August 2021 - Arch-excludes - Fedora Mailing-Lists

Architecture specific change in rpms/teem.git

by githook-noreply＠fedoraproject.org

The package rpms/teem.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/teem.git/commit/?id=593f4aa56a75b.... Change: +%ifarch %{arm64} ppc64le s390x Thanks. Full change: ============ commit 78c8bfa63ee9200e45b439952cccee2508142cdc Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Aug 21 11:07:13 2021 -0400 Remove EPEL workarounds from Fedora spec file diff --git a/teem.spec b/teem.spec index a7f8e03..1913581 100644 --- a/teem.spec +++ b/teem.spec @@ -141,7 +141,7 @@ Source961: unu-save.1 Patch0: lib_install_dir.patch BuildRequires: gcc-c++ -BuildRequires: cmake3 +BuildRequires: cmake BuildRequires: make BuildRequires: zlib-devel @@ -247,16 +247,16 @@ rm -rvf python %build -%cmake3 \ +%cmake \ -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR=ON \ -DTeem_FFTW3=ON \ -DTeem_LEVMAR=ON -%cmake3_build +%cmake_build %install -%cmake3_install +%cmake_install %if %{with man_pages} install -d %{buildroot}%{_mandir}/man1 @@ -296,12 +296,7 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ # Tests are not parallel-safe %global _smp_mflags -j1 -%ctest3 %{?ctest_excludes} - - -%if 0%{?epel} == 7 -%ldconfig_scriptlets libs -%endif +%ctest %{?ctest_excludes} %files commit 2d230660a820d87784de6faa0fa2c9c025de4659 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Aug 21 11:04:34 2021 -0400 Finish complete set of man pages (adds unu-* man pages) diff --git a/ilk.1 b/ilk.1 index e88f365..ec96d51 100644 --- a/ilk.1 +++ b/ilk.1 @@ -33,7 +33,7 @@ Applies linear (homogenous coordinate) transforms to a given image, using the given kernel for resampling. .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-i\fR <\fIimage\fR> diff --git a/miter.1 b/miter.1 index 254f8b8..c95895c 100644 --- a/miter.1 +++ b/miter.1 @@ -79,7 +79,7 @@ miter \- a simple but effective little volume renderer .RI < filename >] .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-i\fR <\fInsin\fR> diff --git a/mrender.1 b/mrender.1 index c58da9e..b263ee1 100644 --- a/mrender.1 +++ b/mrender.1 @@ -69,7 +69,7 @@ in the output image. .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-i\fR <\fInin\fR> diff --git a/puller.1 b/puller.1 index 45b7635..ec9f9cf 100644 --- a/puller.1 +++ b/puller.1 @@ -139,7 +139,7 @@ puller \- command-line interface to the \(lqpull\(rq library .RI < base >] .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-int\fR <\fIint\fR> diff --git a/teem.spec b/teem.spec index aded044..a7f8e03 100644 --- a/teem.spec +++ b/teem.spec @@ -4,7 +4,8 @@ Version: 1.11.0 Release: %autorelease -b 13 Summary: Libraries for processing and visualizing scientific raster data -# The entire source is LGPLv2+, except files noted at the License fields of certain subpackages. +# The entire source is LGPLv2+, except files noted at the License fields of +# certain subpackages. License: LGPLv2+ # Additionally, the following are removed in %%prep to assert that they do not # contribute to the built package: @@ -71,68 +72,68 @@ Source837: tend-shrink.1 Source838: tend-bfit.1 Source839: tend-satin.1 -#Source900: unu-about.1 -#Source901: unu-env.1 -#Source902: unu-i2w.1 -#Source903: unu-w2i.1 -#Source904: unu-make.1 -#Source905: unu-head.1 -#Source906: unu-data.1 -#Source907: unu-convert.1 -#Source908: unu-resample.1 -#Source909: unu-fft.1 -#Source910: unu-cmedian.1 -#Source911: unu-dist.1 -#Source912: unu-minmax.1 -#Source913: unu-cksum.1 -#Source914: unu-diff.1 -#Source915: unu-quantize.1 -#Source916: unu-unquantize.1 -#Source917: unu-project.1 -#Source918: unu-slice.1 -#Source919: unu-sselect.1 -#Source920: unu-dice.1 -#Source921: unu-splice.1 -#Source922: unu-join.1 -#Source923: unu-crop.1 -#Source924: unu-acrop.1 -#Source925: unu-inset.1 -#Source926: unu-pad.1 -#Source927: unu-reshape.1 -#Source928: unu-permute.1 -#Source929: unu-swap.1 -#Source930: unu-shuffle.1 -#Source931: unu-flip.1 -#Source932: unu-unorient.1 -#Source933: unu-axinfo.1 -#Source934: unu-axinsert.1 -#Source935: unu-axsplit.1 -#Source936: unu-axdelete.1 -#Source937: unu-axmerge.1 -#Source938: unu-tile.1 -#Source939: unu-untile.1 -#Source940: unu-histo.1 -#Source941: unu-dhisto.1 -#Source942: unu-jhisto.1 -#Source943: unu-histax.1 -#Source944: unu-heq.1 -#Source945: unu-gamma.1 -#Source946: unu-1op.1 -#Source947: unu-2op.1 -#Source948: unu-3op.1 -#Source949: unu-affine.1 -#Source950: unu-lut.1 -#Source951: unu-mlut.1 -#Source952: unu-subst.1 -#Source953: unu-rmap.1 -#Source954: unu-mrmap.1 -#Source955: unu-imap.1 -#Source956: unu-lut2.1 -#Source957: unu-ccfind.1 -#Source958: unu-ccadj.1 -#Source959: unu-ccmerge.1 -#Source960: unu-ccsettle.1 -#Source961: unu-save.1 +Source900: unu-about.1 +Source901: unu-env.1 +Source902: unu-i2w.1 +Source903: unu-w2i.1 +Source904: unu-make.1 +Source905: unu-head.1 +Source906: unu-data.1 +Source907: unu-convert.1 +Source908: unu-resample.1 +Source909: unu-fft.1 +Source910: unu-cmedian.1 +Source911: unu-dist.1 +Source912: unu-minmax.1 +Source913: unu-cksum.1 +Source914: unu-diff.1 +Source915: unu-quantize.1 +Source916: unu-unquantize.1 +Source917: unu-project.1 +Source918: unu-slice.1 +Source919: unu-sselect.1 +Source920: unu-dice.1 +Source921: unu-splice.1 +Source922: unu-join.1 +Source923: unu-crop.1 +Source924: unu-acrop.1 +Source925: unu-inset.1 +Source926: unu-pad.1 +Source927: unu-reshape.1 +Source928: unu-permute.1 +Source929: unu-swap.1 +Source930: unu-shuffle.1 +Source931: unu-flip.1 +Source932: unu-unorient.1 +Source933: unu-axinfo.1 +Source934: unu-axinsert.1 +Source935: unu-axsplit.1 +Source936: unu-axdelete.1 +Source937: unu-axmerge.1 +Source938: unu-tile.1 +Source939: unu-untile.1 +Source940: unu-histo.1 +Source941: unu-dhisto.1 +Source942: unu-jhisto.1 +Source943: unu-histax.1 +Source944: unu-heq.1 +Source945: unu-gamma.1 +Source946: unu-1op.1 +Source947: unu-2op.1 +Source948: unu-3op.1 +Source949: unu-affine.1 +Source950: unu-lut.1 +Source951: unu-mlut.1 +Source952: unu-subst.1 +Source953: unu-rmap.1 +Source954: unu-mrmap.1 +Source955: unu-imap.1 +Source956: unu-lut2.1 +Source957: unu-ccfind.1 +Source958: unu-ccadj.1 +Source959: unu-ccmerge.1 +Source960: unu-ccsettle.1 +Source961: unu-save.1 # Patch CMakeLists.txt to fix library install paths to match what Fedora # expects. It is not immediately obvious if this patch is suitable for @@ -269,20 +270,20 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %{SOURCE820} %{SOURCE821} %{SOURCE822} %{SOURCE823} %{SOURCE824} \ %{SOURCE825} %{SOURCE826} %{SOURCE827} %{SOURCE828} %{SOURCE829} \ %{SOURCE830} %{SOURCE831} %{SOURCE832} %{SOURCE833} %{SOURCE834} \ - %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} - #{SOURCE900} #{SOURCE901} #{SOURCE902} #{SOURCE903} #{SOURCE904} \ - #{SOURCE905} #{SOURCE906} #{SOURCE907} #{SOURCE908} #{SOURCE909} \ - #{SOURCE910} #{SOURCE911} #{SOURCE912} #{SOURCE913} #{SOURCE914} \ - #{SOURCE915} #{SOURCE916} #{SOURCE917} #{SOURCE918} #{SOURCE919} \ - #{SOURCE920} #{SOURCE921} #{SOURCE922} #{SOURCE923} #{SOURCE924} \ - #{SOURCE925} #{SOURCE926} #{SOURCE927} #{SOURCE928} #{SOURCE929} \ - #{SOURCE930} #{SOURCE931} #{SOURCE932} #{SOURCE933} #{SOURCE934} \ - #{SOURCE935} #{SOURCE936} #{SOURCE937} #{SOURCE938} #{SOURCE939} \ - #{SOURCE940} #{SOURCE941} #{SOURCE942} #{SOURCE943} #{SOURCE944} \ - #{SOURCE945} #{SOURCE946} #{SOURCE947} #{SOURCE948} #{SOURCE949} \ - #{SOURCE950} #{SOURCE951} #{SOURCE952} #{SOURCE953} #{SOURCE954} \ - #{SOURCE955} #{SOURCE956} #{SOURCE957} #{SOURCE958} #{SOURCE959} \ - #{SOURCE960} #{SOURCE961} + %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} \ + %{SOURCE900} %{SOURCE901} %{SOURCE902} %{SOURCE903} %{SOURCE904} \ + %{SOURCE905} %{SOURCE906} %{SOURCE907} %{SOURCE908} %{SOURCE909} \ + %{SOURCE910} %{SOURCE911} %{SOURCE912} %{SOURCE913} %{SOURCE914} \ + %{SOURCE915} %{SOURCE916} %{SOURCE917} %{SOURCE918} %{SOURCE919} \ + %{SOURCE920} %{SOURCE921} %{SOURCE922} %{SOURCE923} %{SOURCE924} \ + %{SOURCE925} %{SOURCE926} %{SOURCE927} %{SOURCE928} %{SOURCE929} \ + %{SOURCE930} %{SOURCE931} %{SOURCE932} %{SOURCE933} %{SOURCE934} \ + %{SOURCE935} %{SOURCE936} %{SOURCE937} %{SOURCE938} %{SOURCE939} \ + %{SOURCE940} %{SOURCE941} %{SOURCE942} %{SOURCE943} %{SOURCE944} \ + %{SOURCE945} %{SOURCE946} %{SOURCE947} %{SOURCE948} %{SOURCE949} \ + %{SOURCE950} %{SOURCE951} %{SOURCE952} %{SOURCE953} %{SOURCE954} \ + %{SOURCE955} %{SOURCE956} %{SOURCE957} %{SOURCE958} %{SOURCE959} \ + %{SOURCE960} %{SOURCE961} %endif @@ -327,7 +328,7 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %{_mandir}/man1/tend.1* %{_mandir}/man1/tend-*.1* %{_mandir}/man1/unu.1* -#{_mandir}/man1/unu-*.1* +%{_mandir}/man1/unu-*.1* %{_mandir}/man1/vprobe.1* %endif diff --git a/tend-bfit.1 b/tend-bfit.1 index 9269f75..3e72390 100644 --- a/tend-bfit.1 +++ b/tend-bfit.1 @@ -27,7 +27,7 @@ to the range of DWI values along input axis 0, as a function of changing values. .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-i\fR <\fInin\fR> diff --git a/tend-glyph.1 b/tend-glyph.1 index c0ee791..5f8d28a 100644 --- a/tend-glyph.1 +++ b/tend-glyph.1 @@ -124,7 +124,7 @@ and/or .RB \(lq unu\ quantize\ \-b\ 8 \(rq. .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-rt diff --git a/tend-unmf.1 b/tend-unmf.1 index d97b5ce..c2fefd6 100644 --- a/tend-unmf.1 +++ b/tend-unmf.1 @@ -18,7 +18,9 @@ world space, and remove the measurement frame from the .B \-i\fR <\fInin\fR> input diffusion tensor volume (sorry, can\(cqt use usual default of .RB \(lq \- \(rq -for stdin because of hest quirk) +for +.BR stdin (3) +because of hest quirk) .TP .B \-o\fR <\fInout\fR> output tensor volume diff --git a/tend.1 b/tend.1 index 831950d..0dc61a9 100644 --- a/tend.1 +++ b/tend.1 @@ -4,7 +4,7 @@ tend \- diffusion image processing and analysis .SH SYNOPSIS .B tend .I COMMAND -.RI [ OPTION ]... +.RI [ OPTION ]...\: .SH DESCRIPTION .BR tend (1) is a command-line interface to much of the functionality in \(lqten\(rq, a C diff --git a/unu-1op.1 b/unu-1op.1 new file mode 100644 index 0000000..9a7fd67 --- /dev/null +++ b/unu-1op.1 @@ -0,0 +1,177 @@ +.TH UNU\-1OP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-1op \- unary operation on a +.I nrrd +.SH SYNOPSIS +.B unu\ 1op +.RI < operator > +.RB [ \-s , \-\-seed +.RI < seed >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Unary operation on a +.IR nrrd . +.IP \(bu +2n +Uses +.B nrrdArithUnaryOp +.SH OPTIONS +.TP +.I operator +Unary operator. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq \- \(rq: +negative (multiply by +.BR \-1.0 ) +.IP \(bu 2 +.RB \(lq r \(rq: +reciprocal +.RB ( 1.0 / \fIvalue ) +.IP \(bu 2 +.RB \(lq sin \(rq, +.RB \(lq cos \(rq, +.RB \(lq tan \(rq, +.RB \(lq asin \(rq, +.RB \(lq acos \(rq, +.RB \(lq atan \(rq: +same as in C +.IP \(bu 2 +.RB \(lq exp \(rq, +.RB \(lq log \(rq, +.RB \(lq log10 \(rq: +same as in C +.IP \(bu 2 +.RB \(lq log1p \(rq, +.RB \(lq expm1 \(rq: +accurate +.BI log( x +1) +and +.BI exp( x )\-1 +.IP \(bu 2 +.RB \(lq log2 \(rq: +log base 2 +.IP \(bu 2 +.RB \(lq sqrt \(rq, +.RB \(lq cbrt \(rq, +.RB \(lq ceil \(rq, +.RB \(lq floor \(rq: +same as in C +.IP \(bu 2 +.RB \(lq erf \(rq: +error function (integral of Gaussian) +.IP \(bu 2 +.RB \(lq rup \(rq, +.RB \(lq rdn \(rq: +round up or down to integral value +.IP \(bu 2 +.RB \(lq abs \(rq: +absolute value +.IP \(bu 2 +.RB \(lq sgn \(rq: +.BR \-1 , +.BR 0 , +.BR 1 +if value is +.RB < 0 , +.RB == 0 , +or +.RB > 0 +.IP \(bu 2 +.RB \(lq exists \(rq: +.B 1 +iff not +.B NaN +or +.BR + / \-Inf , +.B 0 +otherwise +.IP \(bu 2 +.RB \(lq rand \(rq: +random value in +.BR [0.0,1.0) , +no relation to input +.IP \(bu 2 +.RB \(lq nrand \(rq: +random sample from normal distribution with mean +.B 0.0 +and stdvi +.BR 1.0 , +no relation to input +.IP \(bu 2 +.RB \(lq if \(rq: +if input is non-zero, +.BR 1 , +else +.B 0 +.IP \(bu 2 +.RB \(lq 0 \(rq: +output always +.B 0 +.IP \(bu 2 +.RB \(lq 1 \(rq: +output always +.B 1 +.RE +.TP +.B \-s\fR\ <\fIseed\fR>\ ,\ \fB\-\-seed\fR\ <\fIseed\fR> +seed value for RNG for +.B rand +and +.BR nrand , +so that you can get repeatable results between runs, or, by not using this +option, the RNG seeding will be based on the current time +.RI ( string ) +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +convert input +.I nrrd +to this type prior to doing operation. +Useful when desired output is +.I float +(e.g., with +.BR log1p ), +but input is integral. +By default (not using this option), the types of the input +.IR nrrd s +are left unchanged. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) +.P +.BR abs (3), +.BR acos (3), +.BR asin (3), +.BR atan (3), +.BR cbrt (3), +.BR ceil (3), +.BR cos (3), +.BR erf (3), +.BR exp (3), +.BR expm1 (3), +.BR fabs (3), +.BR floor (3), +.BR isfinite (3), +.BR log (3), +.BR log10 (3), +.BR log1p (3), +.BR log2 (3), +.BR rand (3), +.BR sin (3), +.BR sqrt (3), +.BR tan (3) diff --git a/unu-2op.1 b/unu-2op.1 new file mode 100644 index 0000000..a6678fb --- /dev/null +++ b/unu-2op.1 @@ -0,0 +1,180 @@ +.TH UNU\-2OP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-2op \- binary operation on two +.IR nrrd s, +or on a +.I nrrd +and a constant +.SH SYNOPSIS +.B unu\ 2op +.RI < operator > +.RI < in1 > +.RI < in2 > +.RB [ \-s , \-\-seed +.RI < seed >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-w , \-\-which +.RI < arg >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Binary operation on two +.IR nrrd s, +or on a +.I nrrd +and a constant. +Either the first or second operand can be a +.I float +constant, but not both. +Use +.RB \(lq \- \(rq +for an operand to signify a +.I nrrd +to be read from +.I stdin +(a pipe). +Note, however, that +.RB \(lq \- \(rq +can probably only be used once (reliably). +.IP \(bu +2n +Uses +.B nrrdArithIterBinaryOp +or (with +.BR \-w ) +.B nrrdArithIterBinaryOpSelect +.SH OPTIONS +.TP +.I operator +Binary operator. +Possibilities include: +.RS +7n +.IP \(bu +2n +.RB \(lq + \(rq, +.RB \(lq \- \(rq +.RB \(lq x \(rq +.RB \(lq / \(rq: +add, subtract, multiply, divide +.IP \(bu +2n +.RB \(lq ^ \(rq: +exponentiation +.RB ( pow (3)) +.IP \(bu +2n +.RB \(lq spow \(rq: +signed exponentiation: +.BI sgn( x )pow(abs( x ), p ) +.IP \(bu +2n +.RB \(lq fpow \(rq: +like spow but with curves flipped +.IP \(bu +2n +.RB \(lq % \(rq: +integer modulo +.IP \(bu +2n +.RB \(lq fmod \(rq: +same as +.BR fmod (3) +in C +.IP \(bu +2n +.RB \(lq atan2 \(rq: +same as +.BR atan2 (3) +in C +.IP \(bu +2n +.RB \(lq min \(rq +.RB \(lq max \(rq: +minimum, maximum +.IP \(bu +2n +.RB \(lq lt \(rq +.RB \(lq lte \(rq +.RB \(lq gt \(rq +.RB \(lq gte \(rq: +same as C's +.BR < , +.BR <= , +.BR > , +.B <= +.IP \(bu +2n +.RB \(lq eq \(rq +.RB \(lq neq \(rq: +same as C's +.B == +and +.B != +.IP \(bu +2n +.RB \(lq comp \(rq: +.BR \-1 , +.BR 0 , +or +.B 1 +if 1st value is less than, equal to, or greater than 2nd value +.IP \(bu +2n +.RB \(lq if \(rq: +if 1st value is non-zero, use it, else use 2nd value +.IP \(bu +2n +.RB \(lq exists \(rq: +if 1st value exists, use it, else use 2nd value +.IP \(bu +2n +.RB \(lq nrand \(rq: +scale unit-stdv Gaussian noise by 2nd value and add to first value +.IP \(bu +2n +.RB \(lq rrand \(rq: +sample Rician distribution with 1st value for \(lqtrue\(rq mean, and 2nd value +for sigma +.RE +.TP +.I in1 +First input. +Can be a single value or a +.IR nrrd . +.TP +.I in2 +Second input. +Can be a single value or a +.IR nrrd . +.TP +.B \-s\fR\ <\fIseed\fR>\ ,\ \fB\-\-seed\fR\ <\fIseed\fR> +seed value for RNG for +.BR nrand , +so that you can get repeatable results between runs, or, by not using this +option, the RNG seeding will be based on the current time +.RI ( string ) +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to convert all +.B INPUT +.IR nrrd s +to, prior to doing operation, useful for doing, for instance, the difference +between two +.I unsigned\ char +.IR nrrd s. +This will also determine output type. +By default (not using this option), the types of the input +.IR nrrd s +are left unchanged. +.TP +.B \-w\fR\ <\fIarg\fR>\ ,\ \fB\-\-which\fR\ <\fIarg\fR> +Which argument +.RB ( 0 +or +.BR 1 ) +should be used to determine the shape of the output +.IR nrrd . +By default (not using this option), the first non-constant argument is used. +.RI ( int ); +default: +.RB \(lq \-1 \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) +.P +.BR abs (1), +.BR atan2 (1), +.BR fabs (1), +.BR fmod (1), +.BR pow (1) diff --git a/unu-3op.1 b/unu-3op.1 new file mode 100644 index 0000000..3204054 --- /dev/null +++ b/unu-3op.1 @@ -0,0 +1,171 @@ +.TH UNU\-3OP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-3op \- ternary operation on three +.IR nrrd s +or constants +.SH SYNOPSIS +.B unu\ 3op +.RI < operator > +.RI < in1 > +.RI < in2 > +.RI < in3 > +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-w , \-\-which +.RI < arg >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Ternary operation on three +.IR nrrd s +or constants. +Can have one, two, or three +.IR nrrd s, +but not zero. +Use +.RB \(lq \- \(rq +for an operand to signify a +.I nrrd +to be read from +.I stdin +(a pipe). +Note, however, that +.RB \(lq \- \(rq +can probably only be used once (reliably). +.IP \(bu +2n +Uses +.B nrrdArithIterTernaryOp +or (with +.BR \-w ) +.B nrrdArithIterTernaryOpSelect +.SH OPTIONS +.TP +.I operator +Ternary operator. +Possibilities include: +.RS +7n +.IP \(bu +2n +.RB \(lq + \(rq, +.RB \(lq x \(rq +sum or product of three values +.IP \(bu +2n +.RB \(lq min \(rq, +.RB \(lq max \(rq +minimum, maximum +.IP \(bu +2n +.RB \(lq min_sm \(rq +smoothed minimum function; +.BI min_sm( x ,\ w ,\ M ) +is like +.BI min( x , M ) +but for +.IR x \ >\ M \- w +(with +.IR w \ >\ \fB0 ) +there is a smooth transition from +.I x +to asymptotic to +.I M +.IP \(bu +2n +.RB \(lq max_sm \(rq +smoothed maximum function; +max_sm(m, w, x) +.BI max_sm( m ,\ w ,\ x ) +is like +.BI max( m , x ) +but for +.IR x \ <\ m + w +(with +.IR w \ >\ m ) +there is a smooth transition from +.I x +to asymptotic to +.I m +.IP \(bu +2n +.RB \(lq lt_sm \(rq +1st less than 3rd, smoothed by 2nd +.IP \(bu +2n +.RB \(lq gt_sm \(rq +1st greater than 3rd, smoothed by 2nd +.IP \(bu +2n +.RB \(lq clamp \(rq +2nd value is clamped to range between the 1st and the 3rd +.IP \(bu +2n +.RB \(lq ifelse \(rq +if 1st value non-zero, then 2nd value, else 3rd value +.IP \(bu +2n +.RB \(lq lerp \(rq +linear interpolation between the 2nd and 3rd values, as the 1st value varies +between +.B 0.0 +and +.BR 1.0 , +respectively +.IP \(bu +2n +.RB \(lq exists \(rq +if the 1st value exists, use the 2nd value, otherwise use the 3rd +.IP \(bu +2n +.RB \(lq in_op \(rq +.B 1 +iff 2nd value is > 1st and < 3rd, +.B 0 +otherwise +.IP \(bu +2n +.RB \(lq in_cl \(rq +.B 1 +iff 2nd value is >= 1st and <= 3rd, +.B 0 +otherwise +.IP \(bu +2n +.RB \(lq gauss \(rq +evaluate (at 1st value) Gaussian with mean=2nd and stdv=3rd value +.IP \(bu +2n +.RB \(lq rician \(rq +evaluate (at 1st value) Rician with mean=2nd and stdv=3rd value +.RE +.TP +.I in1 +First input. +Can be a single value or a +.IR nrrd . +.TP +.I in2 +Second input. +Can be a single value or a +.IR nrrd . +.TP +.I in3 +Third input. +Can be a single value or a +.IR nrrd . +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to convert all +.IR nrrd +inputs to, prior to doing operation. +This also determines output type. +By default (not using this option), the types of the input +.IR nrrd s +are left unchanged. +.TP +.B \-w\fR\ <\fIarg\fR>\ ,\ \fB\-\-which\fR\ <\fIarg\fR> +Which argument +.RB ( 0 , +.BR 1 , +or +.BR 2 ) +should be used to determine the shape of the output +.IR nrrd . +By default (not using this option), the first non-constant argument is used. +.RI ( int ); +default: +.RB \(lq \-1 \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-about.1 b/unu-about.1 new file mode 100644 index 0000000..9df6bee --- /dev/null +++ b/unu-about.1 @@ -0,0 +1,9 @@ +.TH UNU\-ABOUT "1" "April 2021" "" "User Commands" +.SH NAME +unu\-about \- information about +.BR unu (1) +and its use +.SH SYNOPSIS +.B unu\ about +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-acrop.1 b/unu-acrop.1 new file mode 100644 index 0000000..cbc595f --- /dev/null +++ b/unu-acrop.1 @@ -0,0 +1,115 @@ +.TH UNU\-ACROP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-acrop \- automatically crop axes based on given measure +.SH SYNOPSIS +.B unu\ acrop +.RB [ \-a , \-\-axes +.RI [< ax0 \ ...>]] +.BR \-m , \-\-measure +.RI < measr > +.RB [ \-f , \-\-frac +.RI < frac >] +.RB [ \-off , \-\-offset +.RI < offset >] +.RB [ \-b , \-\-bounds +.RI < filename >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Automatically crop axes based on given measure. +For the axes that are to be cropped, the slices perpendicular to that axis are +projected down to a scalar with the specified measure. +The resulting 1\-D array is analyzed by determining what portions at the +beginning and end constitute less than some portion of the cumulative array +sum; these ends are cropped off. +The cropping bounds determined here can be saved and applied to other arrays +via the +.RB \(lq \-b \(rq +option. +.IP \(bu +2n +Uses +.B nrrdCropAuto +.SH OPTIONS +.TP +.B \-a\fR\ [<\fIax0\fR\ ...>]\ ,\ \fB\-\-axes\fR\ [<\fIax0\fR\ ...>] +the axes (if any) that should +.B NOT +be cropped (0 or more +.IR unsigned\ int s); +default: \(lq \(rq +.TP +.B \-m\fR\ <\fImeasr\fR>\ ,\ \fB\-\-measure\fR\ <\fImeasr\fR> +How to measure slices (along axes to crop) as scalars, to form 1\-D array +analyzed to determine cropping extent. +All the measures from +.BR unu\-project (1) +can be used, but those that make more sense here include: +.RS +7n +.IP \(bu 2 +.RB \(lq max \(rq, +.RB \(lq mean \(rq, +.RB \(lq median \(rq, +.RB \(lq variance \(rq: +(self-explanatory) +.IP \(bu 2 +.RB \(lq stdv \(rq: +standard deviation +.IP \(bu 2 +.RB \(lq cov \(rq: +coefficient of variation +.IP \(bu 2 +.RB \(lq product \(rq, +.RB \(lq sum \(rq: +product or sum of all values +.IP \(bu 2 +.RB \(lq L1 \(rq, +.RB \(lq L2 \(rq, +.RB \(lq NL2 \(rq, +.RB \(lq RMS \(rq, +.RB \(lq Linf \(rq: +different norms +.RE +.TP +.B \-f\fR\ <\fIfrac\fR>\ ,\ \fB\-\-frac\fR\ <\fIfrac\fR> +threshold of cumulative sum of 1\-D array at which to crop. +Needs to be in interval +.BR [0.0,0.5) . +.RI ( double ); +default: +.RB \(lq 0.1 \(rq +.TP +.B \-off\fR\ <\fIoffset\fR>\ ,\ \fB\-\-offset\fR\ <\fIoffset\fR> +how much to offset the numerically determined cropping; positive offsets means +expanding the interval of kept indices (less cropping) +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-b\fR\ <\fIfilename\fR>\ ,\ \fB\-\-bounds\fR\ <\fIfilename\fR> +if a filename is given here, the automatically determined min and max bounds +for cropping are saved to this file as a 2\-D array; first scanline is for +.BR \-min , +second is for +.BR \-max . +Unfortunately nothing using the +.RB \(lq m \(rq +and +.RB \(lq M \(rq +semantics (above) can currently be saved in the bounds file. +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-project (1) diff --git a/unu-affine.1 b/unu-affine.1 new file mode 100644 index 0000000..5765707 --- /dev/null +++ b/unu-affine.1 @@ -0,0 +1,84 @@ +.TH UNU\-AFFINE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-affine \- affine (lerp) mapping on 5 +.IR nrrd s +or constants +.SH SYNOPSIS +.B unu\ affine +.RI < minIn > +.RI < in > +.RI < maxIn > +.RI < minOut > +.RI < maxOut > +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-clamp +.RI < bool >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Affine (lerp) mapping on 5 +.IR nrrd s +or constants. +All the 5 arguments can be either +.IR nrrd s +or single floating-point values. +When all args are single values, this is subsuming the functionality of the +previous stand-alone +.BR affine (1) +program. +Use +.RB \(lq \- \(rq +for an operand to signify a +.I nrrd +to be read from +.I stdin +(a pipe). +Note, however, that +.RB \(lq \- \(rq +can probably only be used once (reliably). +.IP \(bu +2n +Uses +.B nrrdArithAffine +or +.B nrrdArithIterAffine +.SH OPTIONS +.TP +.I minIn +Lower end of input value range. +.TP +.I in +Input value. +.TP +.I maxIn +Upper end of input value range. +.TP +.I minOut +Lower end of output value range. +.TP +.I maxOut +Upper end of output value range. +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to convert all +.IR nrrd +inputs to, prior to doing operation. +This also determines output type. +By default (not using this option), the types of the input +.IR nrrd s +are left unchanged. +.TP +.B \-clamp\fR\ <\fIbool\fR> +clamp output values to specified output range +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-axdelete.1 b/unu-axdelete.1 new file mode 100644 index 0000000..947c921 --- /dev/null +++ b/unu-axdelete.1 @@ -0,0 +1,42 @@ +.TH UNU\-AXDELETE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axdelete \- remove one or more singleton axes from a +.I nrrd +.SH SYNOPSIS +.B unu\ axdelete +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Remove one or more singleton axes from a +.IR nrrd . +Singleton axes have only a single sample along them. +The underlying linear ordering of the samples is unchanged, and the information +about the other axes is shifted downwards as needed. +As a total hack, if you give \-1 as the axis, this will do a matlab-style +\(lqsqueeze\(rq, in which any and all singleton axes are removed. +.IP \(bu +2n +Uses +.B nrrdAxesDelete +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +dimension (axis index) of the axis to remove +.RI ( unsigned\ int ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axmerge (1) diff --git a/unu-axinfo.1 b/unu-axinfo.1 new file mode 100644 index 0000000..00dd7e9 --- /dev/null +++ b/unu-axinfo.1 @@ -0,0 +1,80 @@ +.TH UNU\-AXINFO "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axinfo \- modify attributes of one or more axes +.SH SYNOPSIS +.B unu\ axinfo +.BR \-a , \-\-axes +.RI < ax0 \ ax1 \ ...> +.RB [ \-l , \-\-label +.RI < label >] +.RB [ \-u , \-\-units +.RI < units >] +.RB [ \-mm , \-\-minmax +.RI < min \ max >] +.RB [ \-sp , \-\-spacing +.RI < spacing >] +.RB [ \-c , \-\-center +.RI < center >] +.RB [ \-k , \-\-kind +.RI < kind >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Modify attributes of one or more axes. +The only attributes which are set are those for which command-line options are +given. +.IP \(bu +2n +Uses no particular function; just sets fields in +.B NrrdAxisInfo +.SH OPTIONS +.TP +.B \-a\fR\ <\fIax0\fR \fIax1\fR\ ...>\ ,\ \fB\-\-axes\fR\ <\fIax0\fR \fIax1\fR\ ...> +the one or more axes that should be modified +(1 or more +.IR unsigned\ int s) +.TP +.B \-l\fR\ <\fIlabel\fR>\ ,\ \fB\-\-label\fR\ <\fIlabel\fR> +label to associate with axis +.RI ( string ) +.TP +.B \-u\fR\ <\fIunits\fR>\ ,\ \fB\-\-units\fR\ <\fIunits\fR> +units of measurement +.RI ( string ) +.TP +.B \-mm\fR\ <\fImin\fR\ \fImax\fR>\ ,\ \fB\-\-minmax\fR\ <\fImin\fR\ \fImax\fR> +units of measurement +min and max values along axis +( 2 +.IR double s) +.TP +.B \-sp\fR\ <\fIspacing\fR>\ ,\ \fB\-\-spacing\fR\ <\fIspacing\fR> +spacing between samples along axis +.RI ( double ) +.TP +.B \-c\fR\ <\fIcenter\fR>\ ,\ \fB\-\-center\fR\ <\fIcenter\fR> +axis centering: +.RB \(lq cell \(rq +or +.RB \(lq node \(rq. +Not using this option leaves the centering as it is on input +.RI ( string ) +.TP +.B \-k\fR\ <\fIkind\fR>\ ,\ \fB\-\-kind\fR\ <\fIkind\fR> +axis kind. +Not using this option leaves the kind as it is on input +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-axinsert.1 b/unu-axinsert.1 new file mode 100644 index 0000000..62f1e0a --- /dev/null +++ b/unu-axinsert.1 @@ -0,0 +1,45 @@ +.TH UNU\-AXINSERT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axinsert \- add a \(lqstub\(rq (length 1) axis to a +.I nrrd +.SH SYNOPSIS +.B unu\ axinsert +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-l , \-\-label +.RI < label >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Add a \(lqstub\(rq (length 1) axis to a +.IR nrrd . +The underlying linear ordering of the samples is unchanged, and the information +about the other axes is shifted upwards as needed. +.IP \(bu +2n +Uses +.B nrrdAxesInsert +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axes\fR\ <\fIaxis\fR> +dimension (axis index) at which to insert the new axis +.RI ( unsigned\ int ) +.TP +.B \-l\fR\ <\fIlabel\fR>\ ,\ \fB\-\-label\fR\ <\fIlabel\fR> +label to associate with axis +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axsplit (1) diff --git a/unu-axmerge.1 b/unu-axmerge.1 new file mode 100644 index 0000000..50e8831 --- /dev/null +++ b/unu-axmerge.1 @@ -0,0 +1,47 @@ +.TH UNU\-AXMERGE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axmerge \- merge two adjacent axes into one +.SH SYNOPSIS +.B unu\ axmerge +.BR \-a , \-\-axis +.RI < ax0 \ ...> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Merge two adjacent axes into one. +A more general version of +.BR unu\-axdelete (1). +The underlying linear ordering of the samples is unchanged, and the information +about the other axes is shifted downwards as needed. +.IP \(bu +2n +Uses +.B nrrdAxesMerge +.SH OPTIONS +.TP +.B \-a\fR\ <\fIax0\fR\ ...>\ ,\ \fB\-\-axis\fR\ <\fIax0\fR\ ...> +axis (or axes) to merge. +Each axis index identified is the lower of the pair of axes that will be +merged. +Saying +.RB \(lq \-a\ 2 \(rq +means to merge axis 2 and axis 3 into axis 2. +If multiple merges are to be done, the indices listed here are for the axes +prior to any merging. +(1 or more +.IR int s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axdelete (1) diff --git a/unu-axsplit.1 b/unu-axsplit.1 new file mode 100644 index 0000000..2577ae8 --- /dev/null +++ b/unu-axsplit.1 @@ -0,0 +1,47 @@ +.TH UNU\-AXSPLIT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axsplit \- split one axis into two axes +.SH SYNOPSIS +.B unu\ axsplit +.BR \-a , \-\-axis +.RI < axis > +.BR \-s , \-\-size +.RI < fast ,\ slow \ sizes> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Split one axis into two axes. +More general version of +.BR unu\-axinsert (1), +since a given axis can be split into fast and slow axes of arbitrary size, as +long as the product of the fast and slow sizes is the same as the original +size. +.IP \(bu +2n +Uses +.B nrrdAxesSplit +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +dimension (axis index) to split at +.RI ( unsigned\ int ) +.TP +.B \-s\fR\ <\fIfast\fR,\ \fIslow\fR\ sizes>\ ,\ \fB\-\-size\fR\ <\fIfast\fR,\ \fIslow\fR\ sizes> +fast and slow axis sizes to produce as result of splitting given axis. +(2 +.IR size_t s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axinsert (1) diff --git a/unu-ccadj.1 b/unu-ccadj.1 new file mode 100644 index 0000000..ec09d85 --- /dev/null +++ b/unu-ccadj.1 @@ -0,0 +1,55 @@ +.TH UNU\-CCADJ "1" "August 2021" "" "User Commands" +.SH NAME +unu\-ccadj \- form adjacency matrix of connected components +.SH SYNOPSIS +.B unu\ ccadj +.BR \-c , \-\-connect +.RI < connectivity > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Form adjecency matrix of connected components. +This operates on +the output of +.BR unu\-ccfind (1). +Output is +.I unsigned\ char +array containing +.B 1 +at locations +.RI ( I , J ) +and +.RI ( J , I ) +if CCs with ids +.I I +and +.I J +are adjacent, according to the chosen style of adjacency. +.IP \(bu +2n +Uses +.B nrrdCCAdjacency +.SH OPTIONS +.TP +.B \-c\fR\ <\fIconnectivity\fR>\ ,\ \fB\-\-connect\fR\ <\fIconnectivity\fR> +what kind of connectivity to use: the number of coordinates that vary in order +to traverse the neighborhood of a given sample. +In 2D: +.RB \(lq 1 \(rq: +4-connected, +.RB \(lq 2 \(rq: +8-connected +.RI ( unsigned\ int ) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-ccfind (1), +.BR unu\-ccmerge (1), +.BR unu\-ccsettle (1) diff --git a/unu-ccfind.1 b/unu-ccfind.1 new file mode 100644 index 0000000..2c4169e --- /dev/null +++ b/unu-ccfind.1 @@ -0,0 +1,64 @@ +.TH UNU\-CCFIND "1" "August 2021" "" "User Commands" +.SH NAME +unu\-ccfind \- find connected components (CCs) +.SH SYNOPSIS +.B unu\ ccfind +.RB [ \-v , \-\-values +.RI < filename >] +.RB [ \-t , \-\-type +.RI < type >] +.BR \-c , \-\-connect +.RI < connectivity > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Find connected components (CCs). +This works on 1-byte and 2-byte integral values, as well as 4-byte +.IR int s. +.IP \(bu +2n +Uses +.B nrrdCCFind +.SH OPTIONS +.TP +.B \-v\fR\ <\fIfilename\fR>\ ,\ \fB\-\-values\fR\ <\fIfilename\fR> +Giving a +.I filename +here allows you to save out the values associated with each connect component. +This can be used later with +.BR unu\-ccmerge (1) \ \-d . +By default, no record of the original CC values is kept. +.RI ( string ) +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to use for output, to store the CC ID values. +By default (not using this option), the type used will be the smallest of +.IR uchar , +.IR ushort , +or +.IR int , +that can represent all the CC ID values. +Using this option allows one to specify the integral type to be used. +.TP +.B \-c\fR\ <\fIconnectivity\fR>\ ,\ \fB\-\-connect\fR\ <\fIconnectivity\fR> +what kind of connectivity to use: the number of coordinates that vary in order +to traverse the neighborhood of a given sample. +In 2D: +.RB \(lq 1 \(rq: +4-connected, +.RB \(lq 2 \(rq: +8-connected +.RI ( unsigned\ int ) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-ccadj (1), +.BR unu\-ccmerge (1), +.BR unu\-ccsettle (1) diff --git a/unu-ccmerge.1 b/unu-ccmerge.1 new file mode 100644 index 0000000..2b263f5 --- /dev/null +++ b/unu-ccmerge.1 @@ -0,0 +1,111 @@ +.TH UNU\-CCMERGE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-ccmerge \- merge CCs with their neighbors, under various constraints +.SH SYNOPSIS +.B unu\ ccmerge +.RB [ \-d , \-\-directed +.RI < dir >] +.RB [ \-s , \-\-size +.RI < max\ size >] +.RB [ \-n , \-\-neighbor +.RI < max\ #\ neigh >] +.BR \-c , \-\-connect +.RI < connectivity > +.RB [ \-revalue ] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-v , \-\-values +.RI < values >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Merge CCs with their neighbors, under various constraints. +This operates on the output of +.BR unu\-ccfind (1). +Merging of a CC is always done into its largest neighbor. +Whether or not to merge can be constrained by one or more of: CC size +.RB (\(lq \-s \(rq), +original CC value being brighter or darker +.RB (\(lq \-d \(rq), +and number of neighbors +.RB (\(lq \-n \(rq). +.IP \(bu +2n +Uses +.B nrrdCCMerge +.SH OPTIONS +.TP +.B \-d\fR\ <\fIdir\fR>\ ,\ \fB\-\-directed\fR\ <\fIdir\fR> +do value-driven merging. +Using (positive) +.RB \(lq 1 \(rq +says that dark islands get merged with bright surrounds, while +.RB \(lq \-1 \(rq +says the opposite. +By default, merging can go either way. +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-s\fR\ <\fImax\ size\fR>\ ,\ \fB\-\-size\fR\ <\fImax\ size\fR> +a cap on the CC size that will be absorbed into its surround. +CCs larger than this are deemed too significant to mess with. +Or, use +.RB \(lq 0 \(rq +to remove any such restriction on merging. +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-n\fR\ <\fImax\ #\ neigh\fR>\ ,\ \fB\-\-neighbor\fR\ <\fImax\ #\ neigh\fR> +a cap on the number of neighbors that a CC may have if it is to be be merged. +.RB \(lq 1 \(rq +allows only islands to be merged, +.RB \(lq 2 \(rq +does merging with bigger of two neighbors, etc, while +.RB \(lq 0 \(rq +says that number of neighbors is no constraint +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-c\fR\ <\fIconnectivity\fR>\ ,\ \fB\-\-connect\fR\ <\fIconnectivity\fR> +what kind of connectivity to use: the number of coordinates that vary in order +to traverse the neighborhood of a given sample. +In 2D: +.RB \(lq 1 \(rq: +4-connected, +.RB \(lq 2 \(rq: +8-connected +.RI ( unsigned\ int ) +.TP +.B \-revalue +If this option is given, then after the merging, the CCs are re-assigned their +original datavalues, as given by the +.RB \(lq \-v \(rq +option +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-v\fR\ <\fIvalues\fR>\ ,\ \fB\-\-values\fR\ <\fIvalues\fR> +result of using +.BR unu\-ccfind (1) \ \-v , +the record of which values were originally associated with each CC. +This is required for value-directed merging (with non-zero +.RB \(lq \-d \(rq +option), or if the +.B \-revalue +option is given, but is not needed otherwise +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-ccfind (1), +.BR unu\-ccadj (1), +.BR unu\-ccsettle (1) diff --git a/unu-ccsettle.1 b/unu-ccsettle.1 new file mode 100644 index 0000000..e5aa503 --- /dev/null +++ b/unu-ccsettle.1 @@ -0,0 +1,40 @@ +.TH UNU\-CCSETTLE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-ccsettle \- remap CC values down to lowest contiguous values +.SH SYNOPSIS +.B unu\ ccsettle +.BR \-i , \-\-input +.RI < nin > +.RB [ \-v , \-\-values +.RI < filename >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Remap CC values down to lowest contiguous values. +.IP \(bu +2n +Uses +.B nrrdCCSettle +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-v\fR\ <\fIfilename\fR>\ ,\ \fB\-\-values\fR\ <\fIfilename\fR> +Giving a +.I filename +here allows you to save out the mapping from new (settled) values to old +values, in the form of a 1-D lookup table +.RI ( string ) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-ccfind (1), +.BR unu\-ccadj (1), +.BR unu\-ccmerge (1) diff --git a/unu-cksum.1 b/unu-cksum.1 new file mode 100644 index 0000000..af6d4b8 --- /dev/null +++ b/unu-cksum.1 @@ -0,0 +1,55 @@ +.TH UNU\-CKSUM "1" "May 2021" "" "User Commands" +.SH NAME +unu\-cksum \- compute 32-bit CRC of +.I nrrd +data (same as via +.BR cksum (1)) +.SH SYNOPSIS +.B unu\ cksum +.BR \-en , \-\-endian +.RI < end > +.RB [ \-pen , \-\-printendian +.RI < bool >] +.RI < nin1 \ ...> +.SH DESCRIPTION +Compute 32-bit CRC of +.I nrrd +data (same as via +.BR cksum (1)). +Unlike other commands, this doesn\(cqt produce a +.IR nrrd . +It only prints to standard out the CRC and byte counts for the input +.IR nrrd (s), +seeking to emulate the formatting of +.BR cksum (1) +output. +.IP \(bu +2n +Uses +.B nrrdCRC32 +.SH OPTIONS +.TP +.B \-en\fR\ <\fIendian\fR>\ ,\ \fB\-\-endian\fR\ <\fIendian\fR> +Endianness in which to compute CRC; +.RB \(lq little \(rq +for Intel and friends; +.RB \(lq big \(rq +for everyone else. +Defaults to endianness of this machine. +.TP +.B \-pen\fR\ <\fIbool\fR>\ ,\ \fB\-\-printendian\fR\ <\fIbool\fR> +whether or not to indicate after the CRC value the endianness with which the +CRC was computed; doing so clarifies that the CRC result depends on endianness +and may remove confusion in comparing results on platforms of different +endianness +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.RI < nin \ ...> +input +.IR nrrd (s) +(1 or more +.IR string s) +.SH "SEE\ ALSO" +.BR unu (1), +.BR cksum (1) diff --git a/unu-cmedian.1 b/unu-cmedian.1 new file mode 100644 index 0000000..685059c --- /dev/null +++ b/unu-cmedian.1 @@ -0,0 +1,98 @@ +.TH UNU\-CMEDIAN "1" "May 2021" "" "User Commands" +.SH NAME +unu\-cmedian \- cheap histogram-based median/mode filtering +.SH SYNOPSIS +.B unu\ cmedian +.BR \-r , \-\-radius +.RI < radius > +.RB [ \-mode ] +.RB [ \-b , \-\-bins +.RI < num >] +.RB [ \-w , \-\-weight +.RI < weight >] +.RB [ \-p , \-\-pad ] +.RB [ \-c , \-\-channel ] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Cheap histogram-based median/mode filtering. +Only works on 1, 2, or 3 dimensions. +The window over which filtering is done is always square, and only a simplistic +weighting scheme is available. +The method is cheap because it does the median or mode based on a histogram, +which enforces a quantization to the number of bins in the histogram, which +probably means a loss of precision for anything except 8-bit data. +Also, integral values can be +recovered exactly only when the number of bins is exactly +.IB min \- max +1 +(as reported by +.BR unu\-minmax (1)). +.IP \(bu +2n +Uses +.BR nrrdCheapMedian , +plus +.B nrrdSlice +and +.B nrrdJoin +in case of +.RB \(lq \-c \(rq +.SH OPTIONS +.TP +.B \-r\fR\ <\fIradius\fR>\ ,\ \fB\-\-radius\fR\ <\fIradius\fR> +how big a window to filter over. +.RB \(lq \-r\ 1 \(rq +leads to a 3x3 window in an image, and a 3x3x3 window in a volume +.RI ( unsigned\ int ) +.TP +.B \-mode +By default, median filtering is done. +Using this option enables mode filtering, in which the most common value is +used as output +.TP +.B \-b\fR\ <\fInum\fR>\ ,\ \fB\-\-bins\fR\ <\fInum\fR> +# of bins in histogram. +It is in your interest to minimize this number, since big histograms mean +slower execution times. +8-bit data needs at most 256 bins. +.RI ( unsigned\ int ); +default: +.RB \(lq 256 \(rq +.TP +.B \-w\fR\ <\fIweight\fR>\ ,\ \fB\-\-weight\fR\ <\fIweight\fR> +How much higher to preferentially weight samples that are closer to the center +of the window. +.RB \(lq 1.0 \(rq +weight means that all samples are uniformly weighted over the window, which +facilitates a simple speed-up. +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-p\fR\ ,\ \fB\-\-pad +Pad the input (with boundary method +.RB \(lq bleed \(rq), +and crop the output, so as to overcome our cheapness and correctly handle the +border. +Obviously, this takes more memory. +.TP +.B \-c\fR\ ,\ \fB\-\-channel +Slice the input along axis 0, run filtering on all slices, and join the results +back together. +This is the way you\(cqd want to process color (multi-channel) images or +volumes. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-minmax (1) diff --git a/unu-convert.1 b/unu-convert.1 new file mode 100644 index 0000000..f3588cd --- /dev/null +++ b/unu-convert.1 @@ -0,0 +1,57 @@ +.TH UNU\-CONVERT "1" "May 2021" "" "User Commands" +.SH NAME +unu\-convert \- convert to another type (as if by cast, w/ optional clamp) +.SH SYNOPSIS +.B unu\ convert +.BR \-t , \-\-type +.RI < type > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-clamp ] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Convert to another type (as if by cast, w/ optional clamp). +By default this does not transform, scale, or intelligently quantize values; it +just copies them from one type to another, which replicates exactly what +you\(cqd get in C when you assign from a variable of one type to another, or +when you cast to a different type. +However, clamping values to the representable range +of the output type is possible with +.RB \(lq \-clamp \(rq. +See also +.BR unu\-quantize (1), +.BR unu\-2op (1) +.BR x , +and +.BR unu\-3op (1) +.BR clamp . +.IP \(bu +2n +Uses +.B nrrdConvert +or +.B nrrdClampConvert +.SH OPTIONS +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to convert to +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-clamp +clamp input values to representable range of values of output type, to avoid +wrap-around problems +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-2op (1), +.BR unu\-3op (1), +.BR unu\-quantize (1) diff --git a/unu-crop.1 b/unu-crop.1 new file mode 100644 index 0000000..b0f9ac8 --- /dev/null +++ b/unu-crop.1 @@ -0,0 +1,85 @@ +.TH UNU\-CROP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-crop \- crop along each axis to make a smaller +.I nrrd +.SH SYNOPSIS +.B unu\ crop +.RB [ \-min , \-\-minimum +.RI [< pos0 \ ...>]] +.RB [ \-max , \-\-maximum +.RI [< pos0 \ ...>]] +.RB [ \-b , \-\-bounds +.RI < filename >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Crop along each axis to make a smaller +.IR nrrd . +.IP \(bu +2n +Uses +.B nrrdCrop +.SH OPTIONS +.TP +.B \-min\fR\ [<\fIpos0\fR\ ...>]\ ,\ \fB\-\-minimum\fR\ [<\fIpos0\fR\ ...>] +low corner of bounding box. +.RS +7n +.IP \(bu +2n +.RI < int > +gives 0-based index +.IP \(bu +2n +.BR M , +.BR M+ <\fIint\fR>, +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.IP +(0 or more +.IR position s). +default: +.RB \(lq 0 \(rq +.TP +.B \-max\fR\ [<\fIpos0\fR\ ...>]\ ,\ \fB\-\-maximum\fR\ [<\fIpos0\fR\ ...>] +high corner of bounding box. +Besides the specification styles described above, there\(cqs also: +.RS +7n +.IP \(bu +2n +.BR m+ <\fIint\fR> +give index relative to minimum. +.RE +.IP +(0 or more +.IR position s). +default: +.RB \(lq 0 \(rq +.TP +.B \-b\fR\ <\fIfilename\fR>\ ,\ \fB\-\-bounds\fR\ <\fIfilename\fR> +a filename given here overrides the +.B \-min +and +.B \-max +options (they don\(cqt need to be used) and provides the cropping bounds as a +2\-D array; first scanline is for +.BR \-min , +second is for +.BR \-max . +Unfortunately the +.RB \(lq m \(rq +and +.RB \(lq M \(rq +semantics (above) are currently not supported in the bounds file. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-data.1 b/unu-data.1 new file mode 100644 index 0000000..e04dc57 --- /dev/null +++ b/unu-data.1 @@ -0,0 +1,55 @@ +.TH UNU\-DATA "1" "May 2021" "" "User Commands" +.SH NAME +unu\-data \- print data segment of a \fInrrd\fR file +.SH SYNOPSIS +.B unu\ data +.RI < nin > +.SH DESCRIPTION +Print data segment of a +.I nrrd +file. +The value of this is to pass the data segment in isolation to a stand-alone +decoder, in case this Teem build lacks an optional data encoding required for a +given nrrd file. +.SS CAVEATS +Will start copying characters from the datafile until EOF is hit, so this +won\(cqt work correctly if the datafile has extraneous content at the end. +Will skip lines (as per +.RB \(lq line\ skip: \(rq +header field) if needed, but can only skip bytes (as per +.RB \(lq byte\ skip: \(rq +if the encoding is NOT a compression. +.IP \(bu +2n +Uses +.B nrrdLoad +with +.B nio->skipData +and +.B nio->keepNrrdDataFileOpen +both +.B true +in the +.I NrrdIoState +.BR nio . +.SH OPTIONS +.TP +.RI < nin > +input +.I nrrd +.RI ( string ) +.SH EXAMPLES +To make +.B vol.raw +contain the uncompressed data from +.B vol.nrrd +which uses +.RB \(lq gz \(rq +encoding: +.in +4n +.EX +.B unu data vol.nrrd | gunzip > vol.raw +.EE +.in +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-head (1) diff --git a/unu-dhisto.1 b/unu-dhisto.1 new file mode 100644 index 0000000..90057d3 --- /dev/null +++ b/unu-dhisto.1 @@ -0,0 +1,55 @@ +.TH UNU\-DHISTO "1" "August 2021" "" "User Commands" +.SH NAME +unu\-dhisto \- create image of 1\-D value histogram +.SH SYNOPSIS +.B unu\ dhisto +.BR \-h , \-\-height +.RI < height > +.RB [ \-nolog ] +.RB [ \-notick ] +.RB [ \-max , \-\-maximum +.RI < max\ #\ hits >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Create image of 1\-D value histogram. +With +.RB \(lq \-nolog \(rq, +this becomes a quick & dirty way of plotting a function. +.IP \(bu +2n +Uses +.B nrrdHistoDraw +.SH OPTIONS +.TP +.B \-h\fR\ <\fIheight\fR>\ ,\ \fB\-\-height\fR\ <\fIheight\fR> +height of output image (horizontal size is determined by number of bins in +input histogram). +.RI ( unsigned\ int ) +.TP +.B \-nolog +do not show the log-scaled histogram with decade tick-marks +.TP +.B \-notick +do not draw the log decade tick marks +.TP +.B \-max\fR\ <\fImax\ #\ hits\fR>\ ,\ \fB\-\-maximum\fR\ <\fImax\ #\ hits\fR> +constrain the top of the drawn histogram to be at this number of hits. +This will either scale the drawn histogram downward or clip its top, depending +on whether the given max is higher or lower than the actual maximum bin count. +By not using this option (the default), the actual maximum bin count is used +.RI \(lq double \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-dice.1 b/unu-dice.1 new file mode 100644 index 0000000..ec458f3 --- /dev/null +++ b/unu-dice.1 @@ -0,0 +1,80 @@ +.TH UNU\-DICE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-dice \- save all slices along one axis into separate files +.SH SYNOPSIS +.B unu\ dice +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-s , \-\-start +.RI < start >] +.RB [ \-ff , \-\-format +.RI < form >] +.RB [ \-l , \-\-limit +.RI < max# >] +.RB [ \-o , \-\-output +.RI < above \ below >] +.SH DESCRIPTION +Save all slices along one axis into separate files. +Calls +.BR unu\-slice (1) +for each position along the indicated axis, and saves out a different +file for each sample along that axis. +.IP \(bu +2n +Uses repeated calls to +.B nrrdSlice +and +.B nrrdSave +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to slice along +.RI ( unsigned\ int ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-s\fR\ <\fIstart\fR>\ ,\ \fB\-\-start\fR\ <\fIstart\fR> +integer value to start numbering with +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ff\fR\ <\fIform\fR>\ ,\ \fB\-\-format\fR\ <\fIform\fR> +a +.BR printf (3)-style +format to use for generating all filenames. +Use this to override the number of characters used to represent the slice +position, or the file format of the output, e.g. +.RB \(lq \-ff\ %03d.ppm \(rq +for +.BR 000.ppm , +.BR 001.ppm , +etc. +By default (not using this option), slices are saved in NRRD format (or PNM or +PNG where possible) with shortest possible filenames. +.RI ( string ) +.TP +.B \-l\fR\ <\fImax#\fR>\ ,\ \fB\-\-limit\fR\ <\fImax#\fR> +a sanity check on how many slice files should be saved out, to prevent +accidentally dicing the wrong axis or the wrong array. +Can raise this value if needed. +.RI ( unsigned\ int ); +default: +.RB \(lq 9999 \(rq +.TP +.B \-o\fR\ <\fIprefix\fR>\ ,\ \fB\-\-output\fR\ <\fIprefix\fR> +output filename +.I prefix +(excluding info set via +.RB \(lq \-ff \(rq, +basically to set path of output files (so be sure to end with +.RB \(lq / \(rq). +.RI ( string ) +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-slice (1) +.P +.BR printf (3) diff --git a/unu-diff.1 b/unu-diff.1 new file mode 100644 index 0000000..a8e7359 --- /dev/null +++ b/unu-diff.1 @@ -0,0 +1,46 @@ +.TH UNU\-DIFF "1" "May 2021" "" "User Commands" +.SH NAME +unu\-diff \- sees if two +.IR nrrd s +are different in any way +.SH SYNOPSIS +.B unu\ diff +.RI < ninA > +.RI < ninB > +.RB [ \-eps , \-\-epsilon +.RI < eps >] +.RB [ \-od , \-\-onlydata ] +.SH DESCRIPTION +Sees if two +.IR nrrd s +are different in any way. +Looks through all fields to see if two given +.IR nrrd s +contain the same information. +Or, array meta-data can be excluded, and comparison only on the data values is +done with the +.B \-od +flag. +.IP \(bu +2n +Uses +.B nrrdCompare +.SH OPTIONS +.TP +.RI < ninA > +First input +.IR nrrd . +.TP +.RI < ninB > +Second input +.IR nrrd . +.TP +.B \-eps\fR\ <\fIeps\fR>\ ,\ \fB\-\-epsilon\fR\ <\fIeps\fR> +threshold for allowable difference in values in data values +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-od\fR\ ,\ \fB\-\-onlydata +Compare data values only, excluding array meta-data +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-dist.1 b/unu-dist.1 new file mode 100644 index 0000000..fb0a97c --- /dev/null +++ b/unu-dist.1 @@ -0,0 +1,71 @@ +.TH UNU\-DIST "1" "May 2021" "" "User Commands" +.SH NAME +unu\-dist \- Euclidean distance transform +.SH SYNOPSIS +.B unu\ dist +.BR \-th , \-\-thresh +.RI < val > +.RB [ \-b , \-\-bias +.RI < val >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-sgn ] +.RB [ \-inv ] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Euclidean distance transform. +Based on \(lqDistance Transforms of Sampled Functions\(rq +by Pedro F. Felzenszwalb and Daniel P. Huttenlocher, +\fICornell Computing and Information Science\fR TR2004\-1963. +This function first thresholds at the specified value and then does the +distance transform of the resulting binary image. +The signed distance (negative values inside object) is also available. +Distances between non-isotropic samples are handled correctly. +.IP \(bu +2n +Uses +.B nrrdDistanceL2 +or +.B nrrdDistanceL2Signed +.SH OPTIONS +.TP +.B \-th\fR\ <\fIval\fR>\ ,\ \fB\-\-thresh\fR\ <\fIval\fR> +threshold value to separate inside from outside +.RI ( double ) +.TP +.B \-b\fR\ <\fIval\fR>\ ,\ \fB\-\-bias\fR\ <\fIval\fR> +if non-zero, bias the distance transform by this amount times the difference in +value from the threshold +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to save output in; default: +.RB \(lq float \(rq +.TP +.B \-sgn +also compute signed (negative) distances inside objects, instead of leaving +them as zero +.TP +.B \-inv +values +.B below +threshold are considered interior to object. +By default (not using this option), values above threshold are considered +interior. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-env.1 b/unu-env.1 new file mode 100644 index 0000000..2b3e8a6 --- /dev/null +++ b/unu-env.1 @@ -0,0 +1,184 @@ +.TH UNU\-ENV "1" "April 2021" "" "User Commands" +.SH NAME +unu\-env \- list relevant environment variables and their values +.SH SYNOPSIS +.B unu\ env +.SH DESCRIPTION +List relevant environment variables and their values. +These environment variables provide a way of setting global variables that can +affect the way Nrrd (and +.BR unu (1)) +operates. +.IP \(bu +2n +Uses +.BR nrrdGetenvBool , +.BR nrrdGetenvEnum , +.BR nrrdGetenvInt , +and +.B nrrdGetenvUInt +.IP +Each variable in the listing below starts with the name of the environment +variable +.RB (\(lq NRRD_ ...\(rq), +what type of value it represents (e.g.\: +.RI \(lq int \(rq, +.RI \(lq bool \(rq), +what the corresponding Nrrd global variable is set to, and a description of the +variable. +In the +.BR unu\-env (1) +command output, the listing also includes what the environment variable is +currently set to. +.IP +.I Bool +variables may be set to true simply by setting the environment variable; +setting the value to +.RI \(lq true \(rq +or +.RI \(lq false \(rq +sets the +.I bool +accordingly. +.I Enum +variables may be set by setting the environment variable to any string that +parses as one of the +.I enum +values. +.I Int +and +.I unsigned\ int +variables are set via a string parse-able as a numeric value. +.IP +In addition to the the +.RB \(lq NRRD_ \(rq +environment variables, there is this one, +.BR UNRRDU_QUIET_QUIT ; +see the +.B ENVIRONMENT +section below. +.SH ENVIRONMENT +.TP +.B UNRRDU_QUIET_QUIT +Determines whether +.BR unu (1) +exits quietly (without error and usage info) when it fails because an input +.I nrrd +read immediately hit +.B EOF +(as happens when many +.BR unu (1) +invocations are piped together). +This is currently detected by seeing if the error message ends with +.RB \(lq [nrrd]\ _nrrdRead:\ immediately\ hit\ EOF \(rq. +.TP +.B NRRD_STATE_KEYVALUEPAIRS_PROPAGATE \fR(\fIbool\fR) +.RB ( nrrdStateKeyValuePairsPropagate \ ==\ true ) +.IP +When +.BR true , +key/value pairs are copied from input +.I nrrd +to output +.I nrrd +just like other basic info that hasn\(cqt just been modified (e.g. type, +dimension, block size). +.TP +.B NRRD_DEFAULT_CENTER \fR(\fIcentering\ enum\fR) +.RB ( nrrdDefaultCenter \ ==\ cell ) +.IP +The type of sample centering to use when none has been set but one has to be +chosen for some operation (e.g. resampling). +.TP +.B NRRD_DEFAULT_WRITE_ENCODING_TYPE \fR(\fIencoding\ enum\fR) +.RB ( nrrdDefaultWriteEncodingType \ ==\ raw ) +.IP +When writing +.IR nrrd s, +what encoding to use. +Only +.BR unu\-save (1) +affords explicit control of output encoding. +.TP +.B NRRD_STATE_KIND_NOOP \fR(\fIbool\fR) +.RB ( nrrdStateKindNoop \ ==\ false ) +.IP +When true, Nrrd makes not even the slightest effort to be smart about setting +the +.RB \(lq kind \(rq +field of an axis after some operation that modified its samples. +.TP +.B NRRD_STATE_VERBOSE_IO \fR(\fIint\fR) +.RB ( nrrdStateVerboseIO \ ==\ 1 ) +.IP +The verbosity level of Nrrd input/output operations. +.TP +.B NRRD_DEFAULT_WRITE_BARE_TEXT \fR(\fIbool\fR) +.RB ( nrrdDefaultWriteBareText \ ==\ 1 ) +.IP +When +.BR false , +text files used for saving +.IR nrrd s +start with comment +.RB (\(lq #\ ... \(rq) +lines containing +.I nrrd +fields. +.TP +.B NRRD_STATE_MEASURE_TYPE \fR(\fIenum\fR) +.RB ( nrrdStateMeasureType \ ==\ float ) +.IP +For measurements +.RB ( unu\-project (1)) +like sum and product, the type of the output result, when one hasn\(cqt been +explicitly requested. +.TP +.B NRRD_STATE_MEASURE_MODE_BINS \fR(\fIint\fR) +.RB ( nrrdStateMeasureModeBins \ ==\ 1024 ) +.IP +When measuring mode but without a given histogram, how many bins to use in the +temporary internal histogram. +.TP +.B NRRD_STATE_MEASURE_HISTO_TYPE \fR(\fIenum\fR) +.RB ( nrrdStateMeasureHistoType \ ==\ float ) +.IP +Output type for most measurements of histograms, when one hasn\(cqt been +explicitly requested +.TP +.B NRRD_STATE_ALWAYS_SET_CONTENT \fR(\fIbool\fR) +.RB ( nrrdStateAlwaysSetContent \ ==\ true ) +.IP +If +.BR true , +the output content string is set even when the input content string is not set. +.TP +.B NRRD_STATE_DISABLE_CONTENT \fR(\fIbool\fR) +.RB ( nrrdStateDisableContent \ ==\ false ) +.IP +If +.BR true , +output content is never set. +.TP +.B NRRD_DEFAULT_WRITE_CHARS_PER_LINE \fR(\fIunsigned\ int\fR) +.RB ( nrrdDefaultWriteCharsPerLine \ ==\ 75 ) +.IP +When using text encoding, maximum # characters allowed per line. +.TP +.B NRRD_DEFAULT_WRITE_VALS_PER_LINE \fR(\fIunsigned\ int\fR) +.RB ( nrrdDefaultWriteValsPerLine \ ==\ 8 ) +.IP +When using text encoding, maximum # values allowed per line +.TP +.B NRRD_STATE_GRAYSCALE_IMAGE_3D \fR(\fIbool\fR) +.RB ( nrrdStateGrayscaleImage3D \ ==\ false ) +.IP +If +.BR true , +reading a 2-D grayscale image results in a 3-D image with a single +sample +.RB ( size = 1 ) +on the first (fastest) axis. +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-project (1), +.BR unu\-save (1) diff --git a/unu-fft.1 b/unu-fft.1 new file mode 100644 index 0000000..3be7157 --- /dev/null +++ b/unu-fft.1 @@ -0,0 +1,107 @@ +.TH UNU\-FFT "1" "May 2021" "" "User Commands" +.SH NAME +unu\-fft \- Fast Fourier Transform of selected axes +.SH SYNOPSIS +.B unu\ fft +.RI < dir > +.BR \-a , \-\-axes +.RI < ax0 \ ...> +.RB [ \-pr , \-\-planrigor +.RI < pr >] +.RB [ \-r , \-\-rescale +.RI < bool >] +.RB [ \-w , \-\-wisdom +.RI < filename >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-ri , \-\-realinput ] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Fast Fourier Transform of selected axes. +Initial attempt at wrapping the FFTW3 library; options are likely to change in +Teem 2.0. +.IP \(bu +2n +Uses +.B nrrdFFT +.SH OPTIONS +.TP +.RI < dir > +forward +.RB (\(lq forw \(rq, +.RB \(lq f \(rq) +or backward/inverse ("back", "b") +.RB (\(lq back \(rq, +.RB \(lq b \(rq) +transform +.TP +.B \-a\fR\ <\fIax0\fR\ ...>\ ,\ \fB\-\-axes\fR\ <\fIax0\fR\ ...> +the one or more axes that should be transformed (1 or more +.IR unsigned\ int s) +.TP +.B \-pr\fR\ <\fIpr\fR>\ ,\ \fB\-\-planrigor\fR\ <\fIpr\fR> +rigor with which fftw plan is constructed. +Options include: +.RS +7n +.IP \(bu 2 +.RB \(lq e \(rq, +.RB \(lq est \(rq, +.RB \(lq estimate \(rq: +only an estimate +.IP \(bu 2 +.RB \(lq m \(rq, +.RB \(lq meas \(rq, +.RB \(lq measure \(rq: +standard amount of measurements of system properties +.IP \(bu 2 +.RB \(lq p \(rq, +.RB \(lq pat \(rq, +.RB \(lq patient \(rq: +slower, more measurements +.IP \(bu 2 +.RB \(lq x \(rq, +.RB \(lq ex \(rq, +.RB \(lq exhaustive \(rq: +slowest, most measurements +.P +default: +.RB \(lq est \(rq +.RE +.TP +.B \-r\fR\ <\fIbool\fR>\ ,\ \fB\-\-rescale\fR\ <\fIbool\fR> +scale fftw output (by sqrt(1/N)) so that forward and backward transforms will +get back to original values +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-w\fR\ <\fIfilename\fR>\ ,\ \fB\-\-wisdom\fR\ <\fIfilename\fR> +A filename here is used to read in fftw wisdom (if the file exists already), +and is used to save out updated wisdom after the transform. +By default (not using this option), no wisdom is read or saved. +.IR Note : +no wisdom is gained (that is, learned by FFTW) with planning rigor +.RB \(lq estimate \(rq. +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-ri\fR\ ,\ \fB\-\-realinput +input is real-valued, so insert new length-2 axis +.B 0 +and set complex component to +.BR 0.0 . +Axes to transform (indicated by +.RB \(lq \-a \(rq +will be incremented accordingly. +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-flip.1 b/unu-flip.1 new file mode 100644 index 0000000..63c86d5 --- /dev/null +++ b/unu-flip.1 @@ -0,0 +1,37 @@ +.TH UNU\-FLIP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-flip \- reverse order of slices along one axis +.SH SYNOPSIS +.B unu\ flip +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Reverse order of slices along one axis. +Special case of +.BR unu\-shuffle (1). +.IP \(bu +2n +Uses +.B nrrdFlip +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to flip along +.RI ( unsigned\ int ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-shuffle (1) diff --git a/unu-gamma.1 b/unu-gamma.1 new file mode 100644 index 0000000..a536802 --- /dev/null +++ b/unu-gamma.1 @@ -0,0 +1,81 @@ +.TH UNU\-GAMMA "1" "August 2021" "" "User Commands" +.SH NAME +unu\-gamma \- brighten or darken values with a gamma +.SH SYNOPSIS +.B unu\ gamma +.BR \-g , \-\-gamma +.RI < gamma > +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Brighten or darken values with a gamma. +Just as in +.BR xv , +the gamma value here is actually the reciprocal of the exponent actually used +to transform the values. +.IP \(bu +2n +Uses +.B nrrdArithGamma +.SH OPTIONS +.TP +.B \-g\fR\ <\fIgamma\fR>\ ,\ \fB\-\-gamma\fR\ <\fIgamma\fR> +.B 1.0 +brightens; gamma < +.B 1.0 +darkens. +Negative gammas invert values (like in +.BR xv ). +.RI ( double ) +.TP +.B \-min\fR\ [<\fIvalue\fR>]\ ,\ \fB\-\-minimum\fR\ [<\fIvalue\fR>] +Value to implicitly map to +.B 0.0 +prior to calling +.BR pow (3). +Defaults to lowest value found in input +.IR nrrd . +.RI ( double ) +.TP +.B \-max\fR\ [<\fIvalue\fR>]\ ,\ \fB\-\-maximum\fR\ [<\fIvalue\fR>] +Value to implicitly map to +.B 1.0 +prior to calling +.BR pow (3). +Defaults to highest value found in input +.IR nrrd . +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) +.P +http://www.trilon.com/xv/ diff --git a/unu-head.1 b/unu-head.1 new file mode 100644 index 0000000..0a3e691 --- /dev/null +++ b/unu-head.1 @@ -0,0 +1,34 @@ +.TH UNU\-HEAD "1" "May 2021" "" "User Commands" +.SH NAME +unu\-head \- print header of one or more \fInrrd\fR files +.SH SYNOPSIS +.B unu\ head +.RI < nin1 \ ...> +.SH DESCRIPTION +Print header of one or more +.I nrrd +files. +The value of this is simply to print the contents of +.I nrrd +headers. +This avoids the use of +.RB \(lq head\ \-\fIN \(rq, +where +.I N +has to be determined manually, which always risks printing raw binary data +(following the header) to screen, which tends to clobber terminal settings, +make pointless beeps, and be annoying. +.IP \(bu +2n +Uses +.B nrrdOneLine +.SH OPTIONS +.TP +.RI < nin1 \ ...> +input +.IR nrrd (s) +(1 or more +.IR string s) +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-data (1), +.BR head (1) diff --git a/unu-heq.1 b/unu-heq.1 new file mode 100644 index 0000000..2d7a955 --- /dev/null +++ b/unu-heq.1 @@ -0,0 +1,82 @@ +.TH UNU\-HEQ "1" "August 2021" "" "User Commands" +.SH NAME +unu\-heq \- perform histogram equalization +.SH SYNOPSIS +.B unu\ heq +.BR \-b , \-\-bin +.RI < bins > +.RB [ \-s , \-\-smart +.RI [< bins >]] +.RB [ \-a , \-\-amount +.RI < amount >] +.RB [ \-m , \-\-map +.RI < filename >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Perform histogram equalization. +If this seems to be doing nothing, try increasing the number of histograms bins +by an order of magnitude or two (or more). +Or, use +.BR unu\-gamma (1) +to warp the values in the direction you know they need to go. +Either of these might work because extremely tall and narrow peaks in the +equalization histogram will produce poor results. +.IP \(bu +2n +Uses +.B nrrdHistoEq +.SH OPTIONS +.TP +.B \-b\fR\ <\fIbins\fR>\ ,\ \fB\-\-bin\fR\ <\fIbins\fR> +# bins to use in histogram that is created in order to calculate the mapping +that achieves the equalization. +.RI ( int ) +.TP +.B \-s\fR\ [<\fIbins\fR>]\ ,\ \fB\-\-smart\fR\ [<\fIbins\fR>] +# bins in value histogram to ignore in calculating the mapping. +Bins are ignored when they get more hits than other bins, and when the values +that fall in them are constant. +This is an effective way to prevent large regions of background value from +distorting the equalization mapping. +(optional +.IR int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-a\fR\ <\fIamount\fR>\ ,\ \fB\-\-amount\fR\ <\fIamount\fR> +extent to which the histogram equalizing mapping should be applied; +.BR 0.0 : +no change, +.BR 1.0 : +full equalization +.RI ( float ); +default: +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +output type; default: +.RB \(lq 1.0 \(rq +.TP +.B \-m\fR\ <\fIfilename\fR>\ ,\ \fB\-\-map\fR\ <\fIfilename\fR> +The value mapping used to achieve histogram equalization is represented by a +univariate regular map. +By giving a filename here, that map can be saved out and applied to other +.IR nrrd s +with +.BR unu\-rmap (1) +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-gamma (1), +.BR unu\-rmap (1) diff --git a/unu-histax.1 b/unu-histax.1 new file mode 100644 index 0000000..4c76380 --- /dev/null +++ b/unu-histax.1 @@ -0,0 +1,94 @@ +.TH UNU\-HISTAX "1" "August 2021" "" "User Commands" +.SH NAME +unu\-histax \- replace each scanline along an axis with its histogram +.SH SYNOPSIS +.B unu\ histax +.BR \-a , \-\-axis +.RI < axis > +.BR \-b , \-\-bin +.RI < bins > +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Replace each scanline along an axis with its histogram. +.IP \(bu +2n +Uses +.B nrrdHistoAxis +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to histogram along +.RI ( unsigned\ int ) +.TP +.B \-b\fR\ <\fIbins\fR>\ ,\ \fB\-\-bin\fR\ <\fIbins\fR> +# of bins in histogram +.RI ( unsigned\ int ) +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +output type; default: +.RB \(lq uint \(rq +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +The value to map to zero, given explicitly as a regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this minimum is specified in terms of the percentage of samples in +input that are lower. +.RB \(lq 0% \(rq +means the lowest input value is used, +.RB \(lq 1% \(rq +means that the 1% of the lowest values are all mapped to zero. +By default (not using this option), the lowest input value is used. +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +The value to map to the highest unsigned integral value, given explicitly as a +regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this maximum is specified in terms of the percentage of samples in +input that are higher. +.RB \(lq 0% \(rq +means the highest input value is used, which is also the default behavior (same +as not using this option). +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-histo.1 b/unu-histo.1 new file mode 100644 index 0000000..e0b34b8 --- /dev/null +++ b/unu-histo.1 @@ -0,0 +1,98 @@ +.TH UNU\-HISTO "1" "August 2021" "" "User Commands" +.SH NAME +unu\-histo \- create 1\-D histogram of values in a +.I nrrd +.SH SYNOPSIS +.B unu\ histo +.BR \-b , \-\-bins +.RI < num > +.RB [ \-w , \-\-weight +.RI < nweight >] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Create 1\-D histogram of values in a +.IR nrrd . +Can explicitly set bounds of histogram domain or can learn these from the data. +.IP \(bu +2n +Uses +.B nrrdHisto +.SH OPTIONS +.TP +.B \-b\fR\ <\fInum\fR>\ ,\ \fB\-\-bins\fR\ <\fInum\fR> +# of bins in histogram +.RI ( unsigned\ int ) +.TP +.B \-w\fR\ <\fInweight\fR>\ ,\ \fB\-\-weight\fR\ <\fInweight\fR> +how to weigh contributions to histogram. +By default (not using this option), the increment is one bin count per sample, +but by giving a +.IR nrrd , +the value in the +.I nrrd +at the corresponding location will be the bin count increment +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Value at low end of histogram, given explicitly as a regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this minimum is specified in terms of the percentage of samples in +input that are lower. +By default (not using this option), the lowest value found in input +.IR nrrd . +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +Value at high end of histogram, given explicitly as a regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this maximum is specified in terms of the percentage of samples in +input that are higher. +Defaults to highest value found in input +.IR nrrd . +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to use for bins in output histogram; default: +.RB \(lq uint \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-i2w.1 b/unu-i2w.1 new file mode 100644 index 0000000..3b29e31 --- /dev/null +++ b/unu-i2w.1 @@ -0,0 +1,58 @@ +.TH UNU\-I2W "1" "April 2021" "" "User Commands" +.SH NAME +unu\-i2w \- converts from 1-D index to world position +.SH SYNOPSIS +.B unu\ i2w +.RI < center > +.RI < minPos > +.RI < maxPos > +.RI < num > +.RI < index > +.SH DESCRIPTION +Converts from 1-D index to world position, given the centering of the data +.RB ( cell +vs. +.BR node ), +the range of positions, and the number of intervals into which position has +been quantized. +This is a demo/utility, which does not actually operate on any +.IR nrrd s. +Previously available as the stand-alone +.B idx2pos +binary. +.P +Uses +.B NRRD_POS +macro +.SH OPTIONS +.TP +.RI < center > +which centering applies to the quantized position. +Possibilities are: +.RS +7n +.IP \(bu 2 +.RB \(lq cell \(rq +for histogram bins, quantized values, and pixels-as-squares +.IP \(bu 2 +.RB \(lq node \(rq +for non-trivially interpolated sample points +.RE +.TP +.RI < minPos > +smallest position associated with index +.B 0 +.RI ( double ) +.TP +.RI < maxPos > +highest position associated with highest index +.RI ( double ) +.TP +.RI < num > +number of intervals into which position has been quantized +.RI ( double ) +.TP +.RI < index > +the input index position, to be converted to world +.RI ( double ) +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-imap.1 b/unu-imap.1 new file mode 100644 index 0000000..c79205f --- /dev/null +++ b/unu-imap.1 @@ -0,0 +1,118 @@ +.TH UNU\-IMAP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-imap \- map +.I nrrd +through +.B irregular +univariate map (\(lqcolormap\(rq) +.SH SYNOPSIS +.B unu\ rmap +.BR \-m , \-\-map +.RI < map > +.RB [ \-l , \-\-length +.RI < aclLen >] +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through +.B irregular +univariate map (\(lqcolormap\(rq). +A map is irregular if the control points are not evenly spaced along the +domain, and hence their position must be explicitly represented in the map. +As +.IR nrrd s, +these maps are necessarily 2D. +Along axis +.BR 0 , +the first value is the location of the control point, and the remaining values +give are the range of the map for that control point. +The output value(s) is the result of linearly interpolating between value(s) +from the map. +.IP \(bu +2n +Uses +.B nrrdApply1DIrregMap +.SH OPTIONS +.TP +.B \-m\fR\ <\fImap\fR>\ ,\ \fB\-\-map\fR\ <\fImap\fR> +irregular map to map input +.I nrrd +through +.TP +.B \-l\fR\ <\fIaclLen\fR>\ ,\ \fB\-\-length\fR\ <\fIaclLen\fR> +length of accelerator array, used to try to speed-up task of finding between +which pair of control points a given value lies. +Not terribly useful for small maps (about 10 points or less). +Use +.B 0 +to turn accelorator off. +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the map domain. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the map\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-rmap (1) diff --git a/unu-inset.1 b/unu-inset.1 new file mode 100644 index 0000000..38059f7 --- /dev/null +++ b/unu-inset.1 @@ -0,0 +1,61 @@ +.TH UNU\-INSET "1" "August 2021" "" "User Commands" +.SH NAME +unu\-inset \- replace a sub-region with a different +.I nrrd +.SH SYNOPSIS +.B unu\ inset +.BR \-min , \-\-minimum +.RI < pos0 \ ...> +.BR \-s , \-\-subset +.RI < nsub > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Replace a sub-region with a different +.IR nrrd . +This is functionally the opposite of +.RB \(lq crop \(rq. +.IP \(bu +2n +Uses +.B nrrdInset +.SH OPTIONS +.TP +.B \-min\fR\ [<\fIpos0\fR\ ...>]\ ,\ \fB\-\-minimum\fR\ [<\fIpos0\fR\ ...>] +coordinates of where to locate sub-volume within input +.IR nrrd . +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0\-based index +.IP \(bu 2 +.BR M , +.BR M\+ <\fIint\fR>, +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.IP +(1 or more +.IR position s) +.TP +.B \-s\fR\ <\fInsub\fR>\ ,\ \fB\-\-subset\fR\ <\fInsub\fR> +sub-region +.IR nrrd . +This is the data to be inset in +.I nin +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-crop (1) diff --git a/unu-jhisto.1 b/unu-jhisto.1 new file mode 100644 index 0000000..861e581 --- /dev/null +++ b/unu-jhisto.1 @@ -0,0 +1,99 @@ +.TH UNU\-JHISTO "1" "August 2021" "" "User Commands" +.SH NAME +unu\-jhisto \- create joint histogram of two or more +.IR nrrd s +.SH SYNOPSIS +.B unu\ jhisto +.BR \-b , \-\-bin +.RI < bins0 \ bins1 \ ...> +.RB [ \-w , \-\-weight +.RI < nweight >] +.RB [ \-min , \-\-minimum +.RI < min0 \ min1 \ ...>] +.RB [ \-max , \-\-maximum +.RI < max0 \ max1 \ ...>] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin0 \ nin1 \ ...>] +.RB [ \-a , \-\-axis +.RI < axis >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Create joint histogram of two or more +.IR nrrd s. +Each axis of the output corresponds to one of the input +.IR nrrd s, +and each bin in the output records the number of corresponding positions in the +inputs with a combination of values represented by the coordinates of the bin. +.IP \(bu +2n +Uses +.B nrrdHistoJoint +.SH OPTIONS +.TP +.B \-b\fR\ <\fIbins0\fR\ \fIbins1\fR\ ...>\ ,\ \fB\-\-bin\fR\ <\fIbins0\fR\ \fIbins1\fR\ ...> +.IR bins < i > +is the number of bins to use along axis +.I i +(of joint histogram), which + represents the values of +.IR nin < i > +(2 or more +.IR size_t s) +.TP +.B \-w\fR\ <\fInweight\fR>\ ,\ \fB\-\-weight\fR\ <\fInweight\fR> +how to weigh contributions to joint histogram. +By default (not using this option), the increment is one bin count per sample, +but by giving a +.IR nrrd , +the value in the +.I nrrd +at the corresponding location will be the bin count increment +.TP +.B \-min\fR\ <\fImin0\fR\ min1\fR\ ...>\ ,\ \fB\-\-minimum\fR\ <\fImin0\fR\ min1\fR\ ...> +.IR min < i > +is the low range of values to be quantized along axis +.IR i ; +use +.RB \(lq nan \(rq +to represent lowest value present +(2 or more +.IR double s) +.TP +.B \-max\fR\ <\fImax0\fR\ max1\fR\ ...>\ ,\ \fB\-\-maximum\fR\ <\fImax0\fR\ max1\fR\ ...> +.IR max < i > +is the high range of values to be quantized along axis +.IR i ; +use +.RB \(lq nan \(rq +to represent highest value present +(2 or more +.IR double s) +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to use for output (the type used to store hit counts in the joint +histogram). +Clamping is done on hit counts so that they never overflow a fixed-point type; +default: +.RB \(lq uint \(rq +.TP +.B \-i\fR\ <\fInin0\fR\ [\fInin1\fR]\ ...>\ ,\ \fB\-\-input\fR\ <\fInin0\fR\ [\fInin1\fR]\ ...> +list of +.IR nrrd s +(one for each axis of joint histogram), or, single +.I nrrd +that will be sliced along specified axis. +(1 or more +.IR nrrd s); +default: +.RB \(lq \- \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-join.1 b/unu-join.1 new file mode 100644 index 0000000..011a0ae --- /dev/null +++ b/unu-join.1 @@ -0,0 +1,89 @@ +.TH UNU\-JOIN "1" "August 2021" "" "User Commands" +.SH NAME +unu\-join \- connect slices and/or slabs into a bigger +.I nrrd +.SH SYNOPSIS +.B unu\ join +.RI [ @file \ ...] +.BR \-i , \-\-input +.RI < nin0 \ ...> +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-incr ] +.RB [ \-l , \-\-label +.RI < label >] +.RB [ \-mm , \-\-minmax +.RI < min \ max >] +.RB [ \-sp , \-\-spacing +.RI < spc >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Connect slices and/or slabs into a bigger +.IR nrrd . +Can stich images into volumes, or tile images side by side, or attach images +onto volumes. +If +there are many many files to name in the +.RB \(lq \-i \(rq +option, and using wildcards won\(cqt work, consider putting the list of +filenames into a separate text file (e.g. +.RB \(lq slices.txt \(rq), +and then name this file as a response file (e.g. +.RB \(lq \-i\ s(a)lices.txt \(rq). +This command now allows you to set the same pieces of +information that previously had to be set with +.BR unu\-axinfo (1): +label, spacing, and min/max. +These can be use whether the join axis is new (because of +.RB \(lq \-incr \(rq) +or not. +.IP \(bu +2n +Uses +.B nrrdJoin +.SH OPTIONS +.TP +.IR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR\ <\fInin0\fR\ ...>\ ,\ \fB\-\-input\fR\ <\fInin0\fR\ ...> +everything to be joined together (1 or more +.IR nrrd s) +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to join along +.RI ( unsigned\ int ) +.TP +.B \-incr +in situations where the join axis is +.B not +among the existing axes of the input +.IR nrrd s, +then this flag signifies that the join axis should be +.BR inserted , +and the output dimension should be one greater than input dimension. +Without this flag, the +.IR nrrd s +are joined side-by-side, along an existing axis. +.TP +.B \-l\fR\ <\fIlabel\fR>\ ,\ \fB\-\-label\fR\ <\fIlabel\fR> +label to associate with join axis +.RI ( string ) +.TP +.B \-mm\fR\ <\fImin\fR\ \fImax\fR>\ ,\ \fB\-\-minmax\fR\ <\fImin\fR\ \fImax\fR> +min and max values along join axis (2 +.IR double s) +.TP +.B \-sp\fR\ <\fIspc\fR>\ ,\ \fB\-\-spacing\fR\ <\fIspc\fR> +spacing between samples along join axis +.RI ( double ) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- (rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axinfo (1) diff --git a/unu-lut.1 b/unu-lut.1 new file mode 100644 index 0000000..1812278 --- /dev/null +++ b/unu-lut.1 @@ -0,0 +1,104 @@ +.TH UNU\-LUT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-lut \- map +.I nrrd +through one univariate lookup table +.SH SYNOPSIS +.B unu\ lut +.BR \-m , \-\-map +.RI < lut > +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through one univariate lookup table (itself represented as a +.IR nrrd ). +The lookup table can be 1D, in which case the output has the same dimension as +the input, or 2D, in which case the output has one more dimension than the +input, and each value is mapped to a scanline (along axis +.BR 0 ) +from the lookup table. +.IP \(bu +2n +Uses +.B nrrdApply1DLut +.SH OPTIONS +.TP +.B \-m\fR\ <\fIlut\fR>\ ,\ \fB\-\-map\fR\ <\fIlut\fR> +lookup table to map input +.I nrrd +through +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the lut domain. +The lut domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the lut\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-mlut (1), +.BR unu\-lut2 (1) diff --git a/unu-lut2.1 b/unu-lut2.1 new file mode 100644 index 0000000..f6871c2 --- /dev/null +++ b/unu-lut2.1 @@ -0,0 +1,114 @@ +.TH UNU\-LUT2 "1" "August 2021" "" "User Commands" +.SH NAME +unu\-lut2 \- map +.I nrrd +through a bivariate lookup table +.SH SYNOPSIS +.B unu\ lut2 +.BR \-m , \-\-map +.RI < lut > +.RB [ \-r , \-\-rescale +.RI < bool \ bool >] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through a bivariate lookup table (itself represented as a +.IR nrrd ). +The lookup table can be 2D, in which case the output has the same dimension as +the input, or 3D, in which case the output has one more dimension than the +input, and each value is mapped to a scanline (along axis +.BR 0 ) +from the lookup table. +In any case, axis +.B 0 +of the input must have length two. +.IP \(bu +2n +Uses +.B nrrdApply2DLut +.SH OPTIONS +.TP +.B \-m\fR\ <\fIlut\fR>\ ,\ \fB\-\-map\fR\ <\fIlut\fR> +lookup table to map input +.I nrrd +through +.TP +.B \-r\fR\ <\fIbool\fR\ \fIbool\fR>\ ,\ \fB\-\-rescale\fR\ <\fIbool\fR\ \fIbool\fR> +rescale one or both of the input values from the input range to the lut domain. +The lut domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +(2 +.IR bool s); +default: +.RB \(lq false\ false \(rq +.TP +.B \-min\fR\ <\fImin0\fR\ \fImin1\fR>\ ,\ \fB\-\-minimum\fR\ <\fImin0\fR\ \fImin1\fR> +Low end of input range. +Defaults to lowest values found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +(2 +.IR double s) +.TP +.B \-max\fR\ <\fImax0\fR\ \fImax1\fR>\ ,\ \fB\-\-maximum\fR\ <\fImax0\fR\ \fImax1\fR> +High end of input range. +Defaults to highest values found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +(2 +.IR double s) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the lut\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-lut (1), +.BR unu\-mlut (1) diff --git a/unu-make.1 b/unu-make.1 new file mode 100644 index 0000000..d5a93b3 --- /dev/null +++ b/unu-make.1 @@ -0,0 +1,383 @@ +.TH UNU\-MAKE "1" "May 2021" "" "User Commands" +.SH NAME +unu\-make \- create a \fInrrd\fR (or \fInrrd\fR header) from scratch +.SH SYNOPSIS +.B unu\ make +.RI [ @file \ ...] +.RB [ \-h ] +.RB [ \-i , \-\-input +.RI < file \ ...>] +.BR \-t , \-\-type +.RI < type > +.BR \-s , \-\-size +.RI < sz0 \ sz1 \ ...> +.RB [ \-fd , \-\-filedim +.RI < dim >] +.RB [ \-sp , \-\-spacing +.RI < sp0 \ sp1 \ ...>] +.RB [ \-th , \-\-thickness +.RI < th0 \ th1 \ ...>] +.RB [ \-k , \-\-kind +.RI < k0 \ k1 \ ...>] +.RB [ \-cn , \-\-centering +.RI < c0 \ c1 \ ...>] +.RB [ \-l , \-\-label +.RI < lb0 \ lb1 \ ...>] +.RB [ \-u , \-\-unit +.RI < un0 \ un1 \ ...>] +.RB [ \-c , \-\-content +.RI < content >] +.RB [ \-ls , \-\-lineskip +.RI < num >] +.RB [ \-bs , \-\-byteskip +.RI < num >] +.RB [ \-e , \-\-encoding +.RI < enc >] +.RB [ \-en , \-\-endian +.RI < end >] +.RB [ \-kv , \-\-keyvalue +.RI < key/val \ ...>] +.RB [ \-spc , \-\-space +.RI < space >] +.RB [ \-orig , \-\-origin +.RI < origin >] +.RB [ \-dirs , \-\-directions +.RI < v0 \ v1 \ ...>] +.RB [ \-mf , \-\-measurementframe +.RI < v0 \ v1 \ ...>] +.RB [ \-spu , \-\-spaceunit +.RI < su0 \ su1 \ ...>] +.RB [ \-o , \-\-output +.RI < nout >] +.RB [ \-od , \-\-outputdata +.RI < name >] +.SH DESCRIPTION +Create a +.I nrrd +(or +.I nrrd +header) from scratch. +The data can be in one or more files, or coming from +.BR stdin (3). +This provides an easy way of specifying the information about some data as to +wrap it in a NRRD file, either to pass on for further +.BR unu (1) +processing, or to save to disk. +Note that with +.RB \(lq \-h \(rq, +this creates a detached +.I nrrd +header file, without ever reading or writing data files. +.P +When using multiple datafiles, the data from each is simply concatenated in +memory (as opposed to interleaving along a faster axis). +Keep in mind that all the options below refer to the finished data segment +resulting from joining all the data pieces together, except for +.RB \(lq \-ls \(rq, +.RB \(lq \-bs \(rq, +and +.RB \(lq \-e \(rq, +which apply (uniformly) to the individual data files. +Use the +.RB \(lq \-fd \(rq, +option when the things being joined together are not slices of the final +result, but slabs or scanlines. +It may be easier to put multiple filenames in a response file; there can be one +or more filenames per line of the response file. You can also use a +.BR sprintf (3)-style +format to identify a numbered range of files, so for example +.RB \(lq \-i\ I.%03d\ 1\ 90\ 1 \(rq +refers to +.BR I.001 ,\ I.002 ,\ ...\ I.090 , +using the inclusive range from the first to the second integer (following the +.BR sprintf (3)-style +format), in steps of the third. +Can optionally give a fourth integer to serve same role as +.RB \(lq \-fd \(rq. +.TP +.B NOTE: +For the +.RB \(lq \-l \(rq +(labels), +.RB \(lq \-u \(rq +(units), and +.RB \(lq \-spu \(rq +(space units) options below, you can use a single unquoted period +.RB ( . ) +to signify an empty string. +This creates a convenient way to convey something that the shell doesn\(cqt +make it easy to convey. +Shell expansion weirdness also requires the use of +quotes +around the arguments to +.RB \(lq \-orig \(rq +(space origin), +.RB \(lq \-dirs \(rq +(space directions), and +.RB \(lq \-mf \(rq +(measurement frame). +.P +Uses various components of file and data IO, but currently there is no library +function that encapsulates the functionality here. +.SH OPTIONS +.TP +.IR @file \ ...\: +response file(s) containing command-line arguments +.TP +.B \-h +Generate header +.BR ONLY : +don\(cqt write out the whole +.IR nrrd , +don\(cqt even bother reading the input data, just output the detached +.I nrrd +header file (usually with a +.RB \(lq .nhdr \(rq +extension) determined by the options below. +The single constraint is that detached headers are incompatible with using +.BR stdin (3) +as the data source. +.TP +.B \-i\fR\ <\fIfile\fR\ ...>\ ,\ \fB\-\-input\fR\ <\fIfile\fR\ ...> +Filename(s) of data file(s); use +.RB \(lq \- \(rq +for +.BR stdin (3). +.BR OR , +can use +.BR sprintf (3)-style +format for identifying a range of numbered files, see above for details. +(1 or more +.IR string s); +default: +.RB \(lq \- \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type of data (e.g.\: +.RB \(lq uchar \(rq, +.RB \(lq int \(rq, +.RB \(lq float \(rq, +.RB \(lq double \(rq, +etc.) +.TP +.B \-s\fR\ <\fIsz0\fR\ \fIsz1\fR\ ...>\ ,\ \fB\-\-size\fR\ <\fIsz0\fR\ \fIsz1\fR\ ...> +number of samples along each axis (and implicit indicator of dimension of +.IR nrrd ) +(1 or more +.IR size_t s) +.TP +.B \-fd\fR\ <\fIdim\fR>\ ,\ \fB\-\-filedim\fR\ <\fIdim\fR> +When using +.B multiple +input data files (to +.RB \(lq \-i \(rq), +what is the dimension of the array data in each individual file. +By default (not using this option), this dimension is assumed to be one less +than the whole data dimension. +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq) +.TP +.B \-sp\fR\ <\fIsp0\fR\ \fIsp1\fR\ ...>\ ,\ \fB\-\-spacing\fR\ <\fIsp0\fR\ \fIsp1\fR\ ...> +spacing between samples on each axis. +Use +.RB \(lq nan \(rq +for any non-spatial axes (e.g. spacing between red, green, and blue along axis +0 of interleaved RGB image data) (1 or more +.IR double s) +.TP +.B \-th\fR\ <\fIth0\fR\ \fIth1\fR\ ...>\ ,\ \fB\-\-thickness\fR\ <\fIth0\fR\ \fIth1\fR\ ...> +thickness of region represented by one sample along each axis. +As with spacing, use +.RB \(lq nan \(rq +for any non-spatial axes. +(1 or more +.IR double s) +.TP +.B \-k\fR\ <\fIk0\fR\ \fIk1\fR\ ...>\ ,\ \fB\-\-kind\fR\ <\fIk0\fR\ \fIk1\fR\ ...> +what \(lqkind\(rq is each axis, from the +.I nrrdKind +.I airEnum +(e.g. +.BR space , +.BR time , +.BR 3-vector , +.BR 3D-masked-symmetric-matrix , +or +.RB \(lq none \(rq +to signify no kind) (1 or more +.IR string s) +.TP +.B \-cn\fR\ <\fIc0\fR\ \fIc1\fR\ ...>\ ,\ \fB\-\-centering\fR\ <\fIc0\fR\ \fIc1\fR\ ...> +kind of centering +.RB ( node +or +.RB cell ) +for each axis, or +.RB \(lq none \(rq +to signify no centering) (1 or more +.IR string s) +.TP +.B \-l\fR\ <\fIlb0\fR\ \fIlb1\fR\ ...>\ ,\ \fB\-\-label\fR\ <\fIlb0\fR\ \fIlb1\fR\ ...> +short string labels for each of the axes (1 or more +.IR string s) +.TP +.B \-u\fR\ <\fIun0\fR\ \fIun1\fR\ ...>\ ,\ \fB\-\-unit\fR\ <\fIun0\fR\ \fIun1\fR\ ...> +short strings giving units for each of the axes (1 or more +.TP +.B \-c\fR\ <\fIcontent\fR>\ ,\ \fB\-\-content\fR\ <\fIcontent\fR> +Specifies the content string of the +.IR nrrd , +which is built upon by many +.I nrrd +functions to record a history of operations +.RI ( string ) +.TP +.B \-ls\fR\ <\fInum\fR>\ ,\ \fB\-\-lineskip\fR\ <\fInum\fR> +number of ascii lines to skip before reading data +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-bs\fR\ <\fInum\fR>\ ,\ \fB\-\-byteskip\fR\ <\fInum\fR> +number of bytes to skip (after skipping ascii lines, if any) before reading +data. +Can use +.RB \(lq \-bs\ \-1 \(rq +to skip a binary header of unknown length in raw-encoded data +.RI ( long int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-e\fR\ <\fIenc\fR>\ ,\ \fB\-\-encoding\fR\ <\fIenc\fR> +encoding of input data. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq raw \(rq +raw encoding +.IP \(bu 2 +.RB \(lq ascii \(rq +ascii values, one scanline per line of text, values within line are delimited +by space, tab, or comma +.IP \(bu 2 +.RB \(lq hex \(rq +two hex digits per byte +.IP \(bu 2 +.RB \(lq gzip \(rq,\ \(lq gz \(rq +gzip compressed raw data +.IP \(bu 2 +.RB \(lq bzip2 \(rq,\ \(lq bz2 \(rq +bzip2 compressed raw data +.P +default: +.RB \(lq raw \(rq +.RE +.TP +.B \-kv\fR\ <\fIkey/val\fR\ ...>\ ,\ \fB\-\-keyvalue\fR\ <\fIkey/val\fR\ ...> +key/value string pairs to be stored in +.IR nrrd . +Each key/value pair must be a single string (put it in +.BR \(dq\(dq s +if the key or the value contain spaces). +The format of each pair is +.RI \(lq key\fB:=\fIvalue \(rq, +with no spaces before or after +.RB \(lq := \(rq. +(1 or more +.IR string s) +.TP +.B \-spc\fR\ <\fIspace\fR>\ ,\ \fB\-\-space\fR\ <\fIspace\fR> +identify the space (e.g.\: +.RB \(lq RAS \(rq, +.RB \(lq LPS \(rq) +in which the array conceptually lives, from the +.I nrrdSpace +.IR airEnum , +which in turn determines the dimension of the space. +Or, use an +.RB integer> 0 +to give the dimension of a space that +.I nrrdSpace +doesn\(cqt know about. +By default (not using this option), the enclosing space is set as unknown. +.RI ( string ) +.TP +.B \-orig\fR\ <\fIorigin\fR>\ ,\ \fB\-\-origin\fR\ <\fIorigin\fR> +.RB ( NOTE: +must quote vector) +the origin in space of the array: the location of the center of the first +sample, of the form +.RB \(lq (x,y,z) \(rq +(or however many coefficients are needed for the chosen space). +Quoting the vector is needed to stop interpretation from the shell +.RI ( string ) +.TP +.B \-dirs\fR\ <\fIv0\fR\ \fIv1\fR\ ...>\ ,\ \fB\-\-directions\fR\ <\fI\fIv0\fR\ \fIv1\fR\ ...> +.RB ( NOTE: +must quote whole vector list) +The \(lqspace directions\(rq: the vectors in space spanned by incrementing (by +one) each axis index (the column vectors of the index-to-world matrix +transform), +.BR OR , +.RB \(lq none \(rq +for non-spatial axes. +Give one vector per axis. +(Quoting around whole vector list, not individually, is needed because of +limitations in the parser) +.RI ( string ) +.TP +.B \-mf\fR\ <\fIv0\fR\ \fIv1\fR\ ...>\ ,\ \fB\-\-measurementframe\fR\ <\fI\fIv0\fR\ \fIv1\fR\ ...> +.RB ( NOTE: +must quote whole vector list) +Each vector is a +.I column +vector of the matrix which transforms from coordinates in measurement frame (in +which the coefficients of vectors and tensors are given) to coordinates of +world space (given with +.RB \(lq \-spc \(rq). +This is not a per-axis field: the column vectors comprise a +.IR D -by- D +square matrix, where +.I D +is the dimension of world space. +.RI ( string ) +.TP +.B \-spu\fR\ <\fIsu0\fR\ \fIsu1\fR\ ...>\ ,\ \fB\-\-spaceunit\fR\ <\fI\fIsu0\fR\ \fIsu1\fR\ ...> +short +.IR string s +giving units with which the coefficients of the space origin and direction +vectors are measured. +(1 or more +.IR string s) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output filename. +If +.RB \(lq \-h \(rq +has been used, the output file is always a detached header. +Otherwise, use extension +.RB \(lq .nrrd \(rq +to signal creation of self-contained +.IR nrrd , +and +.RB \(lq .nhdr \(rq +to signal creating of a detached header with (single) data file. +.RI ( string ); +default: +.RB \(lq \- \(rq +.TP +.B \-od\fR\ <\fIname\fR>\ ,\ \fB\-\-outputdata\fR\ <\fIname\fR> +when +.I not +using +.RB \(lq \-h \(rq +and saving to a +.RB \(lq .nhdr \(rq +file, using this option allows you to explicitly name the data file, instead of +(by default, not using this option) having it be the same filename base as the +header file. +.RI ( string ) +.SH "SEE\ ALSO" +.BR unu (1), +.BR sprintf (3) diff --git a/unu-minmax.1 b/unu-minmax.1 new file mode 100644 index 0000000..11f0533 --- /dev/null +++ b/unu-minmax.1 @@ -0,0 +1,49 @@ +.TH UNU\-MINMAX "1" "May 2021" "" "User Commands" +.SH NAME +unu\-minmax \- print out min and max values in one or more +.IR nrrd s +.SH SYNOPSIS +.B unu\ minmax +.BR \-blind8 +.RI < bool > +.RI < nin1 \ ...> +.SH DESCRIPTION +Print out min and max values in one or more +.IR nrrd s. +Unlike other commands, this doesn\(cqt produce a +.IRnrrd . +It only prints to standard out the min and max values found in the input +.IR nrrd (s), +and it also indicates if there are non-existent values. +.IP \(bu +2n +Uses +.B nrrdRangeNewSet +.SH OPTIONS +.TP +.B \-blind8\fR\ <\fIbool\fR> +whether to blindly assert the range of 8-bit data, without actually going +through the data values, i.e. +.I uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [\-128,127] . +Note that even if you do not use this option, the default +.RB ( false ) +is potentialy over-riding the effect of environment variable +.BR NRRD_STATE_BLIND_8_BIT_RANGE ; +see +.BR unu\-env (1) +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.RI < nin1 \ ...> +input +.IR nrrd (s) +(1 or more +.IR string s) +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-env (1) diff --git a/unu-mlut.1 b/unu-mlut.1 new file mode 100644 index 0000000..e4f0b8a --- /dev/null +++ b/unu-mlut.1 @@ -0,0 +1,115 @@ +.TH UNU\-MLUT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-mlut \- map +.I nrrd +through whole +.I nrrd +of univariate lookup tables +.SH SYNOPSIS +.B unu\ mlut +.BR \-m , \-\-map +.RI < mlut \ ...> +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through whole +.I nrrd +of univariate lookup tables, with one lookup table per element of input +.IR nrrd . +The multiple tables are stored in a +.I nrrd +with a dimension which is either 1 or 2 more than the dimension of the input +.IR nrrd , +resulting in an output which has either the same or one more dimension than the +input, resptectively. +.IP \(bu +2n +Uses +.B nrrdApplyMulti1DLut +.SH OPTIONS +.TP +.B \-m\fR\ <\fIlut\fR>\ ,\ \fB\-\-map\fR\ <\fIlut\fR> +one +.I nrrd +of lookup tables to map input +.I nrrd +through, or, list of +.IR nrrd s +which contain the individual entries of the lookup table at each voxel, which +will be joined together. +(1 or more +.IR nrrd s) +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the lut domain. +The lut domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the lut\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-lut (1) diff --git a/unu-mrmap.1 b/unu-mrmap.1 new file mode 100644 index 0000000..e5ddc68 --- /dev/null +++ b/unu-mrmap.1 @@ -0,0 +1,123 @@ +.TH UNU\-MRMAP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-mrmap \- map +.I nrrd +through whole +.I nrrd +of regular univariate maps +.SH SYNOPSIS +.B unu\ mrmap +.BR \-m , \-\-map +.RI < mmap \ ...> +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through whole +.I nrrd +of regular univariate maps, one map per sample in input. +The +.BI \(lq mmap \(rq +.I nrrd +has the same dimensional constraints as the +.BI \(lq mlut \(rq +.I nrrd +for +.BR unu\-mlut (1). +This functionality is a generalization of +.BR unu\-3op (1) \ lerp : +it allows you to lerp through multiple +.IR nrrd s, +instead of just two. +.IP \(bu +2n +Uses +.B nrrdApplyMulti1DRegMap +.SH OPTIONS +.TP +.B \-m\fR\ <\fImmap\fR>\ ,\ \fB\-\-map\fR\ <\fImmap\fR> +one +.I nrrd +of regular maps to map input +.I nrrd +through, or, list of +.IR nrrd s +which contain the individual entries of the map at each voxel, which will be +joined together. +(1 or more +.IR nrrd s) +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the map domain. +The map domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the map\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-rmap (1), +.BR unu\-mlut (1), +.BR unu\-3op (1) diff --git a/unu-pad.1 b/unu-pad.1 new file mode 100644 index 0000000..608c2fb --- /dev/null +++ b/unu-pad.1 @@ -0,0 +1,92 @@ +.TH UNU\-PAD "1" "August 2021" "" "User Commands" +.SH NAME +unu\-pad \- pad along each axis to make a bigger +.I nrrd +.SH SYNOPSIS +.B unu\ pad +.BR \-min , \-\-minimum +.RI < pos0 \ ...> +.BR \-max , \-\-maximum +.RI < pos0 \ ...> +.RB [ \-b , \-\-boundary +.RI < behavior >] +.RB [ \-v , \-\-value +.RI < val >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Pad along each axis to make a bigger +.IR nrrd . +.IP \(bu +2n +Uses +.B nrrdPad_nva +.SH OPTIONS +.TP +.B \-min\fR\ <\fIpos0\fR\ ...>\ ,\ \fB\-\-minimum\fR\ <\fIpos0\fR\ ...> +low corner of bounding box. +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0\-based index +.IP \(bu 2 +.BR M , +.BR M\+ <\fIint\fR>, +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.IP +(1 or more +.IR position s) +.TP +.B \-max\fR\ <\fIpos0\fR\ ...>\ ,\ \fB\-\-maximum\fR\ <\fIpos0\fR\ ...> +high corner of bounding box. +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0\-based index +.IP \(bu 2 +.BR M , +.BR M\+ <\fIint\fR>, +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.IP +(1 or more +.IR position s) +.TP +.B \-b\fR\ <\fIbehavior\fR>\ ,\ \fB\-\-boundary\fR\ <\fIbehavior\fR> +How to handle samples beyond the input bounds: +.RS +7n +.IP \(bu 2 +.RB \(lq pad \(rq: +use some specified value +.IP \(bu 2 +.RB \(lq bleed \(rq: +extend border values outward +.IP \(bu 2 +.RB \(lq mirror \(rq: +repeated reflections +.IP \(bu 2 +.RB \(lq wrap \(rq: +wrap-around to other side +.RE +.IP +default: +.RB \(lq bleed \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-permute.1 b/unu-permute.1 new file mode 100644 index 0000000..5a0eff6 --- /dev/null +++ b/unu-permute.1 @@ -0,0 +1,38 @@ +.TH UNU\-PERMUTE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-permute \- permute ordering of axes +.SH SYNOPSIS +.B unu\ permute +.BR \-p , \-\-permute +.RI < ax0 \ ax1 \ ...> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Permute ordering of axes. +The permutation gives the new ordering of the old axes (in 0-based numbering). +For example, the permutation 0->1, 1->2, 2->0 would be +.RB \(lq 2\ 0\ 1 \(rq. +.IP \(bu +2n +Uses +.B nrrdAxesPermute +.SH OPTIONS +.TP +.B \-p\fR\ <\fIax0\fR \fIax1\fR\ ...>\ ,\ \fB\-\-permute\fR\ <\fIax0\fR \fIax1\fR\ ...> +new axis ordering +(1 or more +.IR unsigned\ int s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-project.1 b/unu-project.1 new file mode 100644 index 0000000..a246329 --- /dev/null +++ b/unu-project.1 @@ -0,0 +1,103 @@ +.TH UNU\-PROJECT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-project \- collapse scanlines to scalars along some axis +.SH SYNOPSIS +.B unu\ project +.BR \-a , \-\-axis +.RI < axis > +.BR \-m , \-\-measure +.RI < measr > +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Collapse scanlines to scalars along some axis. +The scanline is reduced to a single scalar by \(lqmeasuring\(rq all the values +in the scanline with some measure. +The output +.I nrrd +has dimension one less than input (except when the input is itself 1\-D); the +output type depends on the measure in a non-trivial way, or it can be set +explicitly with the +.RB \(lq \-t \(rq +option. +.IP \(bu +2n +Uses +.B nrrdProject +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to project along +.RI ( unsigned\ int ) +.TP +.B \-m\fR\ <\fImeasr\fR>\ ,\ \fB\-\-measure\fR\ <\fImeasr\fR> +How to \(lqmeasure\(rq a scanline, by summarizing all its values with a single +scalar. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq min \(rq, +.RB \(lq max \(rq, +.RB \(lq mean \(rq, +.RB \(lq median \(rq, +.RB \(lq mode \(rq, +.RB \(lq variance \(rq, +.RB \(lq skew \(rq: +(self-explanatory) +.IP \(bu 2 +.RB \(lq intc \(rq, +.RB \(lq slope \(rq, +.RB \(lq error \(rq: +intercept, slope, and error from line fitting +.IP \(bu 2 +.RB \(lq stdv \(rq: +standard deviation +.IP \(bu 2 +.RB \(lq cov \(rq: +coefficient of variation +.IP \(bu 2 +.RB \(lq product \(rq, +.RB \(lq sum \(rq: +product or sum of all values +.IP \(bu 2 +.RB \(lq L1 \(rq, +.RB \(lq L2 \(rq, +.RB \(lq NL2 \(rq, +.RB \(lq RMS \(rq, +.RB \(lq Linf \(rq: +different norms +.IP \(bu 2 +.RB \(lq histo-min \(rq, +.RB \(lq histo-max \(rq, +.RB \(lq histo-mean \(rq, +.RB \(lq histo-median \(rq, +.RB \(lq histo-mode \(rq, +.RB \(lq histo-product \(rq, +.RB \(lq histo-l2 \(rq, +.RB \(lq histo-sum \(rq, +.RB \(lq histo-variance \(rq, +.RB \(lq histo-sd \(rq: +same measures, but for situations where we\(cqre given not the original values, +but a histogram of them. +.RE +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to use for output. +By default (not using this option), the output type is determined +auto-magically. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-quantize.1 b/unu-quantize.1 new file mode 100644 index 0000000..4686f3e --- /dev/null +++ b/unu-quantize.1 @@ -0,0 +1,135 @@ +.TH UNU\-QUANTIZE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-quantize \- quantize values to 8, 16, or 32 bits +.SH SYNOPSIS +.B unu\ quantize +.BR \-b , \-\-bits +.RI < bits > +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-hb , \-\-bins +.RI < bins >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Quantize values to 8, 16, or 32 bits. +Input values can be fixed point (e.g. quantizing ushorts down to uchars) or +floating point. +Values are clamped to the min and max before they are quantized, so there is no +risk of getting +.B 255 +where you expect +.B 0 +(with +.I unsigned char +output, for example). +The min and max can be specified explicitly (as a regular number), or in terms +of percentiles (a number suffixed with +.RB \(lq % \(rq, +no space in between). +This does only linear quantization. +See also +.BR unu\-convert (1), +.BR unu\-2op (1) \ x , +and +.BR unu\-3op (1) \ clamp . +.IP \(bu +2n +Uses +.B nrrdQuantize +.SH OPTIONS +.TP +.B \-b\fR\ <\fIbits\fR>\ ,\ \fB\-\-bits\fR\ <\fIbits\fR> +Number of bits to quantize down to; determines the type of the output +.IR nrrd : +.RS +7n +.IP \(bu 2 +.RB \(lq 8 \(rq: +.I unsigned char +.IP \(bu 2 +.RB \(lq 16 \(rq: +.I unsigned short +.IP \(bu 2 +.RB \(lq 32 \(rq: +.I unsigned int +.RE +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +The value to map to zero, given explicitly as a regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this minimum is specified in terms of the percentage of samples in +input that are lower. +.RB \(lq 0% \(rq +means the lowest input value is used, +.RB \(lq 1% \(rq +means that the 1% of the lowest values are all mapped to zero. +By default (not using this option), the lowest input value is used. +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +The value to map to the highest unsigned integral value, given explicitly as a +regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this maximum is specified in terms of the percentage of samples in +input that are higher. +.RB \(lq 0% \(rq +means the highest input value is used, which is also the default behavior (same +as not using this option). +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-hb\fR\ <\fIbins\fR>\ ,\ \fB\-\-bins\fR\ <\fIbins\fR> +number of bins in histogram of values, for determining min or max by +percentiles. +This has to be large enough so that any errant very high or very low values do +not compress the interesting part of the histogram to an inscrutably small +number of bins. +.RI ( unsigned\ int ); +default: +.RB \(lq 5000 \(rq +.TP +.B \-blind8\fR\ <\fIbins\fR> +if not using +.RB \(lq \-min \(rq +or +.RB \(lq \-max \(rq, +whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed char +is +.BR [-128,127] ) +.RI ( bool ); +default: +.RB \(lq true \(rq, +"true" +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-unquantize (1), +.BR unu\-convert (1), +.BR unu\-2op (1) \ x , +.BR unu\-3op (1) \ clamp diff --git a/unu-resample.1 b/unu-resample.1 new file mode 100644 index 0000000..e08f625 --- /dev/null +++ b/unu-resample.1 @@ -0,0 +1,344 @@ +.TH UNU\-RESAMPLE "1" "May 2021" "" "User Commands" +.SH NAME +unu\-resample \- filtering and {up,down}sampling with a separable kernel +.SH SYNOPSIS +.B unu\ resample +.RB [ \-old ] +.BR \-s , \-\-size +.RI < sz0 \ ...> +.RB [ \-off , \-\-offset +.RI [< off0 \ ...>]] +.RB [ \-min , \-\-minimum +.RI [< min0 \ ...>]] +.RB [ \-max , \-\-maximum +.RI [< max0 \ ...>]] +.RB [ \-k , \-\-kernel +.RI < kern \ ...>] +.RB [ \-nrn ] +.RB [ \-ne , \-\-nonexistent +.RI < behavior >] +.RB [ \-b , \-\-boundary +.RI < behavior >] +.RB [ \-v , \-\-value +.RI < value >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-cheap ] +.RB [ \-c , \-\-center +.RI < center >] +.RB [ \-co , \-\-center\-override ] +.RB [ \-verbose +.RI < v >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Filtering and {up,down}sampling with a separable kernel. +Simplifies access to the +.B NrrdResampleContext +functions by assuming (among other things) that the same kernel is used for +resampling every axis that is being resampled. +Only required option is +.RB \(lq \-s \(rq +to specify which axes to resample and how many output samples to generate. +Resampling kernel +.RB \(lq \-k \(rq +defaults to an interpolating cubic, but many other choices are available. +By default, resampling an axis resamples the full extent of its samples, but it +is possible to offset this range via +.RB \(lq \-off \(rq, +or to crop and/or pad via +.RB \(lq \-min \(rq +and +.RB \(lq \-max \(rq. +The resampling respects the difference between cell- and node-centered data, +but you can over-ride known centering with +.RB \(lq \-co \(rq. +.IP \(bu +2n +Uses the many +.B nrrdResample* +functions operating on a +.B nrrdResampleContext +.SH OPTIONS +.TP +.B \-old +instead of using the new +.B nrrdResampleContext +implementation, use the old +.B nrrdSpatialResample +implementation +.TP +.B \-s\fR\ <\fIsz0\fR\ ...>\ ,\ \fB\-\-size\fR\ <\fIsz0\fR\ ...> +For each axis, information about how many samples in output: +.RS +7n +.IP \(bu 2 +.RB \(lq = \(rq: +leave this axis completely untouched: no resampling whatsoever +.IP \(bu 2 +.RB \(lq x\fIfloat \(rq: +multiply the number of input samples by +.IR float , +and round to the nearest integer, to get the number of output samples. +Use +.RB \(lq x1 \(rq +to resample the axis but leave the number of samples unchanged +.IP \(bu 2 +.RB \(lq /\fIfloat \(rq: +divide number of input samples by +.I float +.IP \(bu 2 +.RB \(lq +=\fIuint \(rq, +.RB \(lq \-=\fIuint \(rq: +add +.I uint +to or subtract +.I uint +from number input samples to get number output samples +.IP \(bu 2 +.RI \(lq uint \(rq: +exact number of output samples +.IP \(bu 2 +.RI \(lq a \(rq: +resample this axis to whatever number of samples preserves the aspect ratio of +other resampled axes. +Currently needs to be used on all but one of the resampled axes, if at all. +.RE +.IP +(1 or more sampling specifications) +.TP +.B \-off\fR\ [<\fIoff0\fR\ ...>]\ ,\ \fB\-\-offset\fR\ [<\fIoff0\fR\ ...>] +For each axis, an offset or shift to the position (in index space) of the lower +end of the sampling domain. +Either +.B \-off +can be used, or +.B \-min +and +.B \-max +together, or none of these (so that, by default, the full domain of the axis is +resampled). +(0 or more +.IR double s); +default: \(lq\(rq +.TP +.B \-min\fR\ [<\fImin0\fR\ ...>]\ ,\ \fB\-\-minimum\fR\ [<\fImin0\fR\ ...>] +For each axis, the lower end (in index space) of the domain of the resampling. +Either +.B \-off +can be used, or +.B \-min +and +.B \-max +together, or none of these (so that, by default, the full domain of the axis is +resampled). +(0 or more +.IR double s); +default: \(lq\(rq +.TP +.B \-max\fR\ [<\fImax0\fR\ ...>]\ ,\ \fB\-\-maximum\fR\ [<\fImax0\fR\ ...>] +For each axis, the upper end (in index space) of the domain of the resampling. +Either +.B \-off +can be used, or +.B \-max +and +.B \-max +together, or none of these (so that, by default, the full domain of the axis is +resampled). +(0 or more +.IR double s); +default: \(lq\(rq +.TP +.B \-k\fR\ <\fIkern\fR>\ , \fB\-\-kernel\fR\ <\fIkern\fR> +The kernel to use for resampling. +Kernels logically live in the input index space for upsampling, and in the +output index space for downsampling. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq box \(rq: +nearest neighbor interpolation on upsampling, and uniform averaging on +downsampling +.IP \(bu 2 +.RB \(lq cheap \(rq: +nearest neighbor interpolation for upsampling, and non-blurring sub-sampling +(pick subset of input samples) on downsampling +.IP \(bu 2 +.RB \(lq tent \(rq: +linear interpolation +.IP \(bu 2 +.RB \(lq cubic:\fIB\fR,\fIC \(rq: +Mitchell/Netravali BC-family of cubics: +.IP +.RB \(lq cubic:1,0 \(rq: +B-spline; maximal blurring +.IP +.RB \(lq cubic:0,0.5 \(rq: +Catmull-Rom; good interpolating kernel +.IP \(bu 2 +.RB \(lq c4h \(rq: +6-sample-support, C^4 continuous, accurate +.IP \(bu 2 +.RB \(lq c4hai \(rq: +discrete pre-filter to make +.B c4h +interpolate +.IP \(bu 2 +.RB \(lq bspl3 \(rq, +.RB \(lq bspl5 \(rq, +.RB \(lq bspl7 \(rq: +cubic (same as +.BR cubic:1,0 ), +quintic, and 7th order B-spline +.IP \(bu 2 +.RB \(lq bspl3ai \(rq, +.RB \(lq bspl5ai \(rq, +.RB \(lq bspl7ai \(rq: +discrete pre-filters to make +.BR bspl3 , +.BR bspl5 , +.B bspl7 +interpolate +.IP \(bu 2 +.RB \(lq hann:\fIR \(rq: +Hann (cosine bell) windowed sinc, radius +.I R +.IP \(bu 2 +.RB \(lq black:\fIR \(rq: +Blackman windowed sinc, radius +.I R +.IP \(bu 2 +.RB \(lq gauss:\fIS\fB,\fIC \(rq: +Gaussian blurring, with standard deviation +.I S +and cut-off at +.I C +standard deviations +.IP \(bu 2 +.RB \(lq dgauss:\fIS\fB,\fIC \(rq: +Lindeberg\(cqs discrete Gaussian. +.RE +.IP +default: +.RB \(lq cubic:0,0.5 \(rq +.TP +.B \-nrn +do NOT do per-pass kernel weight renormalization. +Doing the renormalization is not a performance hit (hence is enabled by +default), and the renormalization is sometimes needed to avoid \(lqgrating\(rq +on non-integral down-sampling. +Disabling the renormalization is needed for correct results with artificially +narrow kernels. +.TP +.B \-ne\fR\ <\fIbehavior\fR>\ , \fB\-\-nonexistent\fR\ <\fIbehavior\fR> +When resampling floating-point values, how to handle non-existent values within +kernel support: +.RS +7n +.IP \(bu 2 +.RB \(lq noop \(rq: +do nothing; let them pollute result +.IP \(bu 2 +.RB \(lq renorm \(rq: +ignore them and renormalize weights of existent values +.IP \(bu 2 +.RB \(lq wght \(rq: +ignore them and simply use weights of existent values +.RE +.IP +default: +.RB \(lq noop \(rq +.TP +.B \-b\fR\ <\fIbehavior\fR>\ , \fB\-\-boundary\fR\ <\fIbehavior\fR> +How to handle samples beyond the input bounds: +.RS +7n +.IP \(bu 2 +.RB \(lq pad \(rq: +use some specified value +.IP \(bu 2 +.RB \(lq bleed \(rq: +extend border values outward +.IP \(bu 2 +.RB \(lq mirror \(rq: +repeated reflections +.IP \(bu 2 +.RB \(lq wrap \(rq: +wrap-around to other side +.RE +.IP +default: +.RB \(lq noop \(rq +.TP +.B \-v\fR\ <\fIvalue\fR>\ , \fB\-\-value\fR\ <\fIvalue\fR> +for +.RB \(lq pad \(rq +boundary behavior, pad with this value +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ , \fB\-\-type\fR\ <\fItype\fR> +type to save output as. +By default (not using this option), the output type is the same as the input +type; default: +.RB \(lq default \(rq +.TP +.B \-cheap +.RI [ DEPRECATED : +the +.RB \(lq \-k\ cheap \(rq +option is the new (and more reliable) way to access this functionality. +.RB \(lq \-cheap \(rq +is only here for legacy use in combination with +.RB \(lq \-old \(rq.] +.IP +When downsampling (reducing number of samples), don\(cqt try to do correct +filtering by scaling kernel to match new (stretched) index space; keep it in +old index space. +When used in conjunction with +.RB \(lq \-k\ box \(rq, +this can implement subsampling which chooses every Nth value. +.TP +.B \-c\fR\ <\fIcenter\fR>\ , \fB\-\-center\fR\ <\fIcenter\fR> +(not available with +.RB \(lq \-old \(rq) +default centering of axes when input +.I nrrd +axes don\(cqt have a known centering: +.RB \(lq cell \(rq +or +.RB \(lq node \(rq; +default: +.RB \(lq cell \(rq +.TP +.B \-co\fR\ , \fB\-\-center-override +(not available with +.RB \(lq \-old \(rq) +centering info specified via +.RB \(lq \-c \(rq +should +.B over-ride +known centering, rather than simply be used when centering is unknown. +.TP +.B \-verbose\fR\ <\fIv\fR> +(not available with +.RB \(lq \-old \(rq) +verbosity level +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ , \fB\-\-input\fR\ <\fInin\fR> +input +.IR nrrd ; +default: +.RB \(lq \- \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ , \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-reshape.1 b/unu-reshape.1 new file mode 100644 index 0000000..f9660dd --- /dev/null +++ b/unu-reshape.1 @@ -0,0 +1,40 @@ +.TH UNU\-RESHAPE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-reshape \- superficially change dimension and/or axes sizes +.SH SYNOPSIS +.B unu\ reshape +.BR \-s , \-\-size +.RI < sz0 \ sz1 \ ...> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Superficially change dimension and/or axes sizes. +The underlying linear ordering of the samples is unchanged, but the reported +dimension or axes sizes are changed. +Identical in concept to Matlab\(cqs +.RB \(lq reshape \(rq +command. +.IP \(bu +2n +Uses +.B nrrdReshape_nva +.SH OPTIONS +.TP +.B \-s\fR\ <\fIsz0\fR \fIsz1\fR\ ...>\ ,\ \fB\-\-size\fR\ <\fI\fIsz0\fR \fIsz1\fR\ ...> +new axes sizes +(1 or more +.IR size_t s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-rmap.1 b/unu-rmap.1 new file mode 100644 index 0000000..ab2a69c --- /dev/null +++ b/unu-rmap.1 @@ -0,0 +1,119 @@ +.TH UNU\-RMAP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-rmap \- map +.I nrrd +through one +.B regular +univariate map (\(lqcolormap\(rq) +.SH SYNOPSIS +.B unu\ rmap +.BR \-m , \-\-map +.RI < map > +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through one +.B regular +univariate map (\(lqcolormap\(rq). +A map is regular if the control points are evenly spaced along the domain, and +hence their position isn\(cqt explicitly represented in the map; the axis +.IR min , +axis +.IR max , +and number of points determine their location. +The map can be a 1D +.I nrrd +(for \(lqgrayscale\(rq), in which case the output has the same dimension as the +input, or a 2D +.I nrrd +(for \(lqcolor\(rq), in which case the output has one more dimension than the +input. +In either case, the output is the result of linearly interpolating between map +points, either scalar values (\(lqgrayscale\(rq), or scanlines along axis +.B 0 +(\(lqcolor\(rq). +.IP \(bu +2n +Uses +.B nrrdApply1DRegMap +.SH OPTIONS +.TP +.B \-m\fR\ <\fImap\fR>\ ,\ \fB\-\-map\fR\ <\fImap\fR> +regular map to map input +.I nrrd +through +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the map domain. +The map domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the map\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-mrmap (1), +.BR unu\-imap (1) diff --git a/unu-save.1 b/unu-save.1 new file mode 100644 index 0000000..ac0d8f8 --- /dev/null +++ b/unu-save.1 @@ -0,0 +1,150 @@ +.TH UNU\-SAVE +.SH NAME +unu\-save \- write +.I nrrd +with specific format, encoding, or endianness +.SH SYNOPSIS +.B unu\ save +.BR \-f , \-\-format +.RI < form > +.RB [ \-e , \-\-encoding +.RI < enc >] +.RB [ \-en , \-\-endian +.RI < end >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.RB [ \-od , \-\-ouputdata +.RI < name >] +.SH DESCRIPTION +Write +.I nrrd +with specific format, encoding, or endianness. +Use +.in +4n +.EX +.B unu\ save\ \-f\ pnm\ |\ xv\ \- +.EE +.in +to view PPM- or PGM-compatible +.IR nrrd s on unix. +EPS output is a EPSF\-3.0 file with +.B BoundingBox +and +.B HiResBoundingBox +DSC comments, and is suitable for inclusion into other PostScript documents. +As a stand-alone file, the image is conveniently centered on an 8.5x11 inch +page, with 0.5 inch margins. +.IP \(bu +2n +Uses various fields in the +.B NrrdIOState +passed to +.B nrrdSave +.SH OPTIONS +.TP +.B \-f\fR\ <\fIform\fR>\ ,\ \fB\-\-format\fR\ <\fIform\fR> +output file format. +Possibilities include: +.RS +7n +.IP \(bu +2n +.RB \(lq nrrd \(rq: +standard +.I nrrd +format +.IP \(bu +2n +.RB \(lq pnm \(rq: +PNM image; PPM for color, PGM for grayscale +.IP \(bu +2n +.RB \(lq text \(rq: +plain ASCII text for 1\-D and 2\-D data +.IP \(bu +2n +.RB \(lq vtk \(rq: +VTK +.RB \(lq STRUCTURED_POINTS \(rq +dataset +.IP \(bu +2n +.RB \(lq png \(rq: +PNG image +.IP \(bu +2n +.RB \(lq eps \(rq: +EPS file +.RE +.TP +.B \-e\fR\ <\fIenc\fR>\ ,\ \fB\-\-encoding\fR\ <\fIenc\fR> +encoding of data in file. +Not all encodings are supported in a given format. +Possibilities include: +.RS +7n +.IP \(bu +2n +.RB \(lq raw \(rq: +raw encoding +.IP \(bu +2n +.RB \(lq ascii \(rq: +print data in ascii +.IP \(bu +2n +.RB \(lq hex \(rq: +two hex digits per byte +.IP \(bu +2n +.RB \(lq gzip \(rq,\ \(lq gz \(rq: +gzip compressed raw data +.IP \(bu +2n +.RB \(lq bzip2 \(rq,\ \(lq bz2 \(rq: +bzip2 compressed raw data +.P +The specifiers for compressions may be followed by a colon +.RB \(lq : \(rq, +followed by an optional digit giving compression \(lqlevel\(rq (for +.BR gzip ) +or \(lqblock size\(rq (for +.BR bzip2 ). +For +.BR gzip , +this can be followed by an optional character for a compression strategy: +.IP \(bu +2n +.RB \(lq d \(rq: +default, Huffman with string match +.IP \(bu +2n +.RB \(lq h \(rq: +Huffman alone +.IP \(bu +2n +.RB \(lq f \(rq: +specialized for filtered data +.P +For example, +.RB \(lq gz \(rq, +.RB \(lq gz:9 \(rq, +.RB \(lq gz:9f \(rq +are all valid +.RE +.TP +.B \-en\fR\ <\fIend\fR>\ ,\ \fB\-\-endian\fR\ <\fIend\fR> +Endianness to save data out as; +.RB \(lq little \(rq +for Intel and friends; +.RB \(lq big \(rq +for everyone else. +Defaults to endianness of this machine +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.TP +.B \-od\fR\ <\fIname\fR>\ ,\ \fB\-\-ouputdata\fR\ <\fIname\fR> +when saving to a +.RB \(lq .nhdr \(rq +file, this option allows you to explicitly name the data file, instead of (by +default, not using this option) having it be the same filename base as the +header file. +.RI ( string ) +.SH "SEE\ ALSO" +.BR unu (1) +.P +http://www.trilon.com/xv/ diff --git a/unu-shuffle.1 b/unu-shuffle.1 new file mode 100644 index 0000000..b2bd05e --- /dev/null +++ b/unu-shuffle.1 @@ -0,0 +1,57 @@ +.TH UNU\-SHUFFLE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-shuffle \- permute slices along one axis +.SH SYNOPSIS +.B unu\ shuffle +.RI [ @file \ ...] +.BR \-p , \-\-permute +.RI < slc0 \ slc1 \ ...> +.RB [ \-inv , \-\-inverse ] +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Permute slices along one axis. +Slices along one axis are re-arranged as units according to the given +permutation (or its inverse). +The permutation tells which old slice to put at each new position. +For example, the shuffle 0->1, 1->2, 2->0 would be +.RB \(lq 2\ 0\ 1 \(rq. +Obviously, if you have to rearrange the many slices of a large dataset, you +should probably store the permutation in a plain text file and use it as a +\(lqresponse file\rq). +.IP \(bu +2n +Uses +.B nrrdShuffle +.SH OPTIONS +.TP +.IR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-p\fR\ <\fIslc0\fR\ \fIslc1\fR\ ...>\ ,\ \fB\-\-permute\fR\ <\fIslc0\fR\ \fIslc1\fR\ ...> +new slice ordering (1 or more +.IR unsigned\ int s) +.TP +.B \-inv\fR\ ,\ \fB\-\-inverse +use inverse of given permutation +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to shuffle along +.RI ( unsigned\ int ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-flip (1) diff --git a/unu-slice.1 b/unu-slice.1 new file mode 100644 index 0000000..fd6a2de --- /dev/null +++ b/unu-slice.1 @@ -0,0 +1,66 @@ +.TH UNU\-SLICE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-slice \- slice along one or more axes at given positions +.SH SYNOPSIS +.B unu\ slice +.BR \-a , \-\-axis +.RI < axis \ ...> +.BR \-p , \-\-position +.RI < pos \ ...> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Slice along one or more axes at given positions. +Output +.I nrrd +dimension is less than input +.I nrrd +dimension by the number of slice axes (except when the input is or gets down to +1\-D). +Can slice on all axes in order to sample a single value from the array. +Per-axis information is preserved. +.IP \(bu +2n +Uses +.B nrrdSlice +(possibly called multiple times) +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR\ ...>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR\ ...> +single axis or multiple axes to slice along. +Giving multiple axes here leads to doing multiple slices (at the corresponding +positions given with +.RB \(lq \-p \(rq. +Multiple axes should be identified in terms of the axis numbering of the +original +.IR nrrd ; +as the slices are done (in the given ordering) the actual slice axis will be +different if previous slices were on lower-numbered (faster) axes. +(1 or more +.IR unsigned\ ints ) +.TP +.B \-p\fR\ <\fIpos\fR>\ ,\ \fB\-\-position\fR\ <\fIpos\fR> +position(s) to slice at: +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0-based index +.IP \(bu 2 +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-splice.1 b/unu-splice.1 new file mode 100644 index 0000000..86d0ca5 --- /dev/null +++ b/unu-splice.1 @@ -0,0 +1,56 @@ +.TH UNU\-SPLICE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-splice \- replace a slice with a different \fInrrd +.SH SYNOPSIS +.B unu\ splice +.BR \-a , \-\-axis +.RI < axis > +.BR \-p , \-\-position +.RI < pos > +.BR \-s , \-\-slice +.RI < nslice > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Replace a slice with a different +.IR nrrd . +This is functionally the opposite of +.RB \(lq slice \(rq. +.IP \(bu +2n +Uses +.B nrrdSplice +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to splice along +.RI ( unsigned\ int ) +.TP +.B \-p\fR\ <\fIpos\fR>\ ,\ \fB\-\-position\fR\ <\fIpos\fR> +position to splice at: +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0-based index +.IP \(bu 2 +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.IR nrrd . +This is the slice to insert into +.I nin +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- (rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-slice (1) diff --git a/unu-sselect.1 b/unu-sselect.1 new file mode 100644 index 0000000..84e21ff --- /dev/null +++ b/unu-sselect.1 @@ -0,0 +1,52 @@ +.TH UNU\-SSELECT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-sselect \- select subset of slices along an axis +.SH SYNOPSIS +.B unu\ sselect +.RB [ \-i , \-\-input +.RI < nin >] +.BR \-a , \-\-axis +.RI < axis > +.BR \-s , \-\-selector +.RI < nline > +.BR \-th +.RI < thresh > +.RB [ \-o , \-\-output +.RI < above \ below >] +.SH DESCRIPTION +Select subset of slices along an axis. +The choice to keep or nix a slice is determined by whether the values in a +given 1\-D line of values is above or below a given threshold. +.IP \(bu +2n +Uses +.B nrrdSliceSelect +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to slice along +.RI ( unsigned\ int ) +.TP +.B \-s\fR\ <\fInline\fR>\ ,\ \fB\-\-selector\fR\ <\fInline\fR> +the 1\-D +.I nrrd +of values to compare with threshold +.TP +.B \-th\fR\ <\fIthresh\fR> +threshold on selector line +.RI ( double ) +.TP +.B \-o\fR\ <\fIabove\fR\ \fIbelow\fR>\ ,\ \fB\-\-output\fR\ <\fIabove\fR\ \fIbelow\fR> +outputs for slices corresponding to values above (first) and below (second) given threshold. +Use +.RB \(lq x \(rq +to say that no output is desired. +(2 +.IR string s); +default: +.RB \(lq \-\ x \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-subst.1 b/unu-subst.1 new file mode 100644 index 0000000..20e639a --- /dev/null +++ b/unu-subst.1 @@ -0,0 +1,55 @@ +.TH UNU\-SUBST "1" "August 2021" "" "User Commands" +.SH NAME +unu\-subst \- map +.I nrrd +through one univariate substitution table +.SH SYNOPSIS +.B unu\ subst +.BR \-s , \-\-subst +.RI < subst > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through one univariate substitution table (itself represented as a +.IR nrrd ). +The substitution table is a +.RI 2\-by\- N +table: a list of pairs giving the old value (to replace) and the the new value +(to change to), in that order. +A plain text file makes this easy. +Unlike with +.BR unu\-lut (1), +.BR unu\-rmap (1), +and +.BR unu\-imap (1), +the output type is the same as the input type, rather than the type of the lut +or map. +.IP \(bu +2n +Uses +.B nrrdApply1DSubstitution +.SH OPTIONS +.TP +.B \-s\fR\ <\fIsubst\fR>\ ,\ \fB\-\-subst\fR\ <\fIsubst\fR> +substitution table to map input +.I nrrd +through +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-lut (1), +.BR unu\-rmap (1), +.BR unu\-imap (1) diff --git a/unu-swap.1 b/unu-swap.1 new file mode 100644 index 0000000..0189d7f --- /dev/null +++ b/unu-swap.1 @@ -0,0 +1,36 @@ +.TH UNU\-SWAP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-swap \- interchange ordering of two axes +.SH SYNOPSIS +.B unu\ swap +.BR \-a , \-\-axis +.RI < axisA \ axisB > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Interchange ordering of two axes. Special case of +.BR unu\-permute (1). +.IP \(bu +2n +Uses +.B nrrdAxesSwap +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxisA\fR\ \fIaxisB\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxisA\fR\ \fIaxisB\fR> +the two axes to switch (0-based numbering) (2 +.IR unsigned\ int s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-permute (1) diff --git a/unu-tile.1 b/unu-tile.1 new file mode 100644 index 0000000..7346ecc --- /dev/null +++ b/unu-tile.1 @@ -0,0 +1,57 @@ +.TH UNU\-TILE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-tile \- tile slices of one axis into two other axes +.SH SYNOPSIS +.B unu\ tile +.BR \-a , \-\-axis +.RI < axSplit \ ax0 \ ax1 > +.BR \-s , \-\-size +.RI < fast \ slow > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Tile slices of one axis into two other axes. +Tiling an array means splitting one axis into fast and slow parts, and then +interleaving those parts into other (existing) axes by doing two axis merges, +which combine an existing axis with part of the split axis. +This reduces the dimension by one. +The three axis arguments all identify axes in the input array as is. +This provides, for example, a simple way of viewing the 128 slices along the +slow axis of a 3\-D volume as a 16x8 tiled array of 2\-D slices, as with +.RB \(lq \-a\ 2\ 0\ 1\ \-s\ 16\ 8 \(rq. +.IP \(bu +2n +Uses +.B nrrdTile2D +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxSplit\fR\ \fIax0\fR\ \fIax1\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxSplit\fR\ \fIax0\fR\ \fIax1\fR> +.I axSplit +is divided and merged with +.I ax0 +and +.I ax1 +(3 +.IR unsigned\ int s) +.TP +.B \-s\fR\ <\fIfast\fR\ \fIslow\fR>\ ,\ \fB\-\-size\fR\ <\fIfast\fR\ \fIslow\fR> +fast and slow axis sizes to produce as result of splitting the +.I axSplit + axis. +(2 +.IR size_t s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-untile (1) diff --git a/unu-unorient.1 b/unu-unorient.1 new file mode 100644 index 0000000..7a078db --- /dev/null +++ b/unu-unorient.1 @@ -0,0 +1,38 @@ +.TH UNU\-UNORIENT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-unorient \- make image orientation be axis-aligned +.SH SYNOPSIS +.B unu\ unorient +.BR \-i , \-\-input +.RI < nin > +.RB [ \-smfo ] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Make image orientation be axis-aligned. +Does various tricks. +.IP \(bu +2n +Uses +.B nrrdOrientationReduce +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +(sorry, can’t use usual default of +.RB \(lq \- \(rq +for +.I stdin +because of hest quirk) +.TP +.B \-smfo +set some axis mins based on space origin (hack) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-unquantize.1 b/unu-unquantize.1 new file mode 100644 index 0000000..9c81558 --- /dev/null +++ b/unu-unquantize.1 @@ -0,0 +1,83 @@ +.TH UNU\-UNQUANTIZE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-unquantize \- recover floating point values from quantized data +.SH SYNOPSIS +.B unu\ unquantize +.BR \-i , \-\-input +.RI < nin > +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-double ] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Recover floating point values from quantized data. +Uses the +.B oldMin +and +.B oldMax +fields in the +.I nrrd +of quantized values to regenerate approximate versions of the original +unquantized values. +Can also override these with +.RB \(lq \-min \(rq +and +.RB \(lq \-max \(rq. +.IP \(bu +2n +Uses +.B nrrdUnquantize +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.IR nrrd . +That this argument is required instead of optional, as with most +.BR unu (1) +commands, is a quirk caused by the need to have +.BR unu\-unquantize (1) +generate usage info, combined with the fact that all the other arguments have +sensible defaults. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Defaults to +.IB nin ->oldMin +if it exists, otherwise +.B 0.0 +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +Defaults to +.IB nin ->oldMax +if it exists, otherwise +.B 1.0 +.RI ( double ) +.TP +.B \-double +If not using +.RB \(lq \-min \(rq +or +.RB \(lq \-max \(rq, +whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed char +is +.BR [-128,127] ) +.RI ( bool ); +default: +.RB \(lq true \(rq, +"true" +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-quantize (1) diff --git a/unu-untile.1 b/unu-untile.1 new file mode 100644 index 0000000..f1674af --- /dev/null +++ b/unu-untile.1 @@ -0,0 +1,90 @@ +.TH UNU\-UNTILE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-untile \- undo +.BR unu\-tile (1): +merge slow parts of two axis splits +.SH SYNOPSIS +.B unu\ untile +.BR \-a , \-\-axis +.RI < axMerge \ ax0 \ ax1 > +.BR \-s , \-\-size +.RI < size0 \ size1 > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Undo +.BR unu\-tile (1): +merge slow parts of two axis splits. +Untiling an array means spliting two axes, permuting the slow parts of those +axes to be adjecent in the axis ordering, and then merging them. +This increases the dimension by one. +Undoing a +.BR unu\-tile (1) +uses the same +.RB \(lq \-s \(rq +argument, and +sometimes a different +.RB \(lq \-a \(rq +argument, as demonstrated here for a 3\-D array: +.IP +.RB \(lq unu\ untile\ \-a\ 2\ 0\ 1 \(rq +undoes +.RB \(lq unu\ tile\ \-a\ 2\ 0\ 1 \(rq +.IP +.RB \(lq unu\ untile\ \-a\ 1\ 0\ 1 \(rq +undoes +.RB \(lq unu\ tile\ \-a\ 1\ 0\ 2 \(rq +.IP +.RB \(lq unu\ untile\ \-a\ 0\ 0\ 1 \(rq +undoes +.RB \(lq unu\ tile\ \-a\ 0\ 1\ 2 \(rq. +.IP \(bu +2n +Uses +.B nrrdUntile2D +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxMerge\fR\ \fIax0\fR\ \fIax1\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxMerge\fR\ \fIax0\fR\ \fIax1\fR> +the slow parts of axes +.I ax0 +and +.I ax1 +are merged into a (new) axis +.IR axMerge , +with the axis +.I ax0 +part being faster than +.IR ax1 . +(3 +.IR unsigned\ int s) +.TP +.B \-s\fR\ <\fIsize0\fR\ \fIsize1\fR>\ ,\ \fB\-\-size\fR\ <\fIsize0\fR\ \fIsize1\fR> +the slow parts of axes +.I ax0 +and +.I ax1 +are taken to have size +.I size0 +and +.IR size1 , +respectively, and axis +.I axMerge +will have size +.IB size0 * size1\fR. +(2 +.IR size_t s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-tile (1) diff --git a/unu-w2i.1 b/unu-w2i.1 new file mode 100644 index 0000000..17dd885 --- /dev/null +++ b/unu-w2i.1 @@ -0,0 +1,58 @@ +.TH UNU\-W2I "1" "April 2021" "" "User Commands" +.SH NAME +unu\-w2i \- converts from 1-D world to index position +.SH SYNOPSIS +.B unu\ w2i +.RI < center > +.RI < minPos > +.RI < maxPos > +.RI < num > +.RI < world > +.SH DESCRIPTION +Converts from 1-D world to index position, given the centering of the data +.RB ( cell +vs. +.BR node ), +the range of positions, and the number of intervals into which position has +been quantized. +This is a demo/utility, which does not actually operate on any +.IR nrrd s. +Previously available as the stand-alone +.B pos2idx +binary. +.P +Uses +.B NRRD_IDX +macro +.SH OPTIONS +.TP +.RI < center > +which centering applies to the quantized position. +Possibilities are: +.RS +7n +.IP \(bu 2 +.RB \(lq cell \(rq +for histogram bins, quantized values, and pixels-as-squares +.IP \(bu 2 +.RB \(lq node \(rq +for non-trivially interpolated sample points +.RE +.TP +.RI < minPos > +smallest position associated with index +.B 0 +.RI ( double ) +.TP +.RI < maxPos > +highest position associated with highest index +.RI ( double ) +.TP +.RI < num > +number of intervals into which position has been quantized +.RI ( double ) +.TP +.RI < world > +the input world position, to be converted to index +.RI ( double ) +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu.1 b/unu.1 index 6f8b611..cb49b63 100644 --- a/unu.1 +++ b/unu.1 @@ -4,7 +4,7 @@ unu \- Utah Nrrd Utilities command-line interface .SH SYNOPSIS .B unu .I COMMAND -.RI [ OPTION ]... +.RI [ OPTION ]...\: .SH DESCRIPTION .BR unu (1) is a command-line interface to much of the functionality in \(lqnrrd\(rq, a C @@ -116,11 +116,11 @@ Formats available: Nrrd data encodings available: .B raw ascii hex gz bz2 .SH COMMANDS -\" .P -\" Each of the following has a corresponding man page: for example, -\" .BR unu\-about (1) -\" for -\" .RB \(lq unu\ about \(rq. +.P +Each of the following has a corresponding man page: for example, +.BR unu\-about (1) +for +.RB \(lq unu\ about \(rq. .SS unu about Information about this program and its use .SS unu env @@ -303,6 +303,9 @@ Remap CC values down to lowest contiguous values Write .I nrrd with specific format, encoding, or endianness +.SH ENVIRONMENT +See +.BR unu\-env (1). .SH "SEE\ ALSO" .BR gprobe (1), .BR ilk (1), @@ -312,67 +315,66 @@ with specific format, encoding, or endianness .BR overrgb (1), .BR puller (1), .BR tend (1), -.BR vprobe (1) -\" .BR vprobe (1), -\" .BR unu-1op (1), -\" .BR unu-2op (1), -\" .BR unu-3op (1), -\" .BR unu-about (1), -\" .BR unu-acrop (1), -\" .BR unu-affine (1), -\" .BR unu-axdelete (1), -\" .BR unu-axinfo (1), -\" .BR unu-axinsert (1), -\" .BR unu-axmerge (1), -\" .BR unu-axsplit (1), -\" .BR unu-ccadj (1), -\" .BR unu-ccfind (1), -\" .BR unu-ccmerge (1), -\" .BR unu-ccsettle (1), -\" .BR unu-cksum (1), -\" .BR unu-cmedian (1), -\" .BR unu-convert (1), -\" .BR unu-crop (1), -\" .BR unu-data (1), -\" .BR unu-dhisto (1), -\" .BR unu-dice (1), -\" .BR unu-diff (1), -\" .BR unu-dist (1), -\" .BR unu-env (1), -\" .BR unu-fft (1), -\" .BR unu-flip (1), -\" .BR unu-gamma (1), -\" .BR unu-head (1), -\" .BR unu-heq (1), -\" .BR unu-histax (1), -\" .BR unu-histo (1), -\" .BR unu-i2w (1), -\" .BR unu-imap (1), -\" .BR unu-inset (1), -\" .BR unu-jhisto (1), -\" .BR unu-join (1), -\" .BR unu-lut (1), -\" .BR unu-lut2 (1), -\" .BR unu-make (1), -\" .BR unu-minmax (1), -\" .BR unu-mlut (1), -\" .BR unu-mrmap (1), -\" .BR unu-pad (1), -\" .BR unu-permute (1), -\" .BR unu-project (1), -\" .BR unu-quantize (1), -\" .BR unu-resample (1), -\" .BR unu-reshape (1), -\" .BR unu-rmap (1), -\" .BR unu-save (1), -\" .BR unu-shuffle (1), -\" .BR unu-slice (1), -\" .BR unu-splice (1), -\" .BR unu-sselect (1), -\" .BR unu-subst (1), -\" .BR unu-swap (1), -\" .BR unu-tile (1), -\" .BR unu-unorient (1), -\" .BR unu-unquantize (1), -\" .BR unu-untile (1), -\" .BR unu-w2i (1) +.BR vprobe (1), +.BR unu-1op (1), +.BR unu-2op (1), +.BR unu-3op (1), +.BR unu-about (1), +.BR unu-acrop (1), +.BR unu-affine (1), +.BR unu-axdelete (1), +.BR unu-axinfo (1), +.BR unu-axinsert (1), +.BR unu-axmerge (1), +.BR unu-axsplit (1), +.BR unu-ccadj (1), +.BR unu-ccfind (1), +.BR unu-ccmerge (1), +.BR unu-ccsettle (1), +.BR unu-cksum (1), +.BR unu-cmedian (1), +.BR unu-convert (1), +.BR unu-crop (1), +.BR unu-data (1), +.BR unu-dhisto (1), +.BR unu-dice (1), +.BR unu-diff (1), +.BR unu-dist (1), +.BR unu-env (1), +.BR unu-fft (1), +.BR unu-flip (1), +.BR unu-gamma (1), +.BR unu-head (1), +.BR unu-heq (1), +.BR unu-histax (1), +.BR unu-histo (1), +.BR unu-i2w (1), +.BR unu-imap (1), +.BR unu-inset (1), +.BR unu-jhisto (1), +.BR unu-join (1), +.BR unu-lut (1), +.BR unu-lut2 (1), +.BR unu-make (1), +.BR unu-minmax (1), +.BR unu-mlut (1), +.BR unu-mrmap (1), +.BR unu-pad (1), +.BR unu-permute (1), +.BR unu-project (1), +.BR unu-quantize (1), +.BR unu-resample (1), +.BR unu-reshape (1), +.BR unu-rmap (1), +.BR unu-save (1), +.BR unu-shuffle (1), +.BR unu-slice (1), +.BR unu-splice (1), +.BR unu-sselect (1), +.BR unu-subst (1), +.BR unu-swap (1), +.BR unu-tile (1), +.BR unu-unorient (1), +.BR unu-unquantize (1), +.BR unu-untile (1), +.BR unu-w2i (1) commit 516324379066d7660be0b0eaa7e3ff0bd06b27c9 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Wed Jul 21 16:06:33 2021 -0400 Opt in to rpmautospec diff --git a/changelog b/changelog new file mode 100644 index 0000000..833cd80 --- /dev/null +++ b/changelog @@ -0,0 +1,60 @@ +* Tue Apr 13 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-16 +- Finish man pages, except “unu” sub-pages. Start installing man pages. + +* Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 +- Fix typo in lib_install_dir.patch +- Update download URL from HTTP to HTTPS +- Improved package summaries and descriptions +- Adjust whitespace to personal preference +- Fix stray line continuation backslash +- Support EPEL7 +- Build with “levmar” support enabled +- Use stricter file globs, including specifying the so-version +- Add an -examples subpackage so the BSD and zlib licenses can be “contained” + to that subpackage; remove certain unused files with other licenses in %%prep +- Require cmake-filesystem instead of all of CMake in -devel +- More precisely skip overly-strict floating-point tests where required +- Start work on adding a complete set of man pages + +* Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + +* Fri Sep 04 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.11.0-13 +- Use cmake macros to fix build + +* Sat Aug 01 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-12 +- Second attempt - Rebuilt for + https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + +* Wed Jul 29 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-11 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + +* Fri Jan 31 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-10 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + +* Sat Jul 27 2019 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-9 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild + +* Sun Feb 03 2019 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild + +* Sat Jul 14 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild + +* Fri Feb 09 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-6 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild + +* Thu Aug 03 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild + +* Thu Jul 27 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild + +* Sat Feb 11 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild + +* Fri Feb 05 2016 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild + +* Wed Nov 25 2015 Dmitry Mikhirev <mikhirev(a)gmail.com> 1.11.0-1 +- Initial package diff --git a/teem.spec b/teem.spec index 5c62687..aded044 100644 --- a/teem.spec +++ b/teem.spec @@ -1,7 +1,7 @@ Name: teem Version: 1.11.0 %global so_version 1 -Release: 16%{?dist} +Release: %autorelease -b 13 Summary: Libraries for processing and visualizing scientific raster data # The entire source is LGPLv2+, except files noted at the License fields of certain subpackages. @@ -351,63 +351,4 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %changelog -* Tue Apr 13 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-16 -- Finish man pages, except “unu” sub-pages. Start installing man pages. - -* Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 -- Fix typo in lib_install_dir.patch -- Update download URL from HTTP to HTTPS -- Improved package summaries and descriptions -- Adjust whitespace to personal preference -- Fix stray line continuation backslash -- Support EPEL7 -- Build with “levmar” support enabled -- Use stricter file globs, including specifying the so-version -- Add an -examples subpackage so the BSD and zlib licenses can be “contained” - to that subpackage; remove certain unused files with other licenses in %%prep -- Require cmake-filesystem instead of all of CMake in -devel -- More precisely skip overly-strict floating-point tests where required -- Start work on adding a complete set of man pages - -* Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild - -* Fri Sep 04 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.11.0-13 -- Use cmake macros to fix build - -* Sat Aug 01 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-12 -- Second attempt - Rebuilt for - https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Wed Jul 29 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-11 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Fri Jan 31 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-10 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - -* Sat Jul 27 2019 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-9 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild - -* Sun Feb 03 2019 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-8 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild - -* Sat Jul 14 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild - -* Fri Feb 09 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-6 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild - -* Thu Aug 03 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild - -* Thu Jul 27 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-4 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild - -* Sat Feb 11 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild - -* Fri Feb 05 2016 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild - -* Wed Nov 25 2015 Dmitry Mikhirev <mikhirev(a)gmail.com> 1.11.0-1 -- Initial package +%autochangelog commit 7dd3eb9d51ce2c2984ed8f6c467d7483da181c65 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 13 12:04:10 2021 -0400 Finish man pages, except “unu” sub-pages. Start installing man pages. diff --git a/ilk.1 b/ilk.1 index 51b2915..e88f365 100644 --- a/ilk.1 +++ b/ilk.1 @@ -33,7 +33,7 @@ Applies linear (homogenous coordinate) transforms to a given image, using the given kernel for resampling. .SH OPTIONS .TP -.BR @file \ ... +.IR @file \ ... response file(s) containing command-line arguments .TP .B \-i\fR <\fIimage\fR> diff --git a/miter.1 b/miter.1 index 75d7ef4..254f8b8 100644 --- a/miter.1 +++ b/miter.1 @@ -79,7 +79,7 @@ miter \- a simple but effective little volume renderer .RI < filename >] .SH OPTIONS .TP -.BR @file \ ... +.IR @file \ ... response file(s) containing command-line arguments .TP .B \-i\fR <\fInsin\fR> diff --git a/mrender.1 b/mrender.1 index f619ac2..c58da9e 100644 --- a/mrender.1 +++ b/mrender.1 @@ -69,7 +69,7 @@ in the output image. .SH OPTIONS .TP -.BR @file \ ... +.IR @file \ ... response file(s) containing command-line arguments .TP .B \-i\fR <\fInin\fR> diff --git a/overrgb.1 b/overrgb.1 index 538bf57..a9e2a0c 100644 --- a/overrgb.1 +++ b/overrgb.1 @@ -31,9 +31,6 @@ have to be the same size as the input image; it will be resampled (with linear interpolation) to fit. .SH OPTIONS .TP -.BR @file \ ... -response file(s) containing command-line arguments -.TP .B \-i\fR <\fInin\fR> input nrrd to composite .RI ( nrrd ) diff --git a/puller.1 b/puller.1 index fb03592..45b7635 100644 --- a/puller.1 +++ b/puller.1 @@ -3,7 +3,7 @@ puller \- command-line interface to the \(lqpull\(rq library .SH SYNOPSIS .B puller -.RB [ @file \ ...] +.RI [ @file \ ...] .RB [ \-int .RI < int >] .RB [ \-enr @@ -139,7 +139,7 @@ puller \- command-line interface to the \(lqpull\(rq library .RI < base >] .SH OPTIONS .TP -.BR @file \ ... +.IR @file \ ... response file(s) containing command-line arguments .TP .B \-int\fR <\fIint\fR> diff --git a/teem.spec b/teem.spec index 61764d0..5c62687 100644 --- a/teem.spec +++ b/teem.spec @@ -1,11 +1,7 @@ -# Writing man pages is a work in progress. We do not install them until we have -# a complete set. -%bcond_with man_pages - Name: teem Version: 1.11.0 %global so_version 1 -Release: 15%{?dist} +Release: 16%{?dist} Summary: Libraries for processing and visualizing scientific raster data # The entire source is LGPLv2+, except files noted at the License fields of certain subpackages. @@ -45,36 +41,36 @@ Source807: tend-mconv.1 Source808: tend-msim.1 Source809: tend-make.1 Source810: tend-avg.1 -#Source811: tend-helix.1 -#Source812: tend-sten.1 -#Source813: tend-glyph.1 -#Source814: tend-ellipse.1 -#Source815: tend-anplot.1 -#Source816: tend-anvol.1 -#Source817: tend-anscale.1 -#Source818: tend-anhist.1 -#Source819: tend-triple.1 -#Source820: tend-tconv.1 -#Source821: tend-point.1 -#Source822: tend-slice.1 -#Source823: tend-norm.1 -#Source824: tend-fiber.1 -#Source825: tend-eval.1 -#Source826: tend-evalpow.1 -#Source827: tend-evalclamp.1 -#Source828: tend-evaladd.1 -#Source829: tend-evalmul.1 -#Source830: tend-log.1 -#Source831: tend-exp.1 -#Source832: tend-evec.1 -#Source833: tend-evecrgb.1 -#Source834: tend-evq.1 -#Source835: tend-unmf.1 -#Source836: tend-expand.1 -#Source837: tend-shrink.1 -#Source838: tend-bfit.1 -#Source839: tend-satin.1 -# +Source811: tend-helix.1 +Source812: tend-sten.1 +Source813: tend-glyph.1 +Source814: tend-ellipse.1 +Source815: tend-anplot.1 +Source816: tend-anvol.1 +Source817: tend-anscale.1 +Source818: tend-anhist.1 +Source819: tend-triple.1 +Source820: tend-tconv.1 +Source821: tend-point.1 +Source822: tend-slice.1 +Source823: tend-norm.1 +Source824: tend-fiber.1 +Source825: tend-eval.1 +Source826: tend-evalpow.1 +Source827: tend-evalclamp.1 +Source828: tend-evaladd.1 +Source829: tend-evalmult.1 +Source830: tend-log.1 +Source831: tend-exp.1 +Source832: tend-evec.1 +Source833: tend-evecrgb.1 +Source834: tend-evq.1 +Source835: tend-unmf.1 +Source836: tend-expand.1 +Source837: tend-shrink.1 +Source838: tend-bfit.1 +Source839: tend-satin.1 + #Source900: unu-about.1 #Source901: unu-env.1 #Source902: unu-i2w.1 @@ -273,20 +269,20 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %{SOURCE820} %{SOURCE821} %{SOURCE822} %{SOURCE823} %{SOURCE824} \ %{SOURCE825} %{SOURCE826} %{SOURCE827} %{SOURCE828} %{SOURCE829} \ %{SOURCE830} %{SOURCE831} %{SOURCE832} %{SOURCE833} %{SOURCE834} \ - %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} \ - %{SOURCE900} %{SOURCE901} %{SOURCE902} %{SOURCE903} %{SOURCE904} \ - %{SOURCE905} %{SOURCE906} %{SOURCE907} %{SOURCE908} %{SOURCE909} \ - %{SOURCE910} %{SOURCE911} %{SOURCE912} %{SOURCE913} %{SOURCE914} \ - %{SOURCE915} %{SOURCE916} %{SOURCE917} %{SOURCE918} %{SOURCE919} \ - %{SOURCE920} %{SOURCE921} %{SOURCE922} %{SOURCE923} %{SOURCE924} \ - %{SOURCE925} %{SOURCE926} %{SOURCE927} %{SOURCE928} %{SOURCE929} \ - %{SOURCE930} %{SOURCE931} %{SOURCE932} %{SOURCE933} %{SOURCE934} \ - %{SOURCE935} %{SOURCE936} %{SOURCE937} %{SOURCE938} %{SOURCE939} \ - %{SOURCE940} %{SOURCE941} %{SOURCE942} %{SOURCE943} %{SOURCE944} \ - %{SOURCE945} %{SOURCE946} %{SOURCE947} %{SOURCE948} %{SOURCE949} \ - %{SOURCE950} %{SOURCE951} %{SOURCE952} %{SOURCE953} %{SOURCE954} \ - %{SOURCE955} %{SOURCE956} %{SOURCE957} %{SOURCE958} %{SOURCE959} \ - %{SOURCE960} %{SOURCE961} + %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} + #{SOURCE900} #{SOURCE901} #{SOURCE902} #{SOURCE903} #{SOURCE904} \ + #{SOURCE905} #{SOURCE906} #{SOURCE907} #{SOURCE908} #{SOURCE909} \ + #{SOURCE910} #{SOURCE911} #{SOURCE912} #{SOURCE913} #{SOURCE914} \ + #{SOURCE915} #{SOURCE916} #{SOURCE917} #{SOURCE918} #{SOURCE919} \ + #{SOURCE920} #{SOURCE921} #{SOURCE922} #{SOURCE923} #{SOURCE924} \ + #{SOURCE925} #{SOURCE926} #{SOURCE927} #{SOURCE928} #{SOURCE929} \ + #{SOURCE930} #{SOURCE931} #{SOURCE932} #{SOURCE933} #{SOURCE934} \ + #{SOURCE935} #{SOURCE936} #{SOURCE937} #{SOURCE938} #{SOURCE939} \ + #{SOURCE940} #{SOURCE941} #{SOURCE942} #{SOURCE943} #{SOURCE944} \ + #{SOURCE945} #{SOURCE946} #{SOURCE947} #{SOURCE948} #{SOURCE949} \ + #{SOURCE950} #{SOURCE951} #{SOURCE952} #{SOURCE953} #{SOURCE954} \ + #{SOURCE955} #{SOURCE956} #{SOURCE957} #{SOURCE958} #{SOURCE959} \ + #{SOURCE960} #{SOURCE961} %endif @@ -331,7 +327,7 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %{_mandir}/man1/tend.1* %{_mandir}/man1/tend-*.1* %{_mandir}/man1/unu.1* -%{_mandir}/man1/unu-*.1* +#{_mandir}/man1/unu-*.1* %{_mandir}/man1/vprobe.1* %endif @@ -355,6 +351,9 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %changelog +* Tue Apr 13 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-16 +- Finish man pages, except “unu” sub-pages. Start installing man pages. + * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch - Update download URL from HTTP to HTTPS diff --git a/tend-anhist.1 b/tend-anhist.1 new file mode 100644 index 0000000..a475647 --- /dev/null +++ b/tend-anhist.1 @@ -0,0 +1,61 @@ +.TH TEND\-ANHIST "1" "April 2021" "" "User Commands" +.SH NAME +tend\-anhist \- generate barycentric histograms of anisotropy +.SH SYNOPSIS +.B tend\ anhist +.RB [ \-v +.RI < westin\ version >] +.RB [ \-w +.RI < nweight >] +.B \-r +.RI < res > +.RB [ \-right ] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate barycentric histograms of anisotropy. +The barycentric space used is either one of Westin\(cqs triple of spherical, +linear, and planar anisotropy. +The bin counts in the histogram are weighted by the confidence value. +.SH OPTIONS +.TP +.B \-v\fR <\fIwestin\ version\fR> +Which version of Westin\(cqs anisotropy metric triple to use, either +.RB \(lq 1 \(rq +or +.RB \(lq 2 \(rq +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-w\fR <\fInweight\fR> +how to weigh contributions to histogram. +By default (not using this option), the increment is one bin count per sample, +but by giving a +.IR nrrd , +the value in the +.I nrrd +at the corresponding location will be the bin count increment; default: +\(lq\(rq +.TP +.B \-r\fR <\fIres\fR> +resolution of anisotropy plot +.RI ( int ) +.TP +.B \-right +sample a right-triangle-shaped region, instead of a roughly equilateral +triangle. +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-anplot.1 b/tend-anplot.1 new file mode 100644 index 0000000..44024a6 --- /dev/null +++ b/tend-anplot.1 @@ -0,0 +1,106 @@ +.TH TEND\-ANPLOT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-anplot \- graph anisotropy metric in barycentric coords +.SH SYNOPSIS +.B tend\ anplot +.RB [ \-r +.RI < res >] +.RB [ \-w ] +.RB [ \-hflip ] +.RB [ \-nan ] +.B \-a +.RI < aniso > +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Graph anisotropy metric in barycentric coordinates. +The metrics all vary from +.B 0.0 +to +.BR 1.0 , +and will be sampled in the lower right half of the image. +The plane on which they are sampled is a surface of constant trace. +You may want to use +.in +4n +.EX +.B unu\ resample\ \-s\ =\ x0.57735\ \-k\ tent +.in +.EE +to transform the triangle into a 30-60-90 triangle, and +.in +4n +.EX +.B ilk\ \-t\ 1,\-0.5,0,0,0.866,0\ \-k\ tent\ \-0\ u:0,1\ \-b\ pad\ \-bg\ 0 +.EE +.in +(possibly followed by +.BR teem/src/limntest/triimg ) +to transform the domain into an equilateral triangle. +.SH OPTIONS +.TP +.B \-res\fR <\fIres\fR> +resolution of anisotropy plot +.RI ( int ); +default: +.RB \(lq 256 \(rq +.TP +.B \-w +sample the whole triangle of constant trace, instead of just the sixth of it in +which the eigenvalues have the traditional sorted order. +.TP +.B \-hflip +flip the two bottom corners (swapping the place of linear and planar) +.TP +.B \-nan +set the pixel values outside the triangle to be +.BR NaN , +instead of +.B 0 +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy metric to plot. +All the Westin metrics come in two versions. +Currently supported: +.RS +7n +.IP \(bu 2 +.RB \(lq cl1 \(rq, +.RB \(lq cl2 \(rq: +Westin\(cqs linear +.IP \(bu 2 +.RB \(lq cp1 \(rq, +.RB \(lq cp2 \(rq: +Westin\(cqs planar +.IP \(bu 2 +.RB \(lq ca1 \(rq, +.RB \(lq ca2 \(rq: +Westin\(cqs linear + planar +.IP \(bu 2 +.RB \(lq cs1 \(rq, +.RB \(lq cs2 \(rq: +Westin\(cqs spherical +.IP \(bu 2 +.RB \(lq ct1 \(rq, +.RB \(lq ct2 \(rq: +GK\(cqs anisotropy type (cp/ca) +.IP \(bu 2 +.RB \(lq ra \(rq: +Basser/Pierpaoli relative anisotropy/sqrt(2) +.IP \(bu 2 +.RB \(lq fa \(rq: +Basser/Pierpaoli fractional anisotropy +.IP \(bu 2 +.RB \(lq vf \(rq: +volume fraction = 1\-(Basser/Pierpaoli volume ratio) +.IP \(bu 2 +.RB \(lq tr \(rq: +trace +.RE +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR ilk (1), +.BR unu\-resample (1) diff --git a/tend-anscale.1 b/tend-anscale.1 new file mode 100644 index 0000000..740157d --- /dev/null +++ b/tend-anscale.1 @@ -0,0 +1,44 @@ +.TH TEND\-ANSCALE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-anscale \- scale the anisotropic component of the tensors +.SH SYNOPSIS +.B tend\ anscale +.B \-s +.RI < scale > +.RB [ \-fd ] +.RB [ \-mp ] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Scale the anisotropic component of the tensors. +This maintains the isotropic component of the tensor, and fixes either the +trace or determinant, while scaling up (or down) the \(lqdeviatoric\(rq +component of the tensor. +Good for exaggerating the shape of nearly isotropic tensors. +.SH OPTIONS +.TP +.B \-s\fR <\fIscale\fR> +Amount by which to scale deviatoric component of tensor. +.RI ( float ) +.TP +.B \-fd +instead of fixing the per-sample trace (the default), fix the determinant +(ellipsoid volume) +.TP +.B \-mp +after changing the eigenvalues of the tensor, enforce their non-negative-ness. +By default, no such constraint is imposed. +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-anvol.1 b/tend-anvol.1 new file mode 100644 index 0000000..6c06441 --- /dev/null +++ b/tend-anvol.1 @@ -0,0 +1,75 @@ +.TH TEND\-ANVOL "1" "April 2021" "" "User Commands" +.SH NAME +tend\-anvol \- apply an anisotropy metric to a DT volume +.SH SYNOPSIS +.B tend\ anvol +.B \-a +.RI < aniso > +.RB [ \-t +.RI < thresh >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Apply an anisotropy metric to a DT volume. +The anisotropy value will be zero in the locations which don\(cqt meet the +given confidence threshold. +.SH OPTIONS +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy metric to plot. +All the Westin metrics come in two versions. +Currently supported: +.RS +7n +.IP \(bu 2 +.RB \(lq cl1 \(rq, +.RB \(lq cl2 \(rq: +Westin\(cqs linear +.IP \(bu 2 +.RB \(lq cp1 \(rq, +.RB \(lq cp2 \(rq: +Westin\(cqs planar +.IP \(bu 2 +.RB \(lq ca1 \(rq, +.RB \(lq ca2 \(rq: +Westin\(cqs linear + planar +.IP \(bu 2 +.RB \(lq cs1 \(rq, +.RB \(lq cs2 \(rq: +Westin\(cqs spherical +.IP \(bu 2 +.RB \(lq ct1 \(rq, +.RB \(lq ct2 \(rq: +GK\(cqs anisotropy type (cp/ca) +.IP \(bu 2 +.RB \(lq ra \(rq: +Basser/Pierpaoli relative anisotropy/sqrt(2) +.IP \(bu 2 +.RB \(lq fa \(rq: +Basser/Pierpaoli fractional anisotropy +.IP \(bu 2 +.RB \(lq vf \(rq: +volume fraction = 1\-(Basser/Pierpaoli volume ratio) +.IP \(bu 2 +.RB \(lq tr \(rq: +trace +.RE +.TP +.B \-t\fR <\fIthresh\fR> +confidence threshold +.RI ( float ) +default: +.RB \(lq 0.5 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-bfit.1 b/tend-bfit.1 new file mode 100644 index 0000000..9269f75 --- /dev/null +++ b/tend-bfit.1 @@ -0,0 +1,72 @@ +.TH TEND\-BFIT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-bfit \- non-linear least-squares fitting of \fIb\fR-value curves +.SH SYNOPSIS +.B tend\ bfit +.RI [ @file \ ...] +.RB [ \-i +.RI < nin >] +.B \-b +.RI < b1 \ b2 \ ...> +.RB [ \-w +.RI < w1 \ w2 \ ...>] +.RB [ \-imax +.RI < #\ iter >] +.RB [ \-eps +.RI < epsilon >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Non-linear least-squares fitting of \fIb\fR-value curves. +Axis 0 is replaced by three values: +.IR amp ,\ dec ,\ err , +based on a non-linear least-squares fit of +.IB amp *exp(\- b * dec ) +to the range of DWI values along input axis 0, as a function of changing +.I b +values. +.SH OPTIONS +.TP +.IR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fInin\fR> +Input +.IR nrrd . +List of DWIs from different +.IR b -values +must be along axis 0; default: +.RB \(lq \- \(rq +.TP +.B \-b\fR <\fIb1\fR\ \fIb2\fR\ ...> +.I b +values across axis 0 of input +.I nrrd +(2 or more +.IR double s) +.TP +.B \-w\fR <\fIw1\fR\ \fIw2\fR\ ...> +weights for samples in non-linear fitting (2 or more +.IR double s) +.TP +.B \-imax\fR <\fI#\ iter\fR> +max number of iterations to use in non-linear fitting, or, use +.B 0 +to do only initial linear fit +.RI ( int ); +default: +.RB \(lq 10 \(rq +.TP +.B \-eps\fR <\fIepsilon\fR> +epsilon convergence threshold for non-linear fitting +.RI ( double ); +default: +.RB \(lq 1 \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-ellipse.1 b/tend-ellipse.1 new file mode 100644 index 0000000..13f7913 --- /dev/null +++ b/tend-ellipse.1 @@ -0,0 +1,99 @@ +.TH TEND\-ELLIPSE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-ellipse \- generate postscript renderings of 2D glyphs +.SH SYNOPSIS +.B tend\ ellipse +.RB [ \-ctr +.RI < conf\ thresh >] +.RB [ \-gsc +.RI < scale >] +.RB [ \-dot +.RI < radius >] +.RB [ \-wid +.RI < width >] +.RB [ \-inv ] +.RB [ \-min +.RI < minX \ minY >] +.RB [ \-max +.RI < maxX \ maxY >] +.RB [ \-i +.RI < nin >] +.RB [ \-p +.RI < pos\ array >] +.RB [ \-s +.RI < stn\ array >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate postscript renderings of 2D glyphs. +Not much to look at here. +.SH OPTIONS +.TP +.B \-ctr\fR <\fIconf\ thresh\fR> +Glyphs will be drawn only for tensors with confidence values greater than this +threshold +.RI ( float ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-gsc\fR <\fIscale\fR> +over-all glyph size +.RI ( float ); +default: +.RB \(lq 1 \(rq +.TP +.B \-dot\fR <\fIradius\fR> +radius of little dot to put in middle of ellipse, or +.RB \(lq 0 \(rq +for no such dot +.RI ( float ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-wid\fR <\fIwidth\fR> +width of lines for tractlets +.RI ( float ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-inv +use white ellipses on black background, instead of reverse +.TP +.B \-min\fR <\fIminX\fR \fIminY\fR> +when using +.RB \(lq \-p \(rq, +minimum corner (2 +.IR float s); +default: +.RB \(lq \-1\ \-1 \(rq +.TP +.B \-max\fR <\fImaxX\fR \fImaxY\fR> +when using +.RB \(lq \-p \(rq, +maximum corner (2 +.IR float s); +default: +.RB \(lq 1\ 1 \(rq +.TP +.B \-i\fR <\fInin\fR> +image of 2D tensors; default: +.RB \(lq \- \(rq +.TP +.B \-p\fR <\fIpos\ array\fR> +Instead of being on a grid, tensors are at arbitrary locations, as defined by +this 2-by-N array of +.IR float s); +default: \(lq\(rq +.TP +.B \-s\fR <\fIstn\ array\fR> +Locations given by +.RB \(lq \-p \(rq +have this connectivity; default: \(lq\(rq +.TP +.B \-o\fR <\fInout\fR> +output PostScript file +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-eval.1 b/tend-eval.1 new file mode 100644 index 0000000..de9dc27 --- /dev/null +++ b/tend-eval.1 @@ -0,0 +1,47 @@ +.TH TEND\-EVAL "1" "April 2021" "" "User Commands" +.SH NAME +tend\-eval \- calculate one or more eigenvalues in a DT volume +.SH SYNOPSIS +.B tend\ eval +.B \-c +.RI < c0 \ ...> +.RB [ \-t +.RI < thresh >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-c\fR <\fIc0\fR\ ...> +which eigenvalues should be saved out. +.RB \(lq 0 \(rq +for the largest, +.RB \(lq 1 \(rq +for the middle, +.RB \(lq 2 \(rq +for the smallest, +.RB \(lq 0\ 1 \(rq, +.RB \(lq 1\ 2 \(rq, +.RB \(lq 0\ 1\ 2 \(rq +or similar for more than one (1..3 +.IR int s) +.TP +.B \-t\fR <\fIthresh\fR> +confidence threshold +.RI ( float ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-evec (1) diff --git a/tend-evaladd.1 b/tend-evaladd.1 new file mode 100644 index 0000000..e8754f9 --- /dev/null +++ b/tend-evaladd.1 @@ -0,0 +1,35 @@ +.TH TEND\-EVALADD "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evaladd \- modify shape by adding a constant to all eigenvalues +.SH SYNOPSIS +.B tend\ evaladd +.B \-v +.RI < value > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Modify shape by adding a constant to all eigenvalues. +The orientation of the tensor is unchanged. +Note that unlike +.BR tend\-anscale (1), +this operation can completely change the shape of the tensor. +.SH OPTIONS +.TP +.B \-v\fR <\fIvalue\fR> +Value to add to all eigenvalues +.RI ( float ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-anscale (1) diff --git a/tend-evalclamp.1 b/tend-evalclamp.1 new file mode 100644 index 0000000..b88bd6e --- /dev/null +++ b/tend-evalclamp.1 @@ -0,0 +1,47 @@ +.TH TEND\-EVALCLAMP "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evalclamp \- modify shape by clamping eigenvalues in some range +.SH SYNOPSIS +.B tend\ evalclamp +.B \-min +.RI < min > +.RB [ \-max +.RI < max >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Modify shape by clamping eigenvalues in some range. +The orientation of the tensor is unchanged. +Note that unlike +.BR tend\-anscale (1), +this operation can completely change the shape of the tensor. +.SH OPTIONS +.TP +.B \-min\fR <\fImin\fR> +Eigenvalues are clamped from below by this (the minimum output eigenvalue). +Use +.RB \(lq nan \(rq +to signify that no minimum clamping should be done. +.RI ( float ) +.TP +.B \-max\fR <\fImax\fR> +Eigenvalues are clamped from above by this (the maximum output eigenvalue). +Use +.RB \(lq nan \(rq +to signify that no maximum clamping should be done. +.RI ( float ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-anscale (1) diff --git a/tend-evalmult.1 b/tend-evalmult.1 new file mode 100644 index 0000000..3bf86b0 --- /dev/null +++ b/tend-evalmult.1 @@ -0,0 +1,31 @@ +.TH TEND\-EVALMULT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evalmult \- modify shape by multiplying eigenvalues by a constant +.SH SYNOPSIS +.B tend\ evalmult +.B \-v +.RI < value > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Modify shape by multiplying eigenvalues by a constant. +The orientation of the tensor is unchanged. +.SH OPTIONS +.TP +.B \-v\fR <\fIvalue\fR> +Value to multiply eigenvalues by +.RI ( float ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-evalpow.1 b/tend-evalpow.1 new file mode 100644 index 0000000..9f1adf5 --- /dev/null +++ b/tend-evalpow.1 @@ -0,0 +1,31 @@ +.TH TEND\-EVALPOW "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evalpow \- modify shape by raising eigenvalues to some power +.SH SYNOPSIS +.B tend\ evalpow +.B \-p +.RI < power > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Modify shape by raising eigenvalues to some power. +The orientation of the tensor is unchanged. +.SH OPTIONS +.TP +.B \-p\fR <\fIpower\fR> +Power to which to raise all the eigenvalues. +.RI ( float ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-evec.1 b/tend-evec.1 new file mode 100644 index 0000000..74e7988 --- /dev/null +++ b/tend-evec.1 @@ -0,0 +1,47 @@ +.TH TEND\-EVEC "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evec \- calculate one or more eigenvectors in a DT volume +.SH SYNOPSIS +.B tend\ evec +.B \-c +.RI < c0 \ ...> +.RB [ \-t +.RI < thresh >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-c\fR <\fIc0\fR\ ...> +which eigenvectors should be saved out. +.RB \(lq 0 \(rq +for the largest, +.RB \(lq 1 \(rq +for the middle, +.RB \(lq 2 \(rq +for the smallest, +.RB \(lq 0\ 1 \(rq, +.RB \(lq 1\ 2 \(rq, +.RB \(lq 0\ 1\ 2 \(rq +or similar for more than one (1..3 +.IR int s) +.TP +.B \-t\fR <\fIthresh\fR> +confidence threshold +.RI ( float ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-eval (1) diff --git a/tend-evecrgb.1 b/tend-evecrgb.1 new file mode 100644 index 0000000..94e209c --- /dev/null +++ b/tend-evecrgb.1 @@ -0,0 +1,108 @@ +.TH TEND\-EVECRGB "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evecrgb \- make an RGB volume from an eigenvector and an anisotropy +.SH SYNOPSIS +.B tend\ evecrgb +.B \-c +.RI < evec\ index > +.B \-a +.RI < aniso > +.RB [ \-t +.RI < thresh >] +.RB [ \-bg +.RI < background >] +.RB [ \-gr +.RI < gray >] +.RB [ \-gam +.RI < gamma >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-c\fR <\fIevec\ index\fR> +which eigenvector will be colored. +.RB \(lq 0 \(rq +for the principal, +.RB \(lq 1 \(rq +for the middle, +.RB \(lq 2 \(rq +for the minor +.RI ( unsigned\ int ) +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy to use for modulating the saturation of the colors. +All the Westin metrics come in two versions. +Currently supported: +.RS +7n +.IP \(bu 2 +.RB \(lq cl1 \(rq, +.RB \(lq cl2 \(rq: +Westin\(cqs linear +.IP \(bu 2 +.RB \(lq cp1 \(rq, +.RB \(lq cp2 \(rq: +Westin\(cqs planar +.IP \(bu 2 +.RB \(lq ca1 \(rq, +.RB \(lq ca2 \(rq: +Westin\(cqs linear + planar +.IP \(bu 2 +.RB \(lq cs1 \(rq, +.RB \(lq cs2 \(rq: +Westin\(cqs spherical +.IP \(bu 2 +.RB \(lq ct1 \(rq, +.RB \(lq ct2 \(rq: +GK\(cqs anisotropy type (cp/ca) +.IP \(bu 2 +.RB \(lq ra \(rq: +Basser/Pierpaoli relative anisotropy/sqrt(2) +.IP \(bu 2 +.RB \(lq fa \(rq: +Basser/Pierpaoli fractional anisotropy +.IP \(bu 2 +.RB \(lq vf \(rq: +volume fraction = 1\-(Basser/Pierpaoli volume ratio) +.IP \(bu 2 +.RB \(lq tr \(rq: +trace +.RE +.TP +.B \-t\fR <\fIthresh\fR> +confidence threshold +.RI ( float ) +default: +.RB \(lq 0.5 \(rq +.TP +.B \-bg\fR <\fIbackground\fR> +gray level to use for voxels whose confidence is zero +.RI ( double ) +default: +.RB \(lq 0 \(rq +.TP +.B \-gr\fR <\fIgray\fR> +the gray level to desaturate towards as anisotropy decreases (while confidence +remains 1.0) +.RI ( double ) +default: +.RB \(lq 0 \(rq +.TP +.B \-gam\fR <\fIgamma\fR> +gamma to use on color components +.RI ( double ) +default: +.RB \(lq 1 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-evq.1 b/tend-evq.1 new file mode 100644 index 0000000..2266f75 --- /dev/null +++ b/tend-evq.1 @@ -0,0 +1,93 @@ +.TH TEND\-EVQ "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evq \- quantize directions of diffusion +.SH SYNOPSIS +.B tend\ evq +.RB [ \-c +.RI < evec\ index >] +.B \-a +.RI < aniso > +.RB [ \-ns ] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Quantize directions of diffusion. +Because VTK doesn\(cqt do multi-dimensional colormaps, we have to quantize +directions of diffusion (usually just the principal eigenvector) in order to +create the usual XYZ<->RGB coloring. +Because eigenvector directions are poorly defined in regions of low anisotropy, +the length of the vector (pre-quantization) is modulated by anisotropy, +requiring the selection of some anisotropy metric. +.SH OPTIONS +.TP +.B \-c\fR <\fIevec\ index\fR> +Which eigenvector should be quantized: + +.RB \(lq 0 \(rq +for the direction of fastest diffusion (eigenvector associated with largest +eigenvalue), +.RB \(lq 1 \(rq +or +.RB \(lq 2 \(rq +for other two eigenvectors (associated with middle and smallest eigenvalue) +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy metric to scale the eigenvector with. +All the Westin metrics come in two versions. +Currently supported: +.RS +7n +.IP \(bu 2 +.RB \(lq cl1 \(rq, +.RB \(lq cl2 \(rq: +Westin\(cqs linear +.IP \(bu 2 +.RB \(lq cp1 \(rq, +.RB \(lq cp2 \(rq: +Westin\(cqs planar +.IP \(bu 2 +.RB \(lq ca1 \(rq, +.RB \(lq ca2 \(rq: +Westin\(cqs linear + planar +.IP \(bu 2 +.RB \(lq cs1 \(rq, +.RB \(lq cs2 \(rq: +Westin\(cqs spherical +.IP \(bu 2 +.RB \(lq ct1 \(rq, +.RB \(lq ct2 \(rq: +GK\(cqs anisotropy type (cp/ca) +.IP \(bu 2 +.RB \(lq ra \(rq: +Basser/Pierpaoli relative anisotropy/sqrt(2) +.IP \(bu 2 +.RB \(lq fa \(rq: +Basser/Pierpaoli fractional anisotropy +.IP \(bu 2 +.RB \(lq vf \(rq: +volume fraction = 1\-(Basser/Pierpaoli volume ratio) +.IP \(bu 2 +.RB \(lq tr \(rq: +trace +.RE +.TP +.B \-ns +Don\(cqt attenuate the color by anisotropy. +By default (not using this option), regions with low or no anisotropy are very +dark colors or black +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-exp.1 b/tend-exp.1 new file mode 100644 index 0000000..e01f780 --- /dev/null +++ b/tend-exp.1 @@ -0,0 +1,28 @@ +.TH TEND\-EXP "1" "April 2021" "" "User Commands" +.SH NAME +tend\-exp \- calculates \fBexp()\fR of the tensor +.SH SYNOPSIS +.B tend\ exp +.RB [ \-i +.RI < nin >] +.B \-o +.RI < nout > +.SH DESCRIPTION +Calculates +.B exp() +of the tensor, which is based on +.B exp() +of the eigenvalues. +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-expand.1 b/tend-expand.1 new file mode 100644 index 0000000..7025c54 --- /dev/null +++ b/tend-expand.1 @@ -0,0 +1,72 @@ +.TH TEND\-EXPAND "1" "April 2021" "" "User Commands" +.SH NAME +tend\-expand \- converts masked non-redundant tensor images to redundant +.SH SYNOPSIS +.B tend\ expand +.RB [ \-t +.RI < thresh >] +.RB [ \-s +.RI < scale >] +.B [ \-unmf ] +.B [ \-ro ] +.B [ \-roo ] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Converts masked non-redundant tensor images to redundant. +For +images of 3D tensors, this converts from a 7-value tensor starting with the +confidence/mask value +.BI ( conf ,\ Dxx ,\ Dxy ,\ Dxz ,\ Dyy ,\ Dyz ,\ Dzz ) +to a 9-value tensor +with the full matrix +.BI ( Dxx ,\ Dxy ,\ Dxz ,\ Dxy ,\ Dyy ,\ Dyz ,\ Dxz ,\ Dyz ,\ Dzz ). +This is set to all zeros when the confidence is below the given threshold. +For +images +of 2D tensors, the conversion is from +.BI ( conf ,\ Dxx ,\ Dxy ,\ Dyy ) +to +.BI ( Dxx ,\ Dxy ,\ Dxy ,\ Dyy ). +.SH OPTIONS +.TP +.B \-t\fR <\fIthresh\fR> +confidence level to threshold output tensors at. +Should be between +.B 0.0 +and +.BR 1.0 . +.RI ( float ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-s\fR <\fIscale\fR> +how to scale values before saving as 9-value tensor. +Useful for visualization tools which assume certain characteristic ranges of +eigenvalues +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-unmf +apply and remove the measurement frame, if it exists +.TP +.B \-ro +reduce general image orientation to axis-aligned spacings +.TP +.B \-roo +reduce general image orientation to axis-aligned spacings, while also making +some effort to set axis mins from space origin +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume, with 7 values per sample; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume, with the 9 matrix components per sample +.RI ( string ) +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-shrink (1) diff --git a/tend-fiber.1 b/tend-fiber.1 new file mode 100644 index 0000000..8733a8a --- /dev/null +++ b/tend-fiber.1 @@ -0,0 +1,163 @@ +.TH TEND\-FIBER "1" "April 2021" "" "User Commands" +.SH NAME +tend\-fiber \- fiber tractography, from one or more seeds +.SH SYNOPSIS +.B tend\ fiber +.RB [ \-i +.RI < nin >] +.RB [ \-dwi ] +.RB [ \-s +.RI < seed\ point >] +.RB [ \-ns +.RI < seed\ nrrd >] +.RB [ \-wsp ] +.RB [ \-t +.RI < type >] +.RB [ \-n +.RI < intg >] +.RB [ \-k +.RI < kernel >] +.RB [ \-wp +.RI < which >] +.RB [ \-ap ] +.RB [ \-wspo ] +.RB [ \-step +.RI < step\ size >] +.B \-stop +.RI < stop1 \ ...> +.RB [ \-v +.RI < verbose >] +.RB [ \-nmat +.RI < transform >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Fiber tractography, from one or more seeds. +A fairly complete command-line interface to the +.B tenFiber +API. +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input volume; default: +.RB \(lq \- \(rq +.TP +.B \-dwi +input volume is a DWI volume, not a single tensor volume +.TP +.B \-s\fR <\fIseed\ point\fR> +seed point for fiber; it will propogate in two opposite directions starting +from here (3 +.IR double s); +default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-ns\fR <\fIseed\ nrrd\fR> +3-by-N +.I nrrd +of seedpoints; default: \(lq\(rq +.TP +.B \-wsp +define seedpoint and output path in worldspace. +Otherwise, (without using this option) everything is in index space +.TP +.B \-t\fR <\fItype\fR> +fiber type; defaults to something +.RI ( string ) +.TP +.B \-n\fR <\fIintg\fR> +integration method for fiber tracking; default: +.RB \(lq rk4 \(rq +.TP +.B \-k\fR <\fIkernel\fR> +kernel for reconstructing tensor field; default: +.RB \(lq tent \(rq +.TP +.B \-wp\fR <\fIwhich\fR> +when doing multi-tensor tracking, index of path to follow (made moot by +.RB \(lq \-ap \(rq) +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ap +follow all paths from (all) seedpoint(s), output will be +.IR polydata , +rather than a single 3-by-N +.IR nrrd , +even if only a single path is generated +.TP +.B \-wspo +output should be in worldspace, even if input is not (this feature is unstable +and/or confusing) +.TP +.B \-s\fR <\fIstep\ size\fR> +stepsize along fiber, in world space +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-stop\fR <\fIstop1\fR\ ...> +the conditions that should signify the end of a fiber, or when to discard a +fiber that is done propagating. +Multiple stopping criteria are logically OR-ed and tested at every point along +the fiber. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq aniso:\fR<\fItype\fR>\fB,\fR<\fIthresh >\(rq: +require anisotropy to be above the given threshold. +Which anisotropy type is given as with +.BR tend-anvol (1) +.IP \(bu 2 +.RB \(lq len:\fR<\fIlength >\(rq: +limits the length, in world space, of each fiber half +.IP \(bu 2 +.RB \(lq steps:\fR<\fIN >\(rq: +the number of steps in each fiber half is capped at +.I N +.IP \(bu 2 +.RB \(lq conf:\fR<\fIthresh >\(rq: +requires the tensor confidence value to be above the given +.I thresh +.IP \(bu 2 +.RB \(lq radius:\fR<\fIthresh >\(rq: +requires that the radius of curvature of the fiber stay above given +.I thresh +.IP \(bu 2 +.RB \(lq frac:\fR<\fIF >\(rq: +in multi-tensor tracking, the fraction of the tracked component must stay above +.I F +.IP \(bu 2 +.RB \(lq minlen:\fR<\fIlen >\(rq: +discard fiber if its final whole length is below +.I len +(not really a termination criterion) +.IP \(bu 2 +.RB \(lq minsteps:\fR<\fIN >\(rq: +discard fiber if its final number of steps is below +.I N +(not really a termination criterion) +(1 or more fiber stops) +.RE +.TP +.B \-v\fR <\fIverbose\fR> +verbosity level +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-nmat\fR <\fItransform\fR> +a 4x4 homogenous transform matrix (as a +.IR nrrd , +or just a text file) given with this option will be applied to the output +tractography vertices just prior to output; default: \(lq\(rq +.TP +.B \-o\fR <\fInout\fR> +output fiber(s) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-anvol (1) diff --git a/tend-glyph.1 b/tend-glyph.1 new file mode 100644 index 0000000..c0ee791 --- /dev/null +++ b/tend-glyph.1 @@ -0,0 +1,462 @@ +.TH TEND\-GLYPH "1" "April 2021" "" "User Commands" +.SH NAME +tend\-glyph \- generate postscript or ray-traced renderings of 3D glyphs +.SH SYNOPSIS +.B tend\ glyph +.RI [ @file \ ...] +.RB [ \-rt ] +.RB [ \-v +.RI < level >] +.RB [ \-ctr +.RI < conf\ thresh >] +.RB [ \-a +.RI < aniso >] +.RB [ \-atr +.RI < aniso\ thresh >] +.RB [ \-p +.RI < pos\ array >] +.RB [ \-m +.RI < mask\ vol >] +.RB [ \-mtr +.RI < mask\ thresh >] +.RB [ \-g +.RI < glyph\ shape >] +.RB [ \-sh +.RI < sharpness >] +.RB [ \-gsc +.RI < scale >] +.RB [ \-c +.RI < evector\ # >] +.RB [ \-sat +.RI < saturation >] +.RB [ \-ga +.RI < aniso >] +.RB [ \-am +.RI < aniso\ mod >] +.RB [ \-gg +.RI < gray >] +.RB [ \-gam +.RI < gamma >] +.RB [ \-emap +.RI < env\ map >] +.RB [ \-adsp +.RI < phong >] +.RB [ \-bg +.RI < background >] +.RB [ \-ec +.RI < edge\ rgb >] +.RB [ \-slc +.RI < axis\ pos >] +.RB [ \-si +.RI < slice\ image >] +.RB [ \-off +.RI < slice\ offset >] +.RB [ \-sg +.RI < slice\ gamma >] +.RB [ \-sb +.RI < slice\ bias >] +.B \-fr +.RI < from\ point > +.RB [ \-at +.RI < at\ point >] +.RB [ \-up +.RI < up\ vector >] +.RB [ \-rh ] +.RB [ \-dn +.RI < near\ clip >] +.RB [ \-df +.RI < far\ clip >] +.RB [ \-or ] +.RB [ \-ur +.RI < uMin \ uMax >] +.RB [ \-vr +.RI < vMin \ vMax >] +.RB [ \-fv +.RI < fov >] +.RB [ \-gr +.RI < glyph\ res >] +.RB [ \-wd +.RI < 3\ widths >] +.RB [ \-psc +.RI < scale >] +.RB [ \-ca +.RI < angle >] +.RB [ \-nobg ] +.RB [ \-concave ] +.RB [ \-is +.RI < nx \ ny >] +.RB [ \-ns +.RI < #\ samp >] +.RB [ \-nt +.RI < #\ threads >] +.RB [ \-al +.RI < B \ U \ V \ N \ E >] +.RB [ \-ao ] +.RB [ \-shadow +.RI < s >] +.RB [ \-hack +.RI < hack >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate postscript or ray-traced renderings of 3D glyphs. +Whether the output is postscript or a ray-traced image is controlled by the +initial +.RB \(lq \-rt \(rq +flag (by default, the output is postscript). +Because this is doing viz/graphics, many parameters need to be set. +Use a response file to simplify giving the command-line options which aren\(cqt +changing between invocations. +The postscript output is an EPS file, suitable for including as a figure in +LaTeX, or viewing with ghostview, or distilling into PDF. +The +ray-traced output is a 5 channel +.RI ( R , G , B , A , T ) +.I float +.IR nrrd , +suitable for +.RB \(lq unu\ crop\ \-min\ 0\ 0\ 0\ \-max\ 2\ M\ M \(rq +followed by +.RB \(lq unu\ gamma \(rq +and/or +.RB \(lq unu\ quantize\ \-b\ 8 \(rq. +.SH OPTIONS +.TP +.IR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-rt +generate ray-traced output. +By default (not using this option), postscript output is generated. +.TP +.B \-v\fR <\fIlevel\fR> +verbosity level +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-ctr\fR <\fIconf\ thresh\fR> +Glyphs will be drawn only for tensors with confidence values greater than this +threshold +.RI ( float ) +default: +.RB \(lq 0.5 \(rq +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy metric to use for thresholding the data points to be drawn; +default: +.RB \(lq fa \(rq +.TP +.B \-p\fR <\fIpos\ array\fR> +Instead of being on a grid, tensors are at arbitrary locations, as defined by +this 3-by-N array of floats. +Doing this makes various other options moot; default: \(lq\(rq +.TP +.B \-m\fR <\fImask\ vol\fR> +Scalar volume (if any) for masking region in which glyphs are drawn, in +conjunction with +.RB \(lq \-mtr \(rq +flag; default: \(lq\(rq +.TP +.B \-mtr\fR <\fImask\ thresh\fR> +Glyphs will be drawn only for tensors with mask value greater than this +threshold +.RI ( float ) +default: +.RB \(lq 0.5 \(rq +.TP +.B \-g\fR <\fIglyph\ shape\fR> +shape of glyph to use for display. Possibilities include +.RB \(lq box \(rq, +.RB \(lq sphere \(rq, +.RB \(lq cylinder \(rq, +and +.RB \(lq superquad \(rq; +default: +.RB \(lq box \(rq +.TP +.B \-sh\fR <\fIsharpness\fR> +for superquadric glyphs, how much to sharp edges form as a function of +differences between eigenvalues. +Higher values mean that edges form more easily +.RI ( float ) +default: +.RB \(lq 3.0 \(rq +.TP +.B \-gsc\fR <\fIscale\fR> +over-all glyph size in world-space +.RI ( float ) +default: +.RB \(lq 0.01 \(rq +.TP +.B \-c\fR <\fIevector\ #\fR> +which eigenvector should determine coloring. (formally +.RB \(lq v \(rq) +.RB \(lq 0 \(rq, +.RB \(lq 1 \(rq, +.RB \(lq 2 \(rq, +are principal, medium, and minor +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-sat\fR <\fIsaturation\fR> +maximal saturation to use on glyph colors (use +.B 0.0 +to create a black and white image) +.RI ( float ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-ga\fR <\fIaniso\fR> +Which anisotropy metric to use for modulating the saturation of the glyph +color; default: +.RB \(lq fa \(rq +.TP +.B \-am\fR <\fIaniso\ mod\fR> +How much to modulate glyph color saturation by anisotropy (as chosen by +.RB \(lq \-ga \(rq. +If +.BR 1.0 , +then glyphs for zero anisotropy data points will have no hue. +.RI ( float ) +default: +.RB \(lq 0.0 \(rq +.TP +.B \-gg\fR <\fIgray\fR> +desaturating glyph color due to low anisotropy tends towards this gray level +.RI ( float ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-gam\fR <\fIgamma\fR> +gamma to use on color components (after saturation) +.RI ( float ) +default: +.RB \(lq 0.7 \(rq +.TP +.B \-emap\fR <\fIenv\ map\fR> +environment map to use for shading glyphs. +By default, there is no shading; default: \(lq\(rq +.TP +.B \-adsp\fR <\fIphong\fR> +phong ambient, diffuse, specular components, and specular power (4 +.IR float s); +default: +.RB \(lq 0\ 1\ 0\ 30 \(rq +.TP +.B \-bg\fR <\fIbackground\fR> +background RGB color; each component in range +.B [0.0,1.0] +(3 +.IR float s); +default: +.RB \(lq 1\ 1\ 1 \(rq +.TP +.B \-ec\fR <\fIedge\ rgb\fR> +edge RGB color; each component in range +.B [0.0,1.0] +(3 +.IR float s); +default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-slc\fR <\fIaxis\ pos\fR> +For showing a gray-scale slice of anisotropy: the axis and position along which +to slice. +Use +.RB \(lq \-1\ \-1 \(rq +to signify that no slice should be shown (2 +.IR int s); +default: +.RB \(lq \-1\ \-1 \(rq +.TP +.B \-si\fR <\fIslice\ image\fR> +Instead of showing a slice of the anisotropy used to cull glyphs, show +something else; default: \(lq\(rq +.TP +.B \-off\fR <\fIslice\ offset\fR> +Offset from slice position to render slice at (so that it doesn\(cqt occlude +glyphs). +.RI ( float ) +default: +.RB \(lq 0.0 \(rq +.TP +.B \-sg\fR <\fIslice\ gamma\fR> +Gamma to apply to values on slice. +.RI ( float ) +default: +.RB \(lq 1.7 \(rq +.TP +.B \-sb\fR <\fIslice\ bias\fR> +amount by which to bump up slice gray values prior to gamma. +.RI ( float ) +default: +.RB \(lq 0.05 \(rq +.TP +.B \-fr\fR <\fIfrom\ point\fR> +position of camera, used to determine view vector (3 +.IR double s) +.TP +.B \-at\fR <\fIat\ point\fR> +camera look-at point, used to determine view vector (3 +.IR double s) +.TP +.B \-up\fR <\fIup\ vector\fR> +camera pseudo-up vector, used to determine view coordinates (3 +.IR double s); +default: +.RB \(lq 0\ 0\ 1 \(rq +.TP +.B \-rh +use a right-handed UVN frame (V points down) +.TP +.B \-dn\fR <\fInear\ clip\fR> +position of near clipping plane, relative to look-at point +.RI ( double ); +default: +.RB \(lq \-2 \(rq +.TP +.B \-df\fR <\fIfar\ clip\fR> +position of far clipping plane, relative to look-at point +.RI ( double ); +default: +.RB \(lq 2 \(rq +.TP +.B \-or +use orthogonal projection +.TP +.B \-ur\fR <\fIuMin\fR\ \fIuMax\fR> +range in U direction of image plane (2 +.IR double s); +default: +.RB \(lq \-1\ 1 \(rq +.TP +.B \-vr\fR <\fIvMin\fR\ \fIvMax\fR> +range in V direction of image plane (2 +.IR double s); +default: +.RB \(lq \-1\ 1 \(rq +.TP +.B \-fv\fR <\fIfov\fR> +if not +.BR NaN , +vertical field-of-view, in degrees +.RI ( double ) +.TP +.B \-gr\fR <\fIglyph\ res\fR> +.B postscript only +.IP +resolution of polygonalization of glyphs (all glyphs other than the default +box) +.RI ( int ); +default: +.RB \(lq 10 \(rq +.TP +.B \-wd\fR <\fI3\ widths\fR> +.B postscript only +.IP +width of edges drawn for three kinds of glyph edges: silohuette, crease, +non-crease (3 +.IR float s); +default: +.RB \(lq 0.8\ 0.4\ 0.0 \(rq +.TP +.B \-psc\fR <\fIscale\fR> +.B postscript only +.IP +scaling from screen space units to postscript units (in points) +.RI ( float ); +default: +.RB \(lq 300 \(rq +.TP +.B \-ca\fR <\fIangle\fR> +.B postscript only +.IP +minimum crease angle +.RI ( float ); +default: +.RB \(lq 70 \(rq +.TP +.B \-nobg +.B postscript only +.IP +don\(cqt initially fill with background color +.TP +.B \-concave +use slightly buggy rendering method suitable for concave or self-occluding +objects +.TP +.B \-is\fR <\fInx\fR\ \fIny\fR> +.B ray-traced only +.IP +image size (resolution) to render (2 +.IR int s); +default: +.RB \(lq 256\ 256 \(rq +.TP +.B \-ns\fR <\fI#\ samp\fR> +.B ray-traced only +.IP +number of samples per pixel (must be a square number) +.RI ( int ); +default: +.RB \(lq 4 \(rq +.TP +.B \-nt\fR <\fI#\ threads\fR> +.B ray-traced only +.IP +number of threads to be used for rendering +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-al\fR <\fIB\fR\ \fIU\fR\ \fIV\fR\ \fIN\fR\ \fIE\fR> +.B ray-traced only +.IP +brightness +.RI ( B ), +view-space location +.RI ( U \ V \ N ), +and length of edge +.RI ( E ) +of a square area light source, for getting soft shadows. +Requires lots more samples +.RB \(lq \-ns \(rq +to converge. +Use brightness +.B 0 +(the default) to turn this off, and use environment map-based shading +.RB (\(lq \-emap \(rq) +instead. +(5 +.IR float s); +default: +.RB \(lq 0\ \-1\ \-1\ \-4\ 0.7 \(rq +.TP +.B \-ao +set up 6 area lights in a box to approximate ambient occlusion +.TP +.B \-shadow\fR <\fIs\fR> +the extent to which shadowing occurs +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-hack\fR <\fIhack\fR> +don\(cqt mind me +.RI ( string ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output file +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-helix.1 b/tend-helix.1 new file mode 100644 index 0000000..79326f5 --- /dev/null +++ b/tend-helix.1 @@ -0,0 +1,133 @@ +.TH TEND\-HELIX "1" "April 2021" "" "User Commands" +.SH NAME +tend\-helix \- generate twisting helical tensor field +.SH SYNOPSIS +.B tend\ helix +.RB [ \-s +.RI < size >] +.RB [ \-ip +.RI < image\ orientation >] +.RB [ \-mp +.RI < measurement\ orientation >] +.RB [ \-b +.RI < boundary >] +.RB [ \-r +.RI < little\ radius >] +.RB [ \-R +.RI < big\ radius >] +.RB [ \-S +.RI < spacing >] +.RB [ \-a +.RI < angle >] +.RB [ \-nit ] +.RB [ \-ev +.RI < eigenvalues >] +.RB [ \-bg +.RI < background >] +.RB [ \-v +.RI < verbose >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate twisting helical tensor field. +The main utility of such a field is to debug handling of coordinate systems in +tensor field visualization. +The \(lqspace directions\(rq and \(lqspace origin\(rq fields of the NRRD header +determines the mapping from coordinates in the index space of the image to +coordinates in the world space in which the image is sampled. +The \(lqmeasurement frame\(rq field determines the mapping from the coordinates +of the tensor itself, to coordinates of the world space. +When these are correctly handled, the region of high anisotropy is a +right-handed helix (same as DNA). +Using differing axes sizes (via +.RB \(lq \-s \(rq) +helps make sure that the raster ordering of axes is correct. +In addition, the tensors twist relative to the helix, which exposes handling of +the measurement frame. +If you trace paths guided by the principal eigenvector of the tensors, along +the surface of the helical cylinder, you get another right-handed helix, as if +the the tensor field is modeling the result of twisting a set of fibers into +single-stranded helical bundle. +.SH OPTIONS +.TP +.B \-s\fR <\fIsize\fR> +sizes along fast, medium, and slow axes of the sampled volume, often called +\(lqX\(rq, \(lqY\(rq, and \(lqZ\(rq. +It is best to use slightly different sizes here, to expose errors in +interpreting axis ordering (e.g. \(lq\fB\-s\ 39\ 40\ 41\fR\(rq) (3 \fIint\fRs) +.TP +.B \-ip\fR <\fIimage\ orientation\fR> +quaternion quotient space orientation of image (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-mp\fR <\fImeasurement\ orientation\fR> +quaternion quotient space orientation of measurement frame (3 \fIdouble\fRs); +default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-b\fR <\fIboundary\fR> +parameter governing how fuzzy the boundary between high and low anisotropy is. +Use +.RB \(lq \-b\ 0 \(rq +for no fuzziness +.RI ( double ); +default: +.RB \(lq 10 \(rq +.TP +.B \-r\fR <\fIlittle\ radius\fR> +(minor) radius of cylinder tracing helix +.RI ( double ); +default: +.RB \(lq 30 \(rq +.TP +.B \-R\fR <\fIbig\ radius\fR> +(major) radius of helical turns +.RI ( double ); +default: +.RB \(lq 50 \(rq +.TP +.B \-S\fR <\fIspacing\fR> +spacing between turns of helix (along its axis) +.RI ( double ); +default: +.RB \(lq 100 \(rq +.TP +.B \-a\fR <\fIangle\fR> +maximal angle of twist of tensors along path. +There is no twist at helical core of path, and twist increases linearly with +radius around this path. +Positive twist angle with positive spacing resulting in a right-handed twist +around a right-handed helix. +.RI ( double ); +default: +.RB \(lq 60 \(rq +.TP +.B \-nit +changes behavior of twist angle as function of distance from center of helical +core: instead of increasing linearly as describe above, be at a constant angle +.TP +.B \-ev\fR <\fIeigenvalues\fR> +eigenvalues of tensors (in order) along direction of coil, circumferential +around coil, and radial around coil. +(3 \fIdouble\fRs); default: +.RB \(lq 0.006\ 0.002\ 0.001 \(rq +.TP +.B \-bg\fR <\fIbackground\fR> +eigenvalue of isotropic background +.RI ( double ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-v\fR <\fIverbose\fR> +verbose output +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-o\fR <\fInout\fR> +output file +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-log.1 b/tend-log.1 new file mode 100644 index 0000000..07d328a --- /dev/null +++ b/tend-log.1 @@ -0,0 +1,25 @@ +.TH TEND\-LOG "1" "April 2021" "" "User Commands" +.SH NAME +tend\-log \- calculates logarithm of the tensor +.SH SYNOPSIS +.B tend\ log +.RB [ \-i +.RI < nin >] +.B \-o +.RI < nout > +.SH DESCRIPTION +Calculates logarithm of the tensor, which is based on finding the log of the +eigenvalues. +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-msim.1 b/tend-msim.1 index 2d0b76a..3f37f0b 100644 --- a/tend-msim.1 +++ b/tend-msim.1 @@ -63,7 +63,8 @@ gradient list, one row per diffusion-weighted image .B \-b0\fR <\fIb0\ image\fR> reference non-diffusion-weighted .RB (\(lq B0 \(rq) -image, which may be needed if it isn't part of the given model parameter image +image, which may be needed if it isn\(cqt part of the given model parameter +image .TP .B \-m\fR <\fImodel\fR> model with which to simulate DWIs, which must be specified if it is not @@ -74,7 +75,7 @@ indicated by the first axis in input model image. insert a non-DW .B B0 image at the beginning of the experiment specification (useful if the given -gradient list doesn't already have one) and hence also insert a +gradient list doesn\(cqt already have one) and hence also insert a .B B0 image at the beginning of the output simulated DWIs .RB \(lq bool \(rq diff --git a/tend-norm.1 b/tend-norm.1 new file mode 100644 index 0000000..9d74928 --- /dev/null +++ b/tend-norm.1 @@ -0,0 +1,48 @@ +.TH TEND\-NORM "1" "April 2021" "" "User Commands" +.SH NAME +tend\-norm \- normalize tensor size +.SH SYNOPSIS +.B tend\ norm +.B \-w +.RI < w0 \ w1 \ w2 > +.RB [ \-a +.RI < amount >] +.RB [ \-t +.RI < target >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-w\fR <\fIw0\fR\ \fIw1\fR\ \fIw2\fR> +relative weights to put on major, medium, and minor eigenvalue when performing +normalization (internally rescaled to have a 1.0 L1 norm). +These weightings determine the tensors\(cqs \(lqsize\(rq. +(3 +.IR double s) +.TP +.B \-a\fR <\fIamount\fR> +how much of the normalization to perform +.RI ( float ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-t\fR <\fItarget\fR> +target size, post normalization +.RI ( float ) +default: +.RB \(lq 1.0 \(rq +.TP +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-point.1 b/tend-point.1 new file mode 100644 index 0000000..7e2e55e --- /dev/null +++ b/tend-point.1 @@ -0,0 +1,27 @@ +.TH TEND\-POINT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-point \- describe everything about one sample in a DT volume +.SH SYNOPSIS +.B tend\ point +.B \-p +.RI < x \ y \ z > +.RB [ \-i +.RI < nin >] +.SH OPTIONS +.TP +.TP +.B \-p\fR <\fIx\fR\ \fIy\fR\ \fIz\fR> +coordinates of sample to be described (3 +.IR int s) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output array +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-satin.1 b/tend-satin.1 new file mode 100644 index 0000000..5b6b85f --- /dev/null +++ b/tend-satin.1 @@ -0,0 +1,113 @@ +.TH TEND\-SATIN "1" "April 2021" "" "User Commands" +.SH NAME +tend\-satin \- generate a pretty synthetic DT volume +.SH SYNOPSIS +.B tend\ satin +.RI [ \-t ] +.B \-p +.RI < aniso\ param > +.RB [ \-max +.RI < max\ cal >] +.RB [ \-min +.RI < min\ cal >] +.RB [ \-b +.RI < boundary >] +.RB [ \-br +.RI < ramp >] +.RB [ \-th +.RI < thickness >] +.RB [ \-evsc +.RI < eval\ scale >] +.RB [ \-s +.RI < size >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate a pretty synthetic DT volume. +The surface of a sphere or torus is covered with either linear or planar +anisotropic tensors, or somewhere in between. +.SH OPTIONS +.TP +.B \-t +generate a torus dataset, instead of the default spherical +.TP +.B \-p\fR <\fIaniso\ param\fR> +anisotropy parameter. +.B 0.0 +for one direction of linear (along the equator for spheres, or along the larger +circumference for toruses), +.B 1.0 +for planar, +.B 2.0 +for the other direction of linear (from pole to pole for spheres, or along the +smaller circumference for toruses) +.RI ( float ) +.TP +.B \-max\fR <\fImax\ cal\fR> +maximum anisotropy in dataset, according to the +.RB \(lq ca1 \(rq +anisotropy metric. +.RB \(lq 1.0 \(rq +means completely linear or completely planar anisotropy +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-min\fR <\fImin\ cal\fR> +minimum anisotropy in dataset +.RI ( float ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-b\fR <\fIboundary\fR> +parameter governing how fuzzy the boundary between high and low anisotropy is. +Use +.RB \(lq \-b\ 0 \(rq +for no fuzziness +.RI ( float ); +default: +.RB \(lq 0.05 \(rq +.TP +.B \-br\fR <\fIramp\fR> +how much to ramp up effective +.RI \(lq \-b \(rq +along Y axis. +Use +.RB \(lq \-b\ 0 \(rq +for no such ramping. +.RI ( float ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-th\fR <\fIthickness\fR> +parameter governing how thick region of high anisotropy is +.RI ( float ); +default: +.RB \(lq 0.3 \(rq +.TP +.B \-evsc\fR <\fIeval\ scale\fR> +scaling of eigenvalues +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-s\fR <\fIsize\fR> +dimensions of output volume. +For size +.IR N , +the output is +.IB N \ x\ N \ x\ N +for spheres, and +.BI 2 N \ x\ 2 N \ x\ N +for toruses +.RI ( int ); +default: +.RB \(lq 32 \(rq +.TP +.B \-o\fR <\fInout\fR> +output filename +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-shrink.1 b/tend-shrink.1 new file mode 100644 index 0000000..8c504e1 --- /dev/null +++ b/tend-shrink.1 @@ -0,0 +1,32 @@ +.TH TEND\-SHRINK "1" "April 2021" "" "User Commands" +.SH NAME +tend\-shrink \- converts a 9-value DT volume to a 7-value DT volume +.SH SYNOPSIS +.B tend\ shrink +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Converts a 9-value DT volume to a 7-value DT volume. +The confidence value is set to +.B 1.0 +everywhere. +You can +.BR unu\-splice (1) +or +.B nrrdSplice() +something else in its place later. +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume, with 9 matrix components per sample; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume, with the 7 values per sample +.RI ( string ) +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-expand (1), +.BR unu\-splice (1) diff --git a/tend-sim.1 b/tend-sim.1 index 3761398..c40a192 100644 --- a/tend-sim.1 +++ b/tend-sim.1 @@ -45,7 +45,7 @@ measurement frame. .SH OPTIONS .TP .B \-old -don't use the new +don\(cqt use the new .B tenEstimateContext functionality .TP diff --git a/tend-slice.1 b/tend-slice.1 new file mode 100644 index 0000000..a42335a --- /dev/null +++ b/tend-slice.1 @@ -0,0 +1,45 @@ +.TH TEND\-SLICE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-slice \- slice 3D tensors to get slab/image of 3D/2D tensors +.SH SYNOPSIS +.B tend\ slice +.B \-a +.RI < axis > +.B \-p +.RI < pos > +.RB [ \-d +.RI < dim >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-a\fR <\fIaxis\fR> +axis along which to slice +.RI ( int ) +.TP +.B \-p\fR <\fIpos\fR> +position to slice at +.RI ( int ) +.TP +.B \-d\fR <\fIdim\fR> +dimension of desired tensor output, can be either +.B 2 +or +.B 3 +.RI ( int ); +default: +.RB \(lq 3 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor slice +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-sten.1 b/tend-sten.1 new file mode 100644 index 0000000..e5a13a5 --- /dev/null +++ b/tend-sten.1 @@ -0,0 +1,51 @@ +.TH TEND\-STEN "1" "April 2021" "" "User Commands" +.SH NAME +tend\-sten \- calculate structure tensors from a scalar field +.SH SYNOPSIS +.B tend\ sten +.RB [ \-ds +.RI < diff.\ scale >] +.RB [ \-is +.RI < int.\ scale >] +.RB [ \-df +.RI < downsample\ factor >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Calculate structure tensors from a scalar field. +Not a diffusion tensor, but it is symmetric and positive-definite. +.SH OPTIONS +.TP +.B \-ds\fR <\fIdiff.\ scale\fR> +differentiation scale, in pixels: the radius of the kernel used for +differentation to compute gradient vectors +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-is\fR <\fIint.\ scale\fR> +integration scale, in pixels: the radius of the kernel used for blurring outer +products of gradients in order compute structure tensors +.RI ( int ); +default: +.RB \(lq 2 \(rq +.TP +.B \-df\fR <\fIdownsample\ factor\fR> +the factor by which to downsample when creating volume of structure tensors +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-i\fR <\fInin\fR> +input scalar volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output filename +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-tconv.1 b/tend-tconv.1 new file mode 100644 index 0000000..7949634 --- /dev/null +++ b/tend-tconv.1 @@ -0,0 +1,34 @@ +.TH TEND\-TCONV "1" "April 2021" "" "User Commands" +.SH NAME +tend\-tconv \- convert between different shape triples +.SH SYNOPSIS +.B tend\ tconv +.B \-t +.RI < inType \ outType > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Convert between different shape triples. +The triple can be eigenvalues, +invariants +.BI ( J ,\ K ,\ R )\fR, +and lots of other things. +.SH OPTIONS +.TP +.B \-t\fR <\fIinType\fR\ \fIoutType\fR> +given input and desired output type of triples (2 +.IR tenTripleType s) +.TP +.B \-i\fR <\fInin\fR> +input array of triples; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output array +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-triple.1 b/tend-triple.1 new file mode 100644 index 0000000..21fe16e --- /dev/null +++ b/tend-triple.1 @@ -0,0 +1,33 @@ +.TH TEND\-TRIPLE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-triple \- compute volume of shape triples +.SH SYNOPSIS +.B tend\ triple +.B \-t +.RI < type > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Compute volume of shape triples. +The triple can be eigenvalues, +invariants +.BI ( J ,\ K ,\ R )\fR, +and lots of other things. +.SH OPTIONS +.TP +.B \-t\fR <\fItype\fR> +desired output triple type +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output triple volume +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-unmf.1 b/tend-unmf.1 new file mode 100644 index 0000000..d97b5ce --- /dev/null +++ b/tend-unmf.1 @@ -0,0 +1,29 @@ +.TH TEND\-UNMF "1" "April 2021" "" "User Commands" +.SH NAME +tend\-unmf \- applies and removes the measurement frame +.SH SYNOPSIS +.B tend\ unmf +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Applies and removes the measurement frame. +When the given tensor volume has a measurement frame associated with it, this +will apply the measurement frame transform to all tensors to convert them into +world space, and remove the measurement frame from the +.IR nrrd . +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume (sorry, can\(cqt use usual default of +.RB \(lq \- \(rq +for stdin because of hest quirk) +.TP +.B \-o\fR <\fInout\fR> +output tensor volume +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend.1 b/tend.1 index e61040a..831950d 100644 --- a/tend.1 +++ b/tend.1 @@ -64,206 +64,92 @@ eigenvector, and then quantizes it to an 8-bit PNG: .EE .in .SH OPTIONS +.SH COMMANDS +.P +Each of the following has a corresponding man page: for example, +.BR tend\-about (1) +for +.RB \(lq tend\ about \(rq. .SS tend\ about Information about this program and its use -.P -See -.BR tend\-about (1). .SS tend\ grads Calculate balanced gradient directions for DWI acquisition -.P -See -.BR tend\-grads (1). .SS tend\ epireg Register diffusion-weighted echo-planar images -.P -See -.BR tend\-epireg (1). .SS tend\ bmat Calculate B-matrix given gradient directions -.P -See -.BR tend\-bmat (1). .SS tend\ estim Estimate tensors from a set of DW images -.P -See -.BR tend\-estim (1). .SS tend\ sim Simulate DW images from a tensor field -.P -See -.BR tend\-sim (1). .SS tend\ mfit Estimate models from a set of DW images -.P -See -.BR tend\-mfit (1). .SS tend\ mconv Convert from one model to another -.P -See -.BR tend\-mconv (1). .SS tend\ msim Simulate DW images from an image of models -.P -See -.BR tend\-msim (1). .SS tend\ make Create DT volume from confidence and eigensystem -.P -See -.BR tend\-make (1). .SS tend\ avg Average across tensor volumes -.P -See -.BR tend\-avg (1). .SS tend\ helix Generate twisting helical tensor field -.P -See -.BR tend\-helix (1). .SS tend\ sten Calculate structure tensors from a scalar field -.P -See -.BR tend\-sten (1). .SS tend\ glyph Generate postscript or ray-traced renderings of 3D glyphs -.P -See -.BR tend\-glyph (1). .SS tend\ ellipse Generate postscript renderings of 2D glyphs -.P -See -.BR tend\-ellipse (1). .SS tend\ anplot Graph anisotropy metric in barycentric coords -.P -See -.BR tend\-anplot (1). .SS tend\ anvol Apply an anisotropy metric to a DT volume -.P -See -.BR tend\-anvol (1). .SS tend\ anscale Scale the anisotropic component of the tensors -.P -See -.BR tend\-anscale (1). .SS tend\ anhist Generate barycentric histograms of anisotropy -.P -See -.BR tend\-anhist (1). .SS tend\ triple Compute volume of shape triples -.P -See -.BR tend\-triple (1). .SS tend\ tconv Convert between different shape triples -.P -See -.BR tend\-tconv (1). .SS tend\ point Describe everything about one sample in a DT volume -.P -See -.BR tend\-point (1). .SS tend\ slice Slice 3D tensors to get slab/image of 3D/2D tensors -.P -See -.BR tend\-slice (1). .SS tend\ norm Normalize tensor size -.P -See -.BR tend\-norm (1). .SS tend\ fiber Fiber tractography, from one or more seeds -.P -See -.BR tend\-fiber (1). .SS tend\ eval Calculate one or more eigenvalues in a DT volume -.P -See -.BR tend\-eval (1). .SS tend\ evalpow Modify shape by raising eigenvalues to some power -.P -See -.BR tend\-evalpow (1). .SS tend\ evalclamp Modify shape by clamping eigenvalues in some range -.P -See -.BR tend\-evalclamp (1). .SS tend\ evaladd Modify shape by adding a constant to all eigenvalues -.P -See -.BR tend\-evaladd (1). -.SS tend\ evalmul +.SS tend\ evalmult Modify shape by multiplying eigenvalues by a constant -.P -See -.BR tend\-evalmul (1). .SS tend\ log Calculates logarithm of the tensor -.P -See -.BR tend\-log (1). .SS tend\ exp Calculates \fBexp()\fR of the tensor -.P -See -.BR tend\-exp (1). .SS tend\ evec Calculate one or more eigenvectors in a DT volume -.P -See -.BR tend\-evec (1). .SS tend\ evecrgb Make an RGB volume from an eigenvector and an anisotropy -.P -See -.BR tend\-evecrgb (1). .SS tend\ evq Quantize directions of diffusion -.P -See -.BR tend\-evq (1). .SS tend\ unmf Applies and removes the measurement frame -.P -See -.BR tend\-unmf (1). .SS tend\ expand Converts masked non-redundant tensor images to redundant -.P -See -.BR tend\-expand (1). .SS tend\ shrink Converts a 9-value DT volume to a 7-value DT volume -.P -See -.BR tend\-shrink (1). .SS tend\ bfit Non-linear least-squares fitting of b-value curves -.P -See -.BR tend\-bfit (1). .SS tend\ satin Generate a pretty synthetic DT volume -.P -See -.BR tend\-satin (1). .SH "SEE\ ALSO" .BR gprobe (1), .BR ilk (1), @@ -288,7 +174,7 @@ See .BR tend\-eval (1), .BR tend\-evaladd (1), .BR tend\-evalclamp (1), -.BR tend\-evalmul (1), +.BR tend\-evalmult (1), .BR tend\-evalpow (1), .BR tend\-evec (1), .BR tend\-evecrgb (1), diff --git a/unu.1 b/unu.1 index ef710be..6f8b611 100644 --- a/unu.1 +++ b/unu.1 @@ -115,6 +115,194 @@ Formats available: .P Nrrd data encodings available: .B raw ascii hex gz bz2 +.SH COMMANDS +\" .P +\" Each of the following has a corresponding man page: for example, +\" .BR unu\-about (1) +\" for +\" .RB \(lq unu\ about \(rq. +.SS unu about +Information about this program and its use +.SS unu env +List relevant environment variables and their values +.SS unu i2w +Convert from 1-D index to world position +.SS unu w2i +Convert from 1-D world to index position +.SS unu make +Create a +.I nrrd +(or +.I nrrd +header) from scratch +.SS unu head +Print header of one or more +.I nrrd +files +.SS unu data +Print data segment of a +.I nrrd +file +.SS unu convert +Convert to another type (as if by cast, w/ optional clamp) +.SS unu resample +Filtering and {up,down}sampling with a separable kernel +.SS unu fft +Fast Fourier Transform of selected axes +.SS unu cmedian +Cheap histogram-based median/mode filtering +.SS unu dist +Euclidean distance transform +.SS unu minmax +Print out min and max values in one or more +.IR nrrd s +.SS unu cksum +Compute 32-bit CRC of +.I nrrd +data (same as via +.BR cksum (1)) +.SS unu diff +Sees if two +.IR nrrd s +are different in any way +.SS unu quantize +Quantize values to 8, 16, or 32 bits +.SS unu unquantize +Recover floating point values from quantized data +.SS unu project +Collapse scanlines to scalars along some axis +.SS unu slice +Slice along one or more axes at given positions +.SS unu sselect +Select subset of slices along an axis +.SS unu dice +Save all slices along one axis into separate files +.SS unu splice +Replace a slice with a different +.I nrrd +.SS unu join +Connect slices and/or slabs into a bigger +.I nrrd +.SS unu crop +Crop along each axis to make a smaller +.I nrrd +.SS unu acrop +Automatically crop axes based on given measure +.SS unu inset +Replace a sub-region with a different +.I nrrd +.SS unu pad +Pad along each axis to make a bigger +.I nrrd +.SS unu reshape +Superficially change dimension and/or axes sizes +.SS unu permute +Permute ordering of axes +.SS unu swap +Interchange ordering of two axes +.SS unu shuffle +Permute slices along one axis +.SS unu flip +Reverse order of slices along one axis +.SS unu unorient +Make image orientation be axis-aligned +.SS unu axinfo +Modify attributes of one or more axes +.SS unu axinsert +Add a \(lqstub\(rq (length 1) axis to a +.I nrrd +.SS unu axsplit +Split one axis into two axes +.SS unu axdelete +Remove one or more singleton axes from a +.I nrrd +.SS unu axmerge +Merge two adjacent axes into one +.SS unu tile +Tile slices of one axis into two other axes +.SS unu untile +Undo +.BR unu\-tile (1): +merge slow parts of two axis splits +.SS unu histo +Create 1-D histogram of values in a +.I nrrd +.SS unu dhisto +Create image of 1-D value histogram +.SS unu jhisto +Create joint histogram of two or more +.IR nrrd s +.SS unu histax +Replace each scanline along an axis with its histogram +.SS unu heq +Perform histogram equalization +.SS unu gamma +Brighten or darken values with a gamma +.SS unu 1op +Unary operation on a +.I nrrd +.SS unu 2op +Binary operation on two +.IR nrrd s, +or on a +.I nrrd +and a constant +.SS unu 3op +Ternary operation on three +.IR nrrd s +or constants +.SS unu affine +Affine (lerp) mapping on 5 +.IR nrrd s +or constants +.SS unu lut +Map +.I nrrd +through one univariate lookup table +.SS unu mlut +Map +.I nrrd +through whole +.I nrrd +of univariate lookup tables +.SS unu subst +Map +.I nrrd +through a univariate substitution table +.SS unu rmap +Map +.I nrrd +through one +.B regular +univariate map (\(lqcolormap\(rq) +.SS unu mrmap +Map +.I nrrd +through a whole +.I nrrd +of regular univariate maps +.SS unu imap +Map +.I nrrd +through +.B irregular +univariate map (\(lqcolormap\(rq) +.SS unu lut2 +Map +.I nrrd +through a bivariate lookup table +.SS unu ccfind +Find connected components (CCs) +.SS unu ccadj +Form adjecency matrix of connected components +.SS unu ccmerge +Merge CCs with their neighbors, under various constraints +.SS unu ccsettle +Remap CC values down to lowest contiguous values +.SS unu save +Write +.I nrrd +with specific format, encoding, or endianness .SH "SEE\ ALSO" .BR gprobe (1), .BR ilk (1), @@ -125,3 +313,66 @@ Nrrd data encodings available: .BR puller (1), .BR tend (1), .BR vprobe (1) +\" .BR vprobe (1), +\" .BR unu-1op (1), +\" .BR unu-2op (1), +\" .BR unu-3op (1), +\" .BR unu-about (1), +\" .BR unu-acrop (1), +\" .BR unu-affine (1), +\" .BR unu-axdelete (1), +\" .BR unu-axinfo (1), +\" .BR unu-axinsert (1), +\" .BR unu-axmerge (1), +\" .BR unu-axsplit (1), +\" .BR unu-ccadj (1), +\" .BR unu-ccfind (1), +\" .BR unu-ccmerge (1), +\" .BR unu-ccsettle (1), +\" .BR unu-cksum (1), +\" .BR unu-cmedian (1), +\" .BR unu-convert (1), +\" .BR unu-crop (1), +\" .BR unu-data (1), +\" .BR unu-dhisto (1), +\" .BR unu-dice (1), +\" .BR unu-diff (1), +\" .BR unu-dist (1), +\" .BR unu-env (1), +\" .BR unu-fft (1), +\" .BR unu-flip (1), +\" .BR unu-gamma (1), +\" .BR unu-head (1), +\" .BR unu-heq (1), +\" .BR unu-histax (1), +\" .BR unu-histo (1), +\" .BR unu-i2w (1), +\" .BR unu-imap (1), +\" .BR unu-inset (1), +\" .BR unu-jhisto (1), +\" .BR unu-join (1), +\" .BR unu-lut (1), +\" .BR unu-lut2 (1), +\" .BR unu-make (1), +\" .BR unu-minmax (1), +\" .BR unu-mlut (1), +\" .BR unu-mrmap (1), +\" .BR unu-pad (1), +\" .BR unu-permute (1), +\" .BR unu-project (1), +\" .BR unu-quantize (1), +\" .BR unu-resample (1), +\" .BR unu-reshape (1), +\" .BR unu-rmap (1), +\" .BR unu-save (1), +\" .BR unu-shuffle (1), +\" .BR unu-slice (1), +\" .BR unu-splice (1), +\" .BR unu-sselect (1), +\" .BR unu-subst (1), +\" .BR unu-swap (1), +\" .BR unu-tile (1), +\" .BR unu-unorient (1), +\" .BR unu-unquantize (1), +\" .BR unu-untile (1), +\" .BR unu-w2i (1) commit 8d05a3a34a29ea41d5b2ca9712f366ef4f57a1b2 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 6 12:03:06 2021 -0400 Add an rpmlintrc file diff --git a/teem.rpmlintrc b/teem.rpmlintrc new file mode 100644 index 0000000..890462c --- /dev/null +++ b/teem.rpmlintrc @@ -0,0 +1,5 @@ +# These are not real spelling errors... +addFilter(r'spelling-error .*($en_US$| en_US) (resample|datasets|' + r'tractography|unu) ') +# Indeed, there is no dedicated documentation for some subpackages. +addFilter(r' no-documentation$') commit d09ed97c6dc65490fb502eeb6baaae9b3b304a14 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 6 11:59:36 2021 -0400 rewrap description diff --git a/teem.spec b/teem.spec index 563e3b5..61764d0 100644 --- a/teem.spec +++ b/teem.spec @@ -182,8 +182,8 @@ Strengths of Teem Slicer. • Teem is light-weight: The libraries are written with an eye towards minimizing the annoyance of getting data in an out, by using the simplest - possible constructs for the job, and by supporting combinations of operations - that arise in common practice. + possible constructs for the job, and by supporting combinations of + operations that arise in common practice. • Teem is coherent: There is a consistent logic to how information is represented, and uniformity in the APIs across libraries. • Teem is portable: All the code is written in plain ANSI C, so it compiles commit b3cb082255b1984b8f5a864a4576729446f37aee Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 6 11:36:04 2021 -0400 Fix single-threading tests diff --git a/teem.spec b/teem.spec index b69288c..563e3b5 100644 --- a/teem.spec +++ b/teem.spec @@ -298,7 +298,8 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %endif # Tests are not parallel-safe -%ctest3 %{?ctest_excludes} -j1 +%global _smp_mflags -j1 +%ctest3 %{?ctest_excludes} %if 0%{?epel} == 7 commit ba847837bef28947baf576882c1463ada7d0ae7f Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 6 11:34:57 2021 -0400 Start work on adding a complete set of man pages diff --git a/gprobe.1 b/gprobe.1 new file mode 100644 index 0000000..4f35b12 --- /dev/null +++ b/gprobe.1 @@ -0,0 +1,264 @@ +.TH GPROBE "1" "April 2021" "" "User Commands" +.SH NAME +gprobe \- shows off the functionality of the gage library +.SH SYNOPSIS +.B gprobe +.B \-i +.RI < nin > +.B \-k +.RI < kind > +.RB [ \-v +.RI < verbosity >] +.B \-q +.RI < query > +.RB [ \-gmc +.RI < min\ gradmag >] +.RB [ \-ofs ] +.RB [ \-seed +.RI < N >] +.RB [ \-c +.RI < bool >] +.RB [ \-k00 +.RI < kern00 >] +.RB [ \-k11 +.RI < kern11 >] +.RB [ \-k22 +.RI < kern22 >] +.RB [ \-rn ] +.RB [ \-ssn +.RI < SS\ # >] +.RB [ \-ssr +.RI < scale\ range >] +.RB [ \-kssb +.RI < kernel >] +.RB [ \-kssr +.RI < kernel >] +.RB [ \-ssu ] +.RB [ \-sso ] +.RB [ \-ssnd ] +.RB [ \-ssnb +.RI < bias >] +.RB [ \-ssf +.RI < SS\ read/save\ format >] +.RB [ \-s +.RI < sclX \ xclY \ sxlZ >] +.RB [ \-ssp +.RI < pos >] +.RB [ \-pg +.RI < nrrd >] +.RB [ \-pi +.RI < nrrd >] +.RB [ \-pp +.RI < pos \ ...>] +.RB [ \-eps +.RI < epsilon >] +.RB [ \-psi +.RI < p >] +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Shows off the functionality of the gage library. +Uses gageProbe() to query various kinds of volumes to learn various measured or +derived quantities. +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR> +input volume +.TP +.B \-k\fR\ <\fIkind\fR> +\(lqkind\(rq of volume +.RB (\(lq scalar \(rq, +.RB \(lq vector \(rq, +.RB \(lq tensor \(rq, +or +.RB \(lq dwi \(rq) +.TP +.B \-v\fR\ <\fIverbosity\fR> +verbosity level +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-q\fR\ <\fIquery\fR> +the quantity +.RB ( scalar , +.BR vector , +or +.BR matrix ) +to learn by probing +.RI ( string ) +.TP +.B \-gmc\fR\ <\fImin\ gradmag\fR> +For curvature-based queries, use zero when gradient magnitude is below this +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-ofs +If only per-axis spacing is available, use that to contrive full orientation +info +.TP +.B \-seed\fR\ <\fIN\fR> +RNG seed; mostly for debugging +.RI ( unsigned\ int ); +default: +.RB \(lq 42 \(rq +.TP +.B \-c\fR\ <\fIbool\fR> +clamp positions as part of probing +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-k00\fR\ <\fIkern00\fR> +kernel for +.BR gageKernel00 ; +default: +.RB \(lq tent \(rq +.TP +.B \-k11\fR\ <\fIkern11\fR> +kernel for +.BR gageKernel11 ; +default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR\ <\fIkern22\fR> +kernel for +.BR gageKernel22 ; +default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-rn +renormalize kernel weights at each new sample location. +\(lqAccurate\(rq kernels don\(cqt need this; doing it always makes things go +slower +.TP +.B \-ssn\fR\ <\fISS\ #\fR> +how many scale-space samples to evaluate, or, +.B 0 +to turn-off all scale-space behavior +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ssr\fR\ <\fIscale\ range\fR> +range of scales in scale-space (2 +.IR double s); +default: +.RB \(lq nan\ nan \(rq +.TP +.B \-kssb\fR\ <\fIkernel\fR> +blurring kernel, to sample scale space; default: +.RB \(lq dgauss:1,5 \(rq +.TP +.B \-kssr\fR\ <\fIkernel\fR> +kernel for reconstructing from scale space samples +.RB \(lq hermite \(rq +.TP +.B \-ssu +do uniform samples along sigma, and not (by default) samples according to the +effective diffusion scale +.TP +.B \-sso +if not using \(lq\-ssu\(rq, use pre-computed optimal sigmas when possible +.TP +.B \-ssnd +normalize derivatives by scale +.TP +.B \-ssnb\fR\ <\fIbias\fR> +bias on scale-based derivative normalization +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-ssf\fR\ <\fISS\ read/save\ format\fR> +.BR printf (3)\-style +format (including a +.RB \(lq %u \(rq) +for the filenames from which to read pre-blurred volumes computed for the +stack, if they exist and match the stack parameters, and where to save them if +they had to be re-computed. +Leave this as empty string to disable this. +.RI ( string ); +default: \(lq\(rq +.TP +.B \-s\fR\ <\fIsclX\fR\ \fIsclY\fR\ \fIsxlZ\fR> +scaling factor for resampling on each axis +.RB (> 1.0 : +supersampling); use +.RB \(lq \-ssp \(rq +(and +.RB \(lq \-psi \(rq) +to specify scale position of sampling (3 +.IR double s); +default: +.RB \(lq 1\ 1\ 1 \(rq +.TP +.B \-ssp\fR\ <\fIpos\fR> +when using scale-space, scale-position at which to probe +.RI ( double ); +default: +.RB \(lq 0 \(rq +.TP +.B \-pg\fR\ <\fInrrd\fR> +overrides +.RB \(lq \-s \(rq: +2-D +.I nrrd +which specifies origin and direction vectors for sampling grid; default: +\(lq\(rq +.TP +.B \-pi\fR\ <\fInrrd\fR> +overrides +.RB \(lq \-pv \(rq: +probes at this list of 3-vec or 4-vec positions; default: +\(lq\(rq +.TP +.B \-pp\fR\ <\fIpos\fR ...> +overrides +.RB \(lq \-pi \(rq: +only sample at this specified point (3..4 \fIdouble\fRs); default: +.RB \(lq nan\ nan \(rq +.TP +.B \-eps\fR\ <\fIepsilon\fR> +if non-zero, and if query is a scalar, and if using +.RB \(lq \-pp \(rq +to query at a single point, then do +.I epsilon +offset probes to calculate discrete differences, to find the numerical gradient +and hessian (for debugging) +.RI ( double ); +default: +.RB \(lq 0 \(rq +.TP +.B \-psi\fR\ <\fIp\fR> +whether the probe location specification (by any of the four previous flags) +are in index space +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-t\fR\ <\fItype\fR> +type of output volume +.RI ( type ); +default: +.RB \(lq float \(rq +.TP +.B \-o\fR\ <\fInout\fR> +output volume +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR ilk (1), +.BR miter (1), +.BR mrender (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/ilk.1 b/ilk.1 new file mode 100644 index 0000000..51b2915 --- /dev/null +++ b/ilk.1 @@ -0,0 +1,180 @@ +.TH ILK "1" "April 2021" "" "User Commands" +.SH NAME +ilk \- (I)mage (L)inear Trans(X\-\->K)forms +.SH SYNOPSIS +.B ilk +.RI [ @file \ ...] +.RB [ \-i +.RI < image >] +.RB [ \-0 +.RI < origin >] +.B \-t +.RI < xform0 \ ...> +.RB [ \-k +.RI < kernel >] +.RB [ \-min +.RI < xMin \ yMin >] +.RB [ \-max +.RI < xMax \ yMax >] +.RB [ \-b +.RI < boundary >] +.RB [ \-bg +.RI < bg0 \ bg1 \ ...>] +.RB [ \-s +.RI < xSize \ ySize >] +.RB [ \-a +.RI < avg\ # >] +.RB [ \-o +.RI < filename >] +.SH DESCRIPTION +.P +(I)mage (L)inear Trans(X\-\->K)forms. +Applies linear (homogenous coordinate) transforms to a given image, using the +given kernel for resampling. +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fIimage\fR> +input image; default: +.RB \(lq \- \(rq +.TP +.B \-0\fR <\fIorigin\fR> +where to locate +.B (0,0) +prior to applying transforms. +.RS +7n +.IP \(bu 2 +.RB \(lq u:<\fIfloat\fB>,<\fIfloat\fB> \(rq +locate origin in a unit box +.B [0,1]x[0,1] +which covers the original image +.IP \(bu 2 +.RB \(lq p:<\fIfloat\fB>,<\fIfloat\fB> \(rq +locate origin at a particular pixel location, in the index space of the image +.P +default: +.RB \(lq p:0,0 \(rq +.RE +.TP +.B \-t\fR <\fIxform0\fR\ ...> +transform(s) to apply to image. +Transforms are applied in the order in which they appear. +.RS +7n +.IP \(bu 2 +.RB \(lq identity \(rq: +no geometric transform, just resampling +.IP \(bu 2 +.RB \(lq translate:\fIx\fB,\fIy\fB \(rq: +shift image by vector +.BR (\fIx\fB,\fIy\fB) , +as measured in pixels +.IP \(bu 2 +.RB \(lq rotate:\fIang\fB \(rq: +rotate CCW by +.I ang +degrees +.IP \(bu 2 +.RB \(lq scale:\fIxs\fB,\fIys\fB \(rq: +scale by +.I xs +in X, and +.I ys +in Y +.IP \(bu 2 +.RB \(lq shear:\fIfix\fB,\fIamnt\fB \(rq: +shear by +.IR amnt , +keeping fixed the pixels along a direction +.RI < fix > +degrees from the X axis +.IP \(bu 2 +.RB \(lq flip:\fIang\fB \(rq: +flip along axis an angle +.RI < ang > +degrees from the X axis +.IP \(bu 2 +.RB \(lq \fIa\fB,\fIb\fB,\fItx\fB,\fIc\fB,\fId\fB,\fIty\fB \(rq: +specify the transform explicitly in row-major order (opposite of PostScript) +(1 or more 2D transforms) +.RE +.TP +.B \-k\fR <\fIkernel\fR> +reconstruction kernel; default: +.RB \(lq cubic:0,0.5 \(rq +.TP +.B \-min\fR <\fIxMin\fR\ \fIyMin\fR> +lower bounding corner of output image. +Default (by not using this option) is the lower corner of input image. +(2 \fIdouble\fRs) +.TP +.B \-max\fR <\fIxMax\fR\ \fIyMax\fR> +upper bounding corner of output image. +Default (by not using this option) is the upper corner of input image. +(2 \fIdouble\fRs) +.TP +.B \-b\fR <\fIboundary\fR> +what to do when sampling outside original image. +.RS +7n +.IP \(bu 2 +.RB \(lq bleed \(rq: +copy values at image border outward +.IP \(bu 2 +.RB \(lq wrap \(rq: +do wrap-around on image locations +.IP \(bu 2 +.RB \(lq pad \(rq: +use a given background value (via +.RB \(lq \-bg \(rq) +.P +default: +.RB \(lq bleed \(rq +.RE +.TP +.B \-bg\fR <\fIbg0\fR\ \fIbg1\fR\ ...> +background color to use with boundary behavior +.RB \(lq pad \(rq. +Defaults to all zeroes. +(1 or more \fIfloat\fRs) +.TP +.B \-s\fR <\fIxSize\fR\ \fIySize\fR> +For each axis, information about how many samples in output: +.RS +7n +.IP \(bu 2 +.RB \(lq x\fR<\fIfloat\fR> \(rq: +number of output samples is some scaling of the number input of samples; +multiplied by +.RI < float > +.IP \(bu 2 +.RB \(lq \fR<\fIint\fR> \(rq: +specify exact number of samples +(2 sampling specifications) +.P +default: +.RB \(lq x1\ x1 \(rq +.RE +.TP +.B \-a\fR <\fIavg\ #\fR> +number of averages (if there there is only one rotation) +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output +.I nrrd +to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR miter (1), +.BR mrender (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/miter.1 b/miter.1 new file mode 100644 index 0000000..75d7ef4 --- /dev/null +++ b/miter.1 @@ -0,0 +1,287 @@ +.TH MITER "1" "April 2021" "" "User Commands" +.SH NAME +miter \- a simple but effective little volume renderer +.SH SYNOPSIS +.B miter +.RI [ @file \ ...] +.RB [ \-i +.RI < nsin >] +.RB [ \-vi +.RI < nvin >] +.RB [ \-ti +.RI < ntin >] +.B \-txf +.RI < nin \ ...> +.B \-fr +.RI < eye\ pos > +.RB [ \-at +.RI < at\ pos >] +.RB [ \-up +.RI < up\ dir >] +.RB [ \-rh ] +.RB [ \-or ] +.B \-dn +.RI < near > +.B \-di +.RI < image > +.B \-df +.RI < far > +.RB [ \-ar ] +.RB [ \-ur +.RI < uMin\fR\ \fIuMax >] +.RB [ \-vr +.RI < vMin\fR\ \fIvMax >] +.RB [ \-fv +.RI < field\ of\ view >] +.RB [ \-offfr ] +.RB [ \-fr +.RI < fake\ from >] +.RB [ \-turn +.RI < angle >] +.RB [ \-am +.RI < ambient >] +.RB [ \-ld +.RI < light\ pos >] +.RB [ \-is +.RI < image\ size >] +.RB [ \-iss +.RI < scale >] +.RB [ \-ads +.RI < ka\fR\ \fIkd\fR\ \fIks >] +.RB [ \-sp +.RI < spec\ pow >] +.RB [ \-k00 +.RI < kernel >] +.RB [ \-k11 +.RI < kernel >] +.RB [ \-k22 +.RI < kernel >] +.RB [ \-ss +.RI < shading\ spec >] +.RB [ \-ns +.RI < normal\ spec >] +.RB [ \-side +.RI < normal\ side >] +.RB [ \-rn ] +.RB [ \-gmc +.RI < min\ gradmag >] +.RB [ \-step +.RI < size >] +.RB [ \-ref +.RI < size >] +.RB [ \-vp +.RI < verbose pixel >] +.RB [ \-n1 +.RI < near1 >] +.RB [ \-nt +.RI < #\ threads >] +.RB [ \-o +.RI < filename >] +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fInsin\fR> +input scalar volume to render +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-vi\fR <\fInvin\fR> +input vector volume to render +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-ti\fR <\fIntin\fR> +input tensor volume to render +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-txf\fR <\fInin\fR\ ...> +one or more transfer functions (1 or more +.IR nrrd s) +.TP +.B \-fr\fR <\fIeye\ pos\fR> +camera eye point (3 \fIdouble\fRs) +.TP +.B \-at\fR <\fIat\ pos\fR> +camera look-at point (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-up\fR <\fIup\ dir\fR> +camera pseudo-up vector (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 1 \(rq +.TP +.B \-rh +use a right-handed UVN frame (V points down) +.TP +.B \-or +orthogonal (not perspective) projection +.TP +.B \-dn\fR <\fInear\fR> +distance to near clipping plane +.RI ( double ) +.TP +.B \-di\fR <\fIimage\fR> +distance to image plane +.RI ( double ) +.TP +.B \-df\fR <\fIfar\fR> +distance to far clipping plane +.RI ( double ) +.TP +.B \-ur\fR <\fIuMin\fR\ \fIuMax\fR> +range in U direction of image plane (2 +.IR double s) +.TP +.B \-vr\fR <\fIvMin\fR\ \fIvMax\fR> +range in V direction of image plane (2 +.IR double s) +.TP +.B \-fv\fR <\fIfield\ of\ view\fR> +angle (in degrees) vertically subtended by view window +.RI ( double ); +default: +.RB \(lq 20 \(rq +.TP +.B \-offfr +the given eye point +.RB (\(lq \-fr \(rq) +is to be interpreted as an offset from the at point. +.TP +.B \-ffr\fR <\fIfake\ from\fR> +eye point to use for view-dependent transfer functions. +By default (not using this option), the point used is the normally specified +camera eye point. (3 \fIdouble\fRs) +.TP +.B \-turn\fR <\fIangle\fR> +angle (degrees) by which to rotate the from point around true up, for making +stereo pairs. +Positive means move towards positive U (the right) +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-am\fR <\fIambient\fR> +ambient light color (3 \fIfloat\fRs); default: +.RB \(lq 1\ 1\ 1 \(rq +.TP +.B \-ld\fR <\fIlight\ pos\fR> +view space light position (extended to infinity) (3 \fIfloat\fRs); default: +.RB \(lq 0\ 0\ \-1 \(rq +.TP +.B \-is\fR <\fIimage\ size\fR> +image dimensions (2 \fIint\fRs); default: +.RB \(lq 256\ 256 \(rq +.TP +.B \-iss\fR <\fIscale\fR> +scaling of image size (from +.RB \(lq \-is \(rq) +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-ads\fR <\fIka\fR\ \fIkd\fR\ \fIks\fR> +phong components (3 \fIfloat\fRs); default: +.RB \(lq 0.1\ 0.6\ 0.3 \(rq +.TP +.B \-sp\fR <\fIka\fR\ \fIkd\fR\ \fIks\fR> +phong specular power +.RI ( double ); default: +.RB \(lq 30 \(rq +.TP +.B \-k00\fR <\fIkernel\fR> +value reconstruction kernel (\fIkernel specification\fR); default: +.RB \(lq tent \(rq +.TP +.B \-k11\fR <\fIkernel\fR> +first derivative kernel (\fIkernel specification\fR); default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR <\fIkernel\fR> +second derivative kernel (\fIkernel specification\fR); default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-ss\fR <\fIshading\ spec\fR> +how to do shading +.RI ( string ); +default: +.RB \(lq phong:gage(scalar:n) \(rq +.TP +.B \-ns\fR <\fInormal\ spec\fR> +\(lqnormal\(rq to use for those miteVal\(cqs that need one +.RI ( string ); +default: \(lq\(rq +.TP +.B \-side\fR <\fInormal\ side\fR> +how to interpret gradients as normals: +.RS +7n +.IP \(bu 2 +.RB \(lq 1 \(rq: +normal points to lower values (higher == more \(lqinside\(rq) +.IP \(bu 2 +.RB \(lq 0 \(rq: +\(lqtwo-sided\(rq: dot-products are \fBabs()\fR\(cqed +.IP \(bu 2 +.RB \(lq \-1 \(rq: +normal points to higher values (lower == more \(lqinside\(rq) +.P +default: +.RB \(lq 1 \(rq +.RE +.TP +.B \-rn +renormalize kernel weights at each new sample location. +\(lqAccurate\(rq kernels don\(cqt need this; doing it always makes things go +slower +.B \-gmc\fR\ <\fImin\ gradmag\fR> +For curvature-based transfer functions, set curvature to zero when gradient +magnitude is below this +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-step\fR\ <\fIsize\fR> +step size along ray in world space +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-ref\fR\ <\fIsize\fR> +\(lqreference\(rq step size (world space) for doing opacity correction in +compositing +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-vp\fR\ <\fIverbose\ pixel\fR> +pixel for which to turn on verbose messages (2 \fIint\fRs); default: +.RB \(lq \-1\ \-1 \(rq +.TP +.B \-n1\fR\ <\fInear1\fR> +opacity close enough to 1.0 to terminate ray +.RI ( double ); +default: +.RB \(lq 0.99 \(rq +.TP +.B \-nt\fR\ <\fI#\ threads\fR> +number of threads hoover should use +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output nrrd to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/mrender.1 b/mrender.1 new file mode 100644 index 0000000..f619ac2 --- /dev/null +++ b/mrender.1 @@ -0,0 +1,294 @@ +.TH MRENDER "1" "April 2021" "" "User Commands" +.SH NAME +mrender \- a demonstration of hoover, gage, and nrrd measures +.SH SYNOPSIS +.B mrender +.RI [ @file \ ...] +.RB [ \-i +.RI < nin >] +.B \-k +.RI < kind > +.B \-fr +.RI < eye\ pos > +.RB [ \-at +.RI < at\ pos >] +.RB [ \-up +.RI < up\ dir >] +.RB [ \-rh ] +.RB [ \-or ] +.B \-dn +.RI < near > +.B \-di +.RI < image > +.B \-df +.RI < far > +.RB [ \-ar ] +.RB [ \-ur +.RI < uMin\fR\ \fIuMax >] +.RB [ \-vr +.RI < vMin\fR\ \fIvMax >] +.RB [ \-fv +.RI < field\ of\ view >] +.RB [ \-offfr ] +.RB [ \-turn +.RI < angle >] +.RB [ \-is +.RI < image\ size >] +.RB [ \-iss +.RI < scale >] +.RB [ \-k00 +.RI < kernel >] +.RB [ \-k11 +.RI < kernel >] +.RB [ \-k22 +.RI < kernel >] +.RB [ \-rn ] +.B \-q +.RI < query > +.B \-m +.RI < measure > +.RB [ \-gmc +.RI < min\ gradmag >] +.RB [ \-fn +.RI < from\ nan >] +.RB [ \-step +.RB [ \-nt +.RI < #\ threads >] +.RB [ \-vp +.RI < img\ coords >] +.RB [ \-o +.RI < filename >] +.SH DESCRIPTION +.P +Uses hoover to cast rays through a volume (scalar, vector, or tensor), gage to +measure one of various quantities along the rays, and a specified +.I nrrd +measure to reduce all the values along a ray down to one scalar, which is saved +in the output +.RI ( double ) +image. +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fInin\fR> +input +.I nrrd +to render +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-k\fR <\fIkind\fR> +\(lqkind\(rq of volume +.RB (\(lq scalar \(rq, +.RB \(lq vector \(rq, +or +.RB \(lq tensor \(rq) +.RI ( gageKind ) +.TP +.B \-fr\fR <\fIeye\ pos\fR> +camera eye point (3 \fIdouble\fRs) +.TP +.B \-at\fR <\fIat\ pos\fR> +camera look-at point (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-up\fR <\fIup\ dir\fR> +camera pseudo-up vector (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 1 \(rq +.TP +.B \-rh +use a right-handed UVN frame (V points down) +.TP +.B \-or +orthogonal (not perspective) projection +.TP +.B \-dn\fR <\fInear\fR> +distance to near clipping plane +.RI ( double ) +.TP +.B \-di\fR <\fIimage\fR> +distance to image plane +.RI ( double ) +.TP +.B \-df\fR <\fIfar\fR> +distance to far clipping plane +.RI ( double ) +.TP +.B \-ar +near, image, and far plane distances are relative to the +.B at +point, instead of the eye point +.TP +.B \-ur\fR <\fIuMin\fR\ \fIuMax\fR> +range in U direction of image plane (2 +.IR double s); +default: +.RB \(lq nan\ nan \(rq +.TP +.B \-vr\fR <\fIvMin\fR\ \fIvMax\fR> +range in V direction of image plane (2 +.IR double s); +default: +.RB \(lq nan\ nan \(rq +.TP +.B \-fv\fR <\fIfield\ of\ view\fR> +angle (in degrees) vertically subtended by view window +.RI ( double ); +default: +.RB \(lq 20 \(rq +.TP +.B \-offfr +the given eye point +.RB (\(lq \-fr \(rq) +is to be interpreted as an offset from the at point. +.TP +.B \-turn\fR <\fIangle\fR> +angle (degrees) by which to rotate the from point around true up, for making +stereo pairs. +Positive means move towards positive U (the right) +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-is\fR <\fIimage\ size\fR> +image dimensions (2 \fIint\fRs); default: +.RB \(lq 256\ 256 \(rq +.TP +.B \-iss\fR <\fIscale\fR> +scaling of image size (from +.RB \(lq \-is \(rq) +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-k00\fR <\fIkernel\fR> +value reconstruction kernel (\fIkernel specification\fR); default: +.RB \(lq tent \(rq +.TP +.B \-k11\fR <\fIkernel\fR> +first derivative kernel (\fIkernel specification\fR); default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR <\fIkernel\fR> +second derivative kernel (\fIkernel specification\fR); default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-rn +renormalize kernel weights at each new sample location. +\(lqAccurate\(rq kernels don\(cqt need this; doing it always makes things go +slower +.TP +.B \-q\fR <\fIquery\fR> +the quantity +.RB ( scalar , +.BR vector , +or +.BR matrix) +to learn by probing +.RI ( string ) +.TP +.B \-m\fR <\fImeasure\fR> +how to collapse list of ray samples into one scalar. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq min \(rq, +.RB \(lq max \(rq, +.RB \(lq mean \(rq, +.RB \(lq median \(rq, +.RB \(lq mode \(rq, +.RB \(lq variance \(rq, +.RB \(lq skew \(rq: +(self-explanatory) +.IP \(bu 2 +.RB \(lq intc \(rq, +.RB \(lq slope \(rq, +.RB \(lq error \(rq: +intercept, slope, and error from line fitting +.IP \(bu 2 +.RB \(lq stdv \(rq: +standard deviation +.IP \(bu 2 +.RB \(lq cov \(rq: +coefficient of variation +.IP \(bu 2 +.RB \(lq product \(rq, +.RB \(lq sum \(rq: +product or sum of all values +.IP \(bu 2 +.RB \(lq L1 \(rq, +.RB \(lq L2 \(rq, +.RB \(lq NL2 \(rq, +.RB \(lq RMS \(rq, +.RB \(lq Linf \(rq: +different norms +.IP \(bu 2 +.RB \(lq histo\-min \(rq, +.RB \(lq histo\-max \(rq, +.RB \(lq histo\-mean \(rq, +.RB \(lq histo\-median \(rq, +.RB \(lq histo\-mode \(rq, +.RB \(lq histo\-product \(rq, +.RB \(lq histo\-l2 \(rq, +.RB \(lq histo\-sum \(rq, +.RB \(lq histo\-variance \(rq, +.RB \(lq histo\-sd \(rq: +same measures, but for situations where we\(cqre given not the original values, +but a histogram of them. +.RI ( measure ) +.TP +.B \-gmc\fR\ <\fImin\ gradmag\fR> +For curvature-based queries, set answer to zero when gradient magnitude is +below this +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-fn\fR\ <\fIfrom\ nan\fR> +When histo-based measures generate +.B NaN +answers, the value that should be substituted for +.BR NaN . +.RI ( double ); +default: +.RB \(lq nan \(rq +.TP +.B \-step\fR\ <\fIsize\fR> +step size along ray in world space +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-nt\fR\ <\fI#\ threads\fR> +number of threads hoover should use +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-vp\fR\ <\fIimg\ coords\fR> +pixel coordinates for which to turn on verbose debugging messages, or +.RB \(lq \-1\ \-1 \(rq +to disable this. +(2 \fIint\fRs); +default: +.RB \(lq \-1\ \-1 \(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output +.I nrrd +to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/nrrdSanity.1 b/nrrdSanity.1 new file mode 100644 index 0000000..70c577a --- /dev/null +++ b/nrrdSanity.1 @@ -0,0 +1,32 @@ +.TH NRRDSANITY "1" "April 2021" "" "User Commands" +.SH NAME +nrrdSanity \- nrrd sanity check +.SH SYNOPSIS +.B nrrdSanity +.SH DESCRIPTION +.P +.BR nrrdSanity (1) +calls the +.B nrrdSanity() +check to verify the correctness of all the information (set at compile-time) +about the architecture, such as endianness, 32/64-bit, and the size of various +types, as well as running sanity checks on the global default +.RB ( nrrdDefault* ) +and state +.RB ( nrrdState* ) +variables. +.P +As a convenience, +.BR nrrdSanity (1) +also lists the availability of the different formats and data encodings (for +Nrrd files) supported by this build. +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR miter (1), +.BR mrender (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/overrgb.1 b/overrgb.1 new file mode 100644 index 0000000..538bf57 --- /dev/null +++ b/overrgb.1 @@ -0,0 +1,92 @@ +.TH OVERRGB "1" "April 2021" "" "User Commands" +.SH NAME +overrgb \- composites an RGBA nrrd over a background color (or image) +.SH SYNOPSIS +.B overrgb +.B \-i +.RI < nin > +.RB [ \-c +.RI < contrast >] +.RB [ \-cfp +.RI < fixed\ point >] +.RB [ \-g +.RI < gamma >] +.RB [ \-b +.RI < background >] +.RB [ \-bi +.RI < nbg >] +.B \-o +.RI < filename > +.SH DESCRIPTION +.P +Composites an RGBA nrrd over a background color (or image), after doing gamma +correction, then quantizes to an 8-bit image. +Actually, the input nrrd can have more than 4 values per pixel, but only the +first four are used. +If the RGBA nrrd is floating point, the values are taken at face value; if it +is fixed point, the values interpreted as having been quantized (so that 8-bit +RGBA images will act as you expect). +When compositing with a background image, the given background image does not +have to be the same size as the input image; it will be resampled (with linear +interpolation) to fit. +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fInin\fR> +input nrrd to composite +.RI ( nrrd ) +.TP +.B \-c\fR <\fIcontrast\fR> +contrast to apply to RGB values, before gamma. +.RB \(lq 0.0 \(rq +means no change, +.RB \(lq 1.0 \(rq +means thresholding, +.RB \(lq \-1.0 \(rq +means a complete washout. +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-cfp\fR <\fIfixed\ point\fR> +component level that doesn\(cqt change with contrast +.RI ( double ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-g\fR <\fIgamma\fR> +gamma to apply to image data, after contrast +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-b\fR <\fIbackground\fR> +background color to composite against; white is +.BR 1\ 1\ 1 , +not +.BR 255\ 255\ 255 . +(3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-bi\fR <\fInbg\fR> +8-bit RGB background image to composite against +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output PPM image to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/puller.1 b/puller.1 new file mode 100644 index 0000000..fb03592 --- /dev/null +++ b/puller.1 @@ -0,0 +1,591 @@ +.TH PULLER "1" "April 2021" "" "User Commands" +.SH NAME +puller \- command-line interface to the \(lqpull\(rq library +.SH SYNOPSIS +.B puller +.RB [ @file \ ...] +.RB [ \-int +.RI < int >] +.RB [ \-enr +.RI < spec >] +.RB [ \-ens +.RI < spec >] +.RB [ \-enw +.RI < spec >] +.RB [ \-efs +.RI < bool >] +.RB [ \-nave +.RI < bool >] +.RB [ \-cbst +.RI < bool >] +.RB [ \-noadd ] +.RB [ \-usa +.RI < bool >] +.RB [ \-pcet +.RI < bool >] +.RB [ \-nobin ] +.RB [ \-lti +.RI < bool >] +.RB [ \-por +.RI < bool >] +.RB [ \-npcwza +.RI < bool >] +.RB [ \-ubfgl +.RI < bool >] +.RB [ \-ratb +.RI < bool >] +.RB [ \-svec +.RI < vec >] +.RB [ \-gssr +.RI < rad >] +.RB [ \-v +.RI < verbosity >] +.B \-vol +.RI < vol0\ vol1 \ ...> +.B \-info +.RI < info0\ info1 \ ...> +.RB [ \-k00 +.RI < kern00 >] +.RB [ \-k11 +.RI < kern11 >] +.RB [ \-k22 +.RI < kern22 >] +.RB [ \-sscp +.RI < path >] +.RB [ \-kssb +.RI < kernel >] +.RB [ \-kssr +.RI < kernel >] +.RB [ \-nss +.RI < #\ scl\ smpls >] +.RB [ \-np +.RI < #\ points >] +.RB [ \-halton ] +.RB [ \-ppv +.RI < #\ pnts/vox >] +.RB [ \-ppvzr +.RI < z\ range >] +.RB [ \-jit +.RI < jitter >] +.RB [ \-pi +.RI < npos >] +.RB [ \-step +.RI < step >] +.RB [ \-csm +.RI < step >] +.RB [ \-snap +.RI < #\ iters >] +.RB [ \-maxi +.RI < #\ iters >] +.RB [ \-stim +.RI < #\ iters >] +.RB [ \-maxci +.RI < #\ iters >] +.RB [ \-irad +.RI < scale >] +.RB [ \-srad +.RI < scale >] +.RB [ \-bws +.RI < bin\ width >] +.RB [ \-alpha +.RI < alpha >] +.RB [ \-beta +.RI < beta >] +.RB [ \-gamma +.RI < gamma >] +.RB [ \-theta +.RI < theta >] +.RB [ \-wall +.RI < k >] +.RB [ \-eip +.RI < k >] +.RB [ \-ess +.RI < scl >] +.RB [ \-oss +.RI < scl >] +.RB [ \-edmin +.RI < frac >] +.RB [ \-edpcmin +.RI < frac >] +.RB [ \-fnnm +.RI < frac >] +.RB [ \-pcp +.RI < period >] +.RB [ \-iad +.RI < #\ iters >] +.RB [ \-icb +.RI < #\ iters >] +.RB [ \-ac3c +.RI < ac3c >] +.RB [ \-sit +.RI < sit >] +.RB [ \-rng +.RI < seed >] +.RB [ \-pbm +.RI < mod >] +.RB [ \-eiphl +.RI < hl >] +.RB [ \-nt +.RI < #\ threads >] +.RB [ \-nprob +.RI < prob >] +.RB [ \-pprob +.RI < prob >] +.RB [ \-addlog +.RI < fname >] +.RB [ \-o +.RI < nout >] +.RB [ \-eob +.RI < base >] +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-int\fR <\fIint\fR> +inter-particle energy type +.RI ( interaction\ type ); +default: +.RB \(lq justr \(rq +.TP +.B \-enr\fR <\fIspec\fR> +inter-particle energy, radial component +.RI ( energy\ specification ); +default: +.RB \(lq cotan \(rq +.TP +.B \-ens\fR <\fIspec\fR> +inter-particle energy, scale component +.RI ( energy\ specification ); +default: +.RB \(lq zero \(rq +.TP +.B \-enw\fR <\fIspec\fR> +windowing to create locality with additive scale-space interaction +.RB (\(lq \-int\ add \(rq) +.RI ( energy\ specification ); +default: +.RB \(lq butter:16,0.8 \(rq +.TP +.B \-efs\fR <\fIbool\fR> +whether or not strength contributes to particle-image energy +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-nave\fR <\fIbool\fR> +whether or not to nix points at edge of volume, where gage had to invent values +for kernel support +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-cbst\fR <\fIbool\fR> +during initialization, try constraint satisfaction before testing +.B seedThresh +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-noadd +turn off adding during population control +.TP +.B \-usa\fR <\fIbool\fR> +allow volumes to have different shapes +.RB ( false +is safe as different volume sizes are often accidental) +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-pcet\fR <\fIbool\fR> +use neighbor-counting \(lqenough\(rq heuristic to bail out of population +control +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-nobin +turn off spatial binning (which prevents multi-threading from being useful), +for debugging or speed-up measurement +.TP +.B \-lti\fR <\fIbool\fR> +impose +.B liveThresh +on initialization +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-por\fR <\fIbool\fR> +permute points during rebinning +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-npcwza\fR <\fIbool\fR> +no population control with zero alpha +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-ubfgl\fR <\fIbool\fR> +use beta for gamma learning +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-ratb\fR <\fIbool\fR> +be choosy when adding points to bins to avoid overlap +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-svec\fR <\fIvec\fR> +if non-zero (length), vector to use for displaying scale in 3-space (3 +\fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-gssr\fR <\fIrad\fR> +if non-zero (length), scaling of scale to cylindrical tensors +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-v\fR <\fIverbosity\fR> +verbosity level +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-vol\fR <\fIvol0\fR\ \fIvol1\fR\ ...> +input volumes, in format +<\fIfilename\fR>\fB:\fR<\fIkind\fR>\fB:\fR<\fIvolname\fR> +(1 or more \fImeetPullVol\fRs) +.TP +.B \-info\fR <\fIinfo0\fR\ \fIinfo1\fR\ ...> +info definitions, in format +.RI < info >[\fB\-c\fR]\fB:\fR< volname >\fB:\fR< item >[\fB:\fR< zero >\fB:\fR< scale >] +(1 or more \fImeetPullInfo\fRs) +.TP +.B \-k00\fR <\fIkern00\fR> +kernel for +.B gageKernel00 +.RI ( kernel\ specification ); +default: +.RB \(lq cubic:1,0 \(rq +.TP +.B \-k11\fR <\fIkern11\fR> +kernel for +.B gageKernel11 +.RI ( kernel\ specification ); +default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR <\fIkern22\fR> +kernel for +.B gageKernel22 +.RI ( kernel\ specification ); +default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-sscp\fR <\fIpath\fR> +path (without trailing +.BR / ) +for where to read/write pre-blurred volumes for scale-space +.RI ( string ); +default: +.RB \(lq ./ \(rq +.TP +.B \-kssb\fR <\fIkernel\fR> +blurring kernel, to sample scale space +.RI ( kernel\ specification ); +default: +.RB \(lq ds:1,5 \(rq +.TP +.B \-kssr\fR <\fIkernel\fR> +kernel for reconstructing from scale space samples +.RI ( kernel\ specification ); +default: +.RB \(lq hermite \(rq +.TP +.B \-nssr\fR <\fI#\ scl\ smpls\fR> +if using +.RB \(lq \-ppv \(rq; +number of samples along scale axis for each spatial position +.RI ( unsigned\ int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-np\fR <\fI#\ points\fR> +number of points to start in system +.RI ( unsigned\ int ); +default: +.RB \(lq 1000 \(rq +.TP +.B \-halton +use Halton sequence initialization instead of uniform random +.TP +.B \-ppv\fR <\fI#\ p[nts/vox\fR> +number of points per voxel to start in simulation (need to have a seed +threshold volume, overrides +.RB \(lq \-np \(rq) +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ppvzr\fR <\fIz\ range\fR> +range of Z slices (1st num < 2nd num) to do +.B ppv +in, or, +.RB \(lq 1\ 0 \(rq) +for whole volume (2 \fIunsigned\ int\fRs); default: +.RB \(lq 1\ 0 \(rq +.TP +.B \-jit\fR <\fIjitter\fR> +amount of jittering to do with +.B ppv +.RI ( double ); +default: +.RB \(lq 0 \(rq +.TP +.B \-pi\fR <\fInpos\fR> +4-by-N array of positions to start at (overrides +.RB \(lq \-np \(rq +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-step\fR <\fIstep\fR> +initial step size for gradient descent +.RI ( double ); +default: +.RB \(lq 1 \(rq +.TP +.B \-csm\fR <\fIstep\fR> +convergence criterion for constraint satisfaction +.RI ( double ); +default: +.RB \(lq 0.0001 \(rq +.TP +.B \-snap\fR <\fI#\ iters\fR> +if non-zero, # iters between saved snapshots +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-maxi\fR <\fI#\ iters\fR> +if non-zero, max # iterations to run whole system +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-stim\fR <\fI#\ iters\fR> +if non-zero, max # iterations to allow a particle to be stuck before nixing +.RI ( unsigned\ int ); +default: +.RB \(lq 5 \(rq +.TP +.B \-maxci\fR <\fI#\ iters\fR> +if non-zero, max # iterations for contraint enforcement +.RI ( unsigned\ int ); +default: +.RB \(lq 15 \(rq +.TP +.B \-irad\fR <\fIscale\fR> +particle radius in spatial domain +.RI ( double ); +default: +.RB \(lq 1 \(rq +.TP +.B \-srad\fR <\fIscale\fR> +particle radius in scale domain +.RI ( double ); +default: +.RB \(lq 1 \(rq +.TP +.B \-bws\fR <\fIbin\ width\fR> +spatial bin width as multiple of spatial radius +.RI ( double ); +default: +.RB \(lq 1.001 \(rq +.TP +.B \-alpha\fR <\fIalpha\fR> +blend between particle-image (\fIalpha\fR=\fB0\fR) and inter-particle +(\fIalpha\fR=\fB1\fR) energies +.RI ( double ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-beta\fR <\fIbeta\fR> +when using +.B Phi2 +energy, blend between pure space repulsion (\fIbeta\fR=\fB0\fR) and scale +attraction (\fIbeta\fR=\fB1\fR) +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-gamma\fR <\fIgamma\fR> +scaling factor on energy from strength +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-theta\fR <\fItheta\fR> +slope of increasing +.B livethresh +with respect to scale +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-wall\fR <\fIk\fR> +spring constant on walls +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-eip\fR <\fIk\fR> +amount by which it\(cqs okay for +.B per-particle +energy to increase during gradient descent process +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-ess\fR <\fIscl\fR> +when energy goes up instead of down, scale step size by this +.RI ( double ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-oss\fR <\fIscl\fR> +opportunistic scaling (hopefully up, >1) of step size on every iteration +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-edmin\fR <\fIfrac\fR> +convergence threshold: stop when fractional improvement (decrease) in energy +dips below this +.RI ( double ); +default: +.RB \(lq 0.0001 \(rq +.TP +.B \-edpcmin\fR <\fIfrac\fR> +population control is triggered when energy improvement goes below this +threshold +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-fnnm\fR <\fIfrac\fR> +don\(cqt nix if this fraction (or more) of neighbors have been nixed +.RI ( double ); +default: +.RB \(lq 0.25 \(rq +.TP +.B \-pcp\fR <\fIperiod\fR> +# iters to wait between attempts at population control +.RI ( unsigned\ int ); +default: +.RB \(lq 20 \(rq +.TP +.B \-iad\fR <\fI#\ iters\fR> +# iters to run descent on tentative new points during PC +.RI ( unsigned\ int ); +default: +.RB \(lq 10 \(rq +.TP +.B \-icb\fR <\fI#\ iters\fR> +periodicity of calling rendering callback +.RI ( unsigned\ int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-ac3c\fR <\fIac3c\fR> +allow codimensions 3 constraints +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-sit\fR <\fIsit\fR> +scale is tau +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-rng\fR <\fIseed\fR> +base seed value for RNGs +.RI ( unsigned\ int ); +default: +.RB \(lq 42 \(rq +.TP +.B \-pbm\fR <\fImod\fR> +progress bin mod +.RI ( unsigned\ int ); +default: +.RB \(lq 50 \(rq +.TP +.B \-eiphl\fR <\fIhl\fR> +half-life of +.BR energyIncreasePermute (\(lq \-eip \(rq) +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-nt\fR <\fI#\ threads\fR> +number of threads hoover should use +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-nprob\fR <\fIprob\fR> +do full neighbor discovery with this probability +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-pprob\fR <\fIprob\fR> +probe local image values with this probability +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-addlog\fR <\fIfname\fR> +name of file in which to log all particle additions +.RI ( string ); +default: \(lq\(rq +.TP +.B \-o\fR <\fInout\fR> +filename for saving computed positions +.RI ( string ); +default: +.RB \(lq \- \(rq +.TP +.B \-eob\fR <\fIbase\fR> +save extra info (besides position), and use this string as the base of the +filenames. +Not using this eans the extra info is not saved. +.RI ( string ); +default: \(lq\(rq +.SH NOTES +.P +Published research using this tool or the \(lqpull\(rq library should cite the +paper: +.in +4n +\fBGordon L. Kindlmann, Ra{\(rs\(aqu}l San Jos{\(rs\(aqe} Est{\(rs\(aqe}par, +Stephen M. Smith, Carl-Fredrik Westin. +Sampling and Visualizing Creases with Scale-Space Particles. +IEEE Trans. on Visualization and Computer Graphics, 15(6):1415-1424 (2009).\fR +.in +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/teem.spec b/teem.spec index 2ebe7a6..b69288c 100644 --- a/teem.spec +++ b/teem.spec @@ -1,3 +1,7 @@ +# Writing man pages is a work in progress. We do not install them until we have +# a complete set. +%bcond_with man_pages + Name: teem Version: 1.11.0 %global so_version 1 @@ -16,8 +20,124 @@ License: LGPLv2+ # python/ctypes/pullDemo.py # python/ctypes/teem-gen.py # python/ctypes/teem.py -URL: https://teem.sourceforge.net +URL: http://teem.sourceforge.net Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... + +Source1: gprobe.1 +Source2: ilk.1 +Source3: miter.1 +Source4: mrender.1 +Source5: nrrdSanity.1 +Source6: overrgb.1 +Source7: puller.1 +Source8: tend.1 +Source9: unu.1 +Source10: vprobe.1 + +Source800: tend-about.1 +Source801: tend-grads.1 +Source802: tend-epireg.1 +Source803: tend-bmat.1 +Source804: tend-estim.1 +Source805: tend-sim.1 +Source806: tend-mfit.1 +Source807: tend-mconv.1 +Source808: tend-msim.1 +Source809: tend-make.1 +Source810: tend-avg.1 +#Source811: tend-helix.1 +#Source812: tend-sten.1 +#Source813: tend-glyph.1 +#Source814: tend-ellipse.1 +#Source815: tend-anplot.1 +#Source816: tend-anvol.1 +#Source817: tend-anscale.1 +#Source818: tend-anhist.1 +#Source819: tend-triple.1 +#Source820: tend-tconv.1 +#Source821: tend-point.1 +#Source822: tend-slice.1 +#Source823: tend-norm.1 +#Source824: tend-fiber.1 +#Source825: tend-eval.1 +#Source826: tend-evalpow.1 +#Source827: tend-evalclamp.1 +#Source828: tend-evaladd.1 +#Source829: tend-evalmul.1 +#Source830: tend-log.1 +#Source831: tend-exp.1 +#Source832: tend-evec.1 +#Source833: tend-evecrgb.1 +#Source834: tend-evq.1 +#Source835: tend-unmf.1 +#Source836: tend-expand.1 +#Source837: tend-shrink.1 +#Source838: tend-bfit.1 +#Source839: tend-satin.1 +# +#Source900: unu-about.1 +#Source901: unu-env.1 +#Source902: unu-i2w.1 +#Source903: unu-w2i.1 +#Source904: unu-make.1 +#Source905: unu-head.1 +#Source906: unu-data.1 +#Source907: unu-convert.1 +#Source908: unu-resample.1 +#Source909: unu-fft.1 +#Source910: unu-cmedian.1 +#Source911: unu-dist.1 +#Source912: unu-minmax.1 +#Source913: unu-cksum.1 +#Source914: unu-diff.1 +#Source915: unu-quantize.1 +#Source916: unu-unquantize.1 +#Source917: unu-project.1 +#Source918: unu-slice.1 +#Source919: unu-sselect.1 +#Source920: unu-dice.1 +#Source921: unu-splice.1 +#Source922: unu-join.1 +#Source923: unu-crop.1 +#Source924: unu-acrop.1 +#Source925: unu-inset.1 +#Source926: unu-pad.1 +#Source927: unu-reshape.1 +#Source928: unu-permute.1 +#Source929: unu-swap.1 +#Source930: unu-shuffle.1 +#Source931: unu-flip.1 +#Source932: unu-unorient.1 +#Source933: unu-axinfo.1 +#Source934: unu-axinsert.1 +#Source935: unu-axsplit.1 +#Source936: unu-axdelete.1 +#Source937: unu-axmerge.1 +#Source938: unu-tile.1 +#Source939: unu-untile.1 +#Source940: unu-histo.1 +#Source941: unu-dhisto.1 +#Source942: unu-jhisto.1 +#Source943: unu-histax.1 +#Source944: unu-heq.1 +#Source945: unu-gamma.1 +#Source946: unu-1op.1 +#Source947: unu-2op.1 +#Source948: unu-3op.1 +#Source949: unu-affine.1 +#Source950: unu-lut.1 +#Source951: unu-mlut.1 +#Source952: unu-subst.1 +#Source953: unu-rmap.1 +#Source954: unu-mrmap.1 +#Source955: unu-imap.1 +#Source956: unu-lut2.1 +#Source957: unu-ccfind.1 +#Source958: unu-ccadj.1 +#Source959: unu-ccmerge.1 +#Source960: unu-ccsettle.1 +#Source961: unu-save.1 + # Patch CMakeLists.txt to fix library install paths to match what Fedora # expects. It is not immediately obvious if this patch is suitable for # sending upstream or not. @@ -141,6 +261,34 @@ rm -rvf python %install %cmake3_install +%if %{with man_pages} +install -d %{buildroot}%{_mandir}/man1 +install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ + %{SOURCE1} %{SOURCE2} %{SOURCE3} %{SOURCE4} %{SOURCE5} %{SOURCE6} \ + %{SOURCE7} %{SOURCE8} %{SOURCE9} %{SOURCE10} \ + %{SOURCE800} %{SOURCE801} %{SOURCE802} %{SOURCE803} %{SOURCE804} \ + %{SOURCE805} %{SOURCE806} %{SOURCE807} %{SOURCE808} %{SOURCE809} \ + %{SOURCE810} %{SOURCE811} %{SOURCE812} %{SOURCE813} %{SOURCE814} \ + %{SOURCE815} %{SOURCE816} %{SOURCE817} %{SOURCE818} %{SOURCE819} \ + %{SOURCE820} %{SOURCE821} %{SOURCE822} %{SOURCE823} %{SOURCE824} \ + %{SOURCE825} %{SOURCE826} %{SOURCE827} %{SOURCE828} %{SOURCE829} \ + %{SOURCE830} %{SOURCE831} %{SOURCE832} %{SOURCE833} %{SOURCE834} \ + %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} \ + %{SOURCE900} %{SOURCE901} %{SOURCE902} %{SOURCE903} %{SOURCE904} \ + %{SOURCE905} %{SOURCE906} %{SOURCE907} %{SOURCE908} %{SOURCE909} \ + %{SOURCE910} %{SOURCE911} %{SOURCE912} %{SOURCE913} %{SOURCE914} \ + %{SOURCE915} %{SOURCE916} %{SOURCE917} %{SOURCE918} %{SOURCE919} \ + %{SOURCE920} %{SOURCE921} %{SOURCE922} %{SOURCE923} %{SOURCE924} \ + %{SOURCE925} %{SOURCE926} %{SOURCE927} %{SOURCE928} %{SOURCE929} \ + %{SOURCE930} %{SOURCE931} %{SOURCE932} %{SOURCE933} %{SOURCE934} \ + %{SOURCE935} %{SOURCE936} %{SOURCE937} %{SOURCE938} %{SOURCE939} \ + %{SOURCE940} %{SOURCE941} %{SOURCE942} %{SOURCE943} %{SOURCE944} \ + %{SOURCE945} %{SOURCE946} %{SOURCE947} %{SOURCE948} %{SOURCE949} \ + %{SOURCE950} %{SOURCE951} %{SOURCE952} %{SOURCE953} %{SOURCE954} \ + %{SOURCE955} %{SOURCE956} %{SOURCE957} %{SOURCE958} %{SOURCE959} \ + %{SOURCE960} %{SOURCE961} +%endif + %check # We must exclude probeSS_ctmr04 and probeSS_ctmr10 on certain architectures @@ -171,6 +319,21 @@ rm -rvf python %{_bindir}/unu %{_bindir}/vprobe +%if %{with man_pages} +%{_mandir}/man1/gprobe.1* +%{_mandir}/man1/ilk.1* +%{_mandir}/man1/miter.1* +%{_mandir}/man1/mrender.1* +%{_mandir}/man1/nrrdSanity.1* +%{_mandir}/man1/overrgb.1* +%{_mandir}/man1/puller.1* +%{_mandir}/man1/tend.1* +%{_mandir}/man1/tend-*.1* +%{_mandir}/man1/unu.1* +%{_mandir}/man1/unu-*.1* +%{_mandir}/man1/vprobe.1* +%endif + %files libs %license LICENSE.txt @@ -193,7 +356,7 @@ rm -rvf python %changelog * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch -- Update URLs from HTTP to HTTPS +- Update download URL from HTTP to HTTPS - Improved package summaries and descriptions - Adjust whitespace to personal preference - Fix stray line continuation backslash @@ -204,6 +367,7 @@ rm -rvf python to that subpackage; remove certain unused files with other licenses in %%prep - Require cmake-filesystem instead of all of CMake in -devel - More precisely skip overly-strict floating-point tests where required +- Start work on adding a complete set of man pages * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild diff --git a/tend-about.1 b/tend-about.1 new file mode 100644 index 0000000..21d8320 --- /dev/null +++ b/tend-about.1 @@ -0,0 +1,9 @@ +.TH TEND\-ABOUT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-about \- information about +.BR tend (1) +and its use +.SH SYNOPSIS +.B tend\ about +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-avg.1 b/tend-avg.1 new file mode 100644 index 0000000..8b67389 --- /dev/null +++ b/tend-avg.1 @@ -0,0 +1,32 @@ +.TH TEND\-AVG "1" "April 2021" "" "User Commands" +.SH NAME +tend\-avg \- average across tensor volumes +.SH SYNOPSIS +.B tend\ avg +.B \-i +.RI < nin1 \ nin2 \ ...> +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Average across tensor volumes. +The output is the same size as the any one of the inputs. +The individual tensors may be averaged in various ways. +.SH OPTIONS +.TP +.B \-i\fR <\fInin1\fR\ \fInin2\fR\ ...> +list of input diffusion tensor volumes (2 or more +.IR nrrd s) +.TP +.B \-t\fR <\fItype\fR> +averaging method; default: +.RB \(lq linear \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-bmat.1 b/tend-bmat.1 new file mode 100644 index 0000000..e0a8c3b --- /dev/null +++ b/tend-bmat.1 @@ -0,0 +1,43 @@ +.TH TEND\-BMAT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-bmat \- calculate B-matrix given gradient directions +.SH SYNOPSIS +.B tend\ bmat +.B \-i +.RI < grads > +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Calculate B-matrix given gradient directions, assuming no diffusion weighting +from the other imaging gradients. +The input is a 3-by-N array of floats or doubles, each row being one of the +gradient directions used for diffusion-weighted imaging. +A plain text file with one gradient per line, no punctuation, is an easy way to +specify this information. +The gradient vector coefficients are used as is, without normalization (since +different gradient strengths are sometimes desired). +The output has one row of the +B-matrix per line, with coefficient ordering +.BR Bxx , +.BR Bxy , +.BR Bxz , +.BR Byy , +.BR Byz , +.BR Bzz , +and with the off-diagonal elements NOT pre-multiplied by 2. +.SH OPTIONS +.TP +.B \-i\fR <\fIgrads\fR> +array of gradient directions +.TP +.B \-o\fR <\fInout\fR> +output B matrix +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-estim (1), +.BR tend\-msim (1), +.BR tend\-sim (1) diff --git a/tend-epireg.1 b/tend-epireg.1 new file mode 100644 index 0000000..cb45cb6 --- /dev/null +++ b/tend-epireg.1 @@ -0,0 +1,139 @@ +.TH TEND\-EPIREG "1" "April 2021" "" "User Commands" +.SH NAME +tend\-epireg \- register diffusion-weighted echo-planar images +.SH SYNOPSIS +.B tend\ epireg +.B \-i +.RI < dwi0\fR\ \fBdwi1 \ ...> +.B \-g +.RI < grads > +.RB [ \-r +.RI < reference >] +.RB [ \-nv ] +.RB [ \-p ] +.RB [ \-bw +.RI < x\fB,\fIy\fB\ blur >] +.RB [ \-t +.RI < DWI\ thresh >] +.RB [ \-ncc ] +.RB [ \-f +.RI < fit\ frac >] +.RB [ \-k +.RI < kernel >] +.RB [ \-s +.RI < start\ # >] +.RB [ \-o +.RI < output/prefix >] +.SH DESCRIPTION +.P +Register diffusion-weighted echo-planar images. +This registration corrects the shear, scale, and translate along the phase +encoding direction (assumed to be the Y (second) axis of the image) caused by +eddy currents from the diffusion-encoding gradients with echo-planar imaging. +The method is based on calculating moments of segmented images, where the +segmentation is a simple procedure based on blurring (optional), thresholding +and connected component analysis. +The registered DWIs are resampled with the chosen kernel, with the separate +DWIs stacked along axis 0. +.SH OPTIONS +.TP +.B \-i\fR <\fIdwi0\fR\ \fIdwi1\fR\ ...> +all the diffusion-weighted images (DWIs), as separate 3D +.IR nrrd s, +.BR OR : +one 4D +.I nrrd +of all DWIs stacked along axis 0 (1 or more +.IR nrrd s) +.TP +.B \-g\fR <\fIgrads\fR> +array of gradient directions, in the same order as the associated DWIs were +given to +.RB \(lq \-i \(rq, +.B OR +.RB \(lq \-g\ kvp \(rq +signifies that gradient directions should be read from the key/value pairs of +the DWI +.RI ( string ) +.TP +.B \-r\fR <\fIreference\fR> +which of the DW volumes (zero-based numbering) should be used as the standard, +to which all other images are transformed. +Using +.B \-1 +(the default) means that 9 intrinsic parameters governing the relationship +between the gradient direction and the resulting distortion are estimated and +fitted, ensuring good registration with the non-diffusion-weighted T2 image +(which is never explicitly used in registration). +Otherwise, by picking a specific DWI, no distortion parameter estimation is +done. +.RI ( int ); +default: +.RB \(lq \-1 \(rq +.TP +.B \-nv +turn OFF verbose mode, and have no idea what stage processing is at. +.TP +.B \-p +save out intermediate steps of processing +.TP +.B \-bw\fR <\fIx\fB,\fIy\ blur\fR> +standard deviations in X and Y directions of gaussian filter used to blur the +DWIs prior to doing segmentation. +This blurring does not effect the final resampling of registered DWIs. +Use +.RB \(lq 0.0\ 0.0 \(rq +to say \(lqno blurring\(rq (2 +.IR float s); +default: +.RB \(lq 1.0\ 2.0 \(rq +.TP +.B \-t\fR <\fIDWI\ thresh\fR> +Threshold value to use on DWIs, to do initial separation of brain and +non-brain. +By default, the threshold is determined automatically by histogram analysis. +.RI ( float ) +.TP +.B \-ncc +do +.B NOT +do connected component (CC) analysis, after thresholding and before moment +calculation. +Doing CC analysis usually gives better results because it converts the +thresholding output into something much closer to a real segmentation +.TP +.B \-f\fR <\fIfit\ frac\fR> +(only meaningful with +.RB \(lq \-r\ \-1 \(rq) +When doing linear fitting of the intrinsic distortion parameters, it is good to +ignore the slices for which the segmentation was poor. +A heuristic is used to rank the slices according to segmentation quality. +This option controls how many of the (best) slices contribute to the fitting. +Use +.RB \(lq 0 \(rq +to disable distortion parameter fitting. +.RI ( float ) +default: +.RB \(lq 0.70 \(rq +.TP +.B \-k\fR <\fIkernel\fR> +kernel for resampling DWIs along the phase-encoding direction during final +registration stage; default: +.RB \(lq cubic:0,0.5 \(rq +.TP +.B \-s\fR <\fIstart\ #\fR> +first number to use in numbered sequence of output files. +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-o\fR <\fIoutput/prefix\ #\fR> +For separate 3D DWI volume inputs: prefix for output filenames; will save out +one (registered) DWI for each input DWI, using the same type as the input. +.BR OR : +For single 4D DWI input: output file name. +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-estim.1 b/tend-estim.1 new file mode 100644 index 0000000..649a1e1 --- /dev/null +++ b/tend-estim.1 @@ -0,0 +1,196 @@ +.TH TEND\-ESTIM "1" "April 2021" "" "User Commands" +.SH NAME +tend\-estim \- estimate tensors from a set of DW images +.SH SYNOPSIS +.B tend\ estim +.RB [ \-old ] +.RB [ \-sigma +.RI < sigma >] +.RB [ \-v +.RI < verbose >] +.RB [ \-est +.RI < estimate\ method >] +.RB [ \-wlsi +.RI < WLS\ iters >] +.RB [ \-fixneg ] +.RB [ \-ee +.RI < filename >] +.RB [ \-eb +.RI < filename >] +.RB [ \-t +.RI < thresh >] +.RB [ \-soft +.RI < soft >] +.RB [ \-scale +.RI < scale >] +.RB [ \-mv +.RI < min\ val >] +.B \-B +.RI < B\-list > +.RB [ \-b +.RI < b >] +.B \-knownB0 +.RI < bool > +.RB [ \-i +.RI < dwi0\fR\ \fIdwi1\fR\ ...>] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Estimate tensors from a set of DW images. +The tensor coefficient weightings associated with each of the DWIs, the +B-matrix, is given either as a separate array, (see +.BR tend\-bmat (1) for +details), or by the key-value pairs in the DWI +.I nrrd +header. +A \(lqconfidence\(rq value is computed with the tensor, based on a soft +thresholding of the sum of all the DWIs, according to the threshold and +softness parameters. +.SH OPTIONS +.TP +.B \-old +instead of the new +.B tenEstimateContext +code, use the old +.B tenEstimateLinear +code +.TP +.B \-sigma\fR <\fIsigma\fR> +Rician noise parameter +.RI ( float ) +.TP +.B \-v\fR <\fIverbose\fR> +verbosity level +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-est\fR <\fIestimate\ method\fR> +estimation method to use. +.RB \(lq lls \(rq: +linear-least squares; default: +.RB \(lq lls \(rq +.TP +.B \-wlsi\fR <\fIWLS\ iters\fR> +when using weighted-least-squares +.RB (\(lq \-est\ wls \(rq), +how many iterations to do after the initial weighted fit. +.RI ( unsigned\ int ) +default: +.RB \(lq 1 \(rq +.TP +.B \-fixneg +after estimating the tensor, ensure that there are no negative eigenvalues by +adding (to all eigenvalues) the amount by which the smallest is negative +(corresponding to increasing the non-DWI image value). +.TP +.B \-ee\fR <\fIfilename\fR> +Giving a filename here allows you to save out the tensor estimation error: a +value which measures how much error there is between the tensor model and the +given diffusion weighted measurements for each sample. +By default, no such error calculation is saved. +.RI ( string ) +.TP +.B \-eb\fR <\fIfilename\fR> +In those cases where there is no B=0 reference image given +.RB (\(lq \-knownB0\ false \(rq), +giving a filename here allows you to save out the +.B B=0 +image which is estimated from the data. +By default, this image value is estimated but not saved. +.RI ( string ) +.TP +.B \-t\fR <\fIthresh\fR> +value at which to threshold the mean DWI value per pixel in order to generate +the \(lqconfidence\(rq mask. +By default, the threshold value is calculated automatically, based on histogram +analysis. +.RI ( double ) +.TP +.B \-soft\fR <\fIsoft\fR> +how fuzzy the confidence boundary should be. +By default, confidence boundary is perfectly sharp +.RI ( float ) +default: +.RB \(lq 0 \(rq +.TP +.B \-scale\fR <\fIscale\fR> +After estimating the tensor, scale all of its elements (but not the confidence +value) by this amount. +Can help with downstream numerical precision if values are very large or small. +.RI ( float ) +default: +.RB \(lq 1 \(rq +.TP +.B \-mv\fR <\fImin\ val\fR> +minimum plausible value (especially important for linear least squares +estimation) +.RI ( double ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-B\fR <\fIB\-list\fR> +6-by-N list of B-matrices characterizing the diffusion weighting for each +image. +.BR tend\-bmat (1) +is one source for such a matrix; see its usage info for specifics on how the +coefficients of the B-matrix are ordered. +An unadorned plain text file is a great way to specify the B-matrix. +.IP +.B OR +.IP +Can say just +.RB \(lq \-B\ kvp \(rq +to try to learn B matrices from key/value pair information in input images. +.IP +.RI ( string ) +.TP +.B \-b\fR <\fIb\fR> +\(lqb\(rq diffusion-weighting factor (units of sec/mm^2) +.RI ( double ) +.TP +.B \-knownB0\fR <\fIbool\fR> +Indicates if the +.B B=0 +non-diffusion-weighted reference image is known, or if it has to be estimated +along with the tensor elements +.RS +7n +.IP \(bu 2 +if +.RB \(lq true \(rq: +in the given list of diffusion gradients or B-matrices, there are one or more +with zero norm, which are simply averaged to find the +.B B=0 +reference image value +.IP \(bu 2 +if +.RB \(lq false \(rq: +there may or may not be diffusion-weighted images among the input; the +.B B=0 +image value is going to be estimated along with the diffusion model +.P +.RI ( bool ) +.RE +.TP +.B \-i\fR <\fIdwi0\fR\ \fIdwi1\fR\ ...> +all the diffusion-weighted images (DWIs), as separate 3D +.IR nrrd s, +.BR OR : +One 4D +.I nrrd +of all DWIs stacked along axis 0 (1 or more +.IR nrrd s); +default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) +.BR tend\-bmat (1), +.BR tend\-msim (1), +.BR tend\-sim (1) diff --git a/tend-grads.1 b/tend-grads.1 new file mode 100644 index 0000000..e92bc8f --- /dev/null +++ b/tend-grads.1 @@ -0,0 +1,162 @@ +.TH TEND\-GRADS "1" "April 2021" "" "User Commands" +.SH NAME +tend\-grads \- calculate balanced gradient directions for DWI acquisition +.SH SYNOPSIS +.B tend\ grads +.RB [ \-n +.RI < #\ dir >] +.RB [ \-i +.RI < grads >] +.RB [ \-seed +.RI < value >] +.RB [ \-step +.RI < step >] +.RB [ \-single ] +.RB [ \-snap +.RI < interval >] +.RB [ \-jitter +.RI < jitter >] +.RB [ \-miniter +.RI < #\ iters >] +.RB [ \-maxiter +.RI < #\ iters >] +.RB [ \-minvelo +.RI < vel >] +.RB [ \-exp +.RI < exponent >] +.RB [ \-dp +.RI < potential\ change >] +.RB [ \-minimprov +.RI < delta >] +.RB [ \-minmean +.RI < len >] +.RB [ \-izv +.RI < insert >] +.RB [ \-o +.RI < filename >] +.SH DESCRIPTION +.P +Composites an RGBA +.I nrrd +over a background color (or image), after doing gamma correction, then +quantizes to an 8-bit image. +Actually, the input +.I nrrd +can have more than 4 values per pixel, but only the first four are used. +If the RGBA +.I nrrd +s floating point, the values are taken at face value; if it is fixed point, the +values interpreted as having been quantized (so that 8-bit RGBA images will act +as you expect). +When compositing with a background image, the given background image does not +have to be the same size as the input image; it will be resampled (with linear +interpolation) to fit. +.SH OPTIONS +.TP +.B \-n\fR <\fI#\ dir\fR> +desired number of diffusion gradient directions +.RI ( int ) +default: +.RB \(lq 6 \(rq +.TP +.B \-i\fR <\fIgrads\fR> +initial gradient directions to start with, instead of default random initial +directions (overrides +.RB \(lq \-n \(rq); +default: \(lq\(rq +.TP +.B \-seed\fR <\fIvalue\fR> +seed value to used with +.B airSrandMT() +.RI ( unsigned\ int ) +default: +.RB \(lq 42 \(rq +.TP +.B \-step\fR <\fIstep\fR> +time increment in solver +.RI ( double ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-single +instead of the default behavior of tracking a pair of antipodal points +(appropriate for determining DWI gradients), use only single points +(appropriate for who knows what). +.TP +.B \-snap\fR <\fIinterval\fR> +specifies an interval between which snapshots of the point positions should be +saved out. +By default (not using this option), there is no such snapshot behavior +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-jitter\fR <\fIjitter\fR> +amount by which to perturb points when given an input +.I nrrd +.RI ( double ) +default: +.RB \(lq 0.1 \(rq +.TP +.B \-miniter\fR <\fI#\ iters\fR> +min number of iterations for which to run the simulation +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-maxiter\fR <\fI#\ iters\fR> +max number of iterations for which to run the simulation +.RI ( int ) +default: +.RB \(lq 1000000 \(rq +.TP +.B \-minvelo\fR <\fIvel\fR> +low threshold on mean velocity of repelling points, at which point repulsion +phase of algorithm terminates. +.RI ( double ) +default: +.RB \(lq 0.00001 \(rq +.TP +.B \-exp\fR <\fIexponent\fR> +the exponent n that determines the potential energy +.BR 1/r^n . +.RI ( double ) +default: +.RB \(lq 1 \(rq +.TP +.B \-dp\fR <\fIpotential\ change\fR> +low threshold on fractional change of potential at which point repulsion phase +of algorithm terminates. +.RI ( double ) +default: +.RB \(lq 0.000000001 \(rq +.TP +.B \-minimprov\fR <\fIdelta\fR> +in the second phase of the algorithm, when stochastically balancing the sign of +the gradients, the (small) improvement in length of mean gradient which +triggers termination (as further improvements are unlikely. +.RI ( double ) +default: +.RB \(lq 0.00005 \(rq +.TP +.B \-minmean\fR <\fIlen\fR> +if length of mean gradient falls below this, finish the balancing phase +.RI ( double ) +default: +.RB \(lq 0.0001 \(rq +.TP +.B \-izv\fR <\fIinsert\fR> +adding zero vector at beginning of grads +.RI ( bool ) +default: +.RB \(lq false \(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output +.I nrrd +to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-make.1 b/tend-make.1 new file mode 100644 index 0000000..c4b7b08 --- /dev/null +++ b/tend-make.1 @@ -0,0 +1,28 @@ +.TH TEND\-MAKE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-make \- create DT volume from confidence and eigensystem +.SH SYNOPSIS +.B tend\ make +.B \-i +.RI < conf \ evals \ evecs > +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Create DT volume from confidence and eigensystem. +The input is in the form of three +.IR nrrd s, +one for confidence values (3D), one for eigenvalues (4D, three evals per +voxel), and one for eigenvectors (4D, nine evec components per voxel). +.SH OPTIONS +.TP +.B \-i\fR <\fIconf\fR\ \fIevals\fR\ \fIevecs\fR> +input diffusion tensor volume (3 +.IR nrrd s) +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-mconv.1 b/tend-mconv.1 new file mode 100644 index 0000000..54a6f07 --- /dev/null +++ b/tend-mconv.1 @@ -0,0 +1,39 @@ +.TH TEND\-MCONV "1" "April 2021" "" "User Commands" +.SH NAME +tend\-mconv \- convert from one model to another +.SH SYNOPSIS +.B tend\ mconv +.B \-mo +.RI < model > +.RB [ \-mi +.RI < model >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-mo\fR <\fImodel\fR> +which model to convert to +.RI ( string ) +.TP +.B \-mi\fR <\fImodel\fR> +model converting from; if not set, will try to determine from input +.I nrrd +.RI ( string ) +.TP +.B \-i\fR <\fInin\fR> +input +.I nrrd +of model parms; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output +.I nrrd +of model parms +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-mfit.1 b/tend-mfit.1 new file mode 100644 index 0000000..fc220b4 --- /dev/null +++ b/tend-mfit.1 @@ -0,0 +1,129 @@ +.TH TEND\-MFIT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-mfit \- estimate models from a set of DW images +.SH SYNOPSIS +.B tend\ mfit +.RB [ \-v +.RI < verbose >] +.B \-m +.RI < model > +.RB [ \-ns +.RI < #\ starts >] +.RB [ \-ml ] +.RB [ \-sigma +.RI < sigma >] +.RB [ \-eps +.RI < eps >] +.RB [ \-mini +.RI < min\ iters >] +.RB [ \-maxi +.RI < max\ iters >] +.B \-knownB0 +.RI < bool > +.RB [ \-t +.RI < type >] +.RB [ \-i +.RI < dwi >] +.RB [ \-o +.RI < nout >] +.RB [ \-eo +.RI < filename >] +.RB [ \-co +.RI < filename >] +.RB [ \-io +.RI < filename >] +.SH OPTIONS +.TP +.B \-v\fR <\fIverbose\fR> +verbosity level +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-m\fR <\fImodel\fR> +which model to fit. +Use optional +.RB \(lq b0+ \(rq +prefix to indicate that the +.B B0 +image should also be saved (independent of whether it was known or had to be +estimated, according to +.RB \(lq \-knownB0 \(rq). +.RI ( string ) +.TP +.B \-ns\fR <\fI#\ starts\fR> +number of random starting points at which to initialize fitting +.RI ( unsigned\ int ) +default: +.RB \(lq 1 \(rq +.TP +.B \-ml +do ML fitting, rather than least-squares, which also requires setting +.RB \(lq \-sigma \(rq +.TP +.B \-sigma\fR <\fIsigma\fR> +Gaussian/Rician noise parameter +.RI ( double ) +.TP +.B \-eps\fR <\fIeps\fR> +convergence epsilon +.RI ( double ) +default: +.RB \(lq 0.01 \(rq +.TP +.B \-mini\fR <\fImin\ iters\fR> +minimum required # iterations for fitting. +.RI ( unsigned\ int ) +default: +.RB \(lq 3 \(rq +.TP +.B \-maxi\fR <\fImax\ iters\fR> +maximum allowable # iterations for fitting. +.RI ( unsigned\ int ) +default: +.RB \(lq 100 \(rq +.TP +.B \-knownB0\fR <\fIbool\fR> +Indicates if the +.B B=0 +non-diffusion-weighted reference image is known +.RB (\(lq true \(rq) +because it appears one or more times amongst the DWIs, or, if it has to be +estimated along with the other model parameters +.RB (\(lq false \(rq) +.RI ( bool ) +.TP +.B \-t\fR <\fItype\fR> +output type of model parameters; default: +.RB \(lq float \(rq +.TP +.B \-i\fR <\fIdwi\fR> +all the diffusion-weighted images in one 4D +.IR nrrd ; +default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output parameter vector image +.RI ( string ) +default: +.RB \(lq \- \(rq +.TP +.B \-eo\fR <\fIfilename\fR> +Giving a filename here allows you to save out the per-sample fitting error. +By default, no such error is saved. +.RI ( string ) +.TP +.B \-co\fR <\fIfilename\fR> +Giving a filename here allows you to save out the per-sample convergence +fraction. +By default, no such error is saved. +.RI ( string ) +.TP +.B \-io\fR <\fIfilename\fR> +Giving a filename here allows you to save out the per-sample number of +iterations needed for fitting. +By default, no such error is saved. +.RI ( string ) +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-msim.1 b/tend-msim.1 new file mode 100644 index 0000000..2d0b76a --- /dev/null +++ b/tend-msim.1 @@ -0,0 +1,111 @@ +.TH TEND\-MSIM "1" "April 2021" "" "User Commands" +.SH NAME +tend\-msim \- simulate DW images from an image of models +.SH SYNOPSIS +.B tend\ msim +.RB [ \-sigma +.RI < sigma >] +.RB [ \-seed +.RI < seed >] +.B \-g +.RI < grad\ list > +.RB [ \-b0 +.RI < b0\ image >] +.RB [ \-i +.RI < model\ image >] +.B \-m +.RI < model > +.RB [ \-ib0 +.RI < bool >] +.RB [ \-b +.RI < b >] +.RB [ \-kvp +.RI < bool >] +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Simulate DW images from an image of models. +The output will be in the same form as the input to +.BR tend\-estim (1). +The B-matrices +.RB (\(lq \-B \(rq) +can be the output from +.BR tend\-bmat (1), +or the gradients can be given directly +.RB (\(lq \-g \(rq); +one of these is required. +Note that the input tensor image +.RB (\(lq \-i \(rq) +is the basis of the output per-axis fields and image orientation. +.B NOTE: +this includes the measurement frame used in the input tensor image, which +implies that the given gradients or B-matrices are already expressed in that +measurement frame. +.SH OPTIONS +.TP +.B \-sigma\fR <\fIsigma\fR> +Gaussian/Rician noise parameter +.RI ( double ) +default: +.RB \(lq 0.0 \(rq +.TP +.B \-seed\fR <\fIseed\fR> +seed value for RNG which creates noise +.RI ( int ) +default: +.RB \(lq 42 \(rq +.TP +.B \-g\fR <\fIgrad\ list\fR> +gradient list, one row per diffusion-weighted image +.TP +.B \-b0\fR <\fIb0\ image\fR> +reference non-diffusion-weighted +.RB (\(lq B0 \(rq) +image, which may be needed if it isn't part of the given model parameter image +.TP +.B \-m\fR <\fImodel\fR> +model with which to simulate DWIs, which must be specified if it is not +indicated by the first axis in input model image. +.RB \(lq string \(rq +.TP +.B \-ib0\fR <\fIbool\fR> +insert a non-DW +.B B0 +image at the beginning of the experiment specification (useful if the given +gradient list doesn't already have one) and hence also insert a +.B B0 +image at the beginning of the output simulated DWIs +.RB \(lq bool \(rq +default: +.RB \(lq false \(rq +.TP +.B \-b\fR <\fIb\fR> +.B b +value for simulated scan +.RB \(lq double \(rq +default: +.RB \(lq 1000 \(rq +.TP +.B \-kvp\fR <\fIbool\fR> +generate key/value pairs in the NRRD header corresponding to the input +.BR b -value +and gradients. +.RB \(lq bool \(rq +default: +.RB \(lq true \(rq +.TP +.B \-t\fR <\fItype\fR> +output type of DWIs; default: +.RB \(lq float \(rq +.TP +.B \-o\fR <\fInout\fR> +output dwis +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-bmat (1), +.BR tend\-estim (1) diff --git a/tend-sim.1 b/tend-sim.1 new file mode 100644 index 0000000..3761398 --- /dev/null +++ b/tend-sim.1 @@ -0,0 +1,101 @@ +.TH TEND\-SIM "1" "April 2021" "" "User Commands" +.SH NAME +tend\-sim \- simulate DW images from a tensor field +.SH SYNOPSIS +.B tend\ sim +.RB [ \-old ] +.RB [ \-sigma +.RI < sigma >] +.RB [ \-seed +.RI < seed >] +.RB [ \-g +.RI < grad\ list >] +.RB [ \-B +.RI < B\ matrix >] +.B \-r +.RI < reference\ field > +.RB [ \-i +.RI < tensor\ field >] +.RB [ \-b +.RI < b >] +.RB [ \-kvp ] +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Simulate DW images from a tensor field. +The output will be in the same form as the input to +.BR tend\-estim (1). +The B-matrices +.RB (\(lq \-B \(rq) +can be the output from +.BR tend\-bmat (1), +or the gradients can be given directly +.RB (\(lq \-g \(rq); +one of these is required. +Note that the input tensor field +.RB (\(lq \-i \(rq) +is the basis of the output per-axis fields and image orientation. +.B NOTE: +this includes the measurement frame used in the input tensor field, which +implies that the given gradients or B-matrices are already expressed in that +measurement frame. +.SH OPTIONS +.TP +.B \-old +don't use the new +.B tenEstimateContext +functionality +.TP +.B \-sigma\fR <\fIsigma\fR> +Rician noise parameter +.RI ( float ) +default: +.RB \(lq 0.0 \(rq +.TP +.B \-seed\fR <\fIseed\fR> +seed value for RNG which creates noise +.RI ( int ) +default: +.RB \(lq 42 \(rq +.TP +.B \-g\fR <\fIgrad\ list\fR> +gradient list, one row per diffusion-weighted image +.TP +.B \-B\fR <\fIB\ matrix\fR> +B matrix, one row per diffusion-weighted image. +Using this overrides the gradient list input via +.RB \(lq \-g \(rq +.TP +.B \-r\fR <\fIreference\ field\fR> +reference anatomical scan, with no diffusion weighting +.TP +.B \-i\fR <\fItensor\ field\fR> +input diffusion tensor field +.TP +.B \-b\fR <\fIb\fR> +.B b +value for simulated scan +.RI ( float ) +default: +.RB \(lq 1000 \(rq +.TP +.B \-kvp +generate key/value pairs in the NRRD header corresponding to the input b-value +and gradients or B-matrices. +.TP +.B \-t\fR <\fItype\fR> +output type of DWIs; default: +.RB \(lq float \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-bmat (1), +.BR tend\-estim (1) diff --git a/tend.1 b/tend.1 new file mode 100644 index 0000000..e61040a --- /dev/null +++ b/tend.1 @@ -0,0 +1,316 @@ +.TH TEND "1" "April 2021" "" "User Commands" +.SH NAME +tend \- diffusion image processing and analysis +.SH SYNOPSIS +.B tend +.I COMMAND +.RI [ OPTION ]... +.SH DESCRIPTION +.BR tend (1) +is a command-line interface to much of the functionality in \(lqten\(rq, a C +library for diffusion image processing. +Ten is one library in the \(lqTeem\(rq collection of libraries. +More information about Teem is at +.UR http://teem.sf.net +http://teem.sf.net +.UE . +A checkout of Teem source is available via: +.in +4n +.EX +.B svn co https://svn.code.sf.net/p/teem/code/teem/trunk teem +.EE +.in +.P +Long-term maintenance of this software depends on funding, and funding depends +on being able to document who is using it for what. +If +.BR tend (1) +or Ten has helped in your research, including for simple one-off experiments or +mundane data hacking, the developers of Teem would love to know. +There are multiple ways of communicating this. +In your publications, consider adding a line such as this in the +Acknowledgments: +.in +4n +Data processing performed with the tend tool, part of the Teem toolkit +available at +.UR http://teem.sf.net +http://teem.sf.net +.UE . +.in +Alternatively, please email +.MT glk(a)uchicago.edu +glk(a)uchicago.edu +.ME +and briefly describe how Teem software has helped in your work. +Please also consider joining the +.UR https://lists.sourceforge.net/lists/listinfo/teem-users +teem\-users mailing list +.UE . +This is the primary forum for feedback, questions, and feature requests. +.P +Like +.BR unu (1), +another Teem command-line binary, it is often useful to chain together invocations of +.BR tend (1) +with pipes, as in the following, which estimates tensors from DWIs, takes a +slice of the tensor volume, computes the standard RGB colormap of the principal +eigenvector, and then quantizes it to an 8-bit PNG: +.in +4n +.EX +\fBtend\ estim\ \-i\ dwi.nhdr\ \-B\ kvp\ \-knownB0\ true\ \(rs +\ |\ tend\ slice\ \-a\ 2\ \-p\ 30\ \(rs +\ |\ tend\ evecrgb\ \-c\ 0\ \-a\ cl2\ \-gam\ 1.2\ \(rs +\ |\ unu\ quantize\ \-b\ 8\ \-min\ 0\ \-max\ 1\ \-o\ z30\-rgb.png +.EE +.in +.SH OPTIONS +.SS tend\ about +Information about this program and its use +.P +See +.BR tend\-about (1). +.SS tend\ grads +Calculate balanced gradient directions for DWI acquisition +.P +See +.BR tend\-grads (1). +.SS tend\ epireg +Register diffusion-weighted echo-planar images +.P +See +.BR tend\-epireg (1). +.SS tend\ bmat +Calculate B-matrix given gradient directions +.P +See +.BR tend\-bmat (1). +.SS tend\ estim +Estimate tensors from a set of DW images +.P +See +.BR tend\-estim (1). +.SS tend\ sim +Simulate DW images from a tensor field +.P +See +.BR tend\-sim (1). +.SS tend\ mfit +Estimate models from a set of DW images +.P +See +.BR tend\-mfit (1). +.SS tend\ mconv +Convert from one model to another +.P +See +.BR tend\-mconv (1). +.SS tend\ msim +Simulate DW images from an image of models +.P +See +.BR tend\-msim (1). +.SS tend\ make +Create DT volume from confidence and eigensystem +.P +See +.BR tend\-make (1). +.SS tend\ avg +Average across tensor volumes +.P +See +.BR tend\-avg (1). +.SS tend\ helix +Generate twisting helical tensor field +.P +See +.BR tend\-helix (1). +.SS tend\ sten +Calculate structure tensors from a scalar field +.P +See +.BR tend\-sten (1). +.SS tend\ glyph +Generate postscript or ray-traced renderings of 3D glyphs +.P +See +.BR tend\-glyph (1). +.SS tend\ ellipse +Generate postscript renderings of 2D glyphs +.P +See +.BR tend\-ellipse (1). +.SS tend\ anplot +Graph anisotropy metric in barycentric coords +.P +See +.BR tend\-anplot (1). +.SS tend\ anvol +Apply an anisotropy metric to a DT volume +.P +See +.BR tend\-anvol (1). +.SS tend\ anscale +Scale the anisotropic component of the tensors +.P +See +.BR tend\-anscale (1). +.SS tend\ anhist +Generate barycentric histograms of anisotropy +.P +See +.BR tend\-anhist (1). +.SS tend\ triple +Compute volume of shape triples +.P +See +.BR tend\-triple (1). +.SS tend\ tconv +Convert between different shape triples +.P +See +.BR tend\-tconv (1). +.SS tend\ point +Describe everything about one sample in a DT volume +.P +See +.BR tend\-point (1). +.SS tend\ slice +Slice 3D tensors to get slab/image of 3D/2D tensors +.P +See +.BR tend\-slice (1). +.SS tend\ norm +Normalize tensor size +.P +See +.BR tend\-norm (1). +.SS tend\ fiber +Fiber tractography, from one or more seeds +.P +See +.BR tend\-fiber (1). +.SS tend\ eval +Calculate one or more eigenvalues in a DT volume +.P +See +.BR tend\-eval (1). +.SS tend\ evalpow +Modify shape by raising eigenvalues to some power +.P +See +.BR tend\-evalpow (1). +.SS tend\ evalclamp +Modify shape by clamping eigenvalues in some range +.P +See +.BR tend\-evalclamp (1). +.SS tend\ evaladd +Modify shape by adding a constant to all eigenvalues +.P +See +.BR tend\-evaladd (1). +.SS tend\ evalmul +Modify shape by multiplying eigenvalues by a constant +.P +See +.BR tend\-evalmul (1). +.SS tend\ log +Calculates logarithm of the tensor +.P +See +.BR tend\-log (1). +.SS tend\ exp +Calculates \fBexp()\fR of the tensor +.P +See +.BR tend\-exp (1). +.SS tend\ evec +Calculate one or more eigenvectors in a DT volume +.P +See +.BR tend\-evec (1). +.SS tend\ evecrgb +Make an RGB volume from an eigenvector and an anisotropy +.P +See +.BR tend\-evecrgb (1). +.SS tend\ evq +Quantize directions of diffusion +.P +See +.BR tend\-evq (1). +.SS tend\ unmf +Applies and removes the measurement frame +.P +See +.BR tend\-unmf (1). +.SS tend\ expand +Converts masked non-redundant tensor images to redundant +.P +See +.BR tend\-expand (1). +.SS tend\ shrink +Converts a 9-value DT volume to a 7-value DT volume +.P +See +.BR tend\-shrink (1). +.SS tend\ bfit +Non-linear least-squares fitting of b-value curves +.P +See +.BR tend\-bfit (1). +.SS tend\ satin +Generate a pretty synthetic DT volume +.P +See +.BR tend\-satin (1). +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR unu (1), +.BR vprobe (1), +.BR tend\-about (1), +.BR tend\-anhist (1), +.BR tend\-anplot (1), +.BR tend\-anscale (1), +.BR tend\-anvol (1), +.BR tend\-avg (1), +.BR tend\-bfit (1), +.BR tend\-bmat (1), +.BR tend\-ellipse (1), +.BR tend\-epireg (1), +.BR tend\-estim (1), +.BR tend\-eval (1), +.BR tend\-evaladd (1), +.BR tend\-evalclamp (1), +.BR tend\-evalmul (1), +.BR tend\-evalpow (1), +.BR tend\-evec (1), +.BR tend\-evecrgb (1), +.BR tend\-evq (1), +.BR tend\-exp (1), +.BR tend\-expand (1), +.BR tend\-fiber (1), +.BR tend\-glyph (1), +.BR tend\-grads (1), +.BR tend\-helix (1), +.BR tend\-log (1), +.BR tend\-make (1), +.BR tend\-mconv (1), +.BR tend\-mfit (1), +.BR tend\-msim (1), +.BR tend\-norm (1), +.BR tend\-point (1), +.BR tend\-satin (1), +.BR tend\-shrink (1), +.BR tend\-sim (1), +.BR tend\-slice (1), +.BR tend\-sten (1), +.BR tend\-tconv (1), +.BR tend\-triple (1), +.BR tend\-unmf (1) diff --git a/unu.1 b/unu.1 new file mode 100644 index 0000000..ef710be --- /dev/null +++ b/unu.1 @@ -0,0 +1,127 @@ +.TH UNU "1" "April 2021" "" "User Commands" +.SH NAME +unu \- Utah Nrrd Utilities command-line interface +.SH SYNOPSIS +.B unu +.I COMMAND +.RI [ OPTION ]... +.SH DESCRIPTION +.BR unu (1) +is a command-line interface to much of the functionality in \(lqnrrd\(rq, a C +library for raster data processing. +Nrrd is one library in the \(lqTeem\(rq collection of libraries. +More information about Teem is at +.UR http://teem.sf.net +http://teem.sf.net +.UE . +A checkout of Teem source is available via: +.in +4n +.EX +.B svn co https://svn.code.sf.net/p/teem/code/teem/trunk teem +.EE +.in +.P +Long-term maintenance of this software depends on funding, and funding depends +on being able to document who is using it for what. +If +.BR unu (1) +or Nrrd has helped in your research, including for simple one-off experiments +or mundane data hacking, the developers of Teem would love to know. +There are multiple ways of communicating this. +In your publications, consider adding a line such as this in the +Acknowledgments: +.in +4n +Data processing performed with the unu tool, part of the Teem toolkit available +at +.UR http://teem.sf.net +http://teem.sf.net +.UE . +.in +Alternatively, please email +.MT glk(a)uchicago.edu +glk(a)uchicago.edu +.ME +and briefly describe how Teem software has helped in your work. +Please also consider joining the +.UR https://lists.sourceforge.net/lists/listinfo/teem-users +teem\-users mailing list +.UE . +This is the primary forum for feedback, questions, and feature requests. +.P +A summary list of unu commands is generated by running simply +.RB \(lq unu \(rq. +Running a +.BR unu (1) +command without additional arguments (e.g. \(lq\fBunu\ slice\fR\(rq) +generates its description and usage information. +This includes information (marked with +.RB \(lq *\ Uses\ ... \(rq) +about the underling Nrrd library calls (e.g. \fBnrrdSlice()\fR) that implement +the basic functionality in that +.BR unu (1) +command. +.P +The utility of +.BR unu (1) +is mainly as a pre-processing tool for getting data into a type, encoding, +format, or dimensions best suited for some visualization or rendering task. +Also, slices and projections are effective ways to visually inspect the +contents of a dataset. +Especially useful + commands include +.BR make , +.BR resample , +.BR crop , +.BR slice , +.BR project , +.BR histo , +.BR dhisto , +.BR quantize , +and +.BR save . +.BR unu (1) +can process CT and MRI volume datasets, grayscale and color images, +time-varying volumes of vector fields (5-D arrays), and more. +Currently supported formats are plain text files (2-D float arrays), NRRD, VTK +structured points, and PNG and PNM images. +.RB \(lq unu\ make\ \-bs\ \-1 \(rq +can read from most DICOM files. +.RB \(lq unu\ save \(rq +can generate EPS files. +Supported encodings are raw, ascii, hex, gzip, and bzip2. +.P +Much of the functionality of +.BR unu (1) +derives from chaining multiple invocations together with pipes +.RB (\(lq | \(rq), +minimizing the need to save out intermediate files. +For example, if +.RB (\(lq data.raw.gz \(rq), +is a gzip\(cqed 256\ x\ 256\ x\ 80 volume of raw floats written from a PC, then +the following will save to +.RB (\(lq zsum.png \(rq) +a histogram equalized summation projection along the slowest axis: +.in +4n +.EX +\fBunu\ make\ \-i\ data.raw.gz\ \-t\ float\ \-s\ 256\ 256\ 80\ \-e\ gzip\ \-en\ little\ \(rs +\ |\ unu\ project\ \-a\ 2\ \-m\ sum\ \(rs +\ |\ unu\ heq\ \-b\ 2000\ \-s\ 1\ \(rs +\ |\ unu\ quantize\ \-b\ 8\ \-o\ zsum.png +.EE +.in +.P +Formats available: +.B nrrd pnm png vtk text eps +.P +Nrrd data encodings available: +.B raw ascii hex gz bz2 +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR vprobe (1) diff --git a/vprobe.1 b/vprobe.1 new file mode 100644 index 0000000..bdee507 --- /dev/null +++ b/vprobe.1 @@ -0,0 +1,214 @@ +.TH VPROBE "1" "April 2021" "" "User Commands" +.SH NAME +vprobe \- shows off the functionality of the gage library +.SH SYNOPSIS +.B vprobe +.B \-i +.RI < nin > +.B \-k +.RI < kind > +.RB [ \-v +.RI < verbosity >] +.B \-q +.RI < query > +.RB [ \-s +.RI < sclX \ xclY \ sxlZ >] +.RB [ \-k00 +.RI < kern00 >] +.RB [ \-k11 +.RI < kern11 >] +.RB [ \-k22 +.RI < kern22 >] +.RB [ \-seed +.RI < N >] +.RB [ \-ssn +.RI < SS\ # >] +.RB [ \-ssr +.RI < scale\ range >] +.RB [ \-ssrf +.RI < SS\ read\ format >] +.RB [ \-sssf +.RI < SS\ save\ format >] +.RB [ \-ssw +.RI < SS\ pos >] +.RB [ \-kssb +.RI < kernel >] +.RB [ \-kssr +.RI < kernel >] +.RB [ \-ssu ] +.RB [ \-sso ] +.RB [ \-ssnd ] +.RB [ \-rn ] +.RB [ \-gmc +.RI < min\ gradmag >] +.RB [ \-ofs ] +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Shows off the functionality of the gage library. +Uses gageProbe() to query various kinds of volumes to learn various measured or +derived quantities. +Can set environment variable +.B TEEM_VPROBE_HACK_ZI +to limit probing to a single z slice. +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR> +input volume +.TP +.B \-k\fR\ <\fIkind\fR> +\(lqkind\(rq of volume +.RB (\(lq scalar \(rq, +.RB \(lq vector \(rq, +.RB \(lq tensor \(rq, +or +.RB \(lq dwi \(rq) +.TP +.B \-v\fR\ <\fIverbosity\fR> +verbosity level +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-q\fR\ <\fIquery\fR> +the quantity +.RB ( scalar , +.BR vector , +or +.BR matrix ) +to learn by probing +.RI ( string ) +.TP +.B \-s\fR\ <\fIsclX\fR\ \fIsclY\fR\ \fIsxlZ\fR> +scaling factor for resampling on each axis +.RB (> 1.0 : +supersampling); (3 +.IR double s); +default: +.RB \(lq 1.0\ 1.0\ 1.0 \(rq +.TP +.B \-k00\fR\ <\fIkern00\fR> +kernel for +.BR gageKernel00 ; +default: +.RB \(lq tent \(rq +.TP +.B \-k11\fR\ <\fIkern11\fR> +kernel for +.BR gageKernel11 ; +default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR\ <\fIkern22\fR> +kernel for +.BR gageKernel22 ; +default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-seed\fR\ <\fIN\fR> +RNG seed; mostly for debugging +.RI ( unsigned\ int ); +default: +.RB \(lq 42 \(rq +.TP +.B \-ssn\fR\ <\fISS\ #\fR> +how many scale-space samples to evaluate, or, +.B 0 +to turn-off all scale-space behavior +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ssr\fR\ <\fIscale\ range\fR> +range of scales in scale-space (2 +.IR double s); +default: +.RB \(lq nan\ nan \(rq +.TP +.B \-ssrf\fR\ <\fISS\ read\ format\fR> +.BR printf (3)\-style +format (including a +.RB \(lq %u \(rq) +for the filenames from which to +.I read +pre-blurred volumes computed for the stack +.RI ( string ); +default: \(lq\(rq +.TP +.B \-sssf\fR\ <\fISS\ save\ format\fR> +.BR printf (3)\-style +format (including a +.RB \(lq %u \(rq) +for the filenames from which to +.I save +pre-blurred volumes computed for the stack +.RI ( string ); +default: \(lq\(rq +.TP +.B \-ssw\fR\ <\fISS\ pos\fR> +\(lqworld\(rq)-space position (true sigma) at which to sample in scale-space +.RI ( double ); +default: +.RB \(lq 0 \(rq +.TP +.B \-kssb\fR\ <\fIkernel\fR> +blurring kernel, to sample scale space; default: +.RB \(lq dgauss:1,5 \(rq +.TP +.B \-kssr\fR\ <\fIkernel\fR> +kernel for reconstructing from scale space samples +.RB \(lq hermite \(rq +.TP +.B \-ssu +do uniform samples along sigma, and not (by default) samples according to the +effective diffusion scale +.TP +.B \-sso +if not using \(lq\-ssu\(rq, use pre-computed optimal sigmas when possible +.TP +.B \-ssnd +normalize derivatives by scale +.TP +.B \-rn +renormalize kernel weights at each new sample location. +\(lqAccurate\(rq kernels don\(cqt need this; doing it always makes things go +slower +.TP +.B \-gmc\fR\ <\fImin\ gradmag\fR> +For curvature-based queries, use zero when gradient magnitude is below this +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-ofs +If only per-axis spacing is available, use that to contrive full orientation +info +.TP +.B \-t\fR\ <\fItype\fR> +type of output volume +.RI ( type ); +default: +.RB \(lq float \(rq +.TP +.B \-o\fR\ <\fInout\fR> +output volume +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH ENVIRONMENT +.TP +.B TEEM_VPROBE_HACK_ZI +If set, probing is limited to a single z slice. +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR miter (1), +.BR mrender (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1) commit 593f4aa56a75b955f0a6b62a4a248954e702945d Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 12:41:10 2021 -0400 More precisely skip overly-strict floating-point tests where required diff --git a/teem.spec b/teem.spec index f97e08f..2ebe7a6 100644 --- a/teem.spec +++ b/teem.spec @@ -143,13 +143,15 @@ rm -rvf python %check -# tests fail on 32-bit arches -# seems that computation accuracy is arch-dependant -%global _smp_mflags -j1 -%ifarch x86_64 -%ctest3 +# We must exclude probeSS_ctmr04 and probeSS_ctmr10 on certain architectures +# due to overly-strict rounding requirements. +%ifarch %{arm64} ppc64le s390x +%global ctest_excludes --exclude-regex '^(probeSS_ctmr(04|10))$' %endif +# Tests are not parallel-safe +%ctest3 %{?ctest_excludes} -j1 + %if 0%{?epel} == 7 %ldconfig_scriptlets libs @@ -201,6 +203,7 @@ rm -rvf python - Add an -examples subpackage so the BSD and zlib licenses can be “contained” to that subpackage; remove certain unused files with other licenses in %%prep - Require cmake-filesystem instead of all of CMake in -devel +- More precisely skip overly-strict floating-point tests where required * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 23e9f5a00538ba4ca386c4cf3cb6384c16caa08a Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:49:36 2021 -0400 Add explicit BR on make (implied by cmake/cmake3) diff --git a/teem.spec b/teem.spec index d1fa1e0..f97e08f 100644 --- a/teem.spec +++ b/teem.spec @@ -25,6 +25,7 @@ Patch0: lib_install_dir.patch BuildRequires: gcc-c++ BuildRequires: cmake3 +BuildRequires: make BuildRequires: zlib-devel BuildRequires: libpng-devel commit db87fd2490d946f17a6d9fc4b18e47d37bebb4b3 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:43:41 2021 -0400 Require cmake-filesystem instead of all of CMake in -devel diff --git a/teem.spec b/teem.spec index d4c3d79..d1fa1e0 100644 --- a/teem.spec +++ b/teem.spec @@ -92,7 +92,7 @@ applications that use Teem. %package devel Summary: Development files for %{name} Requires: %{name}-libs%{?_isa} = %{version}-%{release} -Requires: cmake%{?_isa} +Requires: cmake-filesystem %description devel %{common_description} @@ -199,6 +199,7 @@ rm -rvf python - Use stricter file globs, including specifying the so-version - Add an -examples subpackage so the BSD and zlib licenses can be “contained” to that subpackage; remove certain unused files with other licenses in %%prep +- Require cmake-filesystem instead of all of CMake in -devel * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit e6982c7d45b51e73e424b3235560d9c3d6314908 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:42:16 2021 -0400 Add an -examples subpackage so the BSD and zlib licenses can be “contained” to that subpackage; remove certain unused files with other licenses in %%prep diff --git a/teem.spec b/teem.spec index b3f50d4..d4c3d79 100644 --- a/teem.spec +++ b/teem.spec @@ -4,7 +4,18 @@ Version: 1.11.0 Release: 15%{?dist} Summary: Libraries for processing and visualizing scientific raster data +# The entire source is LGPLv2+, except files noted at the License fields of certain subpackages. License: LGPLv2+ +# Additionally, the following are removed in %%prep to assert that they do not +# contribute to the built package: +# +# zlib: +# arch/win32/include/zlib.h +# MIT: +# python/ctypes/Nrrd.py +# python/ctypes/pullDemo.py +# python/ctypes/teem-gen.py +# python/ctypes/teem.py URL: https://teem.sourceforge.net Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... # Patch CMakeLists.txt to fix library install paths to match what Fedora @@ -89,9 +100,33 @@ The %{name}-devel package contains libraries and header files for developing applications that use Teem. +%package examples +Summary: Examples for developing with for %{name} +# The entire contents of this subpackage are LGPLv2+, except: +# +# zlib: +# UseTeemCMakeDemo/sanity.c +# BSD: +# Examples/sanity/sanity.c +License: LGPLv2+ and zlib and BSD +BuildArch: noarch + +%description examples %{common_description} + +The %{name}-examples package contains examples for developing applications that +use Teem. + + %prep %autosetup -n %{name}-%{version}-src -p1 +# Remove files that, while they have acceptable licenses, we want to assert do +# not contribute to the built RPMs: +# - Not applicable to this platform +rm -rvf arch/win32 +# - Nothing here appears suitable for packaging: +rm -rvf python + %build %cmake3 \ @@ -141,12 +176,17 @@ applications that use Teem. %files devel -%doc Examples/sanity/ %{_includedir}/teem/ %{_libdir}/libteem.so %{_libdir}/cmake/Teem-%{version}/ +%files examples +%license LICENSE.txt +%doc Examples +%doc UseTeemCMakeDemo + + %changelog * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch @@ -156,6 +196,9 @@ applications that use Teem. - Fix stray line continuation backslash - Support EPEL7 - Build with “levmar” support enabled +- Use stricter file globs, including specifying the so-version +- Add an -examples subpackage so the BSD and zlib licenses can be “contained” + to that subpackage; remove certain unused files with other licenses in %%prep * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit f879b4ba5748261a4e94736d94a9aecf9e63a24b Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:22:50 2021 -0400 Use stricter file globs, including specifying the so-version diff --git a/teem.spec b/teem.spec index be5871f..b3f50d4 100644 --- a/teem.spec +++ b/teem.spec @@ -1,5 +1,6 @@ Name: teem Version: 1.11.0 +%global so_version 1 Release: 15%{?dist} Summary: Libraries for processing and visualizing scientific raster data @@ -121,12 +122,22 @@ applications that use Teem. %files %doc README.txt -%{_bindir}/* +%{_bindir}/gprobe +%{_bindir}/ilk +%{_bindir}/miter +%{_bindir}/mrender +%{_bindir}/nrrdSanity +%{_bindir}/overrgb +%{_bindir}/puller +%{_bindir}/tend +%{_bindir}/unu +%{_bindir}/vprobe %files libs %license LICENSE.txt -%{_libdir}/libteem.so.* +%{_libdir}/libteem.so.%{so_version} +%{_libdir}/libteem.so.%{so_version}.* %files devel commit 8e9d83ec6f4083e2e472511cf71e6a4cb303f6f6 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:19:43 2021 -0400 Build with “levmar” support enabled diff --git a/teem.spec b/teem.spec index 5f11edb..be5871f 100644 --- a/teem.spec +++ b/teem.spec @@ -18,6 +18,7 @@ BuildRequires: zlib-devel BuildRequires: libpng-devel BuildRequires: bzip2-devel BuildRequires: fftw-devel +BuildRequires: levmar-devel %global common_description %{expand: What Is Teem? @@ -95,7 +96,8 @@ applications that use Teem. %cmake3 \ -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR=ON \ - -DTeem_FFTW3=ON + -DTeem_FFTW3=ON \ + -DTeem_LEVMAR=ON %cmake3_build @@ -142,6 +144,7 @@ applications that use Teem. - Adjust whitespace to personal preference - Fix stray line continuation backslash - Support EPEL7 +- Build with “levmar” support enabled * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 3d52b904785970205228eea38b1f59eab1e5f7e8 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:18:27 2021 -0400 Rearrange BR’s, and drop gcc (implied by gcc-c++) diff --git a/teem.spec b/teem.spec index 31cd485..5f11edb 100644 --- a/teem.spec +++ b/teem.spec @@ -12,12 +12,12 @@ Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/% Patch0: lib_install_dir.patch BuildRequires: gcc-c++ -BuildRequires: gcc BuildRequires: cmake3 + +BuildRequires: zlib-devel +BuildRequires: libpng-devel BuildRequires: bzip2-devel BuildRequires: fftw-devel -BuildRequires: libpng-devel -BuildRequires: zlib-devel %global common_description %{expand: What Is Teem? commit b4222b2431c0b4975ed3ddbc8bf009cd7af182b3 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:15:50 2021 -0400 Support EPEL7 diff --git a/teem.spec b/teem.spec index a6f7829..31cd485 100644 --- a/teem.spec +++ b/teem.spec @@ -13,7 +13,7 @@ Patch0: lib_install_dir.patch BuildRequires: gcc-c++ BuildRequires: gcc -BuildRequires: cmake +BuildRequires: cmake3 BuildRequires: bzip2-devel BuildRequires: fftw-devel BuildRequires: libpng-devel @@ -92,15 +92,15 @@ applications that use Teem. %build -%cmake \ +%cmake3 \ -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR=ON \ -DTeem_FFTW3=ON -%cmake_build +%cmake3_build %install -%cmake_install +%cmake3_install %check @@ -108,11 +108,13 @@ applications that use Teem. # seems that computation accuracy is arch-dependant %global _smp_mflags -j1 %ifarch x86_64 -%ctest +%ctest3 %endif +%if 0%{?epel} == 7 %ldconfig_scriptlets libs +%endif %files @@ -139,6 +141,7 @@ applications that use Teem. - Improved package summaries and descriptions - Adjust whitespace to personal preference - Fix stray line continuation backslash +- Support EPEL7 * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 59bc546adcb1c818b1406486ff585c265ec7d975 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:06:20 2021 -0400 Fix stray line continuation backslash diff --git a/teem.spec b/teem.spec index 96ea77c..a6f7829 100644 --- a/teem.spec +++ b/teem.spec @@ -95,7 +95,7 @@ applications that use Teem. %cmake \ -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR=ON \ - -DTeem_FFTW3=ON \ + -DTeem_FFTW3=ON %cmake_build @@ -138,6 +138,7 @@ applications that use Teem. - Update URLs from HTTP to HTTPS - Improved package summaries and descriptions - Adjust whitespace to personal preference +- Fix stray line continuation backslash * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 1a749c45beb6a651404240b06296b5561d55e673 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:01:56 2021 -0400 Adjust whitespace to personal preference diff --git a/teem.spec b/teem.spec index 8f24e62..96ea77c 100644 --- a/teem.spec +++ b/teem.spec @@ -1,23 +1,23 @@ -Name: teem -Version: 1.11.0 -Release: 15%{?dist} -Summary: Libraries for processing and visualizing scientific raster data - -License: LGPLv2+ -URL: https://teem.sourceforge.net -Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... +Name: teem +Version: 1.11.0 +Release: 15%{?dist} +Summary: Libraries for processing and visualizing scientific raster data + +License: LGPLv2+ +URL: https://teem.sourceforge.net +Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... # Patch CMakeLists.txt to fix library install paths to match what Fedora # expects. It is not immediately obvious if this patch is suitable for # sending upstream or not. -Patch0: lib_install_dir.patch +Patch0: lib_install_dir.patch BuildRequires: gcc-c++ -BuildRequires: gcc -BuildRequires: cmake -BuildRequires: bzip2-devel -BuildRequires: fftw-devel -BuildRequires: libpng-devel -BuildRequires: zlib-devel +BuildRequires: gcc +BuildRequires: cmake +BuildRequires: bzip2-devel +BuildRequires: fftw-devel +BuildRequires: libpng-devel +BuildRequires: zlib-devel %global common_description %{expand: What Is Teem? @@ -66,6 +66,7 @@ Strengths of Teem The %{name} package contains the command-line tools included with Teem. + %package libs Summary: Libraries files for %{name} @@ -74,10 +75,11 @@ Summary: Libraries files for %{name} The %{name}-libs package contains libraries that may be required at runtime by applications that use Teem. + %package devel Summary: Development files for %{name} -Requires: %{name}-libs%{?_isa} = %{version}-%{release} -Requires: cmake%{?_isa} +Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: cmake%{?_isa} %description devel %{common_description} @@ -100,6 +102,7 @@ applications that use Teem. %install %cmake_install + %check # tests fail on 32-bit arches # seems that computation accuracy is arch-dependant @@ -108,16 +111,20 @@ applications that use Teem. %ctest %endif + %ldconfig_scriptlets libs + %files %doc README.txt %{_bindir}/* + %files libs %license LICENSE.txt %{_libdir}/libteem.so.* + %files devel %doc Examples/sanity/ %{_includedir}/teem/ @@ -130,6 +137,7 @@ applications that use Teem. - Fix typo in lib_install_dir.patch - Update URLs from HTTP to HTTPS - Improved package summaries and descriptions +- Adjust whitespace to personal preference * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 68faf7af85f2054b1476dc60655e208092e76cac Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:00:17 2021 -0400 Improved package summaries and descriptions diff --git a/teem.spec b/teem.spec index 04a9438..8f24e62 100644 --- a/teem.spec +++ b/teem.spec @@ -1,7 +1,7 @@ Name: teem Version: 1.11.0 Release: 15%{?dist} -Summary: Libraries for scientific raster data processing and visualizing +Summary: Libraries for processing and visualizing scientific raster data License: LGPLv2+ URL: https://teem.sourceforge.net @@ -19,41 +19,70 @@ BuildRequires: fftw-devel BuildRequires: libpng-devel BuildRequires: zlib-devel -%description -Teem is a coordinated group of libraries for representing, processing, -and visualizing scientific raster data. Teem includes command-line tools -that permit the library functions to be quickly applied to files and streams, -without having to write any code. The most important and useful libraries -in Teem are: - -- Nrrd (and the unu command-line tool on top of it) supports a range - of operations for transforming N-dimensional raster data (resample, crop, - slice, project, histogram, etc.), as well as the NRRD file format - for storing arrays and their meta-information. -- Gage: fast convolution-based measurements at arbitrary point locations - in volume datasets (scalar, vector, tensor, etc.) -- Mite: a multi-threaded ray-casting volume render with transfer functions - based on any quantity Gage can measure -- Ten: for estimating, processing, and visualizing diffusion tensor fields, - including fiber tractography methods. - +%global common_description %{expand: +What Is Teem? + +Teem is a coordinated group of libraries for representing, processing, and +visualizing scientific raster data. Teem includes command-line tools that +permit the library functions to be quickly applied to files and streams, +without having to write any code. The most important and useful libraries in +Teem are: + + • Nrrd (and the unu command-line tool on top of it) supports a range of + operations for transforming N-dimensional raster data (resample, crop, + slice, project, histogram, etc.), as well as the NRRD file format for + storing arrays and their meta-information. + • Gage: fast convolution-based measurements at arbitrary point locations in + volume datasets (scalar, vector, tensor, etc.) + • Mite: a multi-threaded ray-casting volume render with transfer functions + based on any quantity Gage can measure + • Ten: for estimating, processing, and visualizing diffusion tensor fields, + including fiber tractography methods. + +Strengths of Teem + + • Teem works: Its purpose is to enable research in visualization and image + processing, and research is enabled when simple things are simple to do. + Teem’s functionality and its ease of use have allowed it to become a + component of larger research software projects, such as SCIRun and 3D + Slicer. + • Teem is light-weight: The libraries are written with an eye towards + minimizing the annoyance of getting data in an out, by using the simplest + possible constructs for the job, and by supporting combinations of operations + that arise in common practice. + • Teem is coherent: There is a consistent logic to how information is + represented, and uniformity in the APIs across libraries. + • Teem is portable: All the code is written in plain ANSI C, so it compiles + everywhere, including Windows, using either CMake or GNU Make. A Dashboard + is used to monitor compiler errors and warnings. + • Teem is growing: Some Teem libraries were created years ago and have + remained stable, but new libraries and new functionality are continually + being added. + • Teem is open source: Anyone can use it, and contributions are welcome. Teem + is licensed under the GNU Lesser General Public License, plus exceptions + which facilitate linking Teem into binary-only applications.} + +%description %{common_description} + +The %{name} package contains the command-line tools included with Teem. %package libs -Summary: Libraries for scientific raster data processing and visualizing +Summary: Libraries files for %{name} + +%description libs %{common_description} -%description libs -Teem is a coordinated group of libraries for representing, processing, -and visualizing scientific raster data. +The %{name}-libs package contains libraries that may be required at runtime by +applications that use Teem. %package devel -Summary: Libraries for scientific raster data processing and visualizing +Summary: Development files for %{name} Requires: %{name}-libs%{?_isa} = %{version}-%{release} Requires: cmake%{?_isa} -%description devel -Teem is a coordinated group of libraries for representing, processing, -and visualizing scientific raster data. This package contains development -files. +%description devel %{common_description} + +The %{name}-devel package contains libraries and header files for developing +applications that use Teem. %prep @@ -100,6 +129,7 @@ files. * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch - Update URLs from HTTP to HTTPS +- Improved package summaries and descriptions * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 45277db33360db4931556c3c678c8df5a42d11f9 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 08:50:07 2021 -0400 Update hash in sources file from MD5 to SHA-512 diff --git a/sources b/sources index f09a911..4a5f2e5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -6b9737e8b7640e18eaf281e830fe59d1 teem-1.11.0-src.tar.gz +SHA512 (teem-1.11.0-src.tar.gz) = 48b171a12db0f02dcfdaa87aa84464c651d661fa66201dc966b3cd5a8134c5bad1dad8987ffcc5d7c21c5d14c2eb617d48200410a1bda19008ef743c093ed575 commit ea786f8048639405a91a5ebb7ef9ed932b514674 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 08:48:37 2021 -0400 Update URLs from HTTP to HTTPS diff --git a/teem.spec b/teem.spec index 272c4b9..04a9438 100644 --- a/teem.spec +++ b/teem.spec @@ -4,8 +4,8 @@ Release: 15%{?dist} Summary: Libraries for scientific raster data processing and visualizing License: LGPLv2+ -URL: http://teem.sourceforge.net -Source0: http://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{v... +URL: https://teem.sourceforge.net +Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... # Patch CMakeLists.txt to fix library install paths to match what Fedora # expects. It is not immediately obvious if this patch is suitable for # sending upstream or not. @@ -99,6 +99,7 @@ files. %changelog * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch +- Update URLs from HTTP to HTTPS * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 5e008cd008b4422253f4aa2edc846e49efcb41cb Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 08:48:27 2021 -0400 Add a comment about lib_install_dir.patch diff --git a/teem.spec b/teem.spec index 6c490a4..272c4b9 100644 --- a/teem.spec +++ b/teem.spec @@ -6,6 +6,9 @@ Summary: Libraries for scientific raster data processing and visualizing License: LGPLv2+ URL: http://teem.sourceforge.net Source0: http://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{v... +# Patch CMakeLists.txt to fix library install paths to match what Fedora +# expects. It is not immediately obvious if this patch is suitable for +# sending upstream or not. Patch0: lib_install_dir.patch BuildRequires: gcc-c++ commit 427091f9585922ee66a43470d65ea1a17726f334 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 08:35:58 2021 -0400 Fix typo in lib_install_dir.patch diff --git a/lib_install_dir.patch b/lib_install_dir.patch index ba4a5be..c39fed0 100644 --- a/lib_install_dir.patch +++ b/lib_install_dir.patch @@ -6,7 +6,7 @@ Index: teem-1.11.0-src/CMakeLists.txt # RPATH stuff, and mac will ingore the INSTALL_RPATH. Make sure for # macs to set BUILD_WITH_INSTALL_RPATH OFF and set INSTALL_NAME_DIR. # I belive INSTALL_NAME_DIR will be ignored on linux. -+SET(LIB_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib CACHE PATH "Lirary installation directory.") ++SET(LIB_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib CACHE PATH "Library installation directory.") SET_TARGET_PROPERTIES(teem PROPERTIES BUILD_WITH_INSTALL_RPATH OFF - INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib diff --git a/teem.spec b/teem.spec index 77f8aa7..6c490a4 100644 --- a/teem.spec +++ b/teem.spec @@ -1,6 +1,6 @@ Name: teem Version: 1.11.0 -Release: 14%{?dist} +Release: 15%{?dist} Summary: Libraries for scientific raster data processing and visualizing License: LGPLv2+ @@ -94,6 +94,9 @@ files. %changelog +* Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 +- Fix typo in lib_install_dir.patch + * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 6fa79ed60a962b9e204a527bfb1f2de902914f9a Author: Fedora Release Engineering <releng(a)fedoraproject.org> Date: Wed Jan 27 21:44:00 2021 +0000 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild Signed-off-by: Fedora Release Engineering <releng(a)fedoraproject.org> diff --git a/teem.spec b/teem.spec index 2ceb967..77f8aa7 100644 --- a/teem.spec +++ b/teem.spec @@ -1,6 +1,6 @@ Name: teem Version: 1.11.0 -Release: 13%{?dist} +Release: 14%{?dist} Summary: Libraries for scientific raster data processing and visualizing License: LGPLv2+ @@ -94,6 +94,9 @@ files. %changelog +* Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + * Fri Sep 04 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.11.0-13 - Use cmake macros to fix build

2 years, 9 months

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Architecture specific change in rpms/teem.git

by githook-noreply＠fedoraproject.org

The package rpms/teem.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/teem.git/commit/?id=593f4aa56a75b.... Change: +%ifarch %{arm64} ppc64le s390x Thanks. Full change: ============ commit 78c8bfa63ee9200e45b439952cccee2508142cdc Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Aug 21 11:07:13 2021 -0400 Remove EPEL workarounds from Fedora spec file diff --git a/teem.spec b/teem.spec index a7f8e03..1913581 100644 --- a/teem.spec +++ b/teem.spec @@ -141,7 +141,7 @@ Source961: unu-save.1 Patch0: lib_install_dir.patch BuildRequires: gcc-c++ -BuildRequires: cmake3 +BuildRequires: cmake BuildRequires: make BuildRequires: zlib-devel @@ -247,16 +247,16 @@ rm -rvf python %build -%cmake3 \ +%cmake \ -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR=ON \ -DTeem_FFTW3=ON \ -DTeem_LEVMAR=ON -%cmake3_build +%cmake_build %install -%cmake3_install +%cmake_install %if %{with man_pages} install -d %{buildroot}%{_mandir}/man1 @@ -296,12 +296,7 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ # Tests are not parallel-safe %global _smp_mflags -j1 -%ctest3 %{?ctest_excludes} - - -%if 0%{?epel} == 7 -%ldconfig_scriptlets libs -%endif +%ctest %{?ctest_excludes} %files commit 2d230660a820d87784de6faa0fa2c9c025de4659 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Aug 21 11:04:34 2021 -0400 Finish complete set of man pages (adds unu-* man pages) diff --git a/ilk.1 b/ilk.1 index e88f365..ec96d51 100644 --- a/ilk.1 +++ b/ilk.1 @@ -33,7 +33,7 @@ Applies linear (homogenous coordinate) transforms to a given image, using the given kernel for resampling. .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-i\fR <\fIimage\fR> diff --git a/miter.1 b/miter.1 index 254f8b8..c95895c 100644 --- a/miter.1 +++ b/miter.1 @@ -79,7 +79,7 @@ miter \- a simple but effective little volume renderer .RI < filename >] .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-i\fR <\fInsin\fR> diff --git a/mrender.1 b/mrender.1 index c58da9e..b263ee1 100644 --- a/mrender.1 +++ b/mrender.1 @@ -69,7 +69,7 @@ in the output image. .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-i\fR <\fInin\fR> diff --git a/puller.1 b/puller.1 index 45b7635..ec9f9cf 100644 --- a/puller.1 +++ b/puller.1 @@ -139,7 +139,7 @@ puller \- command-line interface to the \(lqpull\(rq library .RI < base >] .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-int\fR <\fIint\fR> diff --git a/teem.spec b/teem.spec index aded044..a7f8e03 100644 --- a/teem.spec +++ b/teem.spec @@ -4,7 +4,8 @@ Version: 1.11.0 Release: %autorelease -b 13 Summary: Libraries for processing and visualizing scientific raster data -# The entire source is LGPLv2+, except files noted at the License fields of certain subpackages. +# The entire source is LGPLv2+, except files noted at the License fields of +# certain subpackages. License: LGPLv2+ # Additionally, the following are removed in %%prep to assert that they do not # contribute to the built package: @@ -71,68 +72,68 @@ Source837: tend-shrink.1 Source838: tend-bfit.1 Source839: tend-satin.1 -#Source900: unu-about.1 -#Source901: unu-env.1 -#Source902: unu-i2w.1 -#Source903: unu-w2i.1 -#Source904: unu-make.1 -#Source905: unu-head.1 -#Source906: unu-data.1 -#Source907: unu-convert.1 -#Source908: unu-resample.1 -#Source909: unu-fft.1 -#Source910: unu-cmedian.1 -#Source911: unu-dist.1 -#Source912: unu-minmax.1 -#Source913: unu-cksum.1 -#Source914: unu-diff.1 -#Source915: unu-quantize.1 -#Source916: unu-unquantize.1 -#Source917: unu-project.1 -#Source918: unu-slice.1 -#Source919: unu-sselect.1 -#Source920: unu-dice.1 -#Source921: unu-splice.1 -#Source922: unu-join.1 -#Source923: unu-crop.1 -#Source924: unu-acrop.1 -#Source925: unu-inset.1 -#Source926: unu-pad.1 -#Source927: unu-reshape.1 -#Source928: unu-permute.1 -#Source929: unu-swap.1 -#Source930: unu-shuffle.1 -#Source931: unu-flip.1 -#Source932: unu-unorient.1 -#Source933: unu-axinfo.1 -#Source934: unu-axinsert.1 -#Source935: unu-axsplit.1 -#Source936: unu-axdelete.1 -#Source937: unu-axmerge.1 -#Source938: unu-tile.1 -#Source939: unu-untile.1 -#Source940: unu-histo.1 -#Source941: unu-dhisto.1 -#Source942: unu-jhisto.1 -#Source943: unu-histax.1 -#Source944: unu-heq.1 -#Source945: unu-gamma.1 -#Source946: unu-1op.1 -#Source947: unu-2op.1 -#Source948: unu-3op.1 -#Source949: unu-affine.1 -#Source950: unu-lut.1 -#Source951: unu-mlut.1 -#Source952: unu-subst.1 -#Source953: unu-rmap.1 -#Source954: unu-mrmap.1 -#Source955: unu-imap.1 -#Source956: unu-lut2.1 -#Source957: unu-ccfind.1 -#Source958: unu-ccadj.1 -#Source959: unu-ccmerge.1 -#Source960: unu-ccsettle.1 -#Source961: unu-save.1 +Source900: unu-about.1 +Source901: unu-env.1 +Source902: unu-i2w.1 +Source903: unu-w2i.1 +Source904: unu-make.1 +Source905: unu-head.1 +Source906: unu-data.1 +Source907: unu-convert.1 +Source908: unu-resample.1 +Source909: unu-fft.1 +Source910: unu-cmedian.1 +Source911: unu-dist.1 +Source912: unu-minmax.1 +Source913: unu-cksum.1 +Source914: unu-diff.1 +Source915: unu-quantize.1 +Source916: unu-unquantize.1 +Source917: unu-project.1 +Source918: unu-slice.1 +Source919: unu-sselect.1 +Source920: unu-dice.1 +Source921: unu-splice.1 +Source922: unu-join.1 +Source923: unu-crop.1 +Source924: unu-acrop.1 +Source925: unu-inset.1 +Source926: unu-pad.1 +Source927: unu-reshape.1 +Source928: unu-permute.1 +Source929: unu-swap.1 +Source930: unu-shuffle.1 +Source931: unu-flip.1 +Source932: unu-unorient.1 +Source933: unu-axinfo.1 +Source934: unu-axinsert.1 +Source935: unu-axsplit.1 +Source936: unu-axdelete.1 +Source937: unu-axmerge.1 +Source938: unu-tile.1 +Source939: unu-untile.1 +Source940: unu-histo.1 +Source941: unu-dhisto.1 +Source942: unu-jhisto.1 +Source943: unu-histax.1 +Source944: unu-heq.1 +Source945: unu-gamma.1 +Source946: unu-1op.1 +Source947: unu-2op.1 +Source948: unu-3op.1 +Source949: unu-affine.1 +Source950: unu-lut.1 +Source951: unu-mlut.1 +Source952: unu-subst.1 +Source953: unu-rmap.1 +Source954: unu-mrmap.1 +Source955: unu-imap.1 +Source956: unu-lut2.1 +Source957: unu-ccfind.1 +Source958: unu-ccadj.1 +Source959: unu-ccmerge.1 +Source960: unu-ccsettle.1 +Source961: unu-save.1 # Patch CMakeLists.txt to fix library install paths to match what Fedora # expects. It is not immediately obvious if this patch is suitable for @@ -269,20 +270,20 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %{SOURCE820} %{SOURCE821} %{SOURCE822} %{SOURCE823} %{SOURCE824} \ %{SOURCE825} %{SOURCE826} %{SOURCE827} %{SOURCE828} %{SOURCE829} \ %{SOURCE830} %{SOURCE831} %{SOURCE832} %{SOURCE833} %{SOURCE834} \ - %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} - #{SOURCE900} #{SOURCE901} #{SOURCE902} #{SOURCE903} #{SOURCE904} \ - #{SOURCE905} #{SOURCE906} #{SOURCE907} #{SOURCE908} #{SOURCE909} \ - #{SOURCE910} #{SOURCE911} #{SOURCE912} #{SOURCE913} #{SOURCE914} \ - #{SOURCE915} #{SOURCE916} #{SOURCE917} #{SOURCE918} #{SOURCE919} \ - #{SOURCE920} #{SOURCE921} #{SOURCE922} #{SOURCE923} #{SOURCE924} \ - #{SOURCE925} #{SOURCE926} #{SOURCE927} #{SOURCE928} #{SOURCE929} \ - #{SOURCE930} #{SOURCE931} #{SOURCE932} #{SOURCE933} #{SOURCE934} \ - #{SOURCE935} #{SOURCE936} #{SOURCE937} #{SOURCE938} #{SOURCE939} \ - #{SOURCE940} #{SOURCE941} #{SOURCE942} #{SOURCE943} #{SOURCE944} \ - #{SOURCE945} #{SOURCE946} #{SOURCE947} #{SOURCE948} #{SOURCE949} \ - #{SOURCE950} #{SOURCE951} #{SOURCE952} #{SOURCE953} #{SOURCE954} \ - #{SOURCE955} #{SOURCE956} #{SOURCE957} #{SOURCE958} #{SOURCE959} \ - #{SOURCE960} #{SOURCE961} + %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} \ + %{SOURCE900} %{SOURCE901} %{SOURCE902} %{SOURCE903} %{SOURCE904} \ + %{SOURCE905} %{SOURCE906} %{SOURCE907} %{SOURCE908} %{SOURCE909} \ + %{SOURCE910} %{SOURCE911} %{SOURCE912} %{SOURCE913} %{SOURCE914} \ + %{SOURCE915} %{SOURCE916} %{SOURCE917} %{SOURCE918} %{SOURCE919} \ + %{SOURCE920} %{SOURCE921} %{SOURCE922} %{SOURCE923} %{SOURCE924} \ + %{SOURCE925} %{SOURCE926} %{SOURCE927} %{SOURCE928} %{SOURCE929} \ + %{SOURCE930} %{SOURCE931} %{SOURCE932} %{SOURCE933} %{SOURCE934} \ + %{SOURCE935} %{SOURCE936} %{SOURCE937} %{SOURCE938} %{SOURCE939} \ + %{SOURCE940} %{SOURCE941} %{SOURCE942} %{SOURCE943} %{SOURCE944} \ + %{SOURCE945} %{SOURCE946} %{SOURCE947} %{SOURCE948} %{SOURCE949} \ + %{SOURCE950} %{SOURCE951} %{SOURCE952} %{SOURCE953} %{SOURCE954} \ + %{SOURCE955} %{SOURCE956} %{SOURCE957} %{SOURCE958} %{SOURCE959} \ + %{SOURCE960} %{SOURCE961} %endif @@ -327,7 +328,7 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %{_mandir}/man1/tend.1* %{_mandir}/man1/tend-*.1* %{_mandir}/man1/unu.1* -#{_mandir}/man1/unu-*.1* +%{_mandir}/man1/unu-*.1* %{_mandir}/man1/vprobe.1* %endif diff --git a/tend-bfit.1 b/tend-bfit.1 index 9269f75..3e72390 100644 --- a/tend-bfit.1 +++ b/tend-bfit.1 @@ -27,7 +27,7 @@ to the range of DWI values along input axis 0, as a function of changing values. .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-i\fR <\fInin\fR> diff --git a/tend-glyph.1 b/tend-glyph.1 index c0ee791..5f8d28a 100644 --- a/tend-glyph.1 +++ b/tend-glyph.1 @@ -124,7 +124,7 @@ and/or .RB \(lq unu\ quantize\ \-b\ 8 \(rq. .SH OPTIONS .TP -.IR @file \ ... +.IR @file \ ...\: response file(s) containing command-line arguments .TP .B \-rt diff --git a/tend-unmf.1 b/tend-unmf.1 index d97b5ce..c2fefd6 100644 --- a/tend-unmf.1 +++ b/tend-unmf.1 @@ -18,7 +18,9 @@ world space, and remove the measurement frame from the .B \-i\fR <\fInin\fR> input diffusion tensor volume (sorry, can\(cqt use usual default of .RB \(lq \- \(rq -for stdin because of hest quirk) +for +.BR stdin (3) +because of hest quirk) .TP .B \-o\fR <\fInout\fR> output tensor volume diff --git a/tend.1 b/tend.1 index 831950d..0dc61a9 100644 --- a/tend.1 +++ b/tend.1 @@ -4,7 +4,7 @@ tend \- diffusion image processing and analysis .SH SYNOPSIS .B tend .I COMMAND -.RI [ OPTION ]... +.RI [ OPTION ]...\: .SH DESCRIPTION .BR tend (1) is a command-line interface to much of the functionality in \(lqten\(rq, a C diff --git a/unu-1op.1 b/unu-1op.1 new file mode 100644 index 0000000..9a7fd67 --- /dev/null +++ b/unu-1op.1 @@ -0,0 +1,177 @@ +.TH UNU\-1OP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-1op \- unary operation on a +.I nrrd +.SH SYNOPSIS +.B unu\ 1op +.RI < operator > +.RB [ \-s , \-\-seed +.RI < seed >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Unary operation on a +.IR nrrd . +.IP \(bu +2n +Uses +.B nrrdArithUnaryOp +.SH OPTIONS +.TP +.I operator +Unary operator. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq \- \(rq: +negative (multiply by +.BR \-1.0 ) +.IP \(bu 2 +.RB \(lq r \(rq: +reciprocal +.RB ( 1.0 / \fIvalue ) +.IP \(bu 2 +.RB \(lq sin \(rq, +.RB \(lq cos \(rq, +.RB \(lq tan \(rq, +.RB \(lq asin \(rq, +.RB \(lq acos \(rq, +.RB \(lq atan \(rq: +same as in C +.IP \(bu 2 +.RB \(lq exp \(rq, +.RB \(lq log \(rq, +.RB \(lq log10 \(rq: +same as in C +.IP \(bu 2 +.RB \(lq log1p \(rq, +.RB \(lq expm1 \(rq: +accurate +.BI log( x +1) +and +.BI exp( x )\-1 +.IP \(bu 2 +.RB \(lq log2 \(rq: +log base 2 +.IP \(bu 2 +.RB \(lq sqrt \(rq, +.RB \(lq cbrt \(rq, +.RB \(lq ceil \(rq, +.RB \(lq floor \(rq: +same as in C +.IP \(bu 2 +.RB \(lq erf \(rq: +error function (integral of Gaussian) +.IP \(bu 2 +.RB \(lq rup \(rq, +.RB \(lq rdn \(rq: +round up or down to integral value +.IP \(bu 2 +.RB \(lq abs \(rq: +absolute value +.IP \(bu 2 +.RB \(lq sgn \(rq: +.BR \-1 , +.BR 0 , +.BR 1 +if value is +.RB < 0 , +.RB == 0 , +or +.RB > 0 +.IP \(bu 2 +.RB \(lq exists \(rq: +.B 1 +iff not +.B NaN +or +.BR + / \-Inf , +.B 0 +otherwise +.IP \(bu 2 +.RB \(lq rand \(rq: +random value in +.BR [0.0,1.0) , +no relation to input +.IP \(bu 2 +.RB \(lq nrand \(rq: +random sample from normal distribution with mean +.B 0.0 +and stdvi +.BR 1.0 , +no relation to input +.IP \(bu 2 +.RB \(lq if \(rq: +if input is non-zero, +.BR 1 , +else +.B 0 +.IP \(bu 2 +.RB \(lq 0 \(rq: +output always +.B 0 +.IP \(bu 2 +.RB \(lq 1 \(rq: +output always +.B 1 +.RE +.TP +.B \-s\fR\ <\fIseed\fR>\ ,\ \fB\-\-seed\fR\ <\fIseed\fR> +seed value for RNG for +.B rand +and +.BR nrand , +so that you can get repeatable results between runs, or, by not using this +option, the RNG seeding will be based on the current time +.RI ( string ) +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +convert input +.I nrrd +to this type prior to doing operation. +Useful when desired output is +.I float +(e.g., with +.BR log1p ), +but input is integral. +By default (not using this option), the types of the input +.IR nrrd s +are left unchanged. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) +.P +.BR abs (3), +.BR acos (3), +.BR asin (3), +.BR atan (3), +.BR cbrt (3), +.BR ceil (3), +.BR cos (3), +.BR erf (3), +.BR exp (3), +.BR expm1 (3), +.BR fabs (3), +.BR floor (3), +.BR isfinite (3), +.BR log (3), +.BR log10 (3), +.BR log1p (3), +.BR log2 (3), +.BR rand (3), +.BR sin (3), +.BR sqrt (3), +.BR tan (3) diff --git a/unu-2op.1 b/unu-2op.1 new file mode 100644 index 0000000..a6678fb --- /dev/null +++ b/unu-2op.1 @@ -0,0 +1,180 @@ +.TH UNU\-2OP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-2op \- binary operation on two +.IR nrrd s, +or on a +.I nrrd +and a constant +.SH SYNOPSIS +.B unu\ 2op +.RI < operator > +.RI < in1 > +.RI < in2 > +.RB [ \-s , \-\-seed +.RI < seed >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-w , \-\-which +.RI < arg >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Binary operation on two +.IR nrrd s, +or on a +.I nrrd +and a constant. +Either the first or second operand can be a +.I float +constant, but not both. +Use +.RB \(lq \- \(rq +for an operand to signify a +.I nrrd +to be read from +.I stdin +(a pipe). +Note, however, that +.RB \(lq \- \(rq +can probably only be used once (reliably). +.IP \(bu +2n +Uses +.B nrrdArithIterBinaryOp +or (with +.BR \-w ) +.B nrrdArithIterBinaryOpSelect +.SH OPTIONS +.TP +.I operator +Binary operator. +Possibilities include: +.RS +7n +.IP \(bu +2n +.RB \(lq + \(rq, +.RB \(lq \- \(rq +.RB \(lq x \(rq +.RB \(lq / \(rq: +add, subtract, multiply, divide +.IP \(bu +2n +.RB \(lq ^ \(rq: +exponentiation +.RB ( pow (3)) +.IP \(bu +2n +.RB \(lq spow \(rq: +signed exponentiation: +.BI sgn( x )pow(abs( x ), p ) +.IP \(bu +2n +.RB \(lq fpow \(rq: +like spow but with curves flipped +.IP \(bu +2n +.RB \(lq % \(rq: +integer modulo +.IP \(bu +2n +.RB \(lq fmod \(rq: +same as +.BR fmod (3) +in C +.IP \(bu +2n +.RB \(lq atan2 \(rq: +same as +.BR atan2 (3) +in C +.IP \(bu +2n +.RB \(lq min \(rq +.RB \(lq max \(rq: +minimum, maximum +.IP \(bu +2n +.RB \(lq lt \(rq +.RB \(lq lte \(rq +.RB \(lq gt \(rq +.RB \(lq gte \(rq: +same as C's +.BR < , +.BR <= , +.BR > , +.B <= +.IP \(bu +2n +.RB \(lq eq \(rq +.RB \(lq neq \(rq: +same as C's +.B == +and +.B != +.IP \(bu +2n +.RB \(lq comp \(rq: +.BR \-1 , +.BR 0 , +or +.B 1 +if 1st value is less than, equal to, or greater than 2nd value +.IP \(bu +2n +.RB \(lq if \(rq: +if 1st value is non-zero, use it, else use 2nd value +.IP \(bu +2n +.RB \(lq exists \(rq: +if 1st value exists, use it, else use 2nd value +.IP \(bu +2n +.RB \(lq nrand \(rq: +scale unit-stdv Gaussian noise by 2nd value and add to first value +.IP \(bu +2n +.RB \(lq rrand \(rq: +sample Rician distribution with 1st value for \(lqtrue\(rq mean, and 2nd value +for sigma +.RE +.TP +.I in1 +First input. +Can be a single value or a +.IR nrrd . +.TP +.I in2 +Second input. +Can be a single value or a +.IR nrrd . +.TP +.B \-s\fR\ <\fIseed\fR>\ ,\ \fB\-\-seed\fR\ <\fIseed\fR> +seed value for RNG for +.BR nrand , +so that you can get repeatable results between runs, or, by not using this +option, the RNG seeding will be based on the current time +.RI ( string ) +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to convert all +.B INPUT +.IR nrrd s +to, prior to doing operation, useful for doing, for instance, the difference +between two +.I unsigned\ char +.IR nrrd s. +This will also determine output type. +By default (not using this option), the types of the input +.IR nrrd s +are left unchanged. +.TP +.B \-w\fR\ <\fIarg\fR>\ ,\ \fB\-\-which\fR\ <\fIarg\fR> +Which argument +.RB ( 0 +or +.BR 1 ) +should be used to determine the shape of the output +.IR nrrd . +By default (not using this option), the first non-constant argument is used. +.RI ( int ); +default: +.RB \(lq \-1 \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) +.P +.BR abs (1), +.BR atan2 (1), +.BR fabs (1), +.BR fmod (1), +.BR pow (1) diff --git a/unu-3op.1 b/unu-3op.1 new file mode 100644 index 0000000..3204054 --- /dev/null +++ b/unu-3op.1 @@ -0,0 +1,171 @@ +.TH UNU\-3OP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-3op \- ternary operation on three +.IR nrrd s +or constants +.SH SYNOPSIS +.B unu\ 3op +.RI < operator > +.RI < in1 > +.RI < in2 > +.RI < in3 > +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-w , \-\-which +.RI < arg >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Ternary operation on three +.IR nrrd s +or constants. +Can have one, two, or three +.IR nrrd s, +but not zero. +Use +.RB \(lq \- \(rq +for an operand to signify a +.I nrrd +to be read from +.I stdin +(a pipe). +Note, however, that +.RB \(lq \- \(rq +can probably only be used once (reliably). +.IP \(bu +2n +Uses +.B nrrdArithIterTernaryOp +or (with +.BR \-w ) +.B nrrdArithIterTernaryOpSelect +.SH OPTIONS +.TP +.I operator +Ternary operator. +Possibilities include: +.RS +7n +.IP \(bu +2n +.RB \(lq + \(rq, +.RB \(lq x \(rq +sum or product of three values +.IP \(bu +2n +.RB \(lq min \(rq, +.RB \(lq max \(rq +minimum, maximum +.IP \(bu +2n +.RB \(lq min_sm \(rq +smoothed minimum function; +.BI min_sm( x ,\ w ,\ M ) +is like +.BI min( x , M ) +but for +.IR x \ >\ M \- w +(with +.IR w \ >\ \fB0 ) +there is a smooth transition from +.I x +to asymptotic to +.I M +.IP \(bu +2n +.RB \(lq max_sm \(rq +smoothed maximum function; +max_sm(m, w, x) +.BI max_sm( m ,\ w ,\ x ) +is like +.BI max( m , x ) +but for +.IR x \ <\ m + w +(with +.IR w \ >\ m ) +there is a smooth transition from +.I x +to asymptotic to +.I m +.IP \(bu +2n +.RB \(lq lt_sm \(rq +1st less than 3rd, smoothed by 2nd +.IP \(bu +2n +.RB \(lq gt_sm \(rq +1st greater than 3rd, smoothed by 2nd +.IP \(bu +2n +.RB \(lq clamp \(rq +2nd value is clamped to range between the 1st and the 3rd +.IP \(bu +2n +.RB \(lq ifelse \(rq +if 1st value non-zero, then 2nd value, else 3rd value +.IP \(bu +2n +.RB \(lq lerp \(rq +linear interpolation between the 2nd and 3rd values, as the 1st value varies +between +.B 0.0 +and +.BR 1.0 , +respectively +.IP \(bu +2n +.RB \(lq exists \(rq +if the 1st value exists, use the 2nd value, otherwise use the 3rd +.IP \(bu +2n +.RB \(lq in_op \(rq +.B 1 +iff 2nd value is > 1st and < 3rd, +.B 0 +otherwise +.IP \(bu +2n +.RB \(lq in_cl \(rq +.B 1 +iff 2nd value is >= 1st and <= 3rd, +.B 0 +otherwise +.IP \(bu +2n +.RB \(lq gauss \(rq +evaluate (at 1st value) Gaussian with mean=2nd and stdv=3rd value +.IP \(bu +2n +.RB \(lq rician \(rq +evaluate (at 1st value) Rician with mean=2nd and stdv=3rd value +.RE +.TP +.I in1 +First input. +Can be a single value or a +.IR nrrd . +.TP +.I in2 +Second input. +Can be a single value or a +.IR nrrd . +.TP +.I in3 +Third input. +Can be a single value or a +.IR nrrd . +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to convert all +.IR nrrd +inputs to, prior to doing operation. +This also determines output type. +By default (not using this option), the types of the input +.IR nrrd s +are left unchanged. +.TP +.B \-w\fR\ <\fIarg\fR>\ ,\ \fB\-\-which\fR\ <\fIarg\fR> +Which argument +.RB ( 0 , +.BR 1 , +or +.BR 2 ) +should be used to determine the shape of the output +.IR nrrd . +By default (not using this option), the first non-constant argument is used. +.RI ( int ); +default: +.RB \(lq \-1 \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-about.1 b/unu-about.1 new file mode 100644 index 0000000..9df6bee --- /dev/null +++ b/unu-about.1 @@ -0,0 +1,9 @@ +.TH UNU\-ABOUT "1" "April 2021" "" "User Commands" +.SH NAME +unu\-about \- information about +.BR unu (1) +and its use +.SH SYNOPSIS +.B unu\ about +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-acrop.1 b/unu-acrop.1 new file mode 100644 index 0000000..cbc595f --- /dev/null +++ b/unu-acrop.1 @@ -0,0 +1,115 @@ +.TH UNU\-ACROP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-acrop \- automatically crop axes based on given measure +.SH SYNOPSIS +.B unu\ acrop +.RB [ \-a , \-\-axes +.RI [< ax0 \ ...>]] +.BR \-m , \-\-measure +.RI < measr > +.RB [ \-f , \-\-frac +.RI < frac >] +.RB [ \-off , \-\-offset +.RI < offset >] +.RB [ \-b , \-\-bounds +.RI < filename >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Automatically crop axes based on given measure. +For the axes that are to be cropped, the slices perpendicular to that axis are +projected down to a scalar with the specified measure. +The resulting 1\-D array is analyzed by determining what portions at the +beginning and end constitute less than some portion of the cumulative array +sum; these ends are cropped off. +The cropping bounds determined here can be saved and applied to other arrays +via the +.RB \(lq \-b \(rq +option. +.IP \(bu +2n +Uses +.B nrrdCropAuto +.SH OPTIONS +.TP +.B \-a\fR\ [<\fIax0\fR\ ...>]\ ,\ \fB\-\-axes\fR\ [<\fIax0\fR\ ...>] +the axes (if any) that should +.B NOT +be cropped (0 or more +.IR unsigned\ int s); +default: \(lq \(rq +.TP +.B \-m\fR\ <\fImeasr\fR>\ ,\ \fB\-\-measure\fR\ <\fImeasr\fR> +How to measure slices (along axes to crop) as scalars, to form 1\-D array +analyzed to determine cropping extent. +All the measures from +.BR unu\-project (1) +can be used, but those that make more sense here include: +.RS +7n +.IP \(bu 2 +.RB \(lq max \(rq, +.RB \(lq mean \(rq, +.RB \(lq median \(rq, +.RB \(lq variance \(rq: +(self-explanatory) +.IP \(bu 2 +.RB \(lq stdv \(rq: +standard deviation +.IP \(bu 2 +.RB \(lq cov \(rq: +coefficient of variation +.IP \(bu 2 +.RB \(lq product \(rq, +.RB \(lq sum \(rq: +product or sum of all values +.IP \(bu 2 +.RB \(lq L1 \(rq, +.RB \(lq L2 \(rq, +.RB \(lq NL2 \(rq, +.RB \(lq RMS \(rq, +.RB \(lq Linf \(rq: +different norms +.RE +.TP +.B \-f\fR\ <\fIfrac\fR>\ ,\ \fB\-\-frac\fR\ <\fIfrac\fR> +threshold of cumulative sum of 1\-D array at which to crop. +Needs to be in interval +.BR [0.0,0.5) . +.RI ( double ); +default: +.RB \(lq 0.1 \(rq +.TP +.B \-off\fR\ <\fIoffset\fR>\ ,\ \fB\-\-offset\fR\ <\fIoffset\fR> +how much to offset the numerically determined cropping; positive offsets means +expanding the interval of kept indices (less cropping) +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-b\fR\ <\fIfilename\fR>\ ,\ \fB\-\-bounds\fR\ <\fIfilename\fR> +if a filename is given here, the automatically determined min and max bounds +for cropping are saved to this file as a 2\-D array; first scanline is for +.BR \-min , +second is for +.BR \-max . +Unfortunately nothing using the +.RB \(lq m \(rq +and +.RB \(lq M \(rq +semantics (above) can currently be saved in the bounds file. +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-project (1) diff --git a/unu-affine.1 b/unu-affine.1 new file mode 100644 index 0000000..5765707 --- /dev/null +++ b/unu-affine.1 @@ -0,0 +1,84 @@ +.TH UNU\-AFFINE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-affine \- affine (lerp) mapping on 5 +.IR nrrd s +or constants +.SH SYNOPSIS +.B unu\ affine +.RI < minIn > +.RI < in > +.RI < maxIn > +.RI < minOut > +.RI < maxOut > +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-clamp +.RI < bool >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Affine (lerp) mapping on 5 +.IR nrrd s +or constants. +All the 5 arguments can be either +.IR nrrd s +or single floating-point values. +When all args are single values, this is subsuming the functionality of the +previous stand-alone +.BR affine (1) +program. +Use +.RB \(lq \- \(rq +for an operand to signify a +.I nrrd +to be read from +.I stdin +(a pipe). +Note, however, that +.RB \(lq \- \(rq +can probably only be used once (reliably). +.IP \(bu +2n +Uses +.B nrrdArithAffine +or +.B nrrdArithIterAffine +.SH OPTIONS +.TP +.I minIn +Lower end of input value range. +.TP +.I in +Input value. +.TP +.I maxIn +Upper end of input value range. +.TP +.I minOut +Lower end of output value range. +.TP +.I maxOut +Upper end of output value range. +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to convert all +.IR nrrd +inputs to, prior to doing operation. +This also determines output type. +By default (not using this option), the types of the input +.IR nrrd s +are left unchanged. +.TP +.B \-clamp\fR\ <\fIbool\fR> +clamp output values to specified output range +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-axdelete.1 b/unu-axdelete.1 new file mode 100644 index 0000000..947c921 --- /dev/null +++ b/unu-axdelete.1 @@ -0,0 +1,42 @@ +.TH UNU\-AXDELETE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axdelete \- remove one or more singleton axes from a +.I nrrd +.SH SYNOPSIS +.B unu\ axdelete +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Remove one or more singleton axes from a +.IR nrrd . +Singleton axes have only a single sample along them. +The underlying linear ordering of the samples is unchanged, and the information +about the other axes is shifted downwards as needed. +As a total hack, if you give \-1 as the axis, this will do a matlab-style +\(lqsqueeze\(rq, in which any and all singleton axes are removed. +.IP \(bu +2n +Uses +.B nrrdAxesDelete +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +dimension (axis index) of the axis to remove +.RI ( unsigned\ int ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axmerge (1) diff --git a/unu-axinfo.1 b/unu-axinfo.1 new file mode 100644 index 0000000..00dd7e9 --- /dev/null +++ b/unu-axinfo.1 @@ -0,0 +1,80 @@ +.TH UNU\-AXINFO "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axinfo \- modify attributes of one or more axes +.SH SYNOPSIS +.B unu\ axinfo +.BR \-a , \-\-axes +.RI < ax0 \ ax1 \ ...> +.RB [ \-l , \-\-label +.RI < label >] +.RB [ \-u , \-\-units +.RI < units >] +.RB [ \-mm , \-\-minmax +.RI < min \ max >] +.RB [ \-sp , \-\-spacing +.RI < spacing >] +.RB [ \-c , \-\-center +.RI < center >] +.RB [ \-k , \-\-kind +.RI < kind >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Modify attributes of one or more axes. +The only attributes which are set are those for which command-line options are +given. +.IP \(bu +2n +Uses no particular function; just sets fields in +.B NrrdAxisInfo +.SH OPTIONS +.TP +.B \-a\fR\ <\fIax0\fR \fIax1\fR\ ...>\ ,\ \fB\-\-axes\fR\ <\fIax0\fR \fIax1\fR\ ...> +the one or more axes that should be modified +(1 or more +.IR unsigned\ int s) +.TP +.B \-l\fR\ <\fIlabel\fR>\ ,\ \fB\-\-label\fR\ <\fIlabel\fR> +label to associate with axis +.RI ( string ) +.TP +.B \-u\fR\ <\fIunits\fR>\ ,\ \fB\-\-units\fR\ <\fIunits\fR> +units of measurement +.RI ( string ) +.TP +.B \-mm\fR\ <\fImin\fR\ \fImax\fR>\ ,\ \fB\-\-minmax\fR\ <\fImin\fR\ \fImax\fR> +units of measurement +min and max values along axis +( 2 +.IR double s) +.TP +.B \-sp\fR\ <\fIspacing\fR>\ ,\ \fB\-\-spacing\fR\ <\fIspacing\fR> +spacing between samples along axis +.RI ( double ) +.TP +.B \-c\fR\ <\fIcenter\fR>\ ,\ \fB\-\-center\fR\ <\fIcenter\fR> +axis centering: +.RB \(lq cell \(rq +or +.RB \(lq node \(rq. +Not using this option leaves the centering as it is on input +.RI ( string ) +.TP +.B \-k\fR\ <\fIkind\fR>\ ,\ \fB\-\-kind\fR\ <\fIkind\fR> +axis kind. +Not using this option leaves the kind as it is on input +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-axinsert.1 b/unu-axinsert.1 new file mode 100644 index 0000000..62f1e0a --- /dev/null +++ b/unu-axinsert.1 @@ -0,0 +1,45 @@ +.TH UNU\-AXINSERT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axinsert \- add a \(lqstub\(rq (length 1) axis to a +.I nrrd +.SH SYNOPSIS +.B unu\ axinsert +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-l , \-\-label +.RI < label >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Add a \(lqstub\(rq (length 1) axis to a +.IR nrrd . +The underlying linear ordering of the samples is unchanged, and the information +about the other axes is shifted upwards as needed. +.IP \(bu +2n +Uses +.B nrrdAxesInsert +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axes\fR\ <\fIaxis\fR> +dimension (axis index) at which to insert the new axis +.RI ( unsigned\ int ) +.TP +.B \-l\fR\ <\fIlabel\fR>\ ,\ \fB\-\-label\fR\ <\fIlabel\fR> +label to associate with axis +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axsplit (1) diff --git a/unu-axmerge.1 b/unu-axmerge.1 new file mode 100644 index 0000000..50e8831 --- /dev/null +++ b/unu-axmerge.1 @@ -0,0 +1,47 @@ +.TH UNU\-AXMERGE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axmerge \- merge two adjacent axes into one +.SH SYNOPSIS +.B unu\ axmerge +.BR \-a , \-\-axis +.RI < ax0 \ ...> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Merge two adjacent axes into one. +A more general version of +.BR unu\-axdelete (1). +The underlying linear ordering of the samples is unchanged, and the information +about the other axes is shifted downwards as needed. +.IP \(bu +2n +Uses +.B nrrdAxesMerge +.SH OPTIONS +.TP +.B \-a\fR\ <\fIax0\fR\ ...>\ ,\ \fB\-\-axis\fR\ <\fIax0\fR\ ...> +axis (or axes) to merge. +Each axis index identified is the lower of the pair of axes that will be +merged. +Saying +.RB \(lq \-a\ 2 \(rq +means to merge axis 2 and axis 3 into axis 2. +If multiple merges are to be done, the indices listed here are for the axes +prior to any merging. +(1 or more +.IR int s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axdelete (1) diff --git a/unu-axsplit.1 b/unu-axsplit.1 new file mode 100644 index 0000000..2577ae8 --- /dev/null +++ b/unu-axsplit.1 @@ -0,0 +1,47 @@ +.TH UNU\-AXSPLIT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-axsplit \- split one axis into two axes +.SH SYNOPSIS +.B unu\ axsplit +.BR \-a , \-\-axis +.RI < axis > +.BR \-s , \-\-size +.RI < fast ,\ slow \ sizes> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Split one axis into two axes. +More general version of +.BR unu\-axinsert (1), +since a given axis can be split into fast and slow axes of arbitrary size, as +long as the product of the fast and slow sizes is the same as the original +size. +.IP \(bu +2n +Uses +.B nrrdAxesSplit +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +dimension (axis index) to split at +.RI ( unsigned\ int ) +.TP +.B \-s\fR\ <\fIfast\fR,\ \fIslow\fR\ sizes>\ ,\ \fB\-\-size\fR\ <\fIfast\fR,\ \fIslow\fR\ sizes> +fast and slow axis sizes to produce as result of splitting given axis. +(2 +.IR size_t s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axinsert (1) diff --git a/unu-ccadj.1 b/unu-ccadj.1 new file mode 100644 index 0000000..ec09d85 --- /dev/null +++ b/unu-ccadj.1 @@ -0,0 +1,55 @@ +.TH UNU\-CCADJ "1" "August 2021" "" "User Commands" +.SH NAME +unu\-ccadj \- form adjacency matrix of connected components +.SH SYNOPSIS +.B unu\ ccadj +.BR \-c , \-\-connect +.RI < connectivity > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Form adjecency matrix of connected components. +This operates on +the output of +.BR unu\-ccfind (1). +Output is +.I unsigned\ char +array containing +.B 1 +at locations +.RI ( I , J ) +and +.RI ( J , I ) +if CCs with ids +.I I +and +.I J +are adjacent, according to the chosen style of adjacency. +.IP \(bu +2n +Uses +.B nrrdCCAdjacency +.SH OPTIONS +.TP +.B \-c\fR\ <\fIconnectivity\fR>\ ,\ \fB\-\-connect\fR\ <\fIconnectivity\fR> +what kind of connectivity to use: the number of coordinates that vary in order +to traverse the neighborhood of a given sample. +In 2D: +.RB \(lq 1 \(rq: +4-connected, +.RB \(lq 2 \(rq: +8-connected +.RI ( unsigned\ int ) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-ccfind (1), +.BR unu\-ccmerge (1), +.BR unu\-ccsettle (1) diff --git a/unu-ccfind.1 b/unu-ccfind.1 new file mode 100644 index 0000000..2c4169e --- /dev/null +++ b/unu-ccfind.1 @@ -0,0 +1,64 @@ +.TH UNU\-CCFIND "1" "August 2021" "" "User Commands" +.SH NAME +unu\-ccfind \- find connected components (CCs) +.SH SYNOPSIS +.B unu\ ccfind +.RB [ \-v , \-\-values +.RI < filename >] +.RB [ \-t , \-\-type +.RI < type >] +.BR \-c , \-\-connect +.RI < connectivity > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Find connected components (CCs). +This works on 1-byte and 2-byte integral values, as well as 4-byte +.IR int s. +.IP \(bu +2n +Uses +.B nrrdCCFind +.SH OPTIONS +.TP +.B \-v\fR\ <\fIfilename\fR>\ ,\ \fB\-\-values\fR\ <\fIfilename\fR> +Giving a +.I filename +here allows you to save out the values associated with each connect component. +This can be used later with +.BR unu\-ccmerge (1) \ \-d . +By default, no record of the original CC values is kept. +.RI ( string ) +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to use for output, to store the CC ID values. +By default (not using this option), the type used will be the smallest of +.IR uchar , +.IR ushort , +or +.IR int , +that can represent all the CC ID values. +Using this option allows one to specify the integral type to be used. +.TP +.B \-c\fR\ <\fIconnectivity\fR>\ ,\ \fB\-\-connect\fR\ <\fIconnectivity\fR> +what kind of connectivity to use: the number of coordinates that vary in order +to traverse the neighborhood of a given sample. +In 2D: +.RB \(lq 1 \(rq: +4-connected, +.RB \(lq 2 \(rq: +8-connected +.RI ( unsigned\ int ) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-ccadj (1), +.BR unu\-ccmerge (1), +.BR unu\-ccsettle (1) diff --git a/unu-ccmerge.1 b/unu-ccmerge.1 new file mode 100644 index 0000000..2b263f5 --- /dev/null +++ b/unu-ccmerge.1 @@ -0,0 +1,111 @@ +.TH UNU\-CCMERGE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-ccmerge \- merge CCs with their neighbors, under various constraints +.SH SYNOPSIS +.B unu\ ccmerge +.RB [ \-d , \-\-directed +.RI < dir >] +.RB [ \-s , \-\-size +.RI < max\ size >] +.RB [ \-n , \-\-neighbor +.RI < max\ #\ neigh >] +.BR \-c , \-\-connect +.RI < connectivity > +.RB [ \-revalue ] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-v , \-\-values +.RI < values >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Merge CCs with their neighbors, under various constraints. +This operates on the output of +.BR unu\-ccfind (1). +Merging of a CC is always done into its largest neighbor. +Whether or not to merge can be constrained by one or more of: CC size +.RB (\(lq \-s \(rq), +original CC value being brighter or darker +.RB (\(lq \-d \(rq), +and number of neighbors +.RB (\(lq \-n \(rq). +.IP \(bu +2n +Uses +.B nrrdCCMerge +.SH OPTIONS +.TP +.B \-d\fR\ <\fIdir\fR>\ ,\ \fB\-\-directed\fR\ <\fIdir\fR> +do value-driven merging. +Using (positive) +.RB \(lq 1 \(rq +says that dark islands get merged with bright surrounds, while +.RB \(lq \-1 \(rq +says the opposite. +By default, merging can go either way. +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-s\fR\ <\fImax\ size\fR>\ ,\ \fB\-\-size\fR\ <\fImax\ size\fR> +a cap on the CC size that will be absorbed into its surround. +CCs larger than this are deemed too significant to mess with. +Or, use +.RB \(lq 0 \(rq +to remove any such restriction on merging. +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-n\fR\ <\fImax\ #\ neigh\fR>\ ,\ \fB\-\-neighbor\fR\ <\fImax\ #\ neigh\fR> +a cap on the number of neighbors that a CC may have if it is to be be merged. +.RB \(lq 1 \(rq +allows only islands to be merged, +.RB \(lq 2 \(rq +does merging with bigger of two neighbors, etc, while +.RB \(lq 0 \(rq +says that number of neighbors is no constraint +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-c\fR\ <\fIconnectivity\fR>\ ,\ \fB\-\-connect\fR\ <\fIconnectivity\fR> +what kind of connectivity to use: the number of coordinates that vary in order +to traverse the neighborhood of a given sample. +In 2D: +.RB \(lq 1 \(rq: +4-connected, +.RB \(lq 2 \(rq: +8-connected +.RI ( unsigned\ int ) +.TP +.B \-revalue +If this option is given, then after the merging, the CCs are re-assigned their +original datavalues, as given by the +.RB \(lq \-v \(rq +option +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-v\fR\ <\fIvalues\fR>\ ,\ \fB\-\-values\fR\ <\fIvalues\fR> +result of using +.BR unu\-ccfind (1) \ \-v , +the record of which values were originally associated with each CC. +This is required for value-directed merging (with non-zero +.RB \(lq \-d \(rq +option), or if the +.B \-revalue +option is given, but is not needed otherwise +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-ccfind (1), +.BR unu\-ccadj (1), +.BR unu\-ccsettle (1) diff --git a/unu-ccsettle.1 b/unu-ccsettle.1 new file mode 100644 index 0000000..e5aa503 --- /dev/null +++ b/unu-ccsettle.1 @@ -0,0 +1,40 @@ +.TH UNU\-CCSETTLE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-ccsettle \- remap CC values down to lowest contiguous values +.SH SYNOPSIS +.B unu\ ccsettle +.BR \-i , \-\-input +.RI < nin > +.RB [ \-v , \-\-values +.RI < filename >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Remap CC values down to lowest contiguous values. +.IP \(bu +2n +Uses +.B nrrdCCSettle +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-v\fR\ <\fIfilename\fR>\ ,\ \fB\-\-values\fR\ <\fIfilename\fR> +Giving a +.I filename +here allows you to save out the mapping from new (settled) values to old +values, in the form of a 1-D lookup table +.RI ( string ) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-ccfind (1), +.BR unu\-ccadj (1), +.BR unu\-ccmerge (1) diff --git a/unu-cksum.1 b/unu-cksum.1 new file mode 100644 index 0000000..af6d4b8 --- /dev/null +++ b/unu-cksum.1 @@ -0,0 +1,55 @@ +.TH UNU\-CKSUM "1" "May 2021" "" "User Commands" +.SH NAME +unu\-cksum \- compute 32-bit CRC of +.I nrrd +data (same as via +.BR cksum (1)) +.SH SYNOPSIS +.B unu\ cksum +.BR \-en , \-\-endian +.RI < end > +.RB [ \-pen , \-\-printendian +.RI < bool >] +.RI < nin1 \ ...> +.SH DESCRIPTION +Compute 32-bit CRC of +.I nrrd +data (same as via +.BR cksum (1)). +Unlike other commands, this doesn\(cqt produce a +.IR nrrd . +It only prints to standard out the CRC and byte counts for the input +.IR nrrd (s), +seeking to emulate the formatting of +.BR cksum (1) +output. +.IP \(bu +2n +Uses +.B nrrdCRC32 +.SH OPTIONS +.TP +.B \-en\fR\ <\fIendian\fR>\ ,\ \fB\-\-endian\fR\ <\fIendian\fR> +Endianness in which to compute CRC; +.RB \(lq little \(rq +for Intel and friends; +.RB \(lq big \(rq +for everyone else. +Defaults to endianness of this machine. +.TP +.B \-pen\fR\ <\fIbool\fR>\ ,\ \fB\-\-printendian\fR\ <\fIbool\fR> +whether or not to indicate after the CRC value the endianness with which the +CRC was computed; doing so clarifies that the CRC result depends on endianness +and may remove confusion in comparing results on platforms of different +endianness +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.RI < nin \ ...> +input +.IR nrrd (s) +(1 or more +.IR string s) +.SH "SEE\ ALSO" +.BR unu (1), +.BR cksum (1) diff --git a/unu-cmedian.1 b/unu-cmedian.1 new file mode 100644 index 0000000..685059c --- /dev/null +++ b/unu-cmedian.1 @@ -0,0 +1,98 @@ +.TH UNU\-CMEDIAN "1" "May 2021" "" "User Commands" +.SH NAME +unu\-cmedian \- cheap histogram-based median/mode filtering +.SH SYNOPSIS +.B unu\ cmedian +.BR \-r , \-\-radius +.RI < radius > +.RB [ \-mode ] +.RB [ \-b , \-\-bins +.RI < num >] +.RB [ \-w , \-\-weight +.RI < weight >] +.RB [ \-p , \-\-pad ] +.RB [ \-c , \-\-channel ] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Cheap histogram-based median/mode filtering. +Only works on 1, 2, or 3 dimensions. +The window over which filtering is done is always square, and only a simplistic +weighting scheme is available. +The method is cheap because it does the median or mode based on a histogram, +which enforces a quantization to the number of bins in the histogram, which +probably means a loss of precision for anything except 8-bit data. +Also, integral values can be +recovered exactly only when the number of bins is exactly +.IB min \- max +1 +(as reported by +.BR unu\-minmax (1)). +.IP \(bu +2n +Uses +.BR nrrdCheapMedian , +plus +.B nrrdSlice +and +.B nrrdJoin +in case of +.RB \(lq \-c \(rq +.SH OPTIONS +.TP +.B \-r\fR\ <\fIradius\fR>\ ,\ \fB\-\-radius\fR\ <\fIradius\fR> +how big a window to filter over. +.RB \(lq \-r\ 1 \(rq +leads to a 3x3 window in an image, and a 3x3x3 window in a volume +.RI ( unsigned\ int ) +.TP +.B \-mode +By default, median filtering is done. +Using this option enables mode filtering, in which the most common value is +used as output +.TP +.B \-b\fR\ <\fInum\fR>\ ,\ \fB\-\-bins\fR\ <\fInum\fR> +# of bins in histogram. +It is in your interest to minimize this number, since big histograms mean +slower execution times. +8-bit data needs at most 256 bins. +.RI ( unsigned\ int ); +default: +.RB \(lq 256 \(rq +.TP +.B \-w\fR\ <\fIweight\fR>\ ,\ \fB\-\-weight\fR\ <\fIweight\fR> +How much higher to preferentially weight samples that are closer to the center +of the window. +.RB \(lq 1.0 \(rq +weight means that all samples are uniformly weighted over the window, which +facilitates a simple speed-up. +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-p\fR\ ,\ \fB\-\-pad +Pad the input (with boundary method +.RB \(lq bleed \(rq), +and crop the output, so as to overcome our cheapness and correctly handle the +border. +Obviously, this takes more memory. +.TP +.B \-c\fR\ ,\ \fB\-\-channel +Slice the input along axis 0, run filtering on all slices, and join the results +back together. +This is the way you\(cqd want to process color (multi-channel) images or +volumes. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-minmax (1) diff --git a/unu-convert.1 b/unu-convert.1 new file mode 100644 index 0000000..f3588cd --- /dev/null +++ b/unu-convert.1 @@ -0,0 +1,57 @@ +.TH UNU\-CONVERT "1" "May 2021" "" "User Commands" +.SH NAME +unu\-convert \- convert to another type (as if by cast, w/ optional clamp) +.SH SYNOPSIS +.B unu\ convert +.BR \-t , \-\-type +.RI < type > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-clamp ] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Convert to another type (as if by cast, w/ optional clamp). +By default this does not transform, scale, or intelligently quantize values; it +just copies them from one type to another, which replicates exactly what +you\(cqd get in C when you assign from a variable of one type to another, or +when you cast to a different type. +However, clamping values to the representable range +of the output type is possible with +.RB \(lq \-clamp \(rq. +See also +.BR unu\-quantize (1), +.BR unu\-2op (1) +.BR x , +and +.BR unu\-3op (1) +.BR clamp . +.IP \(bu +2n +Uses +.B nrrdConvert +or +.B nrrdClampConvert +.SH OPTIONS +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to convert to +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-clamp +clamp input values to representable range of values of output type, to avoid +wrap-around problems +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-2op (1), +.BR unu\-3op (1), +.BR unu\-quantize (1) diff --git a/unu-crop.1 b/unu-crop.1 new file mode 100644 index 0000000..b0f9ac8 --- /dev/null +++ b/unu-crop.1 @@ -0,0 +1,85 @@ +.TH UNU\-CROP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-crop \- crop along each axis to make a smaller +.I nrrd +.SH SYNOPSIS +.B unu\ crop +.RB [ \-min , \-\-minimum +.RI [< pos0 \ ...>]] +.RB [ \-max , \-\-maximum +.RI [< pos0 \ ...>]] +.RB [ \-b , \-\-bounds +.RI < filename >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Crop along each axis to make a smaller +.IR nrrd . +.IP \(bu +2n +Uses +.B nrrdCrop +.SH OPTIONS +.TP +.B \-min\fR\ [<\fIpos0\fR\ ...>]\ ,\ \fB\-\-minimum\fR\ [<\fIpos0\fR\ ...>] +low corner of bounding box. +.RS +7n +.IP \(bu +2n +.RI < int > +gives 0-based index +.IP \(bu +2n +.BR M , +.BR M+ <\fIint\fR>, +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.IP +(0 or more +.IR position s). +default: +.RB \(lq 0 \(rq +.TP +.B \-max\fR\ [<\fIpos0\fR\ ...>]\ ,\ \fB\-\-maximum\fR\ [<\fIpos0\fR\ ...>] +high corner of bounding box. +Besides the specification styles described above, there\(cqs also: +.RS +7n +.IP \(bu +2n +.BR m+ <\fIint\fR> +give index relative to minimum. +.RE +.IP +(0 or more +.IR position s). +default: +.RB \(lq 0 \(rq +.TP +.B \-b\fR\ <\fIfilename\fR>\ ,\ \fB\-\-bounds\fR\ <\fIfilename\fR> +a filename given here overrides the +.B \-min +and +.B \-max +options (they don\(cqt need to be used) and provides the cropping bounds as a +2\-D array; first scanline is for +.BR \-min , +second is for +.BR \-max . +Unfortunately the +.RB \(lq m \(rq +and +.RB \(lq M \(rq +semantics (above) are currently not supported in the bounds file. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-data.1 b/unu-data.1 new file mode 100644 index 0000000..e04dc57 --- /dev/null +++ b/unu-data.1 @@ -0,0 +1,55 @@ +.TH UNU\-DATA "1" "May 2021" "" "User Commands" +.SH NAME +unu\-data \- print data segment of a \fInrrd\fR file +.SH SYNOPSIS +.B unu\ data +.RI < nin > +.SH DESCRIPTION +Print data segment of a +.I nrrd +file. +The value of this is to pass the data segment in isolation to a stand-alone +decoder, in case this Teem build lacks an optional data encoding required for a +given nrrd file. +.SS CAVEATS +Will start copying characters from the datafile until EOF is hit, so this +won\(cqt work correctly if the datafile has extraneous content at the end. +Will skip lines (as per +.RB \(lq line\ skip: \(rq +header field) if needed, but can only skip bytes (as per +.RB \(lq byte\ skip: \(rq +if the encoding is NOT a compression. +.IP \(bu +2n +Uses +.B nrrdLoad +with +.B nio->skipData +and +.B nio->keepNrrdDataFileOpen +both +.B true +in the +.I NrrdIoState +.BR nio . +.SH OPTIONS +.TP +.RI < nin > +input +.I nrrd +.RI ( string ) +.SH EXAMPLES +To make +.B vol.raw +contain the uncompressed data from +.B vol.nrrd +which uses +.RB \(lq gz \(rq +encoding: +.in +4n +.EX +.B unu data vol.nrrd | gunzip > vol.raw +.EE +.in +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-head (1) diff --git a/unu-dhisto.1 b/unu-dhisto.1 new file mode 100644 index 0000000..90057d3 --- /dev/null +++ b/unu-dhisto.1 @@ -0,0 +1,55 @@ +.TH UNU\-DHISTO "1" "August 2021" "" "User Commands" +.SH NAME +unu\-dhisto \- create image of 1\-D value histogram +.SH SYNOPSIS +.B unu\ dhisto +.BR \-h , \-\-height +.RI < height > +.RB [ \-nolog ] +.RB [ \-notick ] +.RB [ \-max , \-\-maximum +.RI < max\ #\ hits >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Create image of 1\-D value histogram. +With +.RB \(lq \-nolog \(rq, +this becomes a quick & dirty way of plotting a function. +.IP \(bu +2n +Uses +.B nrrdHistoDraw +.SH OPTIONS +.TP +.B \-h\fR\ <\fIheight\fR>\ ,\ \fB\-\-height\fR\ <\fIheight\fR> +height of output image (horizontal size is determined by number of bins in +input histogram). +.RI ( unsigned\ int ) +.TP +.B \-nolog +do not show the log-scaled histogram with decade tick-marks +.TP +.B \-notick +do not draw the log decade tick marks +.TP +.B \-max\fR\ <\fImax\ #\ hits\fR>\ ,\ \fB\-\-maximum\fR\ <\fImax\ #\ hits\fR> +constrain the top of the drawn histogram to be at this number of hits. +This will either scale the drawn histogram downward or clip its top, depending +on whether the given max is higher or lower than the actual maximum bin count. +By not using this option (the default), the actual maximum bin count is used +.RI \(lq double \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-dice.1 b/unu-dice.1 new file mode 100644 index 0000000..ec458f3 --- /dev/null +++ b/unu-dice.1 @@ -0,0 +1,80 @@ +.TH UNU\-DICE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-dice \- save all slices along one axis into separate files +.SH SYNOPSIS +.B unu\ dice +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-s , \-\-start +.RI < start >] +.RB [ \-ff , \-\-format +.RI < form >] +.RB [ \-l , \-\-limit +.RI < max# >] +.RB [ \-o , \-\-output +.RI < above \ below >] +.SH DESCRIPTION +Save all slices along one axis into separate files. +Calls +.BR unu\-slice (1) +for each position along the indicated axis, and saves out a different +file for each sample along that axis. +.IP \(bu +2n +Uses repeated calls to +.B nrrdSlice +and +.B nrrdSave +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to slice along +.RI ( unsigned\ int ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-s\fR\ <\fIstart\fR>\ ,\ \fB\-\-start\fR\ <\fIstart\fR> +integer value to start numbering with +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ff\fR\ <\fIform\fR>\ ,\ \fB\-\-format\fR\ <\fIform\fR> +a +.BR printf (3)-style +format to use for generating all filenames. +Use this to override the number of characters used to represent the slice +position, or the file format of the output, e.g. +.RB \(lq \-ff\ %03d.ppm \(rq +for +.BR 000.ppm , +.BR 001.ppm , +etc. +By default (not using this option), slices are saved in NRRD format (or PNM or +PNG where possible) with shortest possible filenames. +.RI ( string ) +.TP +.B \-l\fR\ <\fImax#\fR>\ ,\ \fB\-\-limit\fR\ <\fImax#\fR> +a sanity check on how many slice files should be saved out, to prevent +accidentally dicing the wrong axis or the wrong array. +Can raise this value if needed. +.RI ( unsigned\ int ); +default: +.RB \(lq 9999 \(rq +.TP +.B \-o\fR\ <\fIprefix\fR>\ ,\ \fB\-\-output\fR\ <\fIprefix\fR> +output filename +.I prefix +(excluding info set via +.RB \(lq \-ff \(rq, +basically to set path of output files (so be sure to end with +.RB \(lq / \(rq). +.RI ( string ) +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-slice (1) +.P +.BR printf (3) diff --git a/unu-diff.1 b/unu-diff.1 new file mode 100644 index 0000000..a8e7359 --- /dev/null +++ b/unu-diff.1 @@ -0,0 +1,46 @@ +.TH UNU\-DIFF "1" "May 2021" "" "User Commands" +.SH NAME +unu\-diff \- sees if two +.IR nrrd s +are different in any way +.SH SYNOPSIS +.B unu\ diff +.RI < ninA > +.RI < ninB > +.RB [ \-eps , \-\-epsilon +.RI < eps >] +.RB [ \-od , \-\-onlydata ] +.SH DESCRIPTION +Sees if two +.IR nrrd s +are different in any way. +Looks through all fields to see if two given +.IR nrrd s +contain the same information. +Or, array meta-data can be excluded, and comparison only on the data values is +done with the +.B \-od +flag. +.IP \(bu +2n +Uses +.B nrrdCompare +.SH OPTIONS +.TP +.RI < ninA > +First input +.IR nrrd . +.TP +.RI < ninB > +Second input +.IR nrrd . +.TP +.B \-eps\fR\ <\fIeps\fR>\ ,\ \fB\-\-epsilon\fR\ <\fIeps\fR> +threshold for allowable difference in values in data values +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-od\fR\ ,\ \fB\-\-onlydata +Compare data values only, excluding array meta-data +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-dist.1 b/unu-dist.1 new file mode 100644 index 0000000..fb0a97c --- /dev/null +++ b/unu-dist.1 @@ -0,0 +1,71 @@ +.TH UNU\-DIST "1" "May 2021" "" "User Commands" +.SH NAME +unu\-dist \- Euclidean distance transform +.SH SYNOPSIS +.B unu\ dist +.BR \-th , \-\-thresh +.RI < val > +.RB [ \-b , \-\-bias +.RI < val >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-sgn ] +.RB [ \-inv ] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Euclidean distance transform. +Based on \(lqDistance Transforms of Sampled Functions\(rq +by Pedro F. Felzenszwalb and Daniel P. Huttenlocher, +\fICornell Computing and Information Science\fR TR2004\-1963. +This function first thresholds at the specified value and then does the +distance transform of the resulting binary image. +The signed distance (negative values inside object) is also available. +Distances between non-isotropic samples are handled correctly. +.IP \(bu +2n +Uses +.B nrrdDistanceL2 +or +.B nrrdDistanceL2Signed +.SH OPTIONS +.TP +.B \-th\fR\ <\fIval\fR>\ ,\ \fB\-\-thresh\fR\ <\fIval\fR> +threshold value to separate inside from outside +.RI ( double ) +.TP +.B \-b\fR\ <\fIval\fR>\ ,\ \fB\-\-bias\fR\ <\fIval\fR> +if non-zero, bias the distance transform by this amount times the difference in +value from the threshold +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to save output in; default: +.RB \(lq float \(rq +.TP +.B \-sgn +also compute signed (negative) distances inside objects, instead of leaving +them as zero +.TP +.B \-inv +values +.B below +threshold are considered interior to object. +By default (not using this option), values above threshold are considered +interior. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-env.1 b/unu-env.1 new file mode 100644 index 0000000..2b3e8a6 --- /dev/null +++ b/unu-env.1 @@ -0,0 +1,184 @@ +.TH UNU\-ENV "1" "April 2021" "" "User Commands" +.SH NAME +unu\-env \- list relevant environment variables and their values +.SH SYNOPSIS +.B unu\ env +.SH DESCRIPTION +List relevant environment variables and their values. +These environment variables provide a way of setting global variables that can +affect the way Nrrd (and +.BR unu (1)) +operates. +.IP \(bu +2n +Uses +.BR nrrdGetenvBool , +.BR nrrdGetenvEnum , +.BR nrrdGetenvInt , +and +.B nrrdGetenvUInt +.IP +Each variable in the listing below starts with the name of the environment +variable +.RB (\(lq NRRD_ ...\(rq), +what type of value it represents (e.g.\: +.RI \(lq int \(rq, +.RI \(lq bool \(rq), +what the corresponding Nrrd global variable is set to, and a description of the +variable. +In the +.BR unu\-env (1) +command output, the listing also includes what the environment variable is +currently set to. +.IP +.I Bool +variables may be set to true simply by setting the environment variable; +setting the value to +.RI \(lq true \(rq +or +.RI \(lq false \(rq +sets the +.I bool +accordingly. +.I Enum +variables may be set by setting the environment variable to any string that +parses as one of the +.I enum +values. +.I Int +and +.I unsigned\ int +variables are set via a string parse-able as a numeric value. +.IP +In addition to the the +.RB \(lq NRRD_ \(rq +environment variables, there is this one, +.BR UNRRDU_QUIET_QUIT ; +see the +.B ENVIRONMENT +section below. +.SH ENVIRONMENT +.TP +.B UNRRDU_QUIET_QUIT +Determines whether +.BR unu (1) +exits quietly (without error and usage info) when it fails because an input +.I nrrd +read immediately hit +.B EOF +(as happens when many +.BR unu (1) +invocations are piped together). +This is currently detected by seeing if the error message ends with +.RB \(lq [nrrd]\ _nrrdRead:\ immediately\ hit\ EOF \(rq. +.TP +.B NRRD_STATE_KEYVALUEPAIRS_PROPAGATE \fR(\fIbool\fR) +.RB ( nrrdStateKeyValuePairsPropagate \ ==\ true ) +.IP +When +.BR true , +key/value pairs are copied from input +.I nrrd +to output +.I nrrd +just like other basic info that hasn\(cqt just been modified (e.g. type, +dimension, block size). +.TP +.B NRRD_DEFAULT_CENTER \fR(\fIcentering\ enum\fR) +.RB ( nrrdDefaultCenter \ ==\ cell ) +.IP +The type of sample centering to use when none has been set but one has to be +chosen for some operation (e.g. resampling). +.TP +.B NRRD_DEFAULT_WRITE_ENCODING_TYPE \fR(\fIencoding\ enum\fR) +.RB ( nrrdDefaultWriteEncodingType \ ==\ raw ) +.IP +When writing +.IR nrrd s, +what encoding to use. +Only +.BR unu\-save (1) +affords explicit control of output encoding. +.TP +.B NRRD_STATE_KIND_NOOP \fR(\fIbool\fR) +.RB ( nrrdStateKindNoop \ ==\ false ) +.IP +When true, Nrrd makes not even the slightest effort to be smart about setting +the +.RB \(lq kind \(rq +field of an axis after some operation that modified its samples. +.TP +.B NRRD_STATE_VERBOSE_IO \fR(\fIint\fR) +.RB ( nrrdStateVerboseIO \ ==\ 1 ) +.IP +The verbosity level of Nrrd input/output operations. +.TP +.B NRRD_DEFAULT_WRITE_BARE_TEXT \fR(\fIbool\fR) +.RB ( nrrdDefaultWriteBareText \ ==\ 1 ) +.IP +When +.BR false , +text files used for saving +.IR nrrd s +start with comment +.RB (\(lq #\ ... \(rq) +lines containing +.I nrrd +fields. +.TP +.B NRRD_STATE_MEASURE_TYPE \fR(\fIenum\fR) +.RB ( nrrdStateMeasureType \ ==\ float ) +.IP +For measurements +.RB ( unu\-project (1)) +like sum and product, the type of the output result, when one hasn\(cqt been +explicitly requested. +.TP +.B NRRD_STATE_MEASURE_MODE_BINS \fR(\fIint\fR) +.RB ( nrrdStateMeasureModeBins \ ==\ 1024 ) +.IP +When measuring mode but without a given histogram, how many bins to use in the +temporary internal histogram. +.TP +.B NRRD_STATE_MEASURE_HISTO_TYPE \fR(\fIenum\fR) +.RB ( nrrdStateMeasureHistoType \ ==\ float ) +.IP +Output type for most measurements of histograms, when one hasn\(cqt been +explicitly requested +.TP +.B NRRD_STATE_ALWAYS_SET_CONTENT \fR(\fIbool\fR) +.RB ( nrrdStateAlwaysSetContent \ ==\ true ) +.IP +If +.BR true , +the output content string is set even when the input content string is not set. +.TP +.B NRRD_STATE_DISABLE_CONTENT \fR(\fIbool\fR) +.RB ( nrrdStateDisableContent \ ==\ false ) +.IP +If +.BR true , +output content is never set. +.TP +.B NRRD_DEFAULT_WRITE_CHARS_PER_LINE \fR(\fIunsigned\ int\fR) +.RB ( nrrdDefaultWriteCharsPerLine \ ==\ 75 ) +.IP +When using text encoding, maximum # characters allowed per line. +.TP +.B NRRD_DEFAULT_WRITE_VALS_PER_LINE \fR(\fIunsigned\ int\fR) +.RB ( nrrdDefaultWriteValsPerLine \ ==\ 8 ) +.IP +When using text encoding, maximum # values allowed per line +.TP +.B NRRD_STATE_GRAYSCALE_IMAGE_3D \fR(\fIbool\fR) +.RB ( nrrdStateGrayscaleImage3D \ ==\ false ) +.IP +If +.BR true , +reading a 2-D grayscale image results in a 3-D image with a single +sample +.RB ( size = 1 ) +on the first (fastest) axis. +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-project (1), +.BR unu\-save (1) diff --git a/unu-fft.1 b/unu-fft.1 new file mode 100644 index 0000000..3be7157 --- /dev/null +++ b/unu-fft.1 @@ -0,0 +1,107 @@ +.TH UNU\-FFT "1" "May 2021" "" "User Commands" +.SH NAME +unu\-fft \- Fast Fourier Transform of selected axes +.SH SYNOPSIS +.B unu\ fft +.RI < dir > +.BR \-a , \-\-axes +.RI < ax0 \ ...> +.RB [ \-pr , \-\-planrigor +.RI < pr >] +.RB [ \-r , \-\-rescale +.RI < bool >] +.RB [ \-w , \-\-wisdom +.RI < filename >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-ri , \-\-realinput ] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Fast Fourier Transform of selected axes. +Initial attempt at wrapping the FFTW3 library; options are likely to change in +Teem 2.0. +.IP \(bu +2n +Uses +.B nrrdFFT +.SH OPTIONS +.TP +.RI < dir > +forward +.RB (\(lq forw \(rq, +.RB \(lq f \(rq) +or backward/inverse ("back", "b") +.RB (\(lq back \(rq, +.RB \(lq b \(rq) +transform +.TP +.B \-a\fR\ <\fIax0\fR\ ...>\ ,\ \fB\-\-axes\fR\ <\fIax0\fR\ ...> +the one or more axes that should be transformed (1 or more +.IR unsigned\ int s) +.TP +.B \-pr\fR\ <\fIpr\fR>\ ,\ \fB\-\-planrigor\fR\ <\fIpr\fR> +rigor with which fftw plan is constructed. +Options include: +.RS +7n +.IP \(bu 2 +.RB \(lq e \(rq, +.RB \(lq est \(rq, +.RB \(lq estimate \(rq: +only an estimate +.IP \(bu 2 +.RB \(lq m \(rq, +.RB \(lq meas \(rq, +.RB \(lq measure \(rq: +standard amount of measurements of system properties +.IP \(bu 2 +.RB \(lq p \(rq, +.RB \(lq pat \(rq, +.RB \(lq patient \(rq: +slower, more measurements +.IP \(bu 2 +.RB \(lq x \(rq, +.RB \(lq ex \(rq, +.RB \(lq exhaustive \(rq: +slowest, most measurements +.P +default: +.RB \(lq est \(rq +.RE +.TP +.B \-r\fR\ <\fIbool\fR>\ ,\ \fB\-\-rescale\fR\ <\fIbool\fR> +scale fftw output (by sqrt(1/N)) so that forward and backward transforms will +get back to original values +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-w\fR\ <\fIfilename\fR>\ ,\ \fB\-\-wisdom\fR\ <\fIfilename\fR> +A filename here is used to read in fftw wisdom (if the file exists already), +and is used to save out updated wisdom after the transform. +By default (not using this option), no wisdom is read or saved. +.IR Note : +no wisdom is gained (that is, learned by FFTW) with planning rigor +.RB \(lq estimate \(rq. +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-ri\fR\ ,\ \fB\-\-realinput +input is real-valued, so insert new length-2 axis +.B 0 +and set complex component to +.BR 0.0 . +Axes to transform (indicated by +.RB \(lq \-a \(rq +will be incremented accordingly. +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-flip.1 b/unu-flip.1 new file mode 100644 index 0000000..63c86d5 --- /dev/null +++ b/unu-flip.1 @@ -0,0 +1,37 @@ +.TH UNU\-FLIP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-flip \- reverse order of slices along one axis +.SH SYNOPSIS +.B unu\ flip +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Reverse order of slices along one axis. +Special case of +.BR unu\-shuffle (1). +.IP \(bu +2n +Uses +.B nrrdFlip +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to flip along +.RI ( unsigned\ int ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-shuffle (1) diff --git a/unu-gamma.1 b/unu-gamma.1 new file mode 100644 index 0000000..a536802 --- /dev/null +++ b/unu-gamma.1 @@ -0,0 +1,81 @@ +.TH UNU\-GAMMA "1" "August 2021" "" "User Commands" +.SH NAME +unu\-gamma \- brighten or darken values with a gamma +.SH SYNOPSIS +.B unu\ gamma +.BR \-g , \-\-gamma +.RI < gamma > +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Brighten or darken values with a gamma. +Just as in +.BR xv , +the gamma value here is actually the reciprocal of the exponent actually used +to transform the values. +.IP \(bu +2n +Uses +.B nrrdArithGamma +.SH OPTIONS +.TP +.B \-g\fR\ <\fIgamma\fR>\ ,\ \fB\-\-gamma\fR\ <\fIgamma\fR> +.B 1.0 +brightens; gamma < +.B 1.0 +darkens. +Negative gammas invert values (like in +.BR xv ). +.RI ( double ) +.TP +.B \-min\fR\ [<\fIvalue\fR>]\ ,\ \fB\-\-minimum\fR\ [<\fIvalue\fR>] +Value to implicitly map to +.B 0.0 +prior to calling +.BR pow (3). +Defaults to lowest value found in input +.IR nrrd . +.RI ( double ) +.TP +.B \-max\fR\ [<\fIvalue\fR>]\ ,\ \fB\-\-maximum\fR\ [<\fIvalue\fR>] +Value to implicitly map to +.B 1.0 +prior to calling +.BR pow (3). +Defaults to highest value found in input +.IR nrrd . +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) +.P +http://www.trilon.com/xv/ diff --git a/unu-head.1 b/unu-head.1 new file mode 100644 index 0000000..0a3e691 --- /dev/null +++ b/unu-head.1 @@ -0,0 +1,34 @@ +.TH UNU\-HEAD "1" "May 2021" "" "User Commands" +.SH NAME +unu\-head \- print header of one or more \fInrrd\fR files +.SH SYNOPSIS +.B unu\ head +.RI < nin1 \ ...> +.SH DESCRIPTION +Print header of one or more +.I nrrd +files. +The value of this is simply to print the contents of +.I nrrd +headers. +This avoids the use of +.RB \(lq head\ \-\fIN \(rq, +where +.I N +has to be determined manually, which always risks printing raw binary data +(following the header) to screen, which tends to clobber terminal settings, +make pointless beeps, and be annoying. +.IP \(bu +2n +Uses +.B nrrdOneLine +.SH OPTIONS +.TP +.RI < nin1 \ ...> +input +.IR nrrd (s) +(1 or more +.IR string s) +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-data (1), +.BR head (1) diff --git a/unu-heq.1 b/unu-heq.1 new file mode 100644 index 0000000..2d7a955 --- /dev/null +++ b/unu-heq.1 @@ -0,0 +1,82 @@ +.TH UNU\-HEQ "1" "August 2021" "" "User Commands" +.SH NAME +unu\-heq \- perform histogram equalization +.SH SYNOPSIS +.B unu\ heq +.BR \-b , \-\-bin +.RI < bins > +.RB [ \-s , \-\-smart +.RI [< bins >]] +.RB [ \-a , \-\-amount +.RI < amount >] +.RB [ \-m , \-\-map +.RI < filename >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Perform histogram equalization. +If this seems to be doing nothing, try increasing the number of histograms bins +by an order of magnitude or two (or more). +Or, use +.BR unu\-gamma (1) +to warp the values in the direction you know they need to go. +Either of these might work because extremely tall and narrow peaks in the +equalization histogram will produce poor results. +.IP \(bu +2n +Uses +.B nrrdHistoEq +.SH OPTIONS +.TP +.B \-b\fR\ <\fIbins\fR>\ ,\ \fB\-\-bin\fR\ <\fIbins\fR> +# bins to use in histogram that is created in order to calculate the mapping +that achieves the equalization. +.RI ( int ) +.TP +.B \-s\fR\ [<\fIbins\fR>]\ ,\ \fB\-\-smart\fR\ [<\fIbins\fR>] +# bins in value histogram to ignore in calculating the mapping. +Bins are ignored when they get more hits than other bins, and when the values +that fall in them are constant. +This is an effective way to prevent large regions of background value from +distorting the equalization mapping. +(optional +.IR int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-a\fR\ <\fIamount\fR>\ ,\ \fB\-\-amount\fR\ <\fIamount\fR> +extent to which the histogram equalizing mapping should be applied; +.BR 0.0 : +no change, +.BR 1.0 : +full equalization +.RI ( float ); +default: +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +output type; default: +.RB \(lq 1.0 \(rq +.TP +.B \-m\fR\ <\fIfilename\fR>\ ,\ \fB\-\-map\fR\ <\fIfilename\fR> +The value mapping used to achieve histogram equalization is represented by a +univariate regular map. +By giving a filename here, that map can be saved out and applied to other +.IR nrrd s +with +.BR unu\-rmap (1) +.RI ( string ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-gamma (1), +.BR unu\-rmap (1) diff --git a/unu-histax.1 b/unu-histax.1 new file mode 100644 index 0000000..4c76380 --- /dev/null +++ b/unu-histax.1 @@ -0,0 +1,94 @@ +.TH UNU\-HISTAX "1" "August 2021" "" "User Commands" +.SH NAME +unu\-histax \- replace each scanline along an axis with its histogram +.SH SYNOPSIS +.B unu\ histax +.BR \-a , \-\-axis +.RI < axis > +.BR \-b , \-\-bin +.RI < bins > +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Replace each scanline along an axis with its histogram. +.IP \(bu +2n +Uses +.B nrrdHistoAxis +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to histogram along +.RI ( unsigned\ int ) +.TP +.B \-b\fR\ <\fIbins\fR>\ ,\ \fB\-\-bin\fR\ <\fIbins\fR> +# of bins in histogram +.RI ( unsigned\ int ) +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +output type; default: +.RB \(lq uint \(rq +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +The value to map to zero, given explicitly as a regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this minimum is specified in terms of the percentage of samples in +input that are lower. +.RB \(lq 0% \(rq +means the lowest input value is used, +.RB \(lq 1% \(rq +means that the 1% of the lowest values are all mapped to zero. +By default (not using this option), the lowest input value is used. +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +The value to map to the highest unsigned integral value, given explicitly as a +regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this maximum is specified in terms of the percentage of samples in +input that are higher. +.RB \(lq 0% \(rq +means the highest input value is used, which is also the default behavior (same +as not using this option). +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-histo.1 b/unu-histo.1 new file mode 100644 index 0000000..e0b34b8 --- /dev/null +++ b/unu-histo.1 @@ -0,0 +1,98 @@ +.TH UNU\-HISTO "1" "August 2021" "" "User Commands" +.SH NAME +unu\-histo \- create 1\-D histogram of values in a +.I nrrd +.SH SYNOPSIS +.B unu\ histo +.BR \-b , \-\-bins +.RI < num > +.RB [ \-w , \-\-weight +.RI < nweight >] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Create 1\-D histogram of values in a +.IR nrrd . +Can explicitly set bounds of histogram domain or can learn these from the data. +.IP \(bu +2n +Uses +.B nrrdHisto +.SH OPTIONS +.TP +.B \-b\fR\ <\fInum\fR>\ ,\ \fB\-\-bins\fR\ <\fInum\fR> +# of bins in histogram +.RI ( unsigned\ int ) +.TP +.B \-w\fR\ <\fInweight\fR>\ ,\ \fB\-\-weight\fR\ <\fInweight\fR> +how to weigh contributions to histogram. +By default (not using this option), the increment is one bin count per sample, +but by giving a +.IR nrrd , +the value in the +.I nrrd +at the corresponding location will be the bin count increment +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Value at low end of histogram, given explicitly as a regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this minimum is specified in terms of the percentage of samples in +input that are lower. +By default (not using this option), the lowest value found in input +.IR nrrd . +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +Value at high end of histogram, given explicitly as a regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this maximum is specified in terms of the percentage of samples in +input that are higher. +Defaults to highest value found in input +.IR nrrd . +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to use for bins in output histogram; default: +.RB \(lq uint \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-i2w.1 b/unu-i2w.1 new file mode 100644 index 0000000..3b29e31 --- /dev/null +++ b/unu-i2w.1 @@ -0,0 +1,58 @@ +.TH UNU\-I2W "1" "April 2021" "" "User Commands" +.SH NAME +unu\-i2w \- converts from 1-D index to world position +.SH SYNOPSIS +.B unu\ i2w +.RI < center > +.RI < minPos > +.RI < maxPos > +.RI < num > +.RI < index > +.SH DESCRIPTION +Converts from 1-D index to world position, given the centering of the data +.RB ( cell +vs. +.BR node ), +the range of positions, and the number of intervals into which position has +been quantized. +This is a demo/utility, which does not actually operate on any +.IR nrrd s. +Previously available as the stand-alone +.B idx2pos +binary. +.P +Uses +.B NRRD_POS +macro +.SH OPTIONS +.TP +.RI < center > +which centering applies to the quantized position. +Possibilities are: +.RS +7n +.IP \(bu 2 +.RB \(lq cell \(rq +for histogram bins, quantized values, and pixels-as-squares +.IP \(bu 2 +.RB \(lq node \(rq +for non-trivially interpolated sample points +.RE +.TP +.RI < minPos > +smallest position associated with index +.B 0 +.RI ( double ) +.TP +.RI < maxPos > +highest position associated with highest index +.RI ( double ) +.TP +.RI < num > +number of intervals into which position has been quantized +.RI ( double ) +.TP +.RI < index > +the input index position, to be converted to world +.RI ( double ) +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-imap.1 b/unu-imap.1 new file mode 100644 index 0000000..c79205f --- /dev/null +++ b/unu-imap.1 @@ -0,0 +1,118 @@ +.TH UNU\-IMAP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-imap \- map +.I nrrd +through +.B irregular +univariate map (\(lqcolormap\(rq) +.SH SYNOPSIS +.B unu\ rmap +.BR \-m , \-\-map +.RI < map > +.RB [ \-l , \-\-length +.RI < aclLen >] +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through +.B irregular +univariate map (\(lqcolormap\(rq). +A map is irregular if the control points are not evenly spaced along the +domain, and hence their position must be explicitly represented in the map. +As +.IR nrrd s, +these maps are necessarily 2D. +Along axis +.BR 0 , +the first value is the location of the control point, and the remaining values +give are the range of the map for that control point. +The output value(s) is the result of linearly interpolating between value(s) +from the map. +.IP \(bu +2n +Uses +.B nrrdApply1DIrregMap +.SH OPTIONS +.TP +.B \-m\fR\ <\fImap\fR>\ ,\ \fB\-\-map\fR\ <\fImap\fR> +irregular map to map input +.I nrrd +through +.TP +.B \-l\fR\ <\fIaclLen\fR>\ ,\ \fB\-\-length\fR\ <\fIaclLen\fR> +length of accelerator array, used to try to speed-up task of finding between +which pair of control points a given value lies. +Not terribly useful for small maps (about 10 points or less). +Use +.B 0 +to turn accelorator off. +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the map domain. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the map\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-rmap (1) diff --git a/unu-inset.1 b/unu-inset.1 new file mode 100644 index 0000000..38059f7 --- /dev/null +++ b/unu-inset.1 @@ -0,0 +1,61 @@ +.TH UNU\-INSET "1" "August 2021" "" "User Commands" +.SH NAME +unu\-inset \- replace a sub-region with a different +.I nrrd +.SH SYNOPSIS +.B unu\ inset +.BR \-min , \-\-minimum +.RI < pos0 \ ...> +.BR \-s , \-\-subset +.RI < nsub > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Replace a sub-region with a different +.IR nrrd . +This is functionally the opposite of +.RB \(lq crop \(rq. +.IP \(bu +2n +Uses +.B nrrdInset +.SH OPTIONS +.TP +.B \-min\fR\ [<\fIpos0\fR\ ...>]\ ,\ \fB\-\-minimum\fR\ [<\fIpos0\fR\ ...>] +coordinates of where to locate sub-volume within input +.IR nrrd . +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0\-based index +.IP \(bu 2 +.BR M , +.BR M\+ <\fIint\fR>, +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.IP +(1 or more +.IR position s) +.TP +.B \-s\fR\ <\fInsub\fR>\ ,\ \fB\-\-subset\fR\ <\fInsub\fR> +sub-region +.IR nrrd . +This is the data to be inset in +.I nin +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-crop (1) diff --git a/unu-jhisto.1 b/unu-jhisto.1 new file mode 100644 index 0000000..861e581 --- /dev/null +++ b/unu-jhisto.1 @@ -0,0 +1,99 @@ +.TH UNU\-JHISTO "1" "August 2021" "" "User Commands" +.SH NAME +unu\-jhisto \- create joint histogram of two or more +.IR nrrd s +.SH SYNOPSIS +.B unu\ jhisto +.BR \-b , \-\-bin +.RI < bins0 \ bins1 \ ...> +.RB [ \-w , \-\-weight +.RI < nweight >] +.RB [ \-min , \-\-minimum +.RI < min0 \ min1 \ ...>] +.RB [ \-max , \-\-maximum +.RI < max0 \ max1 \ ...>] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin0 \ nin1 \ ...>] +.RB [ \-a , \-\-axis +.RI < axis >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Create joint histogram of two or more +.IR nrrd s. +Each axis of the output corresponds to one of the input +.IR nrrd s, +and each bin in the output records the number of corresponding positions in the +inputs with a combination of values represented by the coordinates of the bin. +.IP \(bu +2n +Uses +.B nrrdHistoJoint +.SH OPTIONS +.TP +.B \-b\fR\ <\fIbins0\fR\ \fIbins1\fR\ ...>\ ,\ \fB\-\-bin\fR\ <\fIbins0\fR\ \fIbins1\fR\ ...> +.IR bins < i > +is the number of bins to use along axis +.I i +(of joint histogram), which + represents the values of +.IR nin < i > +(2 or more +.IR size_t s) +.TP +.B \-w\fR\ <\fInweight\fR>\ ,\ \fB\-\-weight\fR\ <\fInweight\fR> +how to weigh contributions to joint histogram. +By default (not using this option), the increment is one bin count per sample, +but by giving a +.IR nrrd , +the value in the +.I nrrd +at the corresponding location will be the bin count increment +.TP +.B \-min\fR\ <\fImin0\fR\ min1\fR\ ...>\ ,\ \fB\-\-minimum\fR\ <\fImin0\fR\ min1\fR\ ...> +.IR min < i > +is the low range of values to be quantized along axis +.IR i ; +use +.RB \(lq nan \(rq +to represent lowest value present +(2 or more +.IR double s) +.TP +.B \-max\fR\ <\fImax0\fR\ max1\fR\ ...>\ ,\ \fB\-\-maximum\fR\ <\fImax0\fR\ max1\fR\ ...> +.IR max < i > +is the high range of values to be quantized along axis +.IR i ; +use +.RB \(lq nan \(rq +to represent highest value present +(2 or more +.IR double s) +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to use for output (the type used to store hit counts in the joint +histogram). +Clamping is done on hit counts so that they never overflow a fixed-point type; +default: +.RB \(lq uint \(rq +.TP +.B \-i\fR\ <\fInin0\fR\ [\fInin1\fR]\ ...>\ ,\ \fB\-\-input\fR\ <\fInin0\fR\ [\fInin1\fR]\ ...> +list of +.IR nrrd s +(one for each axis of joint histogram), or, single +.I nrrd +that will be sliced along specified axis. +(1 or more +.IR nrrd s); +default: +.RB \(lq \- \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-join.1 b/unu-join.1 new file mode 100644 index 0000000..011a0ae --- /dev/null +++ b/unu-join.1 @@ -0,0 +1,89 @@ +.TH UNU\-JOIN "1" "August 2021" "" "User Commands" +.SH NAME +unu\-join \- connect slices and/or slabs into a bigger +.I nrrd +.SH SYNOPSIS +.B unu\ join +.RI [ @file \ ...] +.BR \-i , \-\-input +.RI < nin0 \ ...> +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-incr ] +.RB [ \-l , \-\-label +.RI < label >] +.RB [ \-mm , \-\-minmax +.RI < min \ max >] +.RB [ \-sp , \-\-spacing +.RI < spc >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Connect slices and/or slabs into a bigger +.IR nrrd . +Can stich images into volumes, or tile images side by side, or attach images +onto volumes. +If +there are many many files to name in the +.RB \(lq \-i \(rq +option, and using wildcards won\(cqt work, consider putting the list of +filenames into a separate text file (e.g. +.RB \(lq slices.txt \(rq), +and then name this file as a response file (e.g. +.RB \(lq \-i\ s(a)lices.txt \(rq). +This command now allows you to set the same pieces of +information that previously had to be set with +.BR unu\-axinfo (1): +label, spacing, and min/max. +These can be use whether the join axis is new (because of +.RB \(lq \-incr \(rq) +or not. +.IP \(bu +2n +Uses +.B nrrdJoin +.SH OPTIONS +.TP +.IR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR\ <\fInin0\fR\ ...>\ ,\ \fB\-\-input\fR\ <\fInin0\fR\ ...> +everything to be joined together (1 or more +.IR nrrd s) +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to join along +.RI ( unsigned\ int ) +.TP +.B \-incr +in situations where the join axis is +.B not +among the existing axes of the input +.IR nrrd s, +then this flag signifies that the join axis should be +.BR inserted , +and the output dimension should be one greater than input dimension. +Without this flag, the +.IR nrrd s +are joined side-by-side, along an existing axis. +.TP +.B \-l\fR\ <\fIlabel\fR>\ ,\ \fB\-\-label\fR\ <\fIlabel\fR> +label to associate with join axis +.RI ( string ) +.TP +.B \-mm\fR\ <\fImin\fR\ \fImax\fR>\ ,\ \fB\-\-minmax\fR\ <\fImin\fR\ \fImax\fR> +min and max values along join axis (2 +.IR double s) +.TP +.B \-sp\fR\ <\fIspc\fR>\ ,\ \fB\-\-spacing\fR\ <\fIspc\fR> +spacing between samples along join axis +.RI ( double ) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- (rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-axinfo (1) diff --git a/unu-lut.1 b/unu-lut.1 new file mode 100644 index 0000000..1812278 --- /dev/null +++ b/unu-lut.1 @@ -0,0 +1,104 @@ +.TH UNU\-LUT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-lut \- map +.I nrrd +through one univariate lookup table +.SH SYNOPSIS +.B unu\ lut +.BR \-m , \-\-map +.RI < lut > +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through one univariate lookup table (itself represented as a +.IR nrrd ). +The lookup table can be 1D, in which case the output has the same dimension as +the input, or 2D, in which case the output has one more dimension than the +input, and each value is mapped to a scanline (along axis +.BR 0 ) +from the lookup table. +.IP \(bu +2n +Uses +.B nrrdApply1DLut +.SH OPTIONS +.TP +.B \-m\fR\ <\fIlut\fR>\ ,\ \fB\-\-map\fR\ <\fIlut\fR> +lookup table to map input +.I nrrd +through +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the lut domain. +The lut domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the lut\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-mlut (1), +.BR unu\-lut2 (1) diff --git a/unu-lut2.1 b/unu-lut2.1 new file mode 100644 index 0000000..f6871c2 --- /dev/null +++ b/unu-lut2.1 @@ -0,0 +1,114 @@ +.TH UNU\-LUT2 "1" "August 2021" "" "User Commands" +.SH NAME +unu\-lut2 \- map +.I nrrd +through a bivariate lookup table +.SH SYNOPSIS +.B unu\ lut2 +.BR \-m , \-\-map +.RI < lut > +.RB [ \-r , \-\-rescale +.RI < bool \ bool >] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through a bivariate lookup table (itself represented as a +.IR nrrd ). +The lookup table can be 2D, in which case the output has the same dimension as +the input, or 3D, in which case the output has one more dimension than the +input, and each value is mapped to a scanline (along axis +.BR 0 ) +from the lookup table. +In any case, axis +.B 0 +of the input must have length two. +.IP \(bu +2n +Uses +.B nrrdApply2DLut +.SH OPTIONS +.TP +.B \-m\fR\ <\fIlut\fR>\ ,\ \fB\-\-map\fR\ <\fIlut\fR> +lookup table to map input +.I nrrd +through +.TP +.B \-r\fR\ <\fIbool\fR\ \fIbool\fR>\ ,\ \fB\-\-rescale\fR\ <\fIbool\fR\ \fIbool\fR> +rescale one or both of the input values from the input range to the lut domain. +The lut domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +(2 +.IR bool s); +default: +.RB \(lq false\ false \(rq +.TP +.B \-min\fR\ <\fImin0\fR\ \fImin1\fR>\ ,\ \fB\-\-minimum\fR\ <\fImin0\fR\ \fImin1\fR> +Low end of input range. +Defaults to lowest values found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +(2 +.IR double s) +.TP +.B \-max\fR\ <\fImax0\fR\ \fImax1\fR>\ ,\ \fB\-\-maximum\fR\ <\fImax0\fR\ \fImax1\fR> +High end of input range. +Defaults to highest values found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +(2 +.IR double s) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the lut\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-lut (1), +.BR unu\-mlut (1) diff --git a/unu-make.1 b/unu-make.1 new file mode 100644 index 0000000..d5a93b3 --- /dev/null +++ b/unu-make.1 @@ -0,0 +1,383 @@ +.TH UNU\-MAKE "1" "May 2021" "" "User Commands" +.SH NAME +unu\-make \- create a \fInrrd\fR (or \fInrrd\fR header) from scratch +.SH SYNOPSIS +.B unu\ make +.RI [ @file \ ...] +.RB [ \-h ] +.RB [ \-i , \-\-input +.RI < file \ ...>] +.BR \-t , \-\-type +.RI < type > +.BR \-s , \-\-size +.RI < sz0 \ sz1 \ ...> +.RB [ \-fd , \-\-filedim +.RI < dim >] +.RB [ \-sp , \-\-spacing +.RI < sp0 \ sp1 \ ...>] +.RB [ \-th , \-\-thickness +.RI < th0 \ th1 \ ...>] +.RB [ \-k , \-\-kind +.RI < k0 \ k1 \ ...>] +.RB [ \-cn , \-\-centering +.RI < c0 \ c1 \ ...>] +.RB [ \-l , \-\-label +.RI < lb0 \ lb1 \ ...>] +.RB [ \-u , \-\-unit +.RI < un0 \ un1 \ ...>] +.RB [ \-c , \-\-content +.RI < content >] +.RB [ \-ls , \-\-lineskip +.RI < num >] +.RB [ \-bs , \-\-byteskip +.RI < num >] +.RB [ \-e , \-\-encoding +.RI < enc >] +.RB [ \-en , \-\-endian +.RI < end >] +.RB [ \-kv , \-\-keyvalue +.RI < key/val \ ...>] +.RB [ \-spc , \-\-space +.RI < space >] +.RB [ \-orig , \-\-origin +.RI < origin >] +.RB [ \-dirs , \-\-directions +.RI < v0 \ v1 \ ...>] +.RB [ \-mf , \-\-measurementframe +.RI < v0 \ v1 \ ...>] +.RB [ \-spu , \-\-spaceunit +.RI < su0 \ su1 \ ...>] +.RB [ \-o , \-\-output +.RI < nout >] +.RB [ \-od , \-\-outputdata +.RI < name >] +.SH DESCRIPTION +Create a +.I nrrd +(or +.I nrrd +header) from scratch. +The data can be in one or more files, or coming from +.BR stdin (3). +This provides an easy way of specifying the information about some data as to +wrap it in a NRRD file, either to pass on for further +.BR unu (1) +processing, or to save to disk. +Note that with +.RB \(lq \-h \(rq, +this creates a detached +.I nrrd +header file, without ever reading or writing data files. +.P +When using multiple datafiles, the data from each is simply concatenated in +memory (as opposed to interleaving along a faster axis). +Keep in mind that all the options below refer to the finished data segment +resulting from joining all the data pieces together, except for +.RB \(lq \-ls \(rq, +.RB \(lq \-bs \(rq, +and +.RB \(lq \-e \(rq, +which apply (uniformly) to the individual data files. +Use the +.RB \(lq \-fd \(rq, +option when the things being joined together are not slices of the final +result, but slabs or scanlines. +It may be easier to put multiple filenames in a response file; there can be one +or more filenames per line of the response file. You can also use a +.BR sprintf (3)-style +format to identify a numbered range of files, so for example +.RB \(lq \-i\ I.%03d\ 1\ 90\ 1 \(rq +refers to +.BR I.001 ,\ I.002 ,\ ...\ I.090 , +using the inclusive range from the first to the second integer (following the +.BR sprintf (3)-style +format), in steps of the third. +Can optionally give a fourth integer to serve same role as +.RB \(lq \-fd \(rq. +.TP +.B NOTE: +For the +.RB \(lq \-l \(rq +(labels), +.RB \(lq \-u \(rq +(units), and +.RB \(lq \-spu \(rq +(space units) options below, you can use a single unquoted period +.RB ( . ) +to signify an empty string. +This creates a convenient way to convey something that the shell doesn\(cqt +make it easy to convey. +Shell expansion weirdness also requires the use of +quotes +around the arguments to +.RB \(lq \-orig \(rq +(space origin), +.RB \(lq \-dirs \(rq +(space directions), and +.RB \(lq \-mf \(rq +(measurement frame). +.P +Uses various components of file and data IO, but currently there is no library +function that encapsulates the functionality here. +.SH OPTIONS +.TP +.IR @file \ ...\: +response file(s) containing command-line arguments +.TP +.B \-h +Generate header +.BR ONLY : +don\(cqt write out the whole +.IR nrrd , +don\(cqt even bother reading the input data, just output the detached +.I nrrd +header file (usually with a +.RB \(lq .nhdr \(rq +extension) determined by the options below. +The single constraint is that detached headers are incompatible with using +.BR stdin (3) +as the data source. +.TP +.B \-i\fR\ <\fIfile\fR\ ...>\ ,\ \fB\-\-input\fR\ <\fIfile\fR\ ...> +Filename(s) of data file(s); use +.RB \(lq \- \(rq +for +.BR stdin (3). +.BR OR , +can use +.BR sprintf (3)-style +format for identifying a range of numbered files, see above for details. +(1 or more +.IR string s); +default: +.RB \(lq \- \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type of data (e.g.\: +.RB \(lq uchar \(rq, +.RB \(lq int \(rq, +.RB \(lq float \(rq, +.RB \(lq double \(rq, +etc.) +.TP +.B \-s\fR\ <\fIsz0\fR\ \fIsz1\fR\ ...>\ ,\ \fB\-\-size\fR\ <\fIsz0\fR\ \fIsz1\fR\ ...> +number of samples along each axis (and implicit indicator of dimension of +.IR nrrd ) +(1 or more +.IR size_t s) +.TP +.B \-fd\fR\ <\fIdim\fR>\ ,\ \fB\-\-filedim\fR\ <\fIdim\fR> +When using +.B multiple +input data files (to +.RB \(lq \-i \(rq), +what is the dimension of the array data in each individual file. +By default (not using this option), this dimension is assumed to be one less +than the whole data dimension. +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq) +.TP +.B \-sp\fR\ <\fIsp0\fR\ \fIsp1\fR\ ...>\ ,\ \fB\-\-spacing\fR\ <\fIsp0\fR\ \fIsp1\fR\ ...> +spacing between samples on each axis. +Use +.RB \(lq nan \(rq +for any non-spatial axes (e.g. spacing between red, green, and blue along axis +0 of interleaved RGB image data) (1 or more +.IR double s) +.TP +.B \-th\fR\ <\fIth0\fR\ \fIth1\fR\ ...>\ ,\ \fB\-\-thickness\fR\ <\fIth0\fR\ \fIth1\fR\ ...> +thickness of region represented by one sample along each axis. +As with spacing, use +.RB \(lq nan \(rq +for any non-spatial axes. +(1 or more +.IR double s) +.TP +.B \-k\fR\ <\fIk0\fR\ \fIk1\fR\ ...>\ ,\ \fB\-\-kind\fR\ <\fIk0\fR\ \fIk1\fR\ ...> +what \(lqkind\(rq is each axis, from the +.I nrrdKind +.I airEnum +(e.g. +.BR space , +.BR time , +.BR 3-vector , +.BR 3D-masked-symmetric-matrix , +or +.RB \(lq none \(rq +to signify no kind) (1 or more +.IR string s) +.TP +.B \-cn\fR\ <\fIc0\fR\ \fIc1\fR\ ...>\ ,\ \fB\-\-centering\fR\ <\fIc0\fR\ \fIc1\fR\ ...> +kind of centering +.RB ( node +or +.RB cell ) +for each axis, or +.RB \(lq none \(rq +to signify no centering) (1 or more +.IR string s) +.TP +.B \-l\fR\ <\fIlb0\fR\ \fIlb1\fR\ ...>\ ,\ \fB\-\-label\fR\ <\fIlb0\fR\ \fIlb1\fR\ ...> +short string labels for each of the axes (1 or more +.IR string s) +.TP +.B \-u\fR\ <\fIun0\fR\ \fIun1\fR\ ...>\ ,\ \fB\-\-unit\fR\ <\fIun0\fR\ \fIun1\fR\ ...> +short strings giving units for each of the axes (1 or more +.TP +.B \-c\fR\ <\fIcontent\fR>\ ,\ \fB\-\-content\fR\ <\fIcontent\fR> +Specifies the content string of the +.IR nrrd , +which is built upon by many +.I nrrd +functions to record a history of operations +.RI ( string ) +.TP +.B \-ls\fR\ <\fInum\fR>\ ,\ \fB\-\-lineskip\fR\ <\fInum\fR> +number of ascii lines to skip before reading data +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-bs\fR\ <\fInum\fR>\ ,\ \fB\-\-byteskip\fR\ <\fInum\fR> +number of bytes to skip (after skipping ascii lines, if any) before reading +data. +Can use +.RB \(lq \-bs\ \-1 \(rq +to skip a binary header of unknown length in raw-encoded data +.RI ( long int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-e\fR\ <\fIenc\fR>\ ,\ \fB\-\-encoding\fR\ <\fIenc\fR> +encoding of input data. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq raw \(rq +raw encoding +.IP \(bu 2 +.RB \(lq ascii \(rq +ascii values, one scanline per line of text, values within line are delimited +by space, tab, or comma +.IP \(bu 2 +.RB \(lq hex \(rq +two hex digits per byte +.IP \(bu 2 +.RB \(lq gzip \(rq,\ \(lq gz \(rq +gzip compressed raw data +.IP \(bu 2 +.RB \(lq bzip2 \(rq,\ \(lq bz2 \(rq +bzip2 compressed raw data +.P +default: +.RB \(lq raw \(rq +.RE +.TP +.B \-kv\fR\ <\fIkey/val\fR\ ...>\ ,\ \fB\-\-keyvalue\fR\ <\fIkey/val\fR\ ...> +key/value string pairs to be stored in +.IR nrrd . +Each key/value pair must be a single string (put it in +.BR \(dq\(dq s +if the key or the value contain spaces). +The format of each pair is +.RI \(lq key\fB:=\fIvalue \(rq, +with no spaces before or after +.RB \(lq := \(rq. +(1 or more +.IR string s) +.TP +.B \-spc\fR\ <\fIspace\fR>\ ,\ \fB\-\-space\fR\ <\fIspace\fR> +identify the space (e.g.\: +.RB \(lq RAS \(rq, +.RB \(lq LPS \(rq) +in which the array conceptually lives, from the +.I nrrdSpace +.IR airEnum , +which in turn determines the dimension of the space. +Or, use an +.RB integer> 0 +to give the dimension of a space that +.I nrrdSpace +doesn\(cqt know about. +By default (not using this option), the enclosing space is set as unknown. +.RI ( string ) +.TP +.B \-orig\fR\ <\fIorigin\fR>\ ,\ \fB\-\-origin\fR\ <\fIorigin\fR> +.RB ( NOTE: +must quote vector) +the origin in space of the array: the location of the center of the first +sample, of the form +.RB \(lq (x,y,z) \(rq +(or however many coefficients are needed for the chosen space). +Quoting the vector is needed to stop interpretation from the shell +.RI ( string ) +.TP +.B \-dirs\fR\ <\fIv0\fR\ \fIv1\fR\ ...>\ ,\ \fB\-\-directions\fR\ <\fI\fIv0\fR\ \fIv1\fR\ ...> +.RB ( NOTE: +must quote whole vector list) +The \(lqspace directions\(rq: the vectors in space spanned by incrementing (by +one) each axis index (the column vectors of the index-to-world matrix +transform), +.BR OR , +.RB \(lq none \(rq +for non-spatial axes. +Give one vector per axis. +(Quoting around whole vector list, not individually, is needed because of +limitations in the parser) +.RI ( string ) +.TP +.B \-mf\fR\ <\fIv0\fR\ \fIv1\fR\ ...>\ ,\ \fB\-\-measurementframe\fR\ <\fI\fIv0\fR\ \fIv1\fR\ ...> +.RB ( NOTE: +must quote whole vector list) +Each vector is a +.I column +vector of the matrix which transforms from coordinates in measurement frame (in +which the coefficients of vectors and tensors are given) to coordinates of +world space (given with +.RB \(lq \-spc \(rq). +This is not a per-axis field: the column vectors comprise a +.IR D -by- D +square matrix, where +.I D +is the dimension of world space. +.RI ( string ) +.TP +.B \-spu\fR\ <\fIsu0\fR\ \fIsu1\fR\ ...>\ ,\ \fB\-\-spaceunit\fR\ <\fI\fIsu0\fR\ \fIsu1\fR\ ...> +short +.IR string s +giving units with which the coefficients of the space origin and direction +vectors are measured. +(1 or more +.IR string s) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output filename. +If +.RB \(lq \-h \(rq +has been used, the output file is always a detached header. +Otherwise, use extension +.RB \(lq .nrrd \(rq +to signal creation of self-contained +.IR nrrd , +and +.RB \(lq .nhdr \(rq +to signal creating of a detached header with (single) data file. +.RI ( string ); +default: +.RB \(lq \- \(rq +.TP +.B \-od\fR\ <\fIname\fR>\ ,\ \fB\-\-outputdata\fR\ <\fIname\fR> +when +.I not +using +.RB \(lq \-h \(rq +and saving to a +.RB \(lq .nhdr \(rq +file, using this option allows you to explicitly name the data file, instead of +(by default, not using this option) having it be the same filename base as the +header file. +.RI ( string ) +.SH "SEE\ ALSO" +.BR unu (1), +.BR sprintf (3) diff --git a/unu-minmax.1 b/unu-minmax.1 new file mode 100644 index 0000000..11f0533 --- /dev/null +++ b/unu-minmax.1 @@ -0,0 +1,49 @@ +.TH UNU\-MINMAX "1" "May 2021" "" "User Commands" +.SH NAME +unu\-minmax \- print out min and max values in one or more +.IR nrrd s +.SH SYNOPSIS +.B unu\ minmax +.BR \-blind8 +.RI < bool > +.RI < nin1 \ ...> +.SH DESCRIPTION +Print out min and max values in one or more +.IR nrrd s. +Unlike other commands, this doesn\(cqt produce a +.IRnrrd . +It only prints to standard out the min and max values found in the input +.IR nrrd (s), +and it also indicates if there are non-existent values. +.IP \(bu +2n +Uses +.B nrrdRangeNewSet +.SH OPTIONS +.TP +.B \-blind8\fR\ <\fIbool\fR> +whether to blindly assert the range of 8-bit data, without actually going +through the data values, i.e. +.I uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [\-128,127] . +Note that even if you do not use this option, the default +.RB ( false ) +is potentialy over-riding the effect of environment variable +.BR NRRD_STATE_BLIND_8_BIT_RANGE ; +see +.BR unu\-env (1) +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.RI < nin1 \ ...> +input +.IR nrrd (s) +(1 or more +.IR string s) +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-env (1) diff --git a/unu-mlut.1 b/unu-mlut.1 new file mode 100644 index 0000000..e4f0b8a --- /dev/null +++ b/unu-mlut.1 @@ -0,0 +1,115 @@ +.TH UNU\-MLUT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-mlut \- map +.I nrrd +through whole +.I nrrd +of univariate lookup tables +.SH SYNOPSIS +.B unu\ mlut +.BR \-m , \-\-map +.RI < mlut \ ...> +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through whole +.I nrrd +of univariate lookup tables, with one lookup table per element of input +.IR nrrd . +The multiple tables are stored in a +.I nrrd +with a dimension which is either 1 or 2 more than the dimension of the input +.IR nrrd , +resulting in an output which has either the same or one more dimension than the +input, resptectively. +.IP \(bu +2n +Uses +.B nrrdApplyMulti1DLut +.SH OPTIONS +.TP +.B \-m\fR\ <\fIlut\fR>\ ,\ \fB\-\-map\fR\ <\fIlut\fR> +one +.I nrrd +of lookup tables to map input +.I nrrd +through, or, list of +.IR nrrd s +which contain the individual entries of the lookup table at each voxel, which +will be joined together. +(1 or more +.IR nrrd s) +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the lut domain. +The lut domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the lut\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-lut (1) diff --git a/unu-mrmap.1 b/unu-mrmap.1 new file mode 100644 index 0000000..e5ddc68 --- /dev/null +++ b/unu-mrmap.1 @@ -0,0 +1,123 @@ +.TH UNU\-MRMAP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-mrmap \- map +.I nrrd +through whole +.I nrrd +of regular univariate maps +.SH SYNOPSIS +.B unu\ mrmap +.BR \-m , \-\-map +.RI < mmap \ ...> +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through whole +.I nrrd +of regular univariate maps, one map per sample in input. +The +.BI \(lq mmap \(rq +.I nrrd +has the same dimensional constraints as the +.BI \(lq mlut \(rq +.I nrrd +for +.BR unu\-mlut (1). +This functionality is a generalization of +.BR unu\-3op (1) \ lerp : +it allows you to lerp through multiple +.IR nrrd s, +instead of just two. +.IP \(bu +2n +Uses +.B nrrdApplyMulti1DRegMap +.SH OPTIONS +.TP +.B \-m\fR\ <\fImmap\fR>\ ,\ \fB\-\-map\fR\ <\fImmap\fR> +one +.I nrrd +of regular maps to map input +.I nrrd +through, or, list of +.IR nrrd s +which contain the individual entries of the map at each voxel, which will be +joined together. +(1 or more +.IR nrrd s) +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the map domain. +The map domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the map\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-rmap (1), +.BR unu\-mlut (1), +.BR unu\-3op (1) diff --git a/unu-pad.1 b/unu-pad.1 new file mode 100644 index 0000000..608c2fb --- /dev/null +++ b/unu-pad.1 @@ -0,0 +1,92 @@ +.TH UNU\-PAD "1" "August 2021" "" "User Commands" +.SH NAME +unu\-pad \- pad along each axis to make a bigger +.I nrrd +.SH SYNOPSIS +.B unu\ pad +.BR \-min , \-\-minimum +.RI < pos0 \ ...> +.BR \-max , \-\-maximum +.RI < pos0 \ ...> +.RB [ \-b , \-\-boundary +.RI < behavior >] +.RB [ \-v , \-\-value +.RI < val >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Pad along each axis to make a bigger +.IR nrrd . +.IP \(bu +2n +Uses +.B nrrdPad_nva +.SH OPTIONS +.TP +.B \-min\fR\ <\fIpos0\fR\ ...>\ ,\ \fB\-\-minimum\fR\ <\fIpos0\fR\ ...> +low corner of bounding box. +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0\-based index +.IP \(bu 2 +.BR M , +.BR M\+ <\fIint\fR>, +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.IP +(1 or more +.IR position s) +.TP +.B \-max\fR\ <\fIpos0\fR\ ...>\ ,\ \fB\-\-maximum\fR\ <\fIpos0\fR\ ...> +high corner of bounding box. +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0\-based index +.IP \(bu 2 +.BR M , +.BR M\+ <\fIint\fR>, +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.IP +(1 or more +.IR position s) +.TP +.B \-b\fR\ <\fIbehavior\fR>\ ,\ \fB\-\-boundary\fR\ <\fIbehavior\fR> +How to handle samples beyond the input bounds: +.RS +7n +.IP \(bu 2 +.RB \(lq pad \(rq: +use some specified value +.IP \(bu 2 +.RB \(lq bleed \(rq: +extend border values outward +.IP \(bu 2 +.RB \(lq mirror \(rq: +repeated reflections +.IP \(bu 2 +.RB \(lq wrap \(rq: +wrap-around to other side +.RE +.IP +default: +.RB \(lq bleed \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-permute.1 b/unu-permute.1 new file mode 100644 index 0000000..5a0eff6 --- /dev/null +++ b/unu-permute.1 @@ -0,0 +1,38 @@ +.TH UNU\-PERMUTE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-permute \- permute ordering of axes +.SH SYNOPSIS +.B unu\ permute +.BR \-p , \-\-permute +.RI < ax0 \ ax1 \ ...> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Permute ordering of axes. +The permutation gives the new ordering of the old axes (in 0-based numbering). +For example, the permutation 0->1, 1->2, 2->0 would be +.RB \(lq 2\ 0\ 1 \(rq. +.IP \(bu +2n +Uses +.B nrrdAxesPermute +.SH OPTIONS +.TP +.B \-p\fR\ <\fIax0\fR \fIax1\fR\ ...>\ ,\ \fB\-\-permute\fR\ <\fIax0\fR \fIax1\fR\ ...> +new axis ordering +(1 or more +.IR unsigned\ int s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-project.1 b/unu-project.1 new file mode 100644 index 0000000..a246329 --- /dev/null +++ b/unu-project.1 @@ -0,0 +1,103 @@ +.TH UNU\-PROJECT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-project \- collapse scanlines to scalars along some axis +.SH SYNOPSIS +.B unu\ project +.BR \-a , \-\-axis +.RI < axis > +.BR \-m , \-\-measure +.RI < measr > +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Collapse scanlines to scalars along some axis. +The scanline is reduced to a single scalar by \(lqmeasuring\(rq all the values +in the scanline with some measure. +The output +.I nrrd +has dimension one less than input (except when the input is itself 1\-D); the +output type depends on the measure in a non-trivial way, or it can be set +explicitly with the +.RB \(lq \-t \(rq +option. +.IP \(bu +2n +Uses +.B nrrdProject +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to project along +.RI ( unsigned\ int ) +.TP +.B \-m\fR\ <\fImeasr\fR>\ ,\ \fB\-\-measure\fR\ <\fImeasr\fR> +How to \(lqmeasure\(rq a scanline, by summarizing all its values with a single +scalar. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq min \(rq, +.RB \(lq max \(rq, +.RB \(lq mean \(rq, +.RB \(lq median \(rq, +.RB \(lq mode \(rq, +.RB \(lq variance \(rq, +.RB \(lq skew \(rq: +(self-explanatory) +.IP \(bu 2 +.RB \(lq intc \(rq, +.RB \(lq slope \(rq, +.RB \(lq error \(rq: +intercept, slope, and error from line fitting +.IP \(bu 2 +.RB \(lq stdv \(rq: +standard deviation +.IP \(bu 2 +.RB \(lq cov \(rq: +coefficient of variation +.IP \(bu 2 +.RB \(lq product \(rq, +.RB \(lq sum \(rq: +product or sum of all values +.IP \(bu 2 +.RB \(lq L1 \(rq, +.RB \(lq L2 \(rq, +.RB \(lq NL2 \(rq, +.RB \(lq RMS \(rq, +.RB \(lq Linf \(rq: +different norms +.IP \(bu 2 +.RB \(lq histo-min \(rq, +.RB \(lq histo-max \(rq, +.RB \(lq histo-mean \(rq, +.RB \(lq histo-median \(rq, +.RB \(lq histo-mode \(rq, +.RB \(lq histo-product \(rq, +.RB \(lq histo-l2 \(rq, +.RB \(lq histo-sum \(rq, +.RB \(lq histo-variance \(rq, +.RB \(lq histo-sd \(rq: +same measures, but for situations where we\(cqre given not the original values, +but a histogram of them. +.RE +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +type to use for output. +By default (not using this option), the output type is determined +auto-magically. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-quantize.1 b/unu-quantize.1 new file mode 100644 index 0000000..4686f3e --- /dev/null +++ b/unu-quantize.1 @@ -0,0 +1,135 @@ +.TH UNU\-QUANTIZE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-quantize \- quantize values to 8, 16, or 32 bits +.SH SYNOPSIS +.B unu\ quantize +.BR \-b , \-\-bits +.RI < bits > +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-hb , \-\-bins +.RI < bins >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Quantize values to 8, 16, or 32 bits. +Input values can be fixed point (e.g. quantizing ushorts down to uchars) or +floating point. +Values are clamped to the min and max before they are quantized, so there is no +risk of getting +.B 255 +where you expect +.B 0 +(with +.I unsigned char +output, for example). +The min and max can be specified explicitly (as a regular number), or in terms +of percentiles (a number suffixed with +.RB \(lq % \(rq, +no space in between). +This does only linear quantization. +See also +.BR unu\-convert (1), +.BR unu\-2op (1) \ x , +and +.BR unu\-3op (1) \ clamp . +.IP \(bu +2n +Uses +.B nrrdQuantize +.SH OPTIONS +.TP +.B \-b\fR\ <\fIbits\fR>\ ,\ \fB\-\-bits\fR\ <\fIbits\fR> +Number of bits to quantize down to; determines the type of the output +.IR nrrd : +.RS +7n +.IP \(bu 2 +.RB \(lq 8 \(rq: +.I unsigned char +.IP \(bu 2 +.RB \(lq 16 \(rq: +.I unsigned short +.IP \(bu 2 +.RB \(lq 32 \(rq: +.I unsigned int +.RE +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +The value to map to zero, given explicitly as a regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this minimum is specified in terms of the percentage of samples in +input that are lower. +.RB \(lq 0% \(rq +means the lowest input value is used, +.RB \(lq 1% \(rq +means that the 1% of the lowest values are all mapped to zero. +By default (not using this option), the lowest input value is used. +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +The value to map to the highest unsigned integral value, given explicitly as a +regular number, +.BR or , +if the number is given with a +.RB \(lq % \(rq +suffix, this maximum is specified in terms of the percentage of samples in +input that are higher. +.RB \(lq 0% \(rq +means the highest input value is used, which is also the default behavior (same +as not using this option). +.RI ( string ); +default: +.RB \(lq nan \(rq +.TP +.B \-hb\fR\ <\fIbins\fR>\ ,\ \fB\-\-bins\fR\ <\fIbins\fR> +number of bins in histogram of values, for determining min or max by +percentiles. +This has to be large enough so that any errant very high or very low values do +not compress the interesting part of the histogram to an inscrutably small +number of bins. +.RI ( unsigned\ int ); +default: +.RB \(lq 5000 \(rq +.TP +.B \-blind8\fR\ <\fIbins\fR> +if not using +.RB \(lq \-min \(rq +or +.RB \(lq \-max \(rq, +whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed char +is +.BR [-128,127] ) +.RI ( bool ); +default: +.RB \(lq true \(rq, +"true" +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-unquantize (1), +.BR unu\-convert (1), +.BR unu\-2op (1) \ x , +.BR unu\-3op (1) \ clamp diff --git a/unu-resample.1 b/unu-resample.1 new file mode 100644 index 0000000..e08f625 --- /dev/null +++ b/unu-resample.1 @@ -0,0 +1,344 @@ +.TH UNU\-RESAMPLE "1" "May 2021" "" "User Commands" +.SH NAME +unu\-resample \- filtering and {up,down}sampling with a separable kernel +.SH SYNOPSIS +.B unu\ resample +.RB [ \-old ] +.BR \-s , \-\-size +.RI < sz0 \ ...> +.RB [ \-off , \-\-offset +.RI [< off0 \ ...>]] +.RB [ \-min , \-\-minimum +.RI [< min0 \ ...>]] +.RB [ \-max , \-\-maximum +.RI [< max0 \ ...>]] +.RB [ \-k , \-\-kernel +.RI < kern \ ...>] +.RB [ \-nrn ] +.RB [ \-ne , \-\-nonexistent +.RI < behavior >] +.RB [ \-b , \-\-boundary +.RI < behavior >] +.RB [ \-v , \-\-value +.RI < value >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-cheap ] +.RB [ \-c , \-\-center +.RI < center >] +.RB [ \-co , \-\-center\-override ] +.RB [ \-verbose +.RI < v >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Filtering and {up,down}sampling with a separable kernel. +Simplifies access to the +.B NrrdResampleContext +functions by assuming (among other things) that the same kernel is used for +resampling every axis that is being resampled. +Only required option is +.RB \(lq \-s \(rq +to specify which axes to resample and how many output samples to generate. +Resampling kernel +.RB \(lq \-k \(rq +defaults to an interpolating cubic, but many other choices are available. +By default, resampling an axis resamples the full extent of its samples, but it +is possible to offset this range via +.RB \(lq \-off \(rq, +or to crop and/or pad via +.RB \(lq \-min \(rq +and +.RB \(lq \-max \(rq. +The resampling respects the difference between cell- and node-centered data, +but you can over-ride known centering with +.RB \(lq \-co \(rq. +.IP \(bu +2n +Uses the many +.B nrrdResample* +functions operating on a +.B nrrdResampleContext +.SH OPTIONS +.TP +.B \-old +instead of using the new +.B nrrdResampleContext +implementation, use the old +.B nrrdSpatialResample +implementation +.TP +.B \-s\fR\ <\fIsz0\fR\ ...>\ ,\ \fB\-\-size\fR\ <\fIsz0\fR\ ...> +For each axis, information about how many samples in output: +.RS +7n +.IP \(bu 2 +.RB \(lq = \(rq: +leave this axis completely untouched: no resampling whatsoever +.IP \(bu 2 +.RB \(lq x\fIfloat \(rq: +multiply the number of input samples by +.IR float , +and round to the nearest integer, to get the number of output samples. +Use +.RB \(lq x1 \(rq +to resample the axis but leave the number of samples unchanged +.IP \(bu 2 +.RB \(lq /\fIfloat \(rq: +divide number of input samples by +.I float +.IP \(bu 2 +.RB \(lq +=\fIuint \(rq, +.RB \(lq \-=\fIuint \(rq: +add +.I uint +to or subtract +.I uint +from number input samples to get number output samples +.IP \(bu 2 +.RI \(lq uint \(rq: +exact number of output samples +.IP \(bu 2 +.RI \(lq a \(rq: +resample this axis to whatever number of samples preserves the aspect ratio of +other resampled axes. +Currently needs to be used on all but one of the resampled axes, if at all. +.RE +.IP +(1 or more sampling specifications) +.TP +.B \-off\fR\ [<\fIoff0\fR\ ...>]\ ,\ \fB\-\-offset\fR\ [<\fIoff0\fR\ ...>] +For each axis, an offset or shift to the position (in index space) of the lower +end of the sampling domain. +Either +.B \-off +can be used, or +.B \-min +and +.B \-max +together, or none of these (so that, by default, the full domain of the axis is +resampled). +(0 or more +.IR double s); +default: \(lq\(rq +.TP +.B \-min\fR\ [<\fImin0\fR\ ...>]\ ,\ \fB\-\-minimum\fR\ [<\fImin0\fR\ ...>] +For each axis, the lower end (in index space) of the domain of the resampling. +Either +.B \-off +can be used, or +.B \-min +and +.B \-max +together, or none of these (so that, by default, the full domain of the axis is +resampled). +(0 or more +.IR double s); +default: \(lq\(rq +.TP +.B \-max\fR\ [<\fImax0\fR\ ...>]\ ,\ \fB\-\-maximum\fR\ [<\fImax0\fR\ ...>] +For each axis, the upper end (in index space) of the domain of the resampling. +Either +.B \-off +can be used, or +.B \-max +and +.B \-max +together, or none of these (so that, by default, the full domain of the axis is +resampled). +(0 or more +.IR double s); +default: \(lq\(rq +.TP +.B \-k\fR\ <\fIkern\fR>\ , \fB\-\-kernel\fR\ <\fIkern\fR> +The kernel to use for resampling. +Kernels logically live in the input index space for upsampling, and in the +output index space for downsampling. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq box \(rq: +nearest neighbor interpolation on upsampling, and uniform averaging on +downsampling +.IP \(bu 2 +.RB \(lq cheap \(rq: +nearest neighbor interpolation for upsampling, and non-blurring sub-sampling +(pick subset of input samples) on downsampling +.IP \(bu 2 +.RB \(lq tent \(rq: +linear interpolation +.IP \(bu 2 +.RB \(lq cubic:\fIB\fR,\fIC \(rq: +Mitchell/Netravali BC-family of cubics: +.IP +.RB \(lq cubic:1,0 \(rq: +B-spline; maximal blurring +.IP +.RB \(lq cubic:0,0.5 \(rq: +Catmull-Rom; good interpolating kernel +.IP \(bu 2 +.RB \(lq c4h \(rq: +6-sample-support, C^4 continuous, accurate +.IP \(bu 2 +.RB \(lq c4hai \(rq: +discrete pre-filter to make +.B c4h +interpolate +.IP \(bu 2 +.RB \(lq bspl3 \(rq, +.RB \(lq bspl5 \(rq, +.RB \(lq bspl7 \(rq: +cubic (same as +.BR cubic:1,0 ), +quintic, and 7th order B-spline +.IP \(bu 2 +.RB \(lq bspl3ai \(rq, +.RB \(lq bspl5ai \(rq, +.RB \(lq bspl7ai \(rq: +discrete pre-filters to make +.BR bspl3 , +.BR bspl5 , +.B bspl7 +interpolate +.IP \(bu 2 +.RB \(lq hann:\fIR \(rq: +Hann (cosine bell) windowed sinc, radius +.I R +.IP \(bu 2 +.RB \(lq black:\fIR \(rq: +Blackman windowed sinc, radius +.I R +.IP \(bu 2 +.RB \(lq gauss:\fIS\fB,\fIC \(rq: +Gaussian blurring, with standard deviation +.I S +and cut-off at +.I C +standard deviations +.IP \(bu 2 +.RB \(lq dgauss:\fIS\fB,\fIC \(rq: +Lindeberg\(cqs discrete Gaussian. +.RE +.IP +default: +.RB \(lq cubic:0,0.5 \(rq +.TP +.B \-nrn +do NOT do per-pass kernel weight renormalization. +Doing the renormalization is not a performance hit (hence is enabled by +default), and the renormalization is sometimes needed to avoid \(lqgrating\(rq +on non-integral down-sampling. +Disabling the renormalization is needed for correct results with artificially +narrow kernels. +.TP +.B \-ne\fR\ <\fIbehavior\fR>\ , \fB\-\-nonexistent\fR\ <\fIbehavior\fR> +When resampling floating-point values, how to handle non-existent values within +kernel support: +.RS +7n +.IP \(bu 2 +.RB \(lq noop \(rq: +do nothing; let them pollute result +.IP \(bu 2 +.RB \(lq renorm \(rq: +ignore them and renormalize weights of existent values +.IP \(bu 2 +.RB \(lq wght \(rq: +ignore them and simply use weights of existent values +.RE +.IP +default: +.RB \(lq noop \(rq +.TP +.B \-b\fR\ <\fIbehavior\fR>\ , \fB\-\-boundary\fR\ <\fIbehavior\fR> +How to handle samples beyond the input bounds: +.RS +7n +.IP \(bu 2 +.RB \(lq pad \(rq: +use some specified value +.IP \(bu 2 +.RB \(lq bleed \(rq: +extend border values outward +.IP \(bu 2 +.RB \(lq mirror \(rq: +repeated reflections +.IP \(bu 2 +.RB \(lq wrap \(rq: +wrap-around to other side +.RE +.IP +default: +.RB \(lq noop \(rq +.TP +.B \-v\fR\ <\fIvalue\fR>\ , \fB\-\-value\fR\ <\fIvalue\fR> +for +.RB \(lq pad \(rq +boundary behavior, pad with this value +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ , \fB\-\-type\fR\ <\fItype\fR> +type to save output as. +By default (not using this option), the output type is the same as the input +type; default: +.RB \(lq default \(rq +.TP +.B \-cheap +.RI [ DEPRECATED : +the +.RB \(lq \-k\ cheap \(rq +option is the new (and more reliable) way to access this functionality. +.RB \(lq \-cheap \(rq +is only here for legacy use in combination with +.RB \(lq \-old \(rq.] +.IP +When downsampling (reducing number of samples), don\(cqt try to do correct +filtering by scaling kernel to match new (stretched) index space; keep it in +old index space. +When used in conjunction with +.RB \(lq \-k\ box \(rq, +this can implement subsampling which chooses every Nth value. +.TP +.B \-c\fR\ <\fIcenter\fR>\ , \fB\-\-center\fR\ <\fIcenter\fR> +(not available with +.RB \(lq \-old \(rq) +default centering of axes when input +.I nrrd +axes don\(cqt have a known centering: +.RB \(lq cell \(rq +or +.RB \(lq node \(rq; +default: +.RB \(lq cell \(rq +.TP +.B \-co\fR\ , \fB\-\-center-override +(not available with +.RB \(lq \-old \(rq) +centering info specified via +.RB \(lq \-c \(rq +should +.B over-ride +known centering, rather than simply be used when centering is unknown. +.TP +.B \-verbose\fR\ <\fIv\fR> +(not available with +.RB \(lq \-old \(rq) +verbosity level +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-i\fR\ <\fInin\fR>\ , \fB\-\-input\fR\ <\fInin\fR> +input +.IR nrrd ; +default: +.RB \(lq \- \(rq +.TP +.B \-o\fR\ <\fInout\fR>\ , \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-reshape.1 b/unu-reshape.1 new file mode 100644 index 0000000..f9660dd --- /dev/null +++ b/unu-reshape.1 @@ -0,0 +1,40 @@ +.TH UNU\-RESHAPE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-reshape \- superficially change dimension and/or axes sizes +.SH SYNOPSIS +.B unu\ reshape +.BR \-s , \-\-size +.RI < sz0 \ sz1 \ ...> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Superficially change dimension and/or axes sizes. +The underlying linear ordering of the samples is unchanged, but the reported +dimension or axes sizes are changed. +Identical in concept to Matlab\(cqs +.RB \(lq reshape \(rq +command. +.IP \(bu +2n +Uses +.B nrrdReshape_nva +.SH OPTIONS +.TP +.B \-s\fR\ <\fIsz0\fR \fIsz1\fR\ ...>\ ,\ \fB\-\-size\fR\ <\fI\fIsz0\fR \fIsz1\fR\ ...> +new axes sizes +(1 or more +.IR size_t s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-rmap.1 b/unu-rmap.1 new file mode 100644 index 0000000..ab2a69c --- /dev/null +++ b/unu-rmap.1 @@ -0,0 +1,119 @@ +.TH UNU\-RMAP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-rmap \- map +.I nrrd +through one +.B regular +univariate map (\(lqcolormap\(rq) +.SH SYNOPSIS +.B unu\ rmap +.BR \-m , \-\-map +.RI < map > +.RB [ \-r , \-\-rescale ] +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-blind8 +.RI < bool >] +.RB [ \-t , \-\-type +.RI < type >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through one +.B regular +univariate map (\(lqcolormap\(rq). +A map is regular if the control points are evenly spaced along the domain, and +hence their position isn\(cqt explicitly represented in the map; the axis +.IR min , +axis +.IR max , +and number of points determine their location. +The map can be a 1D +.I nrrd +(for \(lqgrayscale\(rq), in which case the output has the same dimension as the +input, or a 2D +.I nrrd +(for \(lqcolor\(rq), in which case the output has one more dimension than the +input. +In either case, the output is the result of linearly interpolating between map +points, either scalar values (\(lqgrayscale\(rq), or scanlines along axis +.B 0 +(\(lqcolor\(rq). +.IP \(bu +2n +Uses +.B nrrdApply1DRegMap +.SH OPTIONS +.TP +.B \-m\fR\ <\fImap\fR>\ ,\ \fB\-\-map\fR\ <\fImap\fR> +regular map to map input +.I nrrd +through +.TP +.B \-r\fR ,\ \fB\-\-rescale +rescale the input values from the input range to the map domain. +The map domain is either explicitly defined by the axis +.IR min , max +along axis +.B 0 +or +.BR 1 , +or, it is implicitly defined as zero to the length of that axis minus one. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Low end of input range. +Defaults to lowest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +High end of input range. +Defaults to highest value found in input +.IR nrrd . +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( double ) +.TP +.B \-blind8\fR\ <\fIbool\fR> +Whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed\ char +is +.BR [-128,127] ). +Explicitly setting this is useful only with rescaling +.RB (\(lq \-r \(rq) +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-t\fR\ <\fItype\fR>\ ,\ \fB\-\-type\fR\ <\fItype\fR> +specify the type +.RB (\(lq int \(rq, +.RB \(lq float \(rq, +etc.) of the output +.IR nrrd . +By default (not using this option), the output type is the map\(cqs type. +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-mrmap (1), +.BR unu\-imap (1) diff --git a/unu-save.1 b/unu-save.1 new file mode 100644 index 0000000..ac0d8f8 --- /dev/null +++ b/unu-save.1 @@ -0,0 +1,150 @@ +.TH UNU\-SAVE +.SH NAME +unu\-save \- write +.I nrrd +with specific format, encoding, or endianness +.SH SYNOPSIS +.B unu\ save +.BR \-f , \-\-format +.RI < form > +.RB [ \-e , \-\-encoding +.RI < enc >] +.RB [ \-en , \-\-endian +.RI < end >] +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.RB [ \-od , \-\-ouputdata +.RI < name >] +.SH DESCRIPTION +Write +.I nrrd +with specific format, encoding, or endianness. +Use +.in +4n +.EX +.B unu\ save\ \-f\ pnm\ |\ xv\ \- +.EE +.in +to view PPM- or PGM-compatible +.IR nrrd s on unix. +EPS output is a EPSF\-3.0 file with +.B BoundingBox +and +.B HiResBoundingBox +DSC comments, and is suitable for inclusion into other PostScript documents. +As a stand-alone file, the image is conveniently centered on an 8.5x11 inch +page, with 0.5 inch margins. +.IP \(bu +2n +Uses various fields in the +.B NrrdIOState +passed to +.B nrrdSave +.SH OPTIONS +.TP +.B \-f\fR\ <\fIform\fR>\ ,\ \fB\-\-format\fR\ <\fIform\fR> +output file format. +Possibilities include: +.RS +7n +.IP \(bu +2n +.RB \(lq nrrd \(rq: +standard +.I nrrd +format +.IP \(bu +2n +.RB \(lq pnm \(rq: +PNM image; PPM for color, PGM for grayscale +.IP \(bu +2n +.RB \(lq text \(rq: +plain ASCII text for 1\-D and 2\-D data +.IP \(bu +2n +.RB \(lq vtk \(rq: +VTK +.RB \(lq STRUCTURED_POINTS \(rq +dataset +.IP \(bu +2n +.RB \(lq png \(rq: +PNG image +.IP \(bu +2n +.RB \(lq eps \(rq: +EPS file +.RE +.TP +.B \-e\fR\ <\fIenc\fR>\ ,\ \fB\-\-encoding\fR\ <\fIenc\fR> +encoding of data in file. +Not all encodings are supported in a given format. +Possibilities include: +.RS +7n +.IP \(bu +2n +.RB \(lq raw \(rq: +raw encoding +.IP \(bu +2n +.RB \(lq ascii \(rq: +print data in ascii +.IP \(bu +2n +.RB \(lq hex \(rq: +two hex digits per byte +.IP \(bu +2n +.RB \(lq gzip \(rq,\ \(lq gz \(rq: +gzip compressed raw data +.IP \(bu +2n +.RB \(lq bzip2 \(rq,\ \(lq bz2 \(rq: +bzip2 compressed raw data +.P +The specifiers for compressions may be followed by a colon +.RB \(lq : \(rq, +followed by an optional digit giving compression \(lqlevel\(rq (for +.BR gzip ) +or \(lqblock size\(rq (for +.BR bzip2 ). +For +.BR gzip , +this can be followed by an optional character for a compression strategy: +.IP \(bu +2n +.RB \(lq d \(rq: +default, Huffman with string match +.IP \(bu +2n +.RB \(lq h \(rq: +Huffman alone +.IP \(bu +2n +.RB \(lq f \(rq: +specialized for filtered data +.P +For example, +.RB \(lq gz \(rq, +.RB \(lq gz:9 \(rq, +.RB \(lq gz:9f \(rq +are all valid +.RE +.TP +.B \-en\fR\ <\fIend\fR>\ ,\ \fB\-\-endian\fR\ <\fIend\fR> +Endianness to save data out as; +.RB \(lq little \(rq +for Intel and friends; +.RB \(lq big \(rq +for everyone else. +Defaults to endianness of this machine +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.TP +.B \-od\fR\ <\fIname\fR>\ ,\ \fB\-\-ouputdata\fR\ <\fIname\fR> +when saving to a +.RB \(lq .nhdr \(rq +file, this option allows you to explicitly name the data file, instead of (by +default, not using this option) having it be the same filename base as the +header file. +.RI ( string ) +.SH "SEE\ ALSO" +.BR unu (1) +.P +http://www.trilon.com/xv/ diff --git a/unu-shuffle.1 b/unu-shuffle.1 new file mode 100644 index 0000000..b2bd05e --- /dev/null +++ b/unu-shuffle.1 @@ -0,0 +1,57 @@ +.TH UNU\-SHUFFLE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-shuffle \- permute slices along one axis +.SH SYNOPSIS +.B unu\ shuffle +.RI [ @file \ ...] +.BR \-p , \-\-permute +.RI < slc0 \ slc1 \ ...> +.RB [ \-inv , \-\-inverse ] +.BR \-a , \-\-axis +.RI < axis > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Permute slices along one axis. +Slices along one axis are re-arranged as units according to the given +permutation (or its inverse). +The permutation tells which old slice to put at each new position. +For example, the shuffle 0->1, 1->2, 2->0 would be +.RB \(lq 2\ 0\ 1 \(rq. +Obviously, if you have to rearrange the many slices of a large dataset, you +should probably store the permutation in a plain text file and use it as a +\(lqresponse file\rq). +.IP \(bu +2n +Uses +.B nrrdShuffle +.SH OPTIONS +.TP +.IR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-p\fR\ <\fIslc0\fR\ \fIslc1\fR\ ...>\ ,\ \fB\-\-permute\fR\ <\fIslc0\fR\ \fIslc1\fR\ ...> +new slice ordering (1 or more +.IR unsigned\ int s) +.TP +.B \-inv\fR\ ,\ \fB\-\-inverse +use inverse of given permutation +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to shuffle along +.RI ( unsigned\ int ) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-flip (1) diff --git a/unu-slice.1 b/unu-slice.1 new file mode 100644 index 0000000..fd6a2de --- /dev/null +++ b/unu-slice.1 @@ -0,0 +1,66 @@ +.TH UNU\-SLICE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-slice \- slice along one or more axes at given positions +.SH SYNOPSIS +.B unu\ slice +.BR \-a , \-\-axis +.RI < axis \ ...> +.BR \-p , \-\-position +.RI < pos \ ...> +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Slice along one or more axes at given positions. +Output +.I nrrd +dimension is less than input +.I nrrd +dimension by the number of slice axes (except when the input is or gets down to +1\-D). +Can slice on all axes in order to sample a single value from the array. +Per-axis information is preserved. +.IP \(bu +2n +Uses +.B nrrdSlice +(possibly called multiple times) +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR\ ...>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR\ ...> +single axis or multiple axes to slice along. +Giving multiple axes here leads to doing multiple slices (at the corresponding +positions given with +.RB \(lq \-p \(rq. +Multiple axes should be identified in terms of the axis numbering of the +original +.IR nrrd ; +as the slices are done (in the given ordering) the actual slice axis will be +different if previous slices were on lower-numbered (faster) axes. +(1 or more +.IR unsigned\ ints ) +.TP +.B \-p\fR\ <\fIpos\fR>\ ,\ \fB\-\-position\fR\ <\fIpos\fR> +position(s) to slice at: +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0-based index +.IP \(bu 2 +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-splice.1 b/unu-splice.1 new file mode 100644 index 0000000..86d0ca5 --- /dev/null +++ b/unu-splice.1 @@ -0,0 +1,56 @@ +.TH UNU\-SPLICE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-splice \- replace a slice with a different \fInrrd +.SH SYNOPSIS +.B unu\ splice +.BR \-a , \-\-axis +.RI < axis > +.BR \-p , \-\-position +.RI < pos > +.BR \-s , \-\-slice +.RI < nslice > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Replace a slice with a different +.IR nrrd . +This is functionally the opposite of +.RB \(lq slice \(rq. +.IP \(bu +2n +Uses +.B nrrdSplice +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to splice along +.RI ( unsigned\ int ) +.TP +.B \-p\fR\ <\fIpos\fR>\ ,\ \fB\-\-position\fR\ <\fIpos\fR> +position to splice at: +.RS +7n +.IP \(bu 2 +.RI < int > +gives 0-based index +.IP \(bu 2 +.BR M\- <\fIint\fR> +give index relative to the last sample on the axis +.RB ( M== \fI#samples \-1 ). +.RE +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.IR nrrd . +This is the slice to insert into +.I nin +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- (rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-slice (1) diff --git a/unu-sselect.1 b/unu-sselect.1 new file mode 100644 index 0000000..84e21ff --- /dev/null +++ b/unu-sselect.1 @@ -0,0 +1,52 @@ +.TH UNU\-SSELECT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-sselect \- select subset of slices along an axis +.SH SYNOPSIS +.B unu\ sselect +.RB [ \-i , \-\-input +.RI < nin >] +.BR \-a , \-\-axis +.RI < axis > +.BR \-s , \-\-selector +.RI < nline > +.BR \-th +.RI < thresh > +.RB [ \-o , \-\-output +.RI < above \ below >] +.SH DESCRIPTION +Select subset of slices along an axis. +The choice to keep or nix a slice is determined by whether the values in a +given 1\-D line of values is above or below a given threshold. +.IP \(bu +2n +Uses +.B nrrdSliceSelect +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-a\fR\ <\fIaxis\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxis\fR> +axis to slice along +.RI ( unsigned\ int ) +.TP +.B \-s\fR\ <\fInline\fR>\ ,\ \fB\-\-selector\fR\ <\fInline\fR> +the 1\-D +.I nrrd +of values to compare with threshold +.TP +.B \-th\fR\ <\fIthresh\fR> +threshold on selector line +.RI ( double ) +.TP +.B \-o\fR\ <\fIabove\fR\ \fIbelow\fR>\ ,\ \fB\-\-output\fR\ <\fIabove\fR\ \fIbelow\fR> +outputs for slices corresponding to values above (first) and below (second) given threshold. +Use +.RB \(lq x \(rq +to say that no output is desired. +(2 +.IR string s); +default: +.RB \(lq \-\ x \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-subst.1 b/unu-subst.1 new file mode 100644 index 0000000..20e639a --- /dev/null +++ b/unu-subst.1 @@ -0,0 +1,55 @@ +.TH UNU\-SUBST "1" "August 2021" "" "User Commands" +.SH NAME +unu\-subst \- map +.I nrrd +through one univariate substitution table +.SH SYNOPSIS +.B unu\ subst +.BR \-s , \-\-subst +.RI < subst > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Map +.I nrrd +through one univariate substitution table (itself represented as a +.IR nrrd ). +The substitution table is a +.RI 2\-by\- N +table: a list of pairs giving the old value (to replace) and the the new value +(to change to), in that order. +A plain text file makes this easy. +Unlike with +.BR unu\-lut (1), +.BR unu\-rmap (1), +and +.BR unu\-imap (1), +the output type is the same as the input type, rather than the type of the lut +or map. +.IP \(bu +2n +Uses +.B nrrdApply1DSubstitution +.SH OPTIONS +.TP +.B \-s\fR\ <\fIsubst\fR>\ ,\ \fB\-\-subst\fR\ <\fIsubst\fR> +substitution table to map input +.I nrrd +through +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-lut (1), +.BR unu\-rmap (1), +.BR unu\-imap (1) diff --git a/unu-swap.1 b/unu-swap.1 new file mode 100644 index 0000000..0189d7f --- /dev/null +++ b/unu-swap.1 @@ -0,0 +1,36 @@ +.TH UNU\-SWAP "1" "August 2021" "" "User Commands" +.SH NAME +unu\-swap \- interchange ordering of two axes +.SH SYNOPSIS +.B unu\ swap +.BR \-a , \-\-axis +.RI < axisA \ axisB > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Interchange ordering of two axes. Special case of +.BR unu\-permute (1). +.IP \(bu +2n +Uses +.B nrrdAxesSwap +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxisA\fR\ \fIaxisB\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxisA\fR\ \fIaxisB\fR> +the two axes to switch (0-based numbering) (2 +.IR unsigned\ int s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-permute (1) diff --git a/unu-tile.1 b/unu-tile.1 new file mode 100644 index 0000000..7346ecc --- /dev/null +++ b/unu-tile.1 @@ -0,0 +1,57 @@ +.TH UNU\-TILE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-tile \- tile slices of one axis into two other axes +.SH SYNOPSIS +.B unu\ tile +.BR \-a , \-\-axis +.RI < axSplit \ ax0 \ ax1 > +.BR \-s , \-\-size +.RI < fast \ slow > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Tile slices of one axis into two other axes. +Tiling an array means splitting one axis into fast and slow parts, and then +interleaving those parts into other (existing) axes by doing two axis merges, +which combine an existing axis with part of the split axis. +This reduces the dimension by one. +The three axis arguments all identify axes in the input array as is. +This provides, for example, a simple way of viewing the 128 slices along the +slow axis of a 3\-D volume as a 16x8 tiled array of 2\-D slices, as with +.RB \(lq \-a\ 2\ 0\ 1\ \-s\ 16\ 8 \(rq. +.IP \(bu +2n +Uses +.B nrrdTile2D +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxSplit\fR\ \fIax0\fR\ \fIax1\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxSplit\fR\ \fIax0\fR\ \fIax1\fR> +.I axSplit +is divided and merged with +.I ax0 +and +.I ax1 +(3 +.IR unsigned\ int s) +.TP +.B \-s\fR\ <\fIfast\fR\ \fIslow\fR>\ ,\ \fB\-\-size\fR\ <\fIfast\fR\ \fIslow\fR> +fast and slow axis sizes to produce as result of splitting the +.I axSplit + axis. +(2 +.IR size_t s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-untile (1) diff --git a/unu-unorient.1 b/unu-unorient.1 new file mode 100644 index 0000000..7a078db --- /dev/null +++ b/unu-unorient.1 @@ -0,0 +1,38 @@ +.TH UNU\-UNORIENT "1" "August 2021" "" "User Commands" +.SH NAME +unu\-unorient \- make image orientation be axis-aligned +.SH SYNOPSIS +.B unu\ unorient +.BR \-i , \-\-input +.RI < nin > +.RB [ \-smfo ] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Make image orientation be axis-aligned. +Does various tricks. +.IP \(bu +2n +Uses +.B nrrdOrientationReduce +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +(sorry, can’t use usual default of +.RB \(lq \- \(rq +for +.I stdin +because of hest quirk) +.TP +.B \-smfo +set some axis mins based on space origin (hack) +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu-unquantize.1 b/unu-unquantize.1 new file mode 100644 index 0000000..9c81558 --- /dev/null +++ b/unu-unquantize.1 @@ -0,0 +1,83 @@ +.TH UNU\-UNQUANTIZE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-unquantize \- recover floating point values from quantized data +.SH SYNOPSIS +.B unu\ unquantize +.BR \-i , \-\-input +.RI < nin > +.RB [ \-min , \-\-minimum +.RI < value >] +.RB [ \-max , \-\-maximum +.RI < value >] +.RB [ \-double ] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Recover floating point values from quantized data. +Uses the +.B oldMin +and +.B oldMax +fields in the +.I nrrd +of quantized values to regenerate approximate versions of the original +unquantized values. +Can also override these with +.RB \(lq \-min \(rq +and +.RB \(lq \-max \(rq. +.IP \(bu +2n +Uses +.B nrrdUnquantize +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.IR nrrd . +That this argument is required instead of optional, as with most +.BR unu (1) +commands, is a quirk caused by the need to have +.BR unu\-unquantize (1) +generate usage info, combined with the fact that all the other arguments have +sensible defaults. +.TP +.B \-min\fR\ <\fIvalue\fR>\ ,\ \fB\-\-minimum\fR\ <\fIvalue\fR> +Defaults to +.IB nin ->oldMin +if it exists, otherwise +.B 0.0 +.RI ( double ) +.TP +.B \-max\fR\ <\fIvalue\fR>\ ,\ \fB\-\-maximum\fR\ <\fIvalue\fR> +Defaults to +.IB nin ->oldMax +if it exists, otherwise +.B 1.0 +.RI ( double ) +.TP +.B \-double +If not using +.RB \(lq \-min \(rq +or +.RB \(lq \-max \(rq, +whether to know the range of 8-bit data blindly +.RI ( uchar +is always +.BR [0,255] , +.I signed char +is +.BR [-128,127] ) +.RI ( bool ); +default: +.RB \(lq true \(rq, +"true" +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-quantize (1) diff --git a/unu-untile.1 b/unu-untile.1 new file mode 100644 index 0000000..f1674af --- /dev/null +++ b/unu-untile.1 @@ -0,0 +1,90 @@ +.TH UNU\-UNTILE "1" "August 2021" "" "User Commands" +.SH NAME +unu\-untile \- undo +.BR unu\-tile (1): +merge slow parts of two axis splits +.SH SYNOPSIS +.B unu\ untile +.BR \-a , \-\-axis +.RI < axMerge \ ax0 \ ax1 > +.BR \-s , \-\-size +.RI < size0 \ size1 > +.RB [ \-i , \-\-input +.RI < nin >] +.RB [ \-o , \-\-output +.RI < nout >] +.SH DESCRIPTION +Undo +.BR unu\-tile (1): +merge slow parts of two axis splits. +Untiling an array means spliting two axes, permuting the slow parts of those +axes to be adjecent in the axis ordering, and then merging them. +This increases the dimension by one. +Undoing a +.BR unu\-tile (1) +uses the same +.RB \(lq \-s \(rq +argument, and +sometimes a different +.RB \(lq \-a \(rq +argument, as demonstrated here for a 3\-D array: +.IP +.RB \(lq unu\ untile\ \-a\ 2\ 0\ 1 \(rq +undoes +.RB \(lq unu\ tile\ \-a\ 2\ 0\ 1 \(rq +.IP +.RB \(lq unu\ untile\ \-a\ 1\ 0\ 1 \(rq +undoes +.RB \(lq unu\ tile\ \-a\ 1\ 0\ 2 \(rq +.IP +.RB \(lq unu\ untile\ \-a\ 0\ 0\ 1 \(rq +undoes +.RB \(lq unu\ tile\ \-a\ 0\ 1\ 2 \(rq. +.IP \(bu +2n +Uses +.B nrrdUntile2D +.SH OPTIONS +.TP +.B \-a\fR\ <\fIaxMerge\fR\ \fIax0\fR\ \fIax1\fR>\ ,\ \fB\-\-axis\fR\ <\fIaxMerge\fR\ \fIax0\fR\ \fIax1\fR> +the slow parts of axes +.I ax0 +and +.I ax1 +are merged into a (new) axis +.IR axMerge , +with the axis +.I ax0 +part being faster than +.IR ax1 . +(3 +.IR unsigned\ int s) +.TP +.B \-s\fR\ <\fIsize0\fR\ \fIsize1\fR>\ ,\ \fB\-\-size\fR\ <\fIsize0\fR\ \fIsize1\fR> +the slow parts of axes +.I ax0 +and +.I ax1 +are taken to have size +.I size0 +and +.IR size1 , +respectively, and axis +.I axMerge +will have size +.IB size0 * size1\fR. +(2 +.IR size_t s) +.TP +.B \-i\fR\ <\fInin\fR>\ ,\ \fB\-\-input\fR\ <\fInin\fR> +input +.I nrrd +.TP +.B \-o\fR\ <\fInout\fR>\ ,\ \fB\-\-output\fR\ <\fInout\fR> +output +.I nrrd +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR unu (1), +.BR unu\-tile (1) diff --git a/unu-w2i.1 b/unu-w2i.1 new file mode 100644 index 0000000..17dd885 --- /dev/null +++ b/unu-w2i.1 @@ -0,0 +1,58 @@ +.TH UNU\-W2I "1" "April 2021" "" "User Commands" +.SH NAME +unu\-w2i \- converts from 1-D world to index position +.SH SYNOPSIS +.B unu\ w2i +.RI < center > +.RI < minPos > +.RI < maxPos > +.RI < num > +.RI < world > +.SH DESCRIPTION +Converts from 1-D world to index position, given the centering of the data +.RB ( cell +vs. +.BR node ), +the range of positions, and the number of intervals into which position has +been quantized. +This is a demo/utility, which does not actually operate on any +.IR nrrd s. +Previously available as the stand-alone +.B pos2idx +binary. +.P +Uses +.B NRRD_IDX +macro +.SH OPTIONS +.TP +.RI < center > +which centering applies to the quantized position. +Possibilities are: +.RS +7n +.IP \(bu 2 +.RB \(lq cell \(rq +for histogram bins, quantized values, and pixels-as-squares +.IP \(bu 2 +.RB \(lq node \(rq +for non-trivially interpolated sample points +.RE +.TP +.RI < minPos > +smallest position associated with index +.B 0 +.RI ( double ) +.TP +.RI < maxPos > +highest position associated with highest index +.RI ( double ) +.TP +.RI < num > +number of intervals into which position has been quantized +.RI ( double ) +.TP +.RI < world > +the input world position, to be converted to index +.RI ( double ) +.SH "SEE\ ALSO" +.BR unu (1) diff --git a/unu.1 b/unu.1 index 6f8b611..cb49b63 100644 --- a/unu.1 +++ b/unu.1 @@ -4,7 +4,7 @@ unu \- Utah Nrrd Utilities command-line interface .SH SYNOPSIS .B unu .I COMMAND -.RI [ OPTION ]... +.RI [ OPTION ]...\: .SH DESCRIPTION .BR unu (1) is a command-line interface to much of the functionality in \(lqnrrd\(rq, a C @@ -116,11 +116,11 @@ Formats available: Nrrd data encodings available: .B raw ascii hex gz bz2 .SH COMMANDS -\" .P -\" Each of the following has a corresponding man page: for example, -\" .BR unu\-about (1) -\" for -\" .RB \(lq unu\ about \(rq. +.P +Each of the following has a corresponding man page: for example, +.BR unu\-about (1) +for +.RB \(lq unu\ about \(rq. .SS unu about Information about this program and its use .SS unu env @@ -303,6 +303,9 @@ Remap CC values down to lowest contiguous values Write .I nrrd with specific format, encoding, or endianness +.SH ENVIRONMENT +See +.BR unu\-env (1). .SH "SEE\ ALSO" .BR gprobe (1), .BR ilk (1), @@ -312,67 +315,66 @@ with specific format, encoding, or endianness .BR overrgb (1), .BR puller (1), .BR tend (1), -.BR vprobe (1) -\" .BR vprobe (1), -\" .BR unu-1op (1), -\" .BR unu-2op (1), -\" .BR unu-3op (1), -\" .BR unu-about (1), -\" .BR unu-acrop (1), -\" .BR unu-affine (1), -\" .BR unu-axdelete (1), -\" .BR unu-axinfo (1), -\" .BR unu-axinsert (1), -\" .BR unu-axmerge (1), -\" .BR unu-axsplit (1), -\" .BR unu-ccadj (1), -\" .BR unu-ccfind (1), -\" .BR unu-ccmerge (1), -\" .BR unu-ccsettle (1), -\" .BR unu-cksum (1), -\" .BR unu-cmedian (1), -\" .BR unu-convert (1), -\" .BR unu-crop (1), -\" .BR unu-data (1), -\" .BR unu-dhisto (1), -\" .BR unu-dice (1), -\" .BR unu-diff (1), -\" .BR unu-dist (1), -\" .BR unu-env (1), -\" .BR unu-fft (1), -\" .BR unu-flip (1), -\" .BR unu-gamma (1), -\" .BR unu-head (1), -\" .BR unu-heq (1), -\" .BR unu-histax (1), -\" .BR unu-histo (1), -\" .BR unu-i2w (1), -\" .BR unu-imap (1), -\" .BR unu-inset (1), -\" .BR unu-jhisto (1), -\" .BR unu-join (1), -\" .BR unu-lut (1), -\" .BR unu-lut2 (1), -\" .BR unu-make (1), -\" .BR unu-minmax (1), -\" .BR unu-mlut (1), -\" .BR unu-mrmap (1), -\" .BR unu-pad (1), -\" .BR unu-permute (1), -\" .BR unu-project (1), -\" .BR unu-quantize (1), -\" .BR unu-resample (1), -\" .BR unu-reshape (1), -\" .BR unu-rmap (1), -\" .BR unu-save (1), -\" .BR unu-shuffle (1), -\" .BR unu-slice (1), -\" .BR unu-splice (1), -\" .BR unu-sselect (1), -\" .BR unu-subst (1), -\" .BR unu-swap (1), -\" .BR unu-tile (1), -\" .BR unu-unorient (1), -\" .BR unu-unquantize (1), -\" .BR unu-untile (1), -\" .BR unu-w2i (1) +.BR vprobe (1), +.BR unu-1op (1), +.BR unu-2op (1), +.BR unu-3op (1), +.BR unu-about (1), +.BR unu-acrop (1), +.BR unu-affine (1), +.BR unu-axdelete (1), +.BR unu-axinfo (1), +.BR unu-axinsert (1), +.BR unu-axmerge (1), +.BR unu-axsplit (1), +.BR unu-ccadj (1), +.BR unu-ccfind (1), +.BR unu-ccmerge (1), +.BR unu-ccsettle (1), +.BR unu-cksum (1), +.BR unu-cmedian (1), +.BR unu-convert (1), +.BR unu-crop (1), +.BR unu-data (1), +.BR unu-dhisto (1), +.BR unu-dice (1), +.BR unu-diff (1), +.BR unu-dist (1), +.BR unu-env (1), +.BR unu-fft (1), +.BR unu-flip (1), +.BR unu-gamma (1), +.BR unu-head (1), +.BR unu-heq (1), +.BR unu-histax (1), +.BR unu-histo (1), +.BR unu-i2w (1), +.BR unu-imap (1), +.BR unu-inset (1), +.BR unu-jhisto (1), +.BR unu-join (1), +.BR unu-lut (1), +.BR unu-lut2 (1), +.BR unu-make (1), +.BR unu-minmax (1), +.BR unu-mlut (1), +.BR unu-mrmap (1), +.BR unu-pad (1), +.BR unu-permute (1), +.BR unu-project (1), +.BR unu-quantize (1), +.BR unu-resample (1), +.BR unu-reshape (1), +.BR unu-rmap (1), +.BR unu-save (1), +.BR unu-shuffle (1), +.BR unu-slice (1), +.BR unu-splice (1), +.BR unu-sselect (1), +.BR unu-subst (1), +.BR unu-swap (1), +.BR unu-tile (1), +.BR unu-unorient (1), +.BR unu-unquantize (1), +.BR unu-untile (1), +.BR unu-w2i (1) commit 516324379066d7660be0b0eaa7e3ff0bd06b27c9 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Wed Jul 21 16:06:33 2021 -0400 Opt in to rpmautospec diff --git a/changelog b/changelog new file mode 100644 index 0000000..833cd80 --- /dev/null +++ b/changelog @@ -0,0 +1,60 @@ +* Tue Apr 13 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-16 +- Finish man pages, except “unu” sub-pages. Start installing man pages. + +* Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 +- Fix typo in lib_install_dir.patch +- Update download URL from HTTP to HTTPS +- Improved package summaries and descriptions +- Adjust whitespace to personal preference +- Fix stray line continuation backslash +- Support EPEL7 +- Build with “levmar” support enabled +- Use stricter file globs, including specifying the so-version +- Add an -examples subpackage so the BSD and zlib licenses can be “contained” + to that subpackage; remove certain unused files with other licenses in %%prep +- Require cmake-filesystem instead of all of CMake in -devel +- More precisely skip overly-strict floating-point tests where required +- Start work on adding a complete set of man pages + +* Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + +* Fri Sep 04 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.11.0-13 +- Use cmake macros to fix build + +* Sat Aug 01 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-12 +- Second attempt - Rebuilt for + https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + +* Wed Jul 29 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-11 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild + +* Fri Jan 31 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-10 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild + +* Sat Jul 27 2019 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-9 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild + +* Sun Feb 03 2019 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-8 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild + +* Sat Jul 14 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-7 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild + +* Fri Feb 09 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-6 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild + +* Thu Aug 03 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-5 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild + +* Thu Jul 27 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-4 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild + +* Sat Feb 11 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-3 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild + +* Fri Feb 05 2016 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild + +* Wed Nov 25 2015 Dmitry Mikhirev <mikhirev(a)gmail.com> 1.11.0-1 +- Initial package diff --git a/teem.spec b/teem.spec index 5c62687..aded044 100644 --- a/teem.spec +++ b/teem.spec @@ -1,7 +1,7 @@ Name: teem Version: 1.11.0 %global so_version 1 -Release: 16%{?dist} +Release: %autorelease -b 13 Summary: Libraries for processing and visualizing scientific raster data # The entire source is LGPLv2+, except files noted at the License fields of certain subpackages. @@ -351,63 +351,4 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %changelog -* Tue Apr 13 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-16 -- Finish man pages, except “unu” sub-pages. Start installing man pages. - -* Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 -- Fix typo in lib_install_dir.patch -- Update download URL from HTTP to HTTPS -- Improved package summaries and descriptions -- Adjust whitespace to personal preference -- Fix stray line continuation backslash -- Support EPEL7 -- Build with “levmar” support enabled -- Use stricter file globs, including specifying the so-version -- Add an -examples subpackage so the BSD and zlib licenses can be “contained” - to that subpackage; remove certain unused files with other licenses in %%prep -- Require cmake-filesystem instead of all of CMake in -devel -- More precisely skip overly-strict floating-point tests where required -- Start work on adding a complete set of man pages - -* Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild - -* Fri Sep 04 2020 Ankur Sinha <ankursinha AT fedoraproject DOT org> - 1.11.0-13 -- Use cmake macros to fix build - -* Sat Aug 01 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-12 -- Second attempt - Rebuilt for - https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Wed Jul 29 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-11 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild - -* Fri Jan 31 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-10 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_32_Mass_Rebuild - -* Sat Jul 27 2019 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-9 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_31_Mass_Rebuild - -* Sun Feb 03 2019 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-8 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_30_Mass_Rebuild - -* Sat Jul 14 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-7 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_29_Mass_Rebuild - -* Fri Feb 09 2018 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-6 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_28_Mass_Rebuild - -* Thu Aug 03 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-5 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Binutils_Mass_Rebuild - -* Thu Jul 27 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-4 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_27_Mass_Rebuild - -* Sat Feb 11 2017 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-3 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_26_Mass_Rebuild - -* Fri Feb 05 2016 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-2 -- Rebuilt for https://fedoraproject.org/wiki/Fedora_24_Mass_Rebuild - -* Wed Nov 25 2015 Dmitry Mikhirev <mikhirev(a)gmail.com> 1.11.0-1 -- Initial package +%autochangelog commit 7dd3eb9d51ce2c2984ed8f6c467d7483da181c65 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 13 12:04:10 2021 -0400 Finish man pages, except “unu” sub-pages. Start installing man pages. diff --git a/ilk.1 b/ilk.1 index 51b2915..e88f365 100644 --- a/ilk.1 +++ b/ilk.1 @@ -33,7 +33,7 @@ Applies linear (homogenous coordinate) transforms to a given image, using the given kernel for resampling. .SH OPTIONS .TP -.BR @file \ ... +.IR @file \ ... response file(s) containing command-line arguments .TP .B \-i\fR <\fIimage\fR> diff --git a/miter.1 b/miter.1 index 75d7ef4..254f8b8 100644 --- a/miter.1 +++ b/miter.1 @@ -79,7 +79,7 @@ miter \- a simple but effective little volume renderer .RI < filename >] .SH OPTIONS .TP -.BR @file \ ... +.IR @file \ ... response file(s) containing command-line arguments .TP .B \-i\fR <\fInsin\fR> diff --git a/mrender.1 b/mrender.1 index f619ac2..c58da9e 100644 --- a/mrender.1 +++ b/mrender.1 @@ -69,7 +69,7 @@ in the output image. .SH OPTIONS .TP -.BR @file \ ... +.IR @file \ ... response file(s) containing command-line arguments .TP .B \-i\fR <\fInin\fR> diff --git a/overrgb.1 b/overrgb.1 index 538bf57..a9e2a0c 100644 --- a/overrgb.1 +++ b/overrgb.1 @@ -31,9 +31,6 @@ have to be the same size as the input image; it will be resampled (with linear interpolation) to fit. .SH OPTIONS .TP -.BR @file \ ... -response file(s) containing command-line arguments -.TP .B \-i\fR <\fInin\fR> input nrrd to composite .RI ( nrrd ) diff --git a/puller.1 b/puller.1 index fb03592..45b7635 100644 --- a/puller.1 +++ b/puller.1 @@ -3,7 +3,7 @@ puller \- command-line interface to the \(lqpull\(rq library .SH SYNOPSIS .B puller -.RB [ @file \ ...] +.RI [ @file \ ...] .RB [ \-int .RI < int >] .RB [ \-enr @@ -139,7 +139,7 @@ puller \- command-line interface to the \(lqpull\(rq library .RI < base >] .SH OPTIONS .TP -.BR @file \ ... +.IR @file \ ... response file(s) containing command-line arguments .TP .B \-int\fR <\fIint\fR> diff --git a/teem.spec b/teem.spec index 61764d0..5c62687 100644 --- a/teem.spec +++ b/teem.spec @@ -1,11 +1,7 @@ -# Writing man pages is a work in progress. We do not install them until we have -# a complete set. -%bcond_with man_pages - Name: teem Version: 1.11.0 %global so_version 1 -Release: 15%{?dist} +Release: 16%{?dist} Summary: Libraries for processing and visualizing scientific raster data # The entire source is LGPLv2+, except files noted at the License fields of certain subpackages. @@ -45,36 +41,36 @@ Source807: tend-mconv.1 Source808: tend-msim.1 Source809: tend-make.1 Source810: tend-avg.1 -#Source811: tend-helix.1 -#Source812: tend-sten.1 -#Source813: tend-glyph.1 -#Source814: tend-ellipse.1 -#Source815: tend-anplot.1 -#Source816: tend-anvol.1 -#Source817: tend-anscale.1 -#Source818: tend-anhist.1 -#Source819: tend-triple.1 -#Source820: tend-tconv.1 -#Source821: tend-point.1 -#Source822: tend-slice.1 -#Source823: tend-norm.1 -#Source824: tend-fiber.1 -#Source825: tend-eval.1 -#Source826: tend-evalpow.1 -#Source827: tend-evalclamp.1 -#Source828: tend-evaladd.1 -#Source829: tend-evalmul.1 -#Source830: tend-log.1 -#Source831: tend-exp.1 -#Source832: tend-evec.1 -#Source833: tend-evecrgb.1 -#Source834: tend-evq.1 -#Source835: tend-unmf.1 -#Source836: tend-expand.1 -#Source837: tend-shrink.1 -#Source838: tend-bfit.1 -#Source839: tend-satin.1 -# +Source811: tend-helix.1 +Source812: tend-sten.1 +Source813: tend-glyph.1 +Source814: tend-ellipse.1 +Source815: tend-anplot.1 +Source816: tend-anvol.1 +Source817: tend-anscale.1 +Source818: tend-anhist.1 +Source819: tend-triple.1 +Source820: tend-tconv.1 +Source821: tend-point.1 +Source822: tend-slice.1 +Source823: tend-norm.1 +Source824: tend-fiber.1 +Source825: tend-eval.1 +Source826: tend-evalpow.1 +Source827: tend-evalclamp.1 +Source828: tend-evaladd.1 +Source829: tend-evalmult.1 +Source830: tend-log.1 +Source831: tend-exp.1 +Source832: tend-evec.1 +Source833: tend-evecrgb.1 +Source834: tend-evq.1 +Source835: tend-unmf.1 +Source836: tend-expand.1 +Source837: tend-shrink.1 +Source838: tend-bfit.1 +Source839: tend-satin.1 + #Source900: unu-about.1 #Source901: unu-env.1 #Source902: unu-i2w.1 @@ -273,20 +269,20 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %{SOURCE820} %{SOURCE821} %{SOURCE822} %{SOURCE823} %{SOURCE824} \ %{SOURCE825} %{SOURCE826} %{SOURCE827} %{SOURCE828} %{SOURCE829} \ %{SOURCE830} %{SOURCE831} %{SOURCE832} %{SOURCE833} %{SOURCE834} \ - %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} \ - %{SOURCE900} %{SOURCE901} %{SOURCE902} %{SOURCE903} %{SOURCE904} \ - %{SOURCE905} %{SOURCE906} %{SOURCE907} %{SOURCE908} %{SOURCE909} \ - %{SOURCE910} %{SOURCE911} %{SOURCE912} %{SOURCE913} %{SOURCE914} \ - %{SOURCE915} %{SOURCE916} %{SOURCE917} %{SOURCE918} %{SOURCE919} \ - %{SOURCE920} %{SOURCE921} %{SOURCE922} %{SOURCE923} %{SOURCE924} \ - %{SOURCE925} %{SOURCE926} %{SOURCE927} %{SOURCE928} %{SOURCE929} \ - %{SOURCE930} %{SOURCE931} %{SOURCE932} %{SOURCE933} %{SOURCE934} \ - %{SOURCE935} %{SOURCE936} %{SOURCE937} %{SOURCE938} %{SOURCE939} \ - %{SOURCE940} %{SOURCE941} %{SOURCE942} %{SOURCE943} %{SOURCE944} \ - %{SOURCE945} %{SOURCE946} %{SOURCE947} %{SOURCE948} %{SOURCE949} \ - %{SOURCE950} %{SOURCE951} %{SOURCE952} %{SOURCE953} %{SOURCE954} \ - %{SOURCE955} %{SOURCE956} %{SOURCE957} %{SOURCE958} %{SOURCE959} \ - %{SOURCE960} %{SOURCE961} + %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} + #{SOURCE900} #{SOURCE901} #{SOURCE902} #{SOURCE903} #{SOURCE904} \ + #{SOURCE905} #{SOURCE906} #{SOURCE907} #{SOURCE908} #{SOURCE909} \ + #{SOURCE910} #{SOURCE911} #{SOURCE912} #{SOURCE913} #{SOURCE914} \ + #{SOURCE915} #{SOURCE916} #{SOURCE917} #{SOURCE918} #{SOURCE919} \ + #{SOURCE920} #{SOURCE921} #{SOURCE922} #{SOURCE923} #{SOURCE924} \ + #{SOURCE925} #{SOURCE926} #{SOURCE927} #{SOURCE928} #{SOURCE929} \ + #{SOURCE930} #{SOURCE931} #{SOURCE932} #{SOURCE933} #{SOURCE934} \ + #{SOURCE935} #{SOURCE936} #{SOURCE937} #{SOURCE938} #{SOURCE939} \ + #{SOURCE940} #{SOURCE941} #{SOURCE942} #{SOURCE943} #{SOURCE944} \ + #{SOURCE945} #{SOURCE946} #{SOURCE947} #{SOURCE948} #{SOURCE949} \ + #{SOURCE950} #{SOURCE951} #{SOURCE952} #{SOURCE953} #{SOURCE954} \ + #{SOURCE955} #{SOURCE956} #{SOURCE957} #{SOURCE958} #{SOURCE959} \ + #{SOURCE960} #{SOURCE961} %endif @@ -331,7 +327,7 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %{_mandir}/man1/tend.1* %{_mandir}/man1/tend-*.1* %{_mandir}/man1/unu.1* -%{_mandir}/man1/unu-*.1* +#{_mandir}/man1/unu-*.1* %{_mandir}/man1/vprobe.1* %endif @@ -355,6 +351,9 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %changelog +* Tue Apr 13 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-16 +- Finish man pages, except “unu” sub-pages. Start installing man pages. + * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch - Update download URL from HTTP to HTTPS diff --git a/tend-anhist.1 b/tend-anhist.1 new file mode 100644 index 0000000..a475647 --- /dev/null +++ b/tend-anhist.1 @@ -0,0 +1,61 @@ +.TH TEND\-ANHIST "1" "April 2021" "" "User Commands" +.SH NAME +tend\-anhist \- generate barycentric histograms of anisotropy +.SH SYNOPSIS +.B tend\ anhist +.RB [ \-v +.RI < westin\ version >] +.RB [ \-w +.RI < nweight >] +.B \-r +.RI < res > +.RB [ \-right ] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate barycentric histograms of anisotropy. +The barycentric space used is either one of Westin\(cqs triple of spherical, +linear, and planar anisotropy. +The bin counts in the histogram are weighted by the confidence value. +.SH OPTIONS +.TP +.B \-v\fR <\fIwestin\ version\fR> +Which version of Westin\(cqs anisotropy metric triple to use, either +.RB \(lq 1 \(rq +or +.RB \(lq 2 \(rq +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-w\fR <\fInweight\fR> +how to weigh contributions to histogram. +By default (not using this option), the increment is one bin count per sample, +but by giving a +.IR nrrd , +the value in the +.I nrrd +at the corresponding location will be the bin count increment; default: +\(lq\(rq +.TP +.B \-r\fR <\fIres\fR> +resolution of anisotropy plot +.RI ( int ) +.TP +.B \-right +sample a right-triangle-shaped region, instead of a roughly equilateral +triangle. +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-anplot.1 b/tend-anplot.1 new file mode 100644 index 0000000..44024a6 --- /dev/null +++ b/tend-anplot.1 @@ -0,0 +1,106 @@ +.TH TEND\-ANPLOT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-anplot \- graph anisotropy metric in barycentric coords +.SH SYNOPSIS +.B tend\ anplot +.RB [ \-r +.RI < res >] +.RB [ \-w ] +.RB [ \-hflip ] +.RB [ \-nan ] +.B \-a +.RI < aniso > +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Graph anisotropy metric in barycentric coordinates. +The metrics all vary from +.B 0.0 +to +.BR 1.0 , +and will be sampled in the lower right half of the image. +The plane on which they are sampled is a surface of constant trace. +You may want to use +.in +4n +.EX +.B unu\ resample\ \-s\ =\ x0.57735\ \-k\ tent +.in +.EE +to transform the triangle into a 30-60-90 triangle, and +.in +4n +.EX +.B ilk\ \-t\ 1,\-0.5,0,0,0.866,0\ \-k\ tent\ \-0\ u:0,1\ \-b\ pad\ \-bg\ 0 +.EE +.in +(possibly followed by +.BR teem/src/limntest/triimg ) +to transform the domain into an equilateral triangle. +.SH OPTIONS +.TP +.B \-res\fR <\fIres\fR> +resolution of anisotropy plot +.RI ( int ); +default: +.RB \(lq 256 \(rq +.TP +.B \-w +sample the whole triangle of constant trace, instead of just the sixth of it in +which the eigenvalues have the traditional sorted order. +.TP +.B \-hflip +flip the two bottom corners (swapping the place of linear and planar) +.TP +.B \-nan +set the pixel values outside the triangle to be +.BR NaN , +instead of +.B 0 +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy metric to plot. +All the Westin metrics come in two versions. +Currently supported: +.RS +7n +.IP \(bu 2 +.RB \(lq cl1 \(rq, +.RB \(lq cl2 \(rq: +Westin\(cqs linear +.IP \(bu 2 +.RB \(lq cp1 \(rq, +.RB \(lq cp2 \(rq: +Westin\(cqs planar +.IP \(bu 2 +.RB \(lq ca1 \(rq, +.RB \(lq ca2 \(rq: +Westin\(cqs linear + planar +.IP \(bu 2 +.RB \(lq cs1 \(rq, +.RB \(lq cs2 \(rq: +Westin\(cqs spherical +.IP \(bu 2 +.RB \(lq ct1 \(rq, +.RB \(lq ct2 \(rq: +GK\(cqs anisotropy type (cp/ca) +.IP \(bu 2 +.RB \(lq ra \(rq: +Basser/Pierpaoli relative anisotropy/sqrt(2) +.IP \(bu 2 +.RB \(lq fa \(rq: +Basser/Pierpaoli fractional anisotropy +.IP \(bu 2 +.RB \(lq vf \(rq: +volume fraction = 1\-(Basser/Pierpaoli volume ratio) +.IP \(bu 2 +.RB \(lq tr \(rq: +trace +.RE +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR ilk (1), +.BR unu\-resample (1) diff --git a/tend-anscale.1 b/tend-anscale.1 new file mode 100644 index 0000000..740157d --- /dev/null +++ b/tend-anscale.1 @@ -0,0 +1,44 @@ +.TH TEND\-ANSCALE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-anscale \- scale the anisotropic component of the tensors +.SH SYNOPSIS +.B tend\ anscale +.B \-s +.RI < scale > +.RB [ \-fd ] +.RB [ \-mp ] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Scale the anisotropic component of the tensors. +This maintains the isotropic component of the tensor, and fixes either the +trace or determinant, while scaling up (or down) the \(lqdeviatoric\(rq +component of the tensor. +Good for exaggerating the shape of nearly isotropic tensors. +.SH OPTIONS +.TP +.B \-s\fR <\fIscale\fR> +Amount by which to scale deviatoric component of tensor. +.RI ( float ) +.TP +.B \-fd +instead of fixing the per-sample trace (the default), fix the determinant +(ellipsoid volume) +.TP +.B \-mp +after changing the eigenvalues of the tensor, enforce their non-negative-ness. +By default, no such constraint is imposed. +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-anvol.1 b/tend-anvol.1 new file mode 100644 index 0000000..6c06441 --- /dev/null +++ b/tend-anvol.1 @@ -0,0 +1,75 @@ +.TH TEND\-ANVOL "1" "April 2021" "" "User Commands" +.SH NAME +tend\-anvol \- apply an anisotropy metric to a DT volume +.SH SYNOPSIS +.B tend\ anvol +.B \-a +.RI < aniso > +.RB [ \-t +.RI < thresh >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Apply an anisotropy metric to a DT volume. +The anisotropy value will be zero in the locations which don\(cqt meet the +given confidence threshold. +.SH OPTIONS +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy metric to plot. +All the Westin metrics come in two versions. +Currently supported: +.RS +7n +.IP \(bu 2 +.RB \(lq cl1 \(rq, +.RB \(lq cl2 \(rq: +Westin\(cqs linear +.IP \(bu 2 +.RB \(lq cp1 \(rq, +.RB \(lq cp2 \(rq: +Westin\(cqs planar +.IP \(bu 2 +.RB \(lq ca1 \(rq, +.RB \(lq ca2 \(rq: +Westin\(cqs linear + planar +.IP \(bu 2 +.RB \(lq cs1 \(rq, +.RB \(lq cs2 \(rq: +Westin\(cqs spherical +.IP \(bu 2 +.RB \(lq ct1 \(rq, +.RB \(lq ct2 \(rq: +GK\(cqs anisotropy type (cp/ca) +.IP \(bu 2 +.RB \(lq ra \(rq: +Basser/Pierpaoli relative anisotropy/sqrt(2) +.IP \(bu 2 +.RB \(lq fa \(rq: +Basser/Pierpaoli fractional anisotropy +.IP \(bu 2 +.RB \(lq vf \(rq: +volume fraction = 1\-(Basser/Pierpaoli volume ratio) +.IP \(bu 2 +.RB \(lq tr \(rq: +trace +.RE +.TP +.B \-t\fR <\fIthresh\fR> +confidence threshold +.RI ( float ) +default: +.RB \(lq 0.5 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-bfit.1 b/tend-bfit.1 new file mode 100644 index 0000000..9269f75 --- /dev/null +++ b/tend-bfit.1 @@ -0,0 +1,72 @@ +.TH TEND\-BFIT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-bfit \- non-linear least-squares fitting of \fIb\fR-value curves +.SH SYNOPSIS +.B tend\ bfit +.RI [ @file \ ...] +.RB [ \-i +.RI < nin >] +.B \-b +.RI < b1 \ b2 \ ...> +.RB [ \-w +.RI < w1 \ w2 \ ...>] +.RB [ \-imax +.RI < #\ iter >] +.RB [ \-eps +.RI < epsilon >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Non-linear least-squares fitting of \fIb\fR-value curves. +Axis 0 is replaced by three values: +.IR amp ,\ dec ,\ err , +based on a non-linear least-squares fit of +.IB amp *exp(\- b * dec ) +to the range of DWI values along input axis 0, as a function of changing +.I b +values. +.SH OPTIONS +.TP +.IR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fInin\fR> +Input +.IR nrrd . +List of DWIs from different +.IR b -values +must be along axis 0; default: +.RB \(lq \- \(rq +.TP +.B \-b\fR <\fIb1\fR\ \fIb2\fR\ ...> +.I b +values across axis 0 of input +.I nrrd +(2 or more +.IR double s) +.TP +.B \-w\fR <\fIw1\fR\ \fIw2\fR\ ...> +weights for samples in non-linear fitting (2 or more +.IR double s) +.TP +.B \-imax\fR <\fI#\ iter\fR> +max number of iterations to use in non-linear fitting, or, use +.B 0 +to do only initial linear fit +.RI ( int ); +default: +.RB \(lq 10 \(rq +.TP +.B \-eps\fR <\fIepsilon\fR> +epsilon convergence threshold for non-linear fitting +.RI ( double ); +default: +.RB \(lq 1 \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-ellipse.1 b/tend-ellipse.1 new file mode 100644 index 0000000..13f7913 --- /dev/null +++ b/tend-ellipse.1 @@ -0,0 +1,99 @@ +.TH TEND\-ELLIPSE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-ellipse \- generate postscript renderings of 2D glyphs +.SH SYNOPSIS +.B tend\ ellipse +.RB [ \-ctr +.RI < conf\ thresh >] +.RB [ \-gsc +.RI < scale >] +.RB [ \-dot +.RI < radius >] +.RB [ \-wid +.RI < width >] +.RB [ \-inv ] +.RB [ \-min +.RI < minX \ minY >] +.RB [ \-max +.RI < maxX \ maxY >] +.RB [ \-i +.RI < nin >] +.RB [ \-p +.RI < pos\ array >] +.RB [ \-s +.RI < stn\ array >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate postscript renderings of 2D glyphs. +Not much to look at here. +.SH OPTIONS +.TP +.B \-ctr\fR <\fIconf\ thresh\fR> +Glyphs will be drawn only for tensors with confidence values greater than this +threshold +.RI ( float ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-gsc\fR <\fIscale\fR> +over-all glyph size +.RI ( float ); +default: +.RB \(lq 1 \(rq +.TP +.B \-dot\fR <\fIradius\fR> +radius of little dot to put in middle of ellipse, or +.RB \(lq 0 \(rq +for no such dot +.RI ( float ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-wid\fR <\fIwidth\fR> +width of lines for tractlets +.RI ( float ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-inv +use white ellipses on black background, instead of reverse +.TP +.B \-min\fR <\fIminX\fR \fIminY\fR> +when using +.RB \(lq \-p \(rq, +minimum corner (2 +.IR float s); +default: +.RB \(lq \-1\ \-1 \(rq +.TP +.B \-max\fR <\fImaxX\fR \fImaxY\fR> +when using +.RB \(lq \-p \(rq, +maximum corner (2 +.IR float s); +default: +.RB \(lq 1\ 1 \(rq +.TP +.B \-i\fR <\fInin\fR> +image of 2D tensors; default: +.RB \(lq \- \(rq +.TP +.B \-p\fR <\fIpos\ array\fR> +Instead of being on a grid, tensors are at arbitrary locations, as defined by +this 2-by-N array of +.IR float s); +default: \(lq\(rq +.TP +.B \-s\fR <\fIstn\ array\fR> +Locations given by +.RB \(lq \-p \(rq +have this connectivity; default: \(lq\(rq +.TP +.B \-o\fR <\fInout\fR> +output PostScript file +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-eval.1 b/tend-eval.1 new file mode 100644 index 0000000..de9dc27 --- /dev/null +++ b/tend-eval.1 @@ -0,0 +1,47 @@ +.TH TEND\-EVAL "1" "April 2021" "" "User Commands" +.SH NAME +tend\-eval \- calculate one or more eigenvalues in a DT volume +.SH SYNOPSIS +.B tend\ eval +.B \-c +.RI < c0 \ ...> +.RB [ \-t +.RI < thresh >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-c\fR <\fIc0\fR\ ...> +which eigenvalues should be saved out. +.RB \(lq 0 \(rq +for the largest, +.RB \(lq 1 \(rq +for the middle, +.RB \(lq 2 \(rq +for the smallest, +.RB \(lq 0\ 1 \(rq, +.RB \(lq 1\ 2 \(rq, +.RB \(lq 0\ 1\ 2 \(rq +or similar for more than one (1..3 +.IR int s) +.TP +.B \-t\fR <\fIthresh\fR> +confidence threshold +.RI ( float ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-evec (1) diff --git a/tend-evaladd.1 b/tend-evaladd.1 new file mode 100644 index 0000000..e8754f9 --- /dev/null +++ b/tend-evaladd.1 @@ -0,0 +1,35 @@ +.TH TEND\-EVALADD "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evaladd \- modify shape by adding a constant to all eigenvalues +.SH SYNOPSIS +.B tend\ evaladd +.B \-v +.RI < value > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Modify shape by adding a constant to all eigenvalues. +The orientation of the tensor is unchanged. +Note that unlike +.BR tend\-anscale (1), +this operation can completely change the shape of the tensor. +.SH OPTIONS +.TP +.B \-v\fR <\fIvalue\fR> +Value to add to all eigenvalues +.RI ( float ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-anscale (1) diff --git a/tend-evalclamp.1 b/tend-evalclamp.1 new file mode 100644 index 0000000..b88bd6e --- /dev/null +++ b/tend-evalclamp.1 @@ -0,0 +1,47 @@ +.TH TEND\-EVALCLAMP "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evalclamp \- modify shape by clamping eigenvalues in some range +.SH SYNOPSIS +.B tend\ evalclamp +.B \-min +.RI < min > +.RB [ \-max +.RI < max >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Modify shape by clamping eigenvalues in some range. +The orientation of the tensor is unchanged. +Note that unlike +.BR tend\-anscale (1), +this operation can completely change the shape of the tensor. +.SH OPTIONS +.TP +.B \-min\fR <\fImin\fR> +Eigenvalues are clamped from below by this (the minimum output eigenvalue). +Use +.RB \(lq nan \(rq +to signify that no minimum clamping should be done. +.RI ( float ) +.TP +.B \-max\fR <\fImax\fR> +Eigenvalues are clamped from above by this (the maximum output eigenvalue). +Use +.RB \(lq nan \(rq +to signify that no maximum clamping should be done. +.RI ( float ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-anscale (1) diff --git a/tend-evalmult.1 b/tend-evalmult.1 new file mode 100644 index 0000000..3bf86b0 --- /dev/null +++ b/tend-evalmult.1 @@ -0,0 +1,31 @@ +.TH TEND\-EVALMULT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evalmult \- modify shape by multiplying eigenvalues by a constant +.SH SYNOPSIS +.B tend\ evalmult +.B \-v +.RI < value > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Modify shape by multiplying eigenvalues by a constant. +The orientation of the tensor is unchanged. +.SH OPTIONS +.TP +.B \-v\fR <\fIvalue\fR> +Value to multiply eigenvalues by +.RI ( float ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-evalpow.1 b/tend-evalpow.1 new file mode 100644 index 0000000..9f1adf5 --- /dev/null +++ b/tend-evalpow.1 @@ -0,0 +1,31 @@ +.TH TEND\-EVALPOW "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evalpow \- modify shape by raising eigenvalues to some power +.SH SYNOPSIS +.B tend\ evalpow +.B \-p +.RI < power > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Modify shape by raising eigenvalues to some power. +The orientation of the tensor is unchanged. +.SH OPTIONS +.TP +.B \-p\fR <\fIpower\fR> +Power to which to raise all the eigenvalues. +.RI ( float ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-evec.1 b/tend-evec.1 new file mode 100644 index 0000000..74e7988 --- /dev/null +++ b/tend-evec.1 @@ -0,0 +1,47 @@ +.TH TEND\-EVEC "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evec \- calculate one or more eigenvectors in a DT volume +.SH SYNOPSIS +.B tend\ evec +.B \-c +.RI < c0 \ ...> +.RB [ \-t +.RI < thresh >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-c\fR <\fIc0\fR\ ...> +which eigenvectors should be saved out. +.RB \(lq 0 \(rq +for the largest, +.RB \(lq 1 \(rq +for the middle, +.RB \(lq 2 \(rq +for the smallest, +.RB \(lq 0\ 1 \(rq, +.RB \(lq 1\ 2 \(rq, +.RB \(lq 0\ 1\ 2 \(rq +or similar for more than one (1..3 +.IR int s) +.TP +.B \-t\fR <\fIthresh\fR> +confidence threshold +.RI ( float ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-eval (1) diff --git a/tend-evecrgb.1 b/tend-evecrgb.1 new file mode 100644 index 0000000..94e209c --- /dev/null +++ b/tend-evecrgb.1 @@ -0,0 +1,108 @@ +.TH TEND\-EVECRGB "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evecrgb \- make an RGB volume from an eigenvector and an anisotropy +.SH SYNOPSIS +.B tend\ evecrgb +.B \-c +.RI < evec\ index > +.B \-a +.RI < aniso > +.RB [ \-t +.RI < thresh >] +.RB [ \-bg +.RI < background >] +.RB [ \-gr +.RI < gray >] +.RB [ \-gam +.RI < gamma >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-c\fR <\fIevec\ index\fR> +which eigenvector will be colored. +.RB \(lq 0 \(rq +for the principal, +.RB \(lq 1 \(rq +for the middle, +.RB \(lq 2 \(rq +for the minor +.RI ( unsigned\ int ) +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy to use for modulating the saturation of the colors. +All the Westin metrics come in two versions. +Currently supported: +.RS +7n +.IP \(bu 2 +.RB \(lq cl1 \(rq, +.RB \(lq cl2 \(rq: +Westin\(cqs linear +.IP \(bu 2 +.RB \(lq cp1 \(rq, +.RB \(lq cp2 \(rq: +Westin\(cqs planar +.IP \(bu 2 +.RB \(lq ca1 \(rq, +.RB \(lq ca2 \(rq: +Westin\(cqs linear + planar +.IP \(bu 2 +.RB \(lq cs1 \(rq, +.RB \(lq cs2 \(rq: +Westin\(cqs spherical +.IP \(bu 2 +.RB \(lq ct1 \(rq, +.RB \(lq ct2 \(rq: +GK\(cqs anisotropy type (cp/ca) +.IP \(bu 2 +.RB \(lq ra \(rq: +Basser/Pierpaoli relative anisotropy/sqrt(2) +.IP \(bu 2 +.RB \(lq fa \(rq: +Basser/Pierpaoli fractional anisotropy +.IP \(bu 2 +.RB \(lq vf \(rq: +volume fraction = 1\-(Basser/Pierpaoli volume ratio) +.IP \(bu 2 +.RB \(lq tr \(rq: +trace +.RE +.TP +.B \-t\fR <\fIthresh\fR> +confidence threshold +.RI ( float ) +default: +.RB \(lq 0.5 \(rq +.TP +.B \-bg\fR <\fIbackground\fR> +gray level to use for voxels whose confidence is zero +.RI ( double ) +default: +.RB \(lq 0 \(rq +.TP +.B \-gr\fR <\fIgray\fR> +the gray level to desaturate towards as anisotropy decreases (while confidence +remains 1.0) +.RI ( double ) +default: +.RB \(lq 0 \(rq +.TP +.B \-gam\fR <\fIgamma\fR> +gamma to use on color components +.RI ( double ) +default: +.RB \(lq 1 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-evq.1 b/tend-evq.1 new file mode 100644 index 0000000..2266f75 --- /dev/null +++ b/tend-evq.1 @@ -0,0 +1,93 @@ +.TH TEND\-EVQ "1" "April 2021" "" "User Commands" +.SH NAME +tend\-evq \- quantize directions of diffusion +.SH SYNOPSIS +.B tend\ evq +.RB [ \-c +.RI < evec\ index >] +.B \-a +.RI < aniso > +.RB [ \-ns ] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Quantize directions of diffusion. +Because VTK doesn\(cqt do multi-dimensional colormaps, we have to quantize +directions of diffusion (usually just the principal eigenvector) in order to +create the usual XYZ<->RGB coloring. +Because eigenvector directions are poorly defined in regions of low anisotropy, +the length of the vector (pre-quantization) is modulated by anisotropy, +requiring the selection of some anisotropy metric. +.SH OPTIONS +.TP +.B \-c\fR <\fIevec\ index\fR> +Which eigenvector should be quantized: + +.RB \(lq 0 \(rq +for the direction of fastest diffusion (eigenvector associated with largest +eigenvalue), +.RB \(lq 1 \(rq +or +.RB \(lq 2 \(rq +for other two eigenvectors (associated with middle and smallest eigenvalue) +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy metric to scale the eigenvector with. +All the Westin metrics come in two versions. +Currently supported: +.RS +7n +.IP \(bu 2 +.RB \(lq cl1 \(rq, +.RB \(lq cl2 \(rq: +Westin\(cqs linear +.IP \(bu 2 +.RB \(lq cp1 \(rq, +.RB \(lq cp2 \(rq: +Westin\(cqs planar +.IP \(bu 2 +.RB \(lq ca1 \(rq, +.RB \(lq ca2 \(rq: +Westin\(cqs linear + planar +.IP \(bu 2 +.RB \(lq cs1 \(rq, +.RB \(lq cs2 \(rq: +Westin\(cqs spherical +.IP \(bu 2 +.RB \(lq ct1 \(rq, +.RB \(lq ct2 \(rq: +GK\(cqs anisotropy type (cp/ca) +.IP \(bu 2 +.RB \(lq ra \(rq: +Basser/Pierpaoli relative anisotropy/sqrt(2) +.IP \(bu 2 +.RB \(lq fa \(rq: +Basser/Pierpaoli fractional anisotropy +.IP \(bu 2 +.RB \(lq vf \(rq: +volume fraction = 1\-(Basser/Pierpaoli volume ratio) +.IP \(bu 2 +.RB \(lq tr \(rq: +trace +.RE +.TP +.B \-ns +Don\(cqt attenuate the color by anisotropy. +By default (not using this option), regions with low or no anisotropy are very +dark colors or black +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-exp.1 b/tend-exp.1 new file mode 100644 index 0000000..e01f780 --- /dev/null +++ b/tend-exp.1 @@ -0,0 +1,28 @@ +.TH TEND\-EXP "1" "April 2021" "" "User Commands" +.SH NAME +tend\-exp \- calculates \fBexp()\fR of the tensor +.SH SYNOPSIS +.B tend\ exp +.RB [ \-i +.RI < nin >] +.B \-o +.RI < nout > +.SH DESCRIPTION +Calculates +.B exp() +of the tensor, which is based on +.B exp() +of the eigenvalues. +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-expand.1 b/tend-expand.1 new file mode 100644 index 0000000..7025c54 --- /dev/null +++ b/tend-expand.1 @@ -0,0 +1,72 @@ +.TH TEND\-EXPAND "1" "April 2021" "" "User Commands" +.SH NAME +tend\-expand \- converts masked non-redundant tensor images to redundant +.SH SYNOPSIS +.B tend\ expand +.RB [ \-t +.RI < thresh >] +.RB [ \-s +.RI < scale >] +.B [ \-unmf ] +.B [ \-ro ] +.B [ \-roo ] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Converts masked non-redundant tensor images to redundant. +For +images of 3D tensors, this converts from a 7-value tensor starting with the +confidence/mask value +.BI ( conf ,\ Dxx ,\ Dxy ,\ Dxz ,\ Dyy ,\ Dyz ,\ Dzz ) +to a 9-value tensor +with the full matrix +.BI ( Dxx ,\ Dxy ,\ Dxz ,\ Dxy ,\ Dyy ,\ Dyz ,\ Dxz ,\ Dyz ,\ Dzz ). +This is set to all zeros when the confidence is below the given threshold. +For +images +of 2D tensors, the conversion is from +.BI ( conf ,\ Dxx ,\ Dxy ,\ Dyy ) +to +.BI ( Dxx ,\ Dxy ,\ Dxy ,\ Dyy ). +.SH OPTIONS +.TP +.B \-t\fR <\fIthresh\fR> +confidence level to threshold output tensors at. +Should be between +.B 0.0 +and +.BR 1.0 . +.RI ( float ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-s\fR <\fIscale\fR> +how to scale values before saving as 9-value tensor. +Useful for visualization tools which assume certain characteristic ranges of +eigenvalues +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-unmf +apply and remove the measurement frame, if it exists +.TP +.B \-ro +reduce general image orientation to axis-aligned spacings +.TP +.B \-roo +reduce general image orientation to axis-aligned spacings, while also making +some effort to set axis mins from space origin +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume, with 7 values per sample; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume, with the 9 matrix components per sample +.RI ( string ) +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-shrink (1) diff --git a/tend-fiber.1 b/tend-fiber.1 new file mode 100644 index 0000000..8733a8a --- /dev/null +++ b/tend-fiber.1 @@ -0,0 +1,163 @@ +.TH TEND\-FIBER "1" "April 2021" "" "User Commands" +.SH NAME +tend\-fiber \- fiber tractography, from one or more seeds +.SH SYNOPSIS +.B tend\ fiber +.RB [ \-i +.RI < nin >] +.RB [ \-dwi ] +.RB [ \-s +.RI < seed\ point >] +.RB [ \-ns +.RI < seed\ nrrd >] +.RB [ \-wsp ] +.RB [ \-t +.RI < type >] +.RB [ \-n +.RI < intg >] +.RB [ \-k +.RI < kernel >] +.RB [ \-wp +.RI < which >] +.RB [ \-ap ] +.RB [ \-wspo ] +.RB [ \-step +.RI < step\ size >] +.B \-stop +.RI < stop1 \ ...> +.RB [ \-v +.RI < verbose >] +.RB [ \-nmat +.RI < transform >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Fiber tractography, from one or more seeds. +A fairly complete command-line interface to the +.B tenFiber +API. +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input volume; default: +.RB \(lq \- \(rq +.TP +.B \-dwi +input volume is a DWI volume, not a single tensor volume +.TP +.B \-s\fR <\fIseed\ point\fR> +seed point for fiber; it will propogate in two opposite directions starting +from here (3 +.IR double s); +default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-ns\fR <\fIseed\ nrrd\fR> +3-by-N +.I nrrd +of seedpoints; default: \(lq\(rq +.TP +.B \-wsp +define seedpoint and output path in worldspace. +Otherwise, (without using this option) everything is in index space +.TP +.B \-t\fR <\fItype\fR> +fiber type; defaults to something +.RI ( string ) +.TP +.B \-n\fR <\fIintg\fR> +integration method for fiber tracking; default: +.RB \(lq rk4 \(rq +.TP +.B \-k\fR <\fIkernel\fR> +kernel for reconstructing tensor field; default: +.RB \(lq tent \(rq +.TP +.B \-wp\fR <\fIwhich\fR> +when doing multi-tensor tracking, index of path to follow (made moot by +.RB \(lq \-ap \(rq) +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ap +follow all paths from (all) seedpoint(s), output will be +.IR polydata , +rather than a single 3-by-N +.IR nrrd , +even if only a single path is generated +.TP +.B \-wspo +output should be in worldspace, even if input is not (this feature is unstable +and/or confusing) +.TP +.B \-s\fR <\fIstep\ size\fR> +stepsize along fiber, in world space +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-stop\fR <\fIstop1\fR\ ...> +the conditions that should signify the end of a fiber, or when to discard a +fiber that is done propagating. +Multiple stopping criteria are logically OR-ed and tested at every point along +the fiber. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq aniso:\fR<\fItype\fR>\fB,\fR<\fIthresh >\(rq: +require anisotropy to be above the given threshold. +Which anisotropy type is given as with +.BR tend-anvol (1) +.IP \(bu 2 +.RB \(lq len:\fR<\fIlength >\(rq: +limits the length, in world space, of each fiber half +.IP \(bu 2 +.RB \(lq steps:\fR<\fIN >\(rq: +the number of steps in each fiber half is capped at +.I N +.IP \(bu 2 +.RB \(lq conf:\fR<\fIthresh >\(rq: +requires the tensor confidence value to be above the given +.I thresh +.IP \(bu 2 +.RB \(lq radius:\fR<\fIthresh >\(rq: +requires that the radius of curvature of the fiber stay above given +.I thresh +.IP \(bu 2 +.RB \(lq frac:\fR<\fIF >\(rq: +in multi-tensor tracking, the fraction of the tracked component must stay above +.I F +.IP \(bu 2 +.RB \(lq minlen:\fR<\fIlen >\(rq: +discard fiber if its final whole length is below +.I len +(not really a termination criterion) +.IP \(bu 2 +.RB \(lq minsteps:\fR<\fIN >\(rq: +discard fiber if its final number of steps is below +.I N +(not really a termination criterion) +(1 or more fiber stops) +.RE +.TP +.B \-v\fR <\fIverbose\fR> +verbosity level +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-nmat\fR <\fItransform\fR> +a 4x4 homogenous transform matrix (as a +.IR nrrd , +or just a text file) given with this option will be applied to the output +tractography vertices just prior to output; default: \(lq\(rq +.TP +.B \-o\fR <\fInout\fR> +output fiber(s) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-anvol (1) diff --git a/tend-glyph.1 b/tend-glyph.1 new file mode 100644 index 0000000..c0ee791 --- /dev/null +++ b/tend-glyph.1 @@ -0,0 +1,462 @@ +.TH TEND\-GLYPH "1" "April 2021" "" "User Commands" +.SH NAME +tend\-glyph \- generate postscript or ray-traced renderings of 3D glyphs +.SH SYNOPSIS +.B tend\ glyph +.RI [ @file \ ...] +.RB [ \-rt ] +.RB [ \-v +.RI < level >] +.RB [ \-ctr +.RI < conf\ thresh >] +.RB [ \-a +.RI < aniso >] +.RB [ \-atr +.RI < aniso\ thresh >] +.RB [ \-p +.RI < pos\ array >] +.RB [ \-m +.RI < mask\ vol >] +.RB [ \-mtr +.RI < mask\ thresh >] +.RB [ \-g +.RI < glyph\ shape >] +.RB [ \-sh +.RI < sharpness >] +.RB [ \-gsc +.RI < scale >] +.RB [ \-c +.RI < evector\ # >] +.RB [ \-sat +.RI < saturation >] +.RB [ \-ga +.RI < aniso >] +.RB [ \-am +.RI < aniso\ mod >] +.RB [ \-gg +.RI < gray >] +.RB [ \-gam +.RI < gamma >] +.RB [ \-emap +.RI < env\ map >] +.RB [ \-adsp +.RI < phong >] +.RB [ \-bg +.RI < background >] +.RB [ \-ec +.RI < edge\ rgb >] +.RB [ \-slc +.RI < axis\ pos >] +.RB [ \-si +.RI < slice\ image >] +.RB [ \-off +.RI < slice\ offset >] +.RB [ \-sg +.RI < slice\ gamma >] +.RB [ \-sb +.RI < slice\ bias >] +.B \-fr +.RI < from\ point > +.RB [ \-at +.RI < at\ point >] +.RB [ \-up +.RI < up\ vector >] +.RB [ \-rh ] +.RB [ \-dn +.RI < near\ clip >] +.RB [ \-df +.RI < far\ clip >] +.RB [ \-or ] +.RB [ \-ur +.RI < uMin \ uMax >] +.RB [ \-vr +.RI < vMin \ vMax >] +.RB [ \-fv +.RI < fov >] +.RB [ \-gr +.RI < glyph\ res >] +.RB [ \-wd +.RI < 3\ widths >] +.RB [ \-psc +.RI < scale >] +.RB [ \-ca +.RI < angle >] +.RB [ \-nobg ] +.RB [ \-concave ] +.RB [ \-is +.RI < nx \ ny >] +.RB [ \-ns +.RI < #\ samp >] +.RB [ \-nt +.RI < #\ threads >] +.RB [ \-al +.RI < B \ U \ V \ N \ E >] +.RB [ \-ao ] +.RB [ \-shadow +.RI < s >] +.RB [ \-hack +.RI < hack >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate postscript or ray-traced renderings of 3D glyphs. +Whether the output is postscript or a ray-traced image is controlled by the +initial +.RB \(lq \-rt \(rq +flag (by default, the output is postscript). +Because this is doing viz/graphics, many parameters need to be set. +Use a response file to simplify giving the command-line options which aren\(cqt +changing between invocations. +The postscript output is an EPS file, suitable for including as a figure in +LaTeX, or viewing with ghostview, or distilling into PDF. +The +ray-traced output is a 5 channel +.RI ( R , G , B , A , T ) +.I float +.IR nrrd , +suitable for +.RB \(lq unu\ crop\ \-min\ 0\ 0\ 0\ \-max\ 2\ M\ M \(rq +followed by +.RB \(lq unu\ gamma \(rq +and/or +.RB \(lq unu\ quantize\ \-b\ 8 \(rq. +.SH OPTIONS +.TP +.IR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-rt +generate ray-traced output. +By default (not using this option), postscript output is generated. +.TP +.B \-v\fR <\fIlevel\fR> +verbosity level +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-ctr\fR <\fIconf\ thresh\fR> +Glyphs will be drawn only for tensors with confidence values greater than this +threshold +.RI ( float ) +default: +.RB \(lq 0.5 \(rq +.TP +.B \-a\fR <\fIaniso\fR> +Which anisotropy metric to use for thresholding the data points to be drawn; +default: +.RB \(lq fa \(rq +.TP +.B \-p\fR <\fIpos\ array\fR> +Instead of being on a grid, tensors are at arbitrary locations, as defined by +this 3-by-N array of floats. +Doing this makes various other options moot; default: \(lq\(rq +.TP +.B \-m\fR <\fImask\ vol\fR> +Scalar volume (if any) for masking region in which glyphs are drawn, in +conjunction with +.RB \(lq \-mtr \(rq +flag; default: \(lq\(rq +.TP +.B \-mtr\fR <\fImask\ thresh\fR> +Glyphs will be drawn only for tensors with mask value greater than this +threshold +.RI ( float ) +default: +.RB \(lq 0.5 \(rq +.TP +.B \-g\fR <\fIglyph\ shape\fR> +shape of glyph to use for display. Possibilities include +.RB \(lq box \(rq, +.RB \(lq sphere \(rq, +.RB \(lq cylinder \(rq, +and +.RB \(lq superquad \(rq; +default: +.RB \(lq box \(rq +.TP +.B \-sh\fR <\fIsharpness\fR> +for superquadric glyphs, how much to sharp edges form as a function of +differences between eigenvalues. +Higher values mean that edges form more easily +.RI ( float ) +default: +.RB \(lq 3.0 \(rq +.TP +.B \-gsc\fR <\fIscale\fR> +over-all glyph size in world-space +.RI ( float ) +default: +.RB \(lq 0.01 \(rq +.TP +.B \-c\fR <\fIevector\ #\fR> +which eigenvector should determine coloring. (formally +.RB \(lq v \(rq) +.RB \(lq 0 \(rq, +.RB \(lq 1 \(rq, +.RB \(lq 2 \(rq, +are principal, medium, and minor +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-sat\fR <\fIsaturation\fR> +maximal saturation to use on glyph colors (use +.B 0.0 +to create a black and white image) +.RI ( float ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-ga\fR <\fIaniso\fR> +Which anisotropy metric to use for modulating the saturation of the glyph +color; default: +.RB \(lq fa \(rq +.TP +.B \-am\fR <\fIaniso\ mod\fR> +How much to modulate glyph color saturation by anisotropy (as chosen by +.RB \(lq \-ga \(rq. +If +.BR 1.0 , +then glyphs for zero anisotropy data points will have no hue. +.RI ( float ) +default: +.RB \(lq 0.0 \(rq +.TP +.B \-gg\fR <\fIgray\fR> +desaturating glyph color due to low anisotropy tends towards this gray level +.RI ( float ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-gam\fR <\fIgamma\fR> +gamma to use on color components (after saturation) +.RI ( float ) +default: +.RB \(lq 0.7 \(rq +.TP +.B \-emap\fR <\fIenv\ map\fR> +environment map to use for shading glyphs. +By default, there is no shading; default: \(lq\(rq +.TP +.B \-adsp\fR <\fIphong\fR> +phong ambient, diffuse, specular components, and specular power (4 +.IR float s); +default: +.RB \(lq 0\ 1\ 0\ 30 \(rq +.TP +.B \-bg\fR <\fIbackground\fR> +background RGB color; each component in range +.B [0.0,1.0] +(3 +.IR float s); +default: +.RB \(lq 1\ 1\ 1 \(rq +.TP +.B \-ec\fR <\fIedge\ rgb\fR> +edge RGB color; each component in range +.B [0.0,1.0] +(3 +.IR float s); +default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-slc\fR <\fIaxis\ pos\fR> +For showing a gray-scale slice of anisotropy: the axis and position along which +to slice. +Use +.RB \(lq \-1\ \-1 \(rq +to signify that no slice should be shown (2 +.IR int s); +default: +.RB \(lq \-1\ \-1 \(rq +.TP +.B \-si\fR <\fIslice\ image\fR> +Instead of showing a slice of the anisotropy used to cull glyphs, show +something else; default: \(lq\(rq +.TP +.B \-off\fR <\fIslice\ offset\fR> +Offset from slice position to render slice at (so that it doesn\(cqt occlude +glyphs). +.RI ( float ) +default: +.RB \(lq 0.0 \(rq +.TP +.B \-sg\fR <\fIslice\ gamma\fR> +Gamma to apply to values on slice. +.RI ( float ) +default: +.RB \(lq 1.7 \(rq +.TP +.B \-sb\fR <\fIslice\ bias\fR> +amount by which to bump up slice gray values prior to gamma. +.RI ( float ) +default: +.RB \(lq 0.05 \(rq +.TP +.B \-fr\fR <\fIfrom\ point\fR> +position of camera, used to determine view vector (3 +.IR double s) +.TP +.B \-at\fR <\fIat\ point\fR> +camera look-at point, used to determine view vector (3 +.IR double s) +.TP +.B \-up\fR <\fIup\ vector\fR> +camera pseudo-up vector, used to determine view coordinates (3 +.IR double s); +default: +.RB \(lq 0\ 0\ 1 \(rq +.TP +.B \-rh +use a right-handed UVN frame (V points down) +.TP +.B \-dn\fR <\fInear\ clip\fR> +position of near clipping plane, relative to look-at point +.RI ( double ); +default: +.RB \(lq \-2 \(rq +.TP +.B \-df\fR <\fIfar\ clip\fR> +position of far clipping plane, relative to look-at point +.RI ( double ); +default: +.RB \(lq 2 \(rq +.TP +.B \-or +use orthogonal projection +.TP +.B \-ur\fR <\fIuMin\fR\ \fIuMax\fR> +range in U direction of image plane (2 +.IR double s); +default: +.RB \(lq \-1\ 1 \(rq +.TP +.B \-vr\fR <\fIvMin\fR\ \fIvMax\fR> +range in V direction of image plane (2 +.IR double s); +default: +.RB \(lq \-1\ 1 \(rq +.TP +.B \-fv\fR <\fIfov\fR> +if not +.BR NaN , +vertical field-of-view, in degrees +.RI ( double ) +.TP +.B \-gr\fR <\fIglyph\ res\fR> +.B postscript only +.IP +resolution of polygonalization of glyphs (all glyphs other than the default +box) +.RI ( int ); +default: +.RB \(lq 10 \(rq +.TP +.B \-wd\fR <\fI3\ widths\fR> +.B postscript only +.IP +width of edges drawn for three kinds of glyph edges: silohuette, crease, +non-crease (3 +.IR float s); +default: +.RB \(lq 0.8\ 0.4\ 0.0 \(rq +.TP +.B \-psc\fR <\fIscale\fR> +.B postscript only +.IP +scaling from screen space units to postscript units (in points) +.RI ( float ); +default: +.RB \(lq 300 \(rq +.TP +.B \-ca\fR <\fIangle\fR> +.B postscript only +.IP +minimum crease angle +.RI ( float ); +default: +.RB \(lq 70 \(rq +.TP +.B \-nobg +.B postscript only +.IP +don\(cqt initially fill with background color +.TP +.B \-concave +use slightly buggy rendering method suitable for concave or self-occluding +objects +.TP +.B \-is\fR <\fInx\fR\ \fIny\fR> +.B ray-traced only +.IP +image size (resolution) to render (2 +.IR int s); +default: +.RB \(lq 256\ 256 \(rq +.TP +.B \-ns\fR <\fI#\ samp\fR> +.B ray-traced only +.IP +number of samples per pixel (must be a square number) +.RI ( int ); +default: +.RB \(lq 4 \(rq +.TP +.B \-nt\fR <\fI#\ threads\fR> +.B ray-traced only +.IP +number of threads to be used for rendering +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-al\fR <\fIB\fR\ \fIU\fR\ \fIV\fR\ \fIN\fR\ \fIE\fR> +.B ray-traced only +.IP +brightness +.RI ( B ), +view-space location +.RI ( U \ V \ N ), +and length of edge +.RI ( E ) +of a square area light source, for getting soft shadows. +Requires lots more samples +.RB \(lq \-ns \(rq +to converge. +Use brightness +.B 0 +(the default) to turn this off, and use environment map-based shading +.RB (\(lq \-emap \(rq) +instead. +(5 +.IR float s); +default: +.RB \(lq 0\ \-1\ \-1\ \-4\ 0.7 \(rq +.TP +.B \-ao +set up 6 area lights in a box to approximate ambient occlusion +.TP +.B \-shadow\fR <\fIs\fR> +the extent to which shadowing occurs +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-hack\fR <\fIhack\fR> +don\(cqt mind me +.RI ( string ) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output file +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-helix.1 b/tend-helix.1 new file mode 100644 index 0000000..79326f5 --- /dev/null +++ b/tend-helix.1 @@ -0,0 +1,133 @@ +.TH TEND\-HELIX "1" "April 2021" "" "User Commands" +.SH NAME +tend\-helix \- generate twisting helical tensor field +.SH SYNOPSIS +.B tend\ helix +.RB [ \-s +.RI < size >] +.RB [ \-ip +.RI < image\ orientation >] +.RB [ \-mp +.RI < measurement\ orientation >] +.RB [ \-b +.RI < boundary >] +.RB [ \-r +.RI < little\ radius >] +.RB [ \-R +.RI < big\ radius >] +.RB [ \-S +.RI < spacing >] +.RB [ \-a +.RI < angle >] +.RB [ \-nit ] +.RB [ \-ev +.RI < eigenvalues >] +.RB [ \-bg +.RI < background >] +.RB [ \-v +.RI < verbose >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate twisting helical tensor field. +The main utility of such a field is to debug handling of coordinate systems in +tensor field visualization. +The \(lqspace directions\(rq and \(lqspace origin\(rq fields of the NRRD header +determines the mapping from coordinates in the index space of the image to +coordinates in the world space in which the image is sampled. +The \(lqmeasurement frame\(rq field determines the mapping from the coordinates +of the tensor itself, to coordinates of the world space. +When these are correctly handled, the region of high anisotropy is a +right-handed helix (same as DNA). +Using differing axes sizes (via +.RB \(lq \-s \(rq) +helps make sure that the raster ordering of axes is correct. +In addition, the tensors twist relative to the helix, which exposes handling of +the measurement frame. +If you trace paths guided by the principal eigenvector of the tensors, along +the surface of the helical cylinder, you get another right-handed helix, as if +the the tensor field is modeling the result of twisting a set of fibers into +single-stranded helical bundle. +.SH OPTIONS +.TP +.B \-s\fR <\fIsize\fR> +sizes along fast, medium, and slow axes of the sampled volume, often called +\(lqX\(rq, \(lqY\(rq, and \(lqZ\(rq. +It is best to use slightly different sizes here, to expose errors in +interpreting axis ordering (e.g. \(lq\fB\-s\ 39\ 40\ 41\fR\(rq) (3 \fIint\fRs) +.TP +.B \-ip\fR <\fIimage\ orientation\fR> +quaternion quotient space orientation of image (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-mp\fR <\fImeasurement\ orientation\fR> +quaternion quotient space orientation of measurement frame (3 \fIdouble\fRs); +default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-b\fR <\fIboundary\fR> +parameter governing how fuzzy the boundary between high and low anisotropy is. +Use +.RB \(lq \-b\ 0 \(rq +for no fuzziness +.RI ( double ); +default: +.RB \(lq 10 \(rq +.TP +.B \-r\fR <\fIlittle\ radius\fR> +(minor) radius of cylinder tracing helix +.RI ( double ); +default: +.RB \(lq 30 \(rq +.TP +.B \-R\fR <\fIbig\ radius\fR> +(major) radius of helical turns +.RI ( double ); +default: +.RB \(lq 50 \(rq +.TP +.B \-S\fR <\fIspacing\fR> +spacing between turns of helix (along its axis) +.RI ( double ); +default: +.RB \(lq 100 \(rq +.TP +.B \-a\fR <\fIangle\fR> +maximal angle of twist of tensors along path. +There is no twist at helical core of path, and twist increases linearly with +radius around this path. +Positive twist angle with positive spacing resulting in a right-handed twist +around a right-handed helix. +.RI ( double ); +default: +.RB \(lq 60 \(rq +.TP +.B \-nit +changes behavior of twist angle as function of distance from center of helical +core: instead of increasing linearly as describe above, be at a constant angle +.TP +.B \-ev\fR <\fIeigenvalues\fR> +eigenvalues of tensors (in order) along direction of coil, circumferential +around coil, and radial around coil. +(3 \fIdouble\fRs); default: +.RB \(lq 0.006\ 0.002\ 0.001 \(rq +.TP +.B \-bg\fR <\fIbackground\fR> +eigenvalue of isotropic background +.RI ( double ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-v\fR <\fIverbose\fR> +verbose output +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-o\fR <\fInout\fR> +output file +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-log.1 b/tend-log.1 new file mode 100644 index 0000000..07d328a --- /dev/null +++ b/tend-log.1 @@ -0,0 +1,25 @@ +.TH TEND\-LOG "1" "April 2021" "" "User Commands" +.SH NAME +tend\-log \- calculates logarithm of the tensor +.SH SYNOPSIS +.B tend\ log +.RB [ \-i +.RI < nin >] +.B \-o +.RI < nout > +.SH DESCRIPTION +Calculates logarithm of the tensor, which is based on finding the log of the +eigenvalues. +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-msim.1 b/tend-msim.1 index 2d0b76a..3f37f0b 100644 --- a/tend-msim.1 +++ b/tend-msim.1 @@ -63,7 +63,8 @@ gradient list, one row per diffusion-weighted image .B \-b0\fR <\fIb0\ image\fR> reference non-diffusion-weighted .RB (\(lq B0 \(rq) -image, which may be needed if it isn't part of the given model parameter image +image, which may be needed if it isn\(cqt part of the given model parameter +image .TP .B \-m\fR <\fImodel\fR> model with which to simulate DWIs, which must be specified if it is not @@ -74,7 +75,7 @@ indicated by the first axis in input model image. insert a non-DW .B B0 image at the beginning of the experiment specification (useful if the given -gradient list doesn't already have one) and hence also insert a +gradient list doesn\(cqt already have one) and hence also insert a .B B0 image at the beginning of the output simulated DWIs .RB \(lq bool \(rq diff --git a/tend-norm.1 b/tend-norm.1 new file mode 100644 index 0000000..9d74928 --- /dev/null +++ b/tend-norm.1 @@ -0,0 +1,48 @@ +.TH TEND\-NORM "1" "April 2021" "" "User Commands" +.SH NAME +tend\-norm \- normalize tensor size +.SH SYNOPSIS +.B tend\ norm +.B \-w +.RI < w0 \ w1 \ w2 > +.RB [ \-a +.RI < amount >] +.RB [ \-t +.RI < target >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-w\fR <\fIw0\fR\ \fIw1\fR\ \fIw2\fR> +relative weights to put on major, medium, and minor eigenvalue when performing +normalization (internally rescaled to have a 1.0 L1 norm). +These weightings determine the tensors\(cqs \(lqsize\(rq. +(3 +.IR double s) +.TP +.B \-a\fR <\fIamount\fR> +how much of the normalization to perform +.RI ( float ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-t\fR <\fItarget\fR> +target size, post normalization +.RI ( float ) +default: +.RB \(lq 1.0 \(rq +.TP +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-point.1 b/tend-point.1 new file mode 100644 index 0000000..7e2e55e --- /dev/null +++ b/tend-point.1 @@ -0,0 +1,27 @@ +.TH TEND\-POINT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-point \- describe everything about one sample in a DT volume +.SH SYNOPSIS +.B tend\ point +.B \-p +.RI < x \ y \ z > +.RB [ \-i +.RI < nin >] +.SH OPTIONS +.TP +.TP +.B \-p\fR <\fIx\fR\ \fIy\fR\ \fIz\fR> +coordinates of sample to be described (3 +.IR int s) +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output array +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-satin.1 b/tend-satin.1 new file mode 100644 index 0000000..5b6b85f --- /dev/null +++ b/tend-satin.1 @@ -0,0 +1,113 @@ +.TH TEND\-SATIN "1" "April 2021" "" "User Commands" +.SH NAME +tend\-satin \- generate a pretty synthetic DT volume +.SH SYNOPSIS +.B tend\ satin +.RI [ \-t ] +.B \-p +.RI < aniso\ param > +.RB [ \-max +.RI < max\ cal >] +.RB [ \-min +.RI < min\ cal >] +.RB [ \-b +.RI < boundary >] +.RB [ \-br +.RI < ramp >] +.RB [ \-th +.RI < thickness >] +.RB [ \-evsc +.RI < eval\ scale >] +.RB [ \-s +.RI < size >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Generate a pretty synthetic DT volume. +The surface of a sphere or torus is covered with either linear or planar +anisotropic tensors, or somewhere in between. +.SH OPTIONS +.TP +.B \-t +generate a torus dataset, instead of the default spherical +.TP +.B \-p\fR <\fIaniso\ param\fR> +anisotropy parameter. +.B 0.0 +for one direction of linear (along the equator for spheres, or along the larger +circumference for toruses), +.B 1.0 +for planar, +.B 2.0 +for the other direction of linear (from pole to pole for spheres, or along the +smaller circumference for toruses) +.RI ( float ) +.TP +.B \-max\fR <\fImax\ cal\fR> +maximum anisotropy in dataset, according to the +.RB \(lq ca1 \(rq +anisotropy metric. +.RB \(lq 1.0 \(rq +means completely linear or completely planar anisotropy +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-min\fR <\fImin\ cal\fR> +minimum anisotropy in dataset +.RI ( float ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-b\fR <\fIboundary\fR> +parameter governing how fuzzy the boundary between high and low anisotropy is. +Use +.RB \(lq \-b\ 0 \(rq +for no fuzziness +.RI ( float ); +default: +.RB \(lq 0.05 \(rq +.TP +.B \-br\fR <\fIramp\fR> +how much to ramp up effective +.RI \(lq \-b \(rq +along Y axis. +Use +.RB \(lq \-b\ 0 \(rq +for no such ramping. +.RI ( float ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-th\fR <\fIthickness\fR> +parameter governing how thick region of high anisotropy is +.RI ( float ); +default: +.RB \(lq 0.3 \(rq +.TP +.B \-evsc\fR <\fIeval\ scale\fR> +scaling of eigenvalues +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-s\fR <\fIsize\fR> +dimensions of output volume. +For size +.IR N , +the output is +.IB N \ x\ N \ x\ N +for spheres, and +.BI 2 N \ x\ 2 N \ x\ N +for toruses +.RI ( int ); +default: +.RB \(lq 32 \(rq +.TP +.B \-o\fR <\fInout\fR> +output filename +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-shrink.1 b/tend-shrink.1 new file mode 100644 index 0000000..8c504e1 --- /dev/null +++ b/tend-shrink.1 @@ -0,0 +1,32 @@ +.TH TEND\-SHRINK "1" "April 2021" "" "User Commands" +.SH NAME +tend\-shrink \- converts a 9-value DT volume to a 7-value DT volume +.SH SYNOPSIS +.B tend\ shrink +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Converts a 9-value DT volume to a 7-value DT volume. +The confidence value is set to +.B 1.0 +everywhere. +You can +.BR unu\-splice (1) +or +.B nrrdSplice() +something else in its place later. +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume, with 9 matrix components per sample; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume, with the 7 values per sample +.RI ( string ) +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-expand (1), +.BR unu\-splice (1) diff --git a/tend-sim.1 b/tend-sim.1 index 3761398..c40a192 100644 --- a/tend-sim.1 +++ b/tend-sim.1 @@ -45,7 +45,7 @@ measurement frame. .SH OPTIONS .TP .B \-old -don't use the new +don\(cqt use the new .B tenEstimateContext functionality .TP diff --git a/tend-slice.1 b/tend-slice.1 new file mode 100644 index 0000000..a42335a --- /dev/null +++ b/tend-slice.1 @@ -0,0 +1,45 @@ +.TH TEND\-SLICE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-slice \- slice 3D tensors to get slab/image of 3D/2D tensors +.SH SYNOPSIS +.B tend\ slice +.B \-a +.RI < axis > +.B \-p +.RI < pos > +.RB [ \-d +.RI < dim >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-a\fR <\fIaxis\fR> +axis along which to slice +.RI ( int ) +.TP +.B \-p\fR <\fIpos\fR> +position to slice at +.RI ( int ) +.TP +.B \-d\fR <\fIdim\fR> +dimension of desired tensor output, can be either +.B 2 +or +.B 3 +.RI ( int ); +default: +.RB \(lq 3 \(rq +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor slice +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-sten.1 b/tend-sten.1 new file mode 100644 index 0000000..e5a13a5 --- /dev/null +++ b/tend-sten.1 @@ -0,0 +1,51 @@ +.TH TEND\-STEN "1" "April 2021" "" "User Commands" +.SH NAME +tend\-sten \- calculate structure tensors from a scalar field +.SH SYNOPSIS +.B tend\ sten +.RB [ \-ds +.RI < diff.\ scale >] +.RB [ \-is +.RI < int.\ scale >] +.RB [ \-df +.RI < downsample\ factor >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Calculate structure tensors from a scalar field. +Not a diffusion tensor, but it is symmetric and positive-definite. +.SH OPTIONS +.TP +.B \-ds\fR <\fIdiff.\ scale\fR> +differentiation scale, in pixels: the radius of the kernel used for +differentation to compute gradient vectors +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-is\fR <\fIint.\ scale\fR> +integration scale, in pixels: the radius of the kernel used for blurring outer +products of gradients in order compute structure tensors +.RI ( int ); +default: +.RB \(lq 2 \(rq +.TP +.B \-df\fR <\fIdownsample\ factor\fR> +the factor by which to downsample when creating volume of structure tensors +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-i\fR <\fInin\fR> +input scalar volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output filename +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-tconv.1 b/tend-tconv.1 new file mode 100644 index 0000000..7949634 --- /dev/null +++ b/tend-tconv.1 @@ -0,0 +1,34 @@ +.TH TEND\-TCONV "1" "April 2021" "" "User Commands" +.SH NAME +tend\-tconv \- convert between different shape triples +.SH SYNOPSIS +.B tend\ tconv +.B \-t +.RI < inType \ outType > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Convert between different shape triples. +The triple can be eigenvalues, +invariants +.BI ( J ,\ K ,\ R )\fR, +and lots of other things. +.SH OPTIONS +.TP +.B \-t\fR <\fIinType\fR\ \fIoutType\fR> +given input and desired output type of triples (2 +.IR tenTripleType s) +.TP +.B \-i\fR <\fInin\fR> +input array of triples; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output array +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-triple.1 b/tend-triple.1 new file mode 100644 index 0000000..21fe16e --- /dev/null +++ b/tend-triple.1 @@ -0,0 +1,33 @@ +.TH TEND\-TRIPLE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-triple \- compute volume of shape triples +.SH SYNOPSIS +.B tend\ triple +.B \-t +.RI < type > +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Compute volume of shape triples. +The triple can be eigenvalues, +invariants +.BI ( J ,\ K ,\ R )\fR, +and lots of other things. +.SH OPTIONS +.TP +.B \-t\fR <\fItype\fR> +desired output triple type +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output triple volume +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-unmf.1 b/tend-unmf.1 new file mode 100644 index 0000000..d97b5ce --- /dev/null +++ b/tend-unmf.1 @@ -0,0 +1,29 @@ +.TH TEND\-UNMF "1" "April 2021" "" "User Commands" +.SH NAME +tend\-unmf \- applies and removes the measurement frame +.SH SYNOPSIS +.B tend\ unmf +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Applies and removes the measurement frame. +When the given tensor volume has a measurement frame associated with it, this +will apply the measurement frame transform to all tensors to convert them into +world space, and remove the measurement frame from the +.IR nrrd . +.SH OPTIONS +.TP +.B \-i\fR <\fInin\fR> +input diffusion tensor volume (sorry, can\(cqt use usual default of +.RB \(lq \- \(rq +for stdin because of hest quirk) +.TP +.B \-o\fR <\fInout\fR> +output tensor volume +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend.1 b/tend.1 index e61040a..831950d 100644 --- a/tend.1 +++ b/tend.1 @@ -64,206 +64,92 @@ eigenvector, and then quantizes it to an 8-bit PNG: .EE .in .SH OPTIONS +.SH COMMANDS +.P +Each of the following has a corresponding man page: for example, +.BR tend\-about (1) +for +.RB \(lq tend\ about \(rq. .SS tend\ about Information about this program and its use -.P -See -.BR tend\-about (1). .SS tend\ grads Calculate balanced gradient directions for DWI acquisition -.P -See -.BR tend\-grads (1). .SS tend\ epireg Register diffusion-weighted echo-planar images -.P -See -.BR tend\-epireg (1). .SS tend\ bmat Calculate B-matrix given gradient directions -.P -See -.BR tend\-bmat (1). .SS tend\ estim Estimate tensors from a set of DW images -.P -See -.BR tend\-estim (1). .SS tend\ sim Simulate DW images from a tensor field -.P -See -.BR tend\-sim (1). .SS tend\ mfit Estimate models from a set of DW images -.P -See -.BR tend\-mfit (1). .SS tend\ mconv Convert from one model to another -.P -See -.BR tend\-mconv (1). .SS tend\ msim Simulate DW images from an image of models -.P -See -.BR tend\-msim (1). .SS tend\ make Create DT volume from confidence and eigensystem -.P -See -.BR tend\-make (1). .SS tend\ avg Average across tensor volumes -.P -See -.BR tend\-avg (1). .SS tend\ helix Generate twisting helical tensor field -.P -See -.BR tend\-helix (1). .SS tend\ sten Calculate structure tensors from a scalar field -.P -See -.BR tend\-sten (1). .SS tend\ glyph Generate postscript or ray-traced renderings of 3D glyphs -.P -See -.BR tend\-glyph (1). .SS tend\ ellipse Generate postscript renderings of 2D glyphs -.P -See -.BR tend\-ellipse (1). .SS tend\ anplot Graph anisotropy metric in barycentric coords -.P -See -.BR tend\-anplot (1). .SS tend\ anvol Apply an anisotropy metric to a DT volume -.P -See -.BR tend\-anvol (1). .SS tend\ anscale Scale the anisotropic component of the tensors -.P -See -.BR tend\-anscale (1). .SS tend\ anhist Generate barycentric histograms of anisotropy -.P -See -.BR tend\-anhist (1). .SS tend\ triple Compute volume of shape triples -.P -See -.BR tend\-triple (1). .SS tend\ tconv Convert between different shape triples -.P -See -.BR tend\-tconv (1). .SS tend\ point Describe everything about one sample in a DT volume -.P -See -.BR tend\-point (1). .SS tend\ slice Slice 3D tensors to get slab/image of 3D/2D tensors -.P -See -.BR tend\-slice (1). .SS tend\ norm Normalize tensor size -.P -See -.BR tend\-norm (1). .SS tend\ fiber Fiber tractography, from one or more seeds -.P -See -.BR tend\-fiber (1). .SS tend\ eval Calculate one or more eigenvalues in a DT volume -.P -See -.BR tend\-eval (1). .SS tend\ evalpow Modify shape by raising eigenvalues to some power -.P -See -.BR tend\-evalpow (1). .SS tend\ evalclamp Modify shape by clamping eigenvalues in some range -.P -See -.BR tend\-evalclamp (1). .SS tend\ evaladd Modify shape by adding a constant to all eigenvalues -.P -See -.BR tend\-evaladd (1). -.SS tend\ evalmul +.SS tend\ evalmult Modify shape by multiplying eigenvalues by a constant -.P -See -.BR tend\-evalmul (1). .SS tend\ log Calculates logarithm of the tensor -.P -See -.BR tend\-log (1). .SS tend\ exp Calculates \fBexp()\fR of the tensor -.P -See -.BR tend\-exp (1). .SS tend\ evec Calculate one or more eigenvectors in a DT volume -.P -See -.BR tend\-evec (1). .SS tend\ evecrgb Make an RGB volume from an eigenvector and an anisotropy -.P -See -.BR tend\-evecrgb (1). .SS tend\ evq Quantize directions of diffusion -.P -See -.BR tend\-evq (1). .SS tend\ unmf Applies and removes the measurement frame -.P -See -.BR tend\-unmf (1). .SS tend\ expand Converts masked non-redundant tensor images to redundant -.P -See -.BR tend\-expand (1). .SS tend\ shrink Converts a 9-value DT volume to a 7-value DT volume -.P -See -.BR tend\-shrink (1). .SS tend\ bfit Non-linear least-squares fitting of b-value curves -.P -See -.BR tend\-bfit (1). .SS tend\ satin Generate a pretty synthetic DT volume -.P -See -.BR tend\-satin (1). .SH "SEE\ ALSO" .BR gprobe (1), .BR ilk (1), @@ -288,7 +174,7 @@ See .BR tend\-eval (1), .BR tend\-evaladd (1), .BR tend\-evalclamp (1), -.BR tend\-evalmul (1), +.BR tend\-evalmult (1), .BR tend\-evalpow (1), .BR tend\-evec (1), .BR tend\-evecrgb (1), diff --git a/unu.1 b/unu.1 index ef710be..6f8b611 100644 --- a/unu.1 +++ b/unu.1 @@ -115,6 +115,194 @@ Formats available: .P Nrrd data encodings available: .B raw ascii hex gz bz2 +.SH COMMANDS +\" .P +\" Each of the following has a corresponding man page: for example, +\" .BR unu\-about (1) +\" for +\" .RB \(lq unu\ about \(rq. +.SS unu about +Information about this program and its use +.SS unu env +List relevant environment variables and their values +.SS unu i2w +Convert from 1-D index to world position +.SS unu w2i +Convert from 1-D world to index position +.SS unu make +Create a +.I nrrd +(or +.I nrrd +header) from scratch +.SS unu head +Print header of one or more +.I nrrd +files +.SS unu data +Print data segment of a +.I nrrd +file +.SS unu convert +Convert to another type (as if by cast, w/ optional clamp) +.SS unu resample +Filtering and {up,down}sampling with a separable kernel +.SS unu fft +Fast Fourier Transform of selected axes +.SS unu cmedian +Cheap histogram-based median/mode filtering +.SS unu dist +Euclidean distance transform +.SS unu minmax +Print out min and max values in one or more +.IR nrrd s +.SS unu cksum +Compute 32-bit CRC of +.I nrrd +data (same as via +.BR cksum (1)) +.SS unu diff +Sees if two +.IR nrrd s +are different in any way +.SS unu quantize +Quantize values to 8, 16, or 32 bits +.SS unu unquantize +Recover floating point values from quantized data +.SS unu project +Collapse scanlines to scalars along some axis +.SS unu slice +Slice along one or more axes at given positions +.SS unu sselect +Select subset of slices along an axis +.SS unu dice +Save all slices along one axis into separate files +.SS unu splice +Replace a slice with a different +.I nrrd +.SS unu join +Connect slices and/or slabs into a bigger +.I nrrd +.SS unu crop +Crop along each axis to make a smaller +.I nrrd +.SS unu acrop +Automatically crop axes based on given measure +.SS unu inset +Replace a sub-region with a different +.I nrrd +.SS unu pad +Pad along each axis to make a bigger +.I nrrd +.SS unu reshape +Superficially change dimension and/or axes sizes +.SS unu permute +Permute ordering of axes +.SS unu swap +Interchange ordering of two axes +.SS unu shuffle +Permute slices along one axis +.SS unu flip +Reverse order of slices along one axis +.SS unu unorient +Make image orientation be axis-aligned +.SS unu axinfo +Modify attributes of one or more axes +.SS unu axinsert +Add a \(lqstub\(rq (length 1) axis to a +.I nrrd +.SS unu axsplit +Split one axis into two axes +.SS unu axdelete +Remove one or more singleton axes from a +.I nrrd +.SS unu axmerge +Merge two adjacent axes into one +.SS unu tile +Tile slices of one axis into two other axes +.SS unu untile +Undo +.BR unu\-tile (1): +merge slow parts of two axis splits +.SS unu histo +Create 1-D histogram of values in a +.I nrrd +.SS unu dhisto +Create image of 1-D value histogram +.SS unu jhisto +Create joint histogram of two or more +.IR nrrd s +.SS unu histax +Replace each scanline along an axis with its histogram +.SS unu heq +Perform histogram equalization +.SS unu gamma +Brighten or darken values with a gamma +.SS unu 1op +Unary operation on a +.I nrrd +.SS unu 2op +Binary operation on two +.IR nrrd s, +or on a +.I nrrd +and a constant +.SS unu 3op +Ternary operation on three +.IR nrrd s +or constants +.SS unu affine +Affine (lerp) mapping on 5 +.IR nrrd s +or constants +.SS unu lut +Map +.I nrrd +through one univariate lookup table +.SS unu mlut +Map +.I nrrd +through whole +.I nrrd +of univariate lookup tables +.SS unu subst +Map +.I nrrd +through a univariate substitution table +.SS unu rmap +Map +.I nrrd +through one +.B regular +univariate map (\(lqcolormap\(rq) +.SS unu mrmap +Map +.I nrrd +through a whole +.I nrrd +of regular univariate maps +.SS unu imap +Map +.I nrrd +through +.B irregular +univariate map (\(lqcolormap\(rq) +.SS unu lut2 +Map +.I nrrd +through a bivariate lookup table +.SS unu ccfind +Find connected components (CCs) +.SS unu ccadj +Form adjecency matrix of connected components +.SS unu ccmerge +Merge CCs with their neighbors, under various constraints +.SS unu ccsettle +Remap CC values down to lowest contiguous values +.SS unu save +Write +.I nrrd +with specific format, encoding, or endianness .SH "SEE\ ALSO" .BR gprobe (1), .BR ilk (1), @@ -125,3 +313,66 @@ Nrrd data encodings available: .BR puller (1), .BR tend (1), .BR vprobe (1) +\" .BR vprobe (1), +\" .BR unu-1op (1), +\" .BR unu-2op (1), +\" .BR unu-3op (1), +\" .BR unu-about (1), +\" .BR unu-acrop (1), +\" .BR unu-affine (1), +\" .BR unu-axdelete (1), +\" .BR unu-axinfo (1), +\" .BR unu-axinsert (1), +\" .BR unu-axmerge (1), +\" .BR unu-axsplit (1), +\" .BR unu-ccadj (1), +\" .BR unu-ccfind (1), +\" .BR unu-ccmerge (1), +\" .BR unu-ccsettle (1), +\" .BR unu-cksum (1), +\" .BR unu-cmedian (1), +\" .BR unu-convert (1), +\" .BR unu-crop (1), +\" .BR unu-data (1), +\" .BR unu-dhisto (1), +\" .BR unu-dice (1), +\" .BR unu-diff (1), +\" .BR unu-dist (1), +\" .BR unu-env (1), +\" .BR unu-fft (1), +\" .BR unu-flip (1), +\" .BR unu-gamma (1), +\" .BR unu-head (1), +\" .BR unu-heq (1), +\" .BR unu-histax (1), +\" .BR unu-histo (1), +\" .BR unu-i2w (1), +\" .BR unu-imap (1), +\" .BR unu-inset (1), +\" .BR unu-jhisto (1), +\" .BR unu-join (1), +\" .BR unu-lut (1), +\" .BR unu-lut2 (1), +\" .BR unu-make (1), +\" .BR unu-minmax (1), +\" .BR unu-mlut (1), +\" .BR unu-mrmap (1), +\" .BR unu-pad (1), +\" .BR unu-permute (1), +\" .BR unu-project (1), +\" .BR unu-quantize (1), +\" .BR unu-resample (1), +\" .BR unu-reshape (1), +\" .BR unu-rmap (1), +\" .BR unu-save (1), +\" .BR unu-shuffle (1), +\" .BR unu-slice (1), +\" .BR unu-splice (1), +\" .BR unu-sselect (1), +\" .BR unu-subst (1), +\" .BR unu-swap (1), +\" .BR unu-tile (1), +\" .BR unu-unorient (1), +\" .BR unu-unquantize (1), +\" .BR unu-untile (1), +\" .BR unu-w2i (1) commit 8d05a3a34a29ea41d5b2ca9712f366ef4f57a1b2 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 6 12:03:06 2021 -0400 Add an rpmlintrc file diff --git a/teem.rpmlintrc b/teem.rpmlintrc new file mode 100644 index 0000000..890462c --- /dev/null +++ b/teem.rpmlintrc @@ -0,0 +1,5 @@ +# These are not real spelling errors... +addFilter(r'spelling-error .*($en_US$| en_US) (resample|datasets|' + r'tractography|unu) ') +# Indeed, there is no dedicated documentation for some subpackages. +addFilter(r' no-documentation$') commit d09ed97c6dc65490fb502eeb6baaae9b3b304a14 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 6 11:59:36 2021 -0400 rewrap description diff --git a/teem.spec b/teem.spec index 563e3b5..61764d0 100644 --- a/teem.spec +++ b/teem.spec @@ -182,8 +182,8 @@ Strengths of Teem Slicer. • Teem is light-weight: The libraries are written with an eye towards minimizing the annoyance of getting data in an out, by using the simplest - possible constructs for the job, and by supporting combinations of operations - that arise in common practice. + possible constructs for the job, and by supporting combinations of + operations that arise in common practice. • Teem is coherent: There is a consistent logic to how information is represented, and uniformity in the APIs across libraries. • Teem is portable: All the code is written in plain ANSI C, so it compiles commit b3cb082255b1984b8f5a864a4576729446f37aee Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 6 11:36:04 2021 -0400 Fix single-threading tests diff --git a/teem.spec b/teem.spec index b69288c..563e3b5 100644 --- a/teem.spec +++ b/teem.spec @@ -298,7 +298,8 @@ install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ %endif # Tests are not parallel-safe -%ctest3 %{?ctest_excludes} -j1 +%global _smp_mflags -j1 +%ctest3 %{?ctest_excludes} %if 0%{?epel} == 7 commit ba847837bef28947baf576882c1463ada7d0ae7f Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Tue Apr 6 11:34:57 2021 -0400 Start work on adding a complete set of man pages diff --git a/gprobe.1 b/gprobe.1 new file mode 100644 index 0000000..4f35b12 --- /dev/null +++ b/gprobe.1 @@ -0,0 +1,264 @@ +.TH GPROBE "1" "April 2021" "" "User Commands" +.SH NAME +gprobe \- shows off the functionality of the gage library +.SH SYNOPSIS +.B gprobe +.B \-i +.RI < nin > +.B \-k +.RI < kind > +.RB [ \-v +.RI < verbosity >] +.B \-q +.RI < query > +.RB [ \-gmc +.RI < min\ gradmag >] +.RB [ \-ofs ] +.RB [ \-seed +.RI < N >] +.RB [ \-c +.RI < bool >] +.RB [ \-k00 +.RI < kern00 >] +.RB [ \-k11 +.RI < kern11 >] +.RB [ \-k22 +.RI < kern22 >] +.RB [ \-rn ] +.RB [ \-ssn +.RI < SS\ # >] +.RB [ \-ssr +.RI < scale\ range >] +.RB [ \-kssb +.RI < kernel >] +.RB [ \-kssr +.RI < kernel >] +.RB [ \-ssu ] +.RB [ \-sso ] +.RB [ \-ssnd ] +.RB [ \-ssnb +.RI < bias >] +.RB [ \-ssf +.RI < SS\ read/save\ format >] +.RB [ \-s +.RI < sclX \ xclY \ sxlZ >] +.RB [ \-ssp +.RI < pos >] +.RB [ \-pg +.RI < nrrd >] +.RB [ \-pi +.RI < nrrd >] +.RB [ \-pp +.RI < pos \ ...>] +.RB [ \-eps +.RI < epsilon >] +.RB [ \-psi +.RI < p >] +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Shows off the functionality of the gage library. +Uses gageProbe() to query various kinds of volumes to learn various measured or +derived quantities. +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR> +input volume +.TP +.B \-k\fR\ <\fIkind\fR> +\(lqkind\(rq of volume +.RB (\(lq scalar \(rq, +.RB \(lq vector \(rq, +.RB \(lq tensor \(rq, +or +.RB \(lq dwi \(rq) +.TP +.B \-v\fR\ <\fIverbosity\fR> +verbosity level +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-q\fR\ <\fIquery\fR> +the quantity +.RB ( scalar , +.BR vector , +or +.BR matrix ) +to learn by probing +.RI ( string ) +.TP +.B \-gmc\fR\ <\fImin\ gradmag\fR> +For curvature-based queries, use zero when gradient magnitude is below this +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-ofs +If only per-axis spacing is available, use that to contrive full orientation +info +.TP +.B \-seed\fR\ <\fIN\fR> +RNG seed; mostly for debugging +.RI ( unsigned\ int ); +default: +.RB \(lq 42 \(rq +.TP +.B \-c\fR\ <\fIbool\fR> +clamp positions as part of probing +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-k00\fR\ <\fIkern00\fR> +kernel for +.BR gageKernel00 ; +default: +.RB \(lq tent \(rq +.TP +.B \-k11\fR\ <\fIkern11\fR> +kernel for +.BR gageKernel11 ; +default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR\ <\fIkern22\fR> +kernel for +.BR gageKernel22 ; +default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-rn +renormalize kernel weights at each new sample location. +\(lqAccurate\(rq kernels don\(cqt need this; doing it always makes things go +slower +.TP +.B \-ssn\fR\ <\fISS\ #\fR> +how many scale-space samples to evaluate, or, +.B 0 +to turn-off all scale-space behavior +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ssr\fR\ <\fIscale\ range\fR> +range of scales in scale-space (2 +.IR double s); +default: +.RB \(lq nan\ nan \(rq +.TP +.B \-kssb\fR\ <\fIkernel\fR> +blurring kernel, to sample scale space; default: +.RB \(lq dgauss:1,5 \(rq +.TP +.B \-kssr\fR\ <\fIkernel\fR> +kernel for reconstructing from scale space samples +.RB \(lq hermite \(rq +.TP +.B \-ssu +do uniform samples along sigma, and not (by default) samples according to the +effective diffusion scale +.TP +.B \-sso +if not using \(lq\-ssu\(rq, use pre-computed optimal sigmas when possible +.TP +.B \-ssnd +normalize derivatives by scale +.TP +.B \-ssnb\fR\ <\fIbias\fR> +bias on scale-based derivative normalization +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-ssf\fR\ <\fISS\ read/save\ format\fR> +.BR printf (3)\-style +format (including a +.RB \(lq %u \(rq) +for the filenames from which to read pre-blurred volumes computed for the +stack, if they exist and match the stack parameters, and where to save them if +they had to be re-computed. +Leave this as empty string to disable this. +.RI ( string ); +default: \(lq\(rq +.TP +.B \-s\fR\ <\fIsclX\fR\ \fIsclY\fR\ \fIsxlZ\fR> +scaling factor for resampling on each axis +.RB (> 1.0 : +supersampling); use +.RB \(lq \-ssp \(rq +(and +.RB \(lq \-psi \(rq) +to specify scale position of sampling (3 +.IR double s); +default: +.RB \(lq 1\ 1\ 1 \(rq +.TP +.B \-ssp\fR\ <\fIpos\fR> +when using scale-space, scale-position at which to probe +.RI ( double ); +default: +.RB \(lq 0 \(rq +.TP +.B \-pg\fR\ <\fInrrd\fR> +overrides +.RB \(lq \-s \(rq: +2-D +.I nrrd +which specifies origin and direction vectors for sampling grid; default: +\(lq\(rq +.TP +.B \-pi\fR\ <\fInrrd\fR> +overrides +.RB \(lq \-pv \(rq: +probes at this list of 3-vec or 4-vec positions; default: +\(lq\(rq +.TP +.B \-pp\fR\ <\fIpos\fR ...> +overrides +.RB \(lq \-pi \(rq: +only sample at this specified point (3..4 \fIdouble\fRs); default: +.RB \(lq nan\ nan \(rq +.TP +.B \-eps\fR\ <\fIepsilon\fR> +if non-zero, and if query is a scalar, and if using +.RB \(lq \-pp \(rq +to query at a single point, then do +.I epsilon +offset probes to calculate discrete differences, to find the numerical gradient +and hessian (for debugging) +.RI ( double ); +default: +.RB \(lq 0 \(rq +.TP +.B \-psi\fR\ <\fIp\fR> +whether the probe location specification (by any of the four previous flags) +are in index space +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-t\fR\ <\fItype\fR> +type of output volume +.RI ( type ); +default: +.RB \(lq float \(rq +.TP +.B \-o\fR\ <\fInout\fR> +output volume +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR ilk (1), +.BR miter (1), +.BR mrender (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/ilk.1 b/ilk.1 new file mode 100644 index 0000000..51b2915 --- /dev/null +++ b/ilk.1 @@ -0,0 +1,180 @@ +.TH ILK "1" "April 2021" "" "User Commands" +.SH NAME +ilk \- (I)mage (L)inear Trans(X\-\->K)forms +.SH SYNOPSIS +.B ilk +.RI [ @file \ ...] +.RB [ \-i +.RI < image >] +.RB [ \-0 +.RI < origin >] +.B \-t +.RI < xform0 \ ...> +.RB [ \-k +.RI < kernel >] +.RB [ \-min +.RI < xMin \ yMin >] +.RB [ \-max +.RI < xMax \ yMax >] +.RB [ \-b +.RI < boundary >] +.RB [ \-bg +.RI < bg0 \ bg1 \ ...>] +.RB [ \-s +.RI < xSize \ ySize >] +.RB [ \-a +.RI < avg\ # >] +.RB [ \-o +.RI < filename >] +.SH DESCRIPTION +.P +(I)mage (L)inear Trans(X\-\->K)forms. +Applies linear (homogenous coordinate) transforms to a given image, using the +given kernel for resampling. +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fIimage\fR> +input image; default: +.RB \(lq \- \(rq +.TP +.B \-0\fR <\fIorigin\fR> +where to locate +.B (0,0) +prior to applying transforms. +.RS +7n +.IP \(bu 2 +.RB \(lq u:<\fIfloat\fB>,<\fIfloat\fB> \(rq +locate origin in a unit box +.B [0,1]x[0,1] +which covers the original image +.IP \(bu 2 +.RB \(lq p:<\fIfloat\fB>,<\fIfloat\fB> \(rq +locate origin at a particular pixel location, in the index space of the image +.P +default: +.RB \(lq p:0,0 \(rq +.RE +.TP +.B \-t\fR <\fIxform0\fR\ ...> +transform(s) to apply to image. +Transforms are applied in the order in which they appear. +.RS +7n +.IP \(bu 2 +.RB \(lq identity \(rq: +no geometric transform, just resampling +.IP \(bu 2 +.RB \(lq translate:\fIx\fB,\fIy\fB \(rq: +shift image by vector +.BR (\fIx\fB,\fIy\fB) , +as measured in pixels +.IP \(bu 2 +.RB \(lq rotate:\fIang\fB \(rq: +rotate CCW by +.I ang +degrees +.IP \(bu 2 +.RB \(lq scale:\fIxs\fB,\fIys\fB \(rq: +scale by +.I xs +in X, and +.I ys +in Y +.IP \(bu 2 +.RB \(lq shear:\fIfix\fB,\fIamnt\fB \(rq: +shear by +.IR amnt , +keeping fixed the pixels along a direction +.RI < fix > +degrees from the X axis +.IP \(bu 2 +.RB \(lq flip:\fIang\fB \(rq: +flip along axis an angle +.RI < ang > +degrees from the X axis +.IP \(bu 2 +.RB \(lq \fIa\fB,\fIb\fB,\fItx\fB,\fIc\fB,\fId\fB,\fIty\fB \(rq: +specify the transform explicitly in row-major order (opposite of PostScript) +(1 or more 2D transforms) +.RE +.TP +.B \-k\fR <\fIkernel\fR> +reconstruction kernel; default: +.RB \(lq cubic:0,0.5 \(rq +.TP +.B \-min\fR <\fIxMin\fR\ \fIyMin\fR> +lower bounding corner of output image. +Default (by not using this option) is the lower corner of input image. +(2 \fIdouble\fRs) +.TP +.B \-max\fR <\fIxMax\fR\ \fIyMax\fR> +upper bounding corner of output image. +Default (by not using this option) is the upper corner of input image. +(2 \fIdouble\fRs) +.TP +.B \-b\fR <\fIboundary\fR> +what to do when sampling outside original image. +.RS +7n +.IP \(bu 2 +.RB \(lq bleed \(rq: +copy values at image border outward +.IP \(bu 2 +.RB \(lq wrap \(rq: +do wrap-around on image locations +.IP \(bu 2 +.RB \(lq pad \(rq: +use a given background value (via +.RB \(lq \-bg \(rq) +.P +default: +.RB \(lq bleed \(rq +.RE +.TP +.B \-bg\fR <\fIbg0\fR\ \fIbg1\fR\ ...> +background color to use with boundary behavior +.RB \(lq pad \(rq. +Defaults to all zeroes. +(1 or more \fIfloat\fRs) +.TP +.B \-s\fR <\fIxSize\fR\ \fIySize\fR> +For each axis, information about how many samples in output: +.RS +7n +.IP \(bu 2 +.RB \(lq x\fR<\fIfloat\fR> \(rq: +number of output samples is some scaling of the number input of samples; +multiplied by +.RI < float > +.IP \(bu 2 +.RB \(lq \fR<\fIint\fR> \(rq: +specify exact number of samples +(2 sampling specifications) +.P +default: +.RB \(lq x1\ x1 \(rq +.RE +.TP +.B \-a\fR <\fIavg\ #\fR> +number of averages (if there there is only one rotation) +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output +.I nrrd +to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR miter (1), +.BR mrender (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/miter.1 b/miter.1 new file mode 100644 index 0000000..75d7ef4 --- /dev/null +++ b/miter.1 @@ -0,0 +1,287 @@ +.TH MITER "1" "April 2021" "" "User Commands" +.SH NAME +miter \- a simple but effective little volume renderer +.SH SYNOPSIS +.B miter +.RI [ @file \ ...] +.RB [ \-i +.RI < nsin >] +.RB [ \-vi +.RI < nvin >] +.RB [ \-ti +.RI < ntin >] +.B \-txf +.RI < nin \ ...> +.B \-fr +.RI < eye\ pos > +.RB [ \-at +.RI < at\ pos >] +.RB [ \-up +.RI < up\ dir >] +.RB [ \-rh ] +.RB [ \-or ] +.B \-dn +.RI < near > +.B \-di +.RI < image > +.B \-df +.RI < far > +.RB [ \-ar ] +.RB [ \-ur +.RI < uMin\fR\ \fIuMax >] +.RB [ \-vr +.RI < vMin\fR\ \fIvMax >] +.RB [ \-fv +.RI < field\ of\ view >] +.RB [ \-offfr ] +.RB [ \-fr +.RI < fake\ from >] +.RB [ \-turn +.RI < angle >] +.RB [ \-am +.RI < ambient >] +.RB [ \-ld +.RI < light\ pos >] +.RB [ \-is +.RI < image\ size >] +.RB [ \-iss +.RI < scale >] +.RB [ \-ads +.RI < ka\fR\ \fIkd\fR\ \fIks >] +.RB [ \-sp +.RI < spec\ pow >] +.RB [ \-k00 +.RI < kernel >] +.RB [ \-k11 +.RI < kernel >] +.RB [ \-k22 +.RI < kernel >] +.RB [ \-ss +.RI < shading\ spec >] +.RB [ \-ns +.RI < normal\ spec >] +.RB [ \-side +.RI < normal\ side >] +.RB [ \-rn ] +.RB [ \-gmc +.RI < min\ gradmag >] +.RB [ \-step +.RI < size >] +.RB [ \-ref +.RI < size >] +.RB [ \-vp +.RI < verbose pixel >] +.RB [ \-n1 +.RI < near1 >] +.RB [ \-nt +.RI < #\ threads >] +.RB [ \-o +.RI < filename >] +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fInsin\fR> +input scalar volume to render +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-vi\fR <\fInvin\fR> +input vector volume to render +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-ti\fR <\fIntin\fR> +input tensor volume to render +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-txf\fR <\fInin\fR\ ...> +one or more transfer functions (1 or more +.IR nrrd s) +.TP +.B \-fr\fR <\fIeye\ pos\fR> +camera eye point (3 \fIdouble\fRs) +.TP +.B \-at\fR <\fIat\ pos\fR> +camera look-at point (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-up\fR <\fIup\ dir\fR> +camera pseudo-up vector (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 1 \(rq +.TP +.B \-rh +use a right-handed UVN frame (V points down) +.TP +.B \-or +orthogonal (not perspective) projection +.TP +.B \-dn\fR <\fInear\fR> +distance to near clipping plane +.RI ( double ) +.TP +.B \-di\fR <\fIimage\fR> +distance to image plane +.RI ( double ) +.TP +.B \-df\fR <\fIfar\fR> +distance to far clipping plane +.RI ( double ) +.TP +.B \-ur\fR <\fIuMin\fR\ \fIuMax\fR> +range in U direction of image plane (2 +.IR double s) +.TP +.B \-vr\fR <\fIvMin\fR\ \fIvMax\fR> +range in V direction of image plane (2 +.IR double s) +.TP +.B \-fv\fR <\fIfield\ of\ view\fR> +angle (in degrees) vertically subtended by view window +.RI ( double ); +default: +.RB \(lq 20 \(rq +.TP +.B \-offfr +the given eye point +.RB (\(lq \-fr \(rq) +is to be interpreted as an offset from the at point. +.TP +.B \-ffr\fR <\fIfake\ from\fR> +eye point to use for view-dependent transfer functions. +By default (not using this option), the point used is the normally specified +camera eye point. (3 \fIdouble\fRs) +.TP +.B \-turn\fR <\fIangle\fR> +angle (degrees) by which to rotate the from point around true up, for making +stereo pairs. +Positive means move towards positive U (the right) +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-am\fR <\fIambient\fR> +ambient light color (3 \fIfloat\fRs); default: +.RB \(lq 1\ 1\ 1 \(rq +.TP +.B \-ld\fR <\fIlight\ pos\fR> +view space light position (extended to infinity) (3 \fIfloat\fRs); default: +.RB \(lq 0\ 0\ \-1 \(rq +.TP +.B \-is\fR <\fIimage\ size\fR> +image dimensions (2 \fIint\fRs); default: +.RB \(lq 256\ 256 \(rq +.TP +.B \-iss\fR <\fIscale\fR> +scaling of image size (from +.RB \(lq \-is \(rq) +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-ads\fR <\fIka\fR\ \fIkd\fR\ \fIks\fR> +phong components (3 \fIfloat\fRs); default: +.RB \(lq 0.1\ 0.6\ 0.3 \(rq +.TP +.B \-sp\fR <\fIka\fR\ \fIkd\fR\ \fIks\fR> +phong specular power +.RI ( double ); default: +.RB \(lq 30 \(rq +.TP +.B \-k00\fR <\fIkernel\fR> +value reconstruction kernel (\fIkernel specification\fR); default: +.RB \(lq tent \(rq +.TP +.B \-k11\fR <\fIkernel\fR> +first derivative kernel (\fIkernel specification\fR); default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR <\fIkernel\fR> +second derivative kernel (\fIkernel specification\fR); default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-ss\fR <\fIshading\ spec\fR> +how to do shading +.RI ( string ); +default: +.RB \(lq phong:gage(scalar:n) \(rq +.TP +.B \-ns\fR <\fInormal\ spec\fR> +\(lqnormal\(rq to use for those miteVal\(cqs that need one +.RI ( string ); +default: \(lq\(rq +.TP +.B \-side\fR <\fInormal\ side\fR> +how to interpret gradients as normals: +.RS +7n +.IP \(bu 2 +.RB \(lq 1 \(rq: +normal points to lower values (higher == more \(lqinside\(rq) +.IP \(bu 2 +.RB \(lq 0 \(rq: +\(lqtwo-sided\(rq: dot-products are \fBabs()\fR\(cqed +.IP \(bu 2 +.RB \(lq \-1 \(rq: +normal points to higher values (lower == more \(lqinside\(rq) +.P +default: +.RB \(lq 1 \(rq +.RE +.TP +.B \-rn +renormalize kernel weights at each new sample location. +\(lqAccurate\(rq kernels don\(cqt need this; doing it always makes things go +slower +.B \-gmc\fR\ <\fImin\ gradmag\fR> +For curvature-based transfer functions, set curvature to zero when gradient +magnitude is below this +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-step\fR\ <\fIsize\fR> +step size along ray in world space +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-ref\fR\ <\fIsize\fR> +\(lqreference\(rq step size (world space) for doing opacity correction in +compositing +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-vp\fR\ <\fIverbose\ pixel\fR> +pixel for which to turn on verbose messages (2 \fIint\fRs); default: +.RB \(lq \-1\ \-1 \(rq +.TP +.B \-n1\fR\ <\fInear1\fR> +opacity close enough to 1.0 to terminate ray +.RI ( double ); +default: +.RB \(lq 0.99 \(rq +.TP +.B \-nt\fR\ <\fI#\ threads\fR> +number of threads hoover should use +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output nrrd to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/mrender.1 b/mrender.1 new file mode 100644 index 0000000..f619ac2 --- /dev/null +++ b/mrender.1 @@ -0,0 +1,294 @@ +.TH MRENDER "1" "April 2021" "" "User Commands" +.SH NAME +mrender \- a demonstration of hoover, gage, and nrrd measures +.SH SYNOPSIS +.B mrender +.RI [ @file \ ...] +.RB [ \-i +.RI < nin >] +.B \-k +.RI < kind > +.B \-fr +.RI < eye\ pos > +.RB [ \-at +.RI < at\ pos >] +.RB [ \-up +.RI < up\ dir >] +.RB [ \-rh ] +.RB [ \-or ] +.B \-dn +.RI < near > +.B \-di +.RI < image > +.B \-df +.RI < far > +.RB [ \-ar ] +.RB [ \-ur +.RI < uMin\fR\ \fIuMax >] +.RB [ \-vr +.RI < vMin\fR\ \fIvMax >] +.RB [ \-fv +.RI < field\ of\ view >] +.RB [ \-offfr ] +.RB [ \-turn +.RI < angle >] +.RB [ \-is +.RI < image\ size >] +.RB [ \-iss +.RI < scale >] +.RB [ \-k00 +.RI < kernel >] +.RB [ \-k11 +.RI < kernel >] +.RB [ \-k22 +.RI < kernel >] +.RB [ \-rn ] +.B \-q +.RI < query > +.B \-m +.RI < measure > +.RB [ \-gmc +.RI < min\ gradmag >] +.RB [ \-fn +.RI < from\ nan >] +.RB [ \-step +.RB [ \-nt +.RI < #\ threads >] +.RB [ \-vp +.RI < img\ coords >] +.RB [ \-o +.RI < filename >] +.SH DESCRIPTION +.P +Uses hoover to cast rays through a volume (scalar, vector, or tensor), gage to +measure one of various quantities along the rays, and a specified +.I nrrd +measure to reduce all the values along a ray down to one scalar, which is saved +in the output +.RI ( double ) +image. +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fInin\fR> +input +.I nrrd +to render +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-k\fR <\fIkind\fR> +\(lqkind\(rq of volume +.RB (\(lq scalar \(rq, +.RB \(lq vector \(rq, +or +.RB \(lq tensor \(rq) +.RI ( gageKind ) +.TP +.B \-fr\fR <\fIeye\ pos\fR> +camera eye point (3 \fIdouble\fRs) +.TP +.B \-at\fR <\fIat\ pos\fR> +camera look-at point (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-up\fR <\fIup\ dir\fR> +camera pseudo-up vector (3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 1 \(rq +.TP +.B \-rh +use a right-handed UVN frame (V points down) +.TP +.B \-or +orthogonal (not perspective) projection +.TP +.B \-dn\fR <\fInear\fR> +distance to near clipping plane +.RI ( double ) +.TP +.B \-di\fR <\fIimage\fR> +distance to image plane +.RI ( double ) +.TP +.B \-df\fR <\fIfar\fR> +distance to far clipping plane +.RI ( double ) +.TP +.B \-ar +near, image, and far plane distances are relative to the +.B at +point, instead of the eye point +.TP +.B \-ur\fR <\fIuMin\fR\ \fIuMax\fR> +range in U direction of image plane (2 +.IR double s); +default: +.RB \(lq nan\ nan \(rq +.TP +.B \-vr\fR <\fIvMin\fR\ \fIvMax\fR> +range in V direction of image plane (2 +.IR double s); +default: +.RB \(lq nan\ nan \(rq +.TP +.B \-fv\fR <\fIfield\ of\ view\fR> +angle (in degrees) vertically subtended by view window +.RI ( double ); +default: +.RB \(lq 20 \(rq +.TP +.B \-offfr +the given eye point +.RB (\(lq \-fr \(rq) +is to be interpreted as an offset from the at point. +.TP +.B \-turn\fR <\fIangle\fR> +angle (degrees) by which to rotate the from point around true up, for making +stereo pairs. +Positive means move towards positive U (the right) +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-is\fR <\fIimage\ size\fR> +image dimensions (2 \fIint\fRs); default: +.RB \(lq 256\ 256 \(rq +.TP +.B \-iss\fR <\fIscale\fR> +scaling of image size (from +.RB \(lq \-is \(rq) +.RI ( float ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-k00\fR <\fIkernel\fR> +value reconstruction kernel (\fIkernel specification\fR); default: +.RB \(lq tent \(rq +.TP +.B \-k11\fR <\fIkernel\fR> +first derivative kernel (\fIkernel specification\fR); default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR <\fIkernel\fR> +second derivative kernel (\fIkernel specification\fR); default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-rn +renormalize kernel weights at each new sample location. +\(lqAccurate\(rq kernels don\(cqt need this; doing it always makes things go +slower +.TP +.B \-q\fR <\fIquery\fR> +the quantity +.RB ( scalar , +.BR vector , +or +.BR matrix) +to learn by probing +.RI ( string ) +.TP +.B \-m\fR <\fImeasure\fR> +how to collapse list of ray samples into one scalar. +Possibilities include: +.RS +7n +.IP \(bu 2 +.RB \(lq min \(rq, +.RB \(lq max \(rq, +.RB \(lq mean \(rq, +.RB \(lq median \(rq, +.RB \(lq mode \(rq, +.RB \(lq variance \(rq, +.RB \(lq skew \(rq: +(self-explanatory) +.IP \(bu 2 +.RB \(lq intc \(rq, +.RB \(lq slope \(rq, +.RB \(lq error \(rq: +intercept, slope, and error from line fitting +.IP \(bu 2 +.RB \(lq stdv \(rq: +standard deviation +.IP \(bu 2 +.RB \(lq cov \(rq: +coefficient of variation +.IP \(bu 2 +.RB \(lq product \(rq, +.RB \(lq sum \(rq: +product or sum of all values +.IP \(bu 2 +.RB \(lq L1 \(rq, +.RB \(lq L2 \(rq, +.RB \(lq NL2 \(rq, +.RB \(lq RMS \(rq, +.RB \(lq Linf \(rq: +different norms +.IP \(bu 2 +.RB \(lq histo\-min \(rq, +.RB \(lq histo\-max \(rq, +.RB \(lq histo\-mean \(rq, +.RB \(lq histo\-median \(rq, +.RB \(lq histo\-mode \(rq, +.RB \(lq histo\-product \(rq, +.RB \(lq histo\-l2 \(rq, +.RB \(lq histo\-sum \(rq, +.RB \(lq histo\-variance \(rq, +.RB \(lq histo\-sd \(rq: +same measures, but for situations where we\(cqre given not the original values, +but a histogram of them. +.RI ( measure ) +.TP +.B \-gmc\fR\ <\fImin\ gradmag\fR> +For curvature-based queries, set answer to zero when gradient magnitude is +below this +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-fn\fR\ <\fIfrom\ nan\fR> +When histo-based measures generate +.B NaN +answers, the value that should be substituted for +.BR NaN . +.RI ( double ); +default: +.RB \(lq nan \(rq +.TP +.B \-step\fR\ <\fIsize\fR> +step size along ray in world space +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-nt\fR\ <\fI#\ threads\fR> +number of threads hoover should use +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-vp\fR\ <\fIimg\ coords\fR> +pixel coordinates for which to turn on verbose debugging messages, or +.RB \(lq \-1\ \-1 \(rq +to disable this. +(2 \fIint\fRs); +default: +.RB \(lq \-1\ \-1 \(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output +.I nrrd +to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/nrrdSanity.1 b/nrrdSanity.1 new file mode 100644 index 0000000..70c577a --- /dev/null +++ b/nrrdSanity.1 @@ -0,0 +1,32 @@ +.TH NRRDSANITY "1" "April 2021" "" "User Commands" +.SH NAME +nrrdSanity \- nrrd sanity check +.SH SYNOPSIS +.B nrrdSanity +.SH DESCRIPTION +.P +.BR nrrdSanity (1) +calls the +.B nrrdSanity() +check to verify the correctness of all the information (set at compile-time) +about the architecture, such as endianness, 32/64-bit, and the size of various +types, as well as running sanity checks on the global default +.RB ( nrrdDefault* ) +and state +.RB ( nrrdState* ) +variables. +.P +As a convenience, +.BR nrrdSanity (1) +also lists the availability of the different formats and data encodings (for +Nrrd files) supported by this build. +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR miter (1), +.BR mrender (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/overrgb.1 b/overrgb.1 new file mode 100644 index 0000000..538bf57 --- /dev/null +++ b/overrgb.1 @@ -0,0 +1,92 @@ +.TH OVERRGB "1" "April 2021" "" "User Commands" +.SH NAME +overrgb \- composites an RGBA nrrd over a background color (or image) +.SH SYNOPSIS +.B overrgb +.B \-i +.RI < nin > +.RB [ \-c +.RI < contrast >] +.RB [ \-cfp +.RI < fixed\ point >] +.RB [ \-g +.RI < gamma >] +.RB [ \-b +.RI < background >] +.RB [ \-bi +.RI < nbg >] +.B \-o +.RI < filename > +.SH DESCRIPTION +.P +Composites an RGBA nrrd over a background color (or image), after doing gamma +correction, then quantizes to an 8-bit image. +Actually, the input nrrd can have more than 4 values per pixel, but only the +first four are used. +If the RGBA nrrd is floating point, the values are taken at face value; if it +is fixed point, the values interpreted as having been quantized (so that 8-bit +RGBA images will act as you expect). +When compositing with a background image, the given background image does not +have to be the same size as the input image; it will be resampled (with linear +interpolation) to fit. +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-i\fR <\fInin\fR> +input nrrd to composite +.RI ( nrrd ) +.TP +.B \-c\fR <\fIcontrast\fR> +contrast to apply to RGB values, before gamma. +.RB \(lq 0.0 \(rq +means no change, +.RB \(lq 1.0 \(rq +means thresholding, +.RB \(lq \-1.0 \(rq +means a complete washout. +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-cfp\fR <\fIfixed\ point\fR> +component level that doesn\(cqt change with contrast +.RI ( double ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-g\fR <\fIgamma\fR> +gamma to apply to image data, after contrast +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-b\fR <\fIbackground\fR> +background color to composite against; white is +.BR 1\ 1\ 1 , +not +.BR 255\ 255\ 255 . +(3 \fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-bi\fR <\fInbg\fR> +8-bit RGB background image to composite against +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output PPM image to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR puller (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/puller.1 b/puller.1 new file mode 100644 index 0000000..fb03592 --- /dev/null +++ b/puller.1 @@ -0,0 +1,591 @@ +.TH PULLER "1" "April 2021" "" "User Commands" +.SH NAME +puller \- command-line interface to the \(lqpull\(rq library +.SH SYNOPSIS +.B puller +.RB [ @file \ ...] +.RB [ \-int +.RI < int >] +.RB [ \-enr +.RI < spec >] +.RB [ \-ens +.RI < spec >] +.RB [ \-enw +.RI < spec >] +.RB [ \-efs +.RI < bool >] +.RB [ \-nave +.RI < bool >] +.RB [ \-cbst +.RI < bool >] +.RB [ \-noadd ] +.RB [ \-usa +.RI < bool >] +.RB [ \-pcet +.RI < bool >] +.RB [ \-nobin ] +.RB [ \-lti +.RI < bool >] +.RB [ \-por +.RI < bool >] +.RB [ \-npcwza +.RI < bool >] +.RB [ \-ubfgl +.RI < bool >] +.RB [ \-ratb +.RI < bool >] +.RB [ \-svec +.RI < vec >] +.RB [ \-gssr +.RI < rad >] +.RB [ \-v +.RI < verbosity >] +.B \-vol +.RI < vol0\ vol1 \ ...> +.B \-info +.RI < info0\ info1 \ ...> +.RB [ \-k00 +.RI < kern00 >] +.RB [ \-k11 +.RI < kern11 >] +.RB [ \-k22 +.RI < kern22 >] +.RB [ \-sscp +.RI < path >] +.RB [ \-kssb +.RI < kernel >] +.RB [ \-kssr +.RI < kernel >] +.RB [ \-nss +.RI < #\ scl\ smpls >] +.RB [ \-np +.RI < #\ points >] +.RB [ \-halton ] +.RB [ \-ppv +.RI < #\ pnts/vox >] +.RB [ \-ppvzr +.RI < z\ range >] +.RB [ \-jit +.RI < jitter >] +.RB [ \-pi +.RI < npos >] +.RB [ \-step +.RI < step >] +.RB [ \-csm +.RI < step >] +.RB [ \-snap +.RI < #\ iters >] +.RB [ \-maxi +.RI < #\ iters >] +.RB [ \-stim +.RI < #\ iters >] +.RB [ \-maxci +.RI < #\ iters >] +.RB [ \-irad +.RI < scale >] +.RB [ \-srad +.RI < scale >] +.RB [ \-bws +.RI < bin\ width >] +.RB [ \-alpha +.RI < alpha >] +.RB [ \-beta +.RI < beta >] +.RB [ \-gamma +.RI < gamma >] +.RB [ \-theta +.RI < theta >] +.RB [ \-wall +.RI < k >] +.RB [ \-eip +.RI < k >] +.RB [ \-ess +.RI < scl >] +.RB [ \-oss +.RI < scl >] +.RB [ \-edmin +.RI < frac >] +.RB [ \-edpcmin +.RI < frac >] +.RB [ \-fnnm +.RI < frac >] +.RB [ \-pcp +.RI < period >] +.RB [ \-iad +.RI < #\ iters >] +.RB [ \-icb +.RI < #\ iters >] +.RB [ \-ac3c +.RI < ac3c >] +.RB [ \-sit +.RI < sit >] +.RB [ \-rng +.RI < seed >] +.RB [ \-pbm +.RI < mod >] +.RB [ \-eiphl +.RI < hl >] +.RB [ \-nt +.RI < #\ threads >] +.RB [ \-nprob +.RI < prob >] +.RB [ \-pprob +.RI < prob >] +.RB [ \-addlog +.RI < fname >] +.RB [ \-o +.RI < nout >] +.RB [ \-eob +.RI < base >] +.SH OPTIONS +.TP +.BR @file \ ... +response file(s) containing command-line arguments +.TP +.B \-int\fR <\fIint\fR> +inter-particle energy type +.RI ( interaction\ type ); +default: +.RB \(lq justr \(rq +.TP +.B \-enr\fR <\fIspec\fR> +inter-particle energy, radial component +.RI ( energy\ specification ); +default: +.RB \(lq cotan \(rq +.TP +.B \-ens\fR <\fIspec\fR> +inter-particle energy, scale component +.RI ( energy\ specification ); +default: +.RB \(lq zero \(rq +.TP +.B \-enw\fR <\fIspec\fR> +windowing to create locality with additive scale-space interaction +.RB (\(lq \-int\ add \(rq) +.RI ( energy\ specification ); +default: +.RB \(lq butter:16,0.8 \(rq +.TP +.B \-efs\fR <\fIbool\fR> +whether or not strength contributes to particle-image energy +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-nave\fR <\fIbool\fR> +whether or not to nix points at edge of volume, where gage had to invent values +for kernel support +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-cbst\fR <\fIbool\fR> +during initialization, try constraint satisfaction before testing +.B seedThresh +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-noadd +turn off adding during population control +.TP +.B \-usa\fR <\fIbool\fR> +allow volumes to have different shapes +.RB ( false +is safe as different volume sizes are often accidental) +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-pcet\fR <\fIbool\fR> +use neighbor-counting \(lqenough\(rq heuristic to bail out of population +control +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-nobin +turn off spatial binning (which prevents multi-threading from being useful), +for debugging or speed-up measurement +.TP +.B \-lti\fR <\fIbool\fR> +impose +.B liveThresh +on initialization +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-por\fR <\fIbool\fR> +permute points during rebinning +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-npcwza\fR <\fIbool\fR> +no population control with zero alpha +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-ubfgl\fR <\fIbool\fR> +use beta for gamma learning +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-ratb\fR <\fIbool\fR> +be choosy when adding points to bins to avoid overlap +.RI ( bool ); +default: +.RB \(lq true \(rq +.TP +.B \-svec\fR <\fIvec\fR> +if non-zero (length), vector to use for displaying scale in 3-space (3 +\fIdouble\fRs); default: +.RB \(lq 0\ 0\ 0 \(rq +.TP +.B \-gssr\fR <\fIrad\fR> +if non-zero (length), scaling of scale to cylindrical tensors +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-v\fR <\fIverbosity\fR> +verbosity level +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-vol\fR <\fIvol0\fR\ \fIvol1\fR\ ...> +input volumes, in format +<\fIfilename\fR>\fB:\fR<\fIkind\fR>\fB:\fR<\fIvolname\fR> +(1 or more \fImeetPullVol\fRs) +.TP +.B \-info\fR <\fIinfo0\fR\ \fIinfo1\fR\ ...> +info definitions, in format +.RI < info >[\fB\-c\fR]\fB:\fR< volname >\fB:\fR< item >[\fB:\fR< zero >\fB:\fR< scale >] +(1 or more \fImeetPullInfo\fRs) +.TP +.B \-k00\fR <\fIkern00\fR> +kernel for +.B gageKernel00 +.RI ( kernel\ specification ); +default: +.RB \(lq cubic:1,0 \(rq +.TP +.B \-k11\fR <\fIkern11\fR> +kernel for +.B gageKernel11 +.RI ( kernel\ specification ); +default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR <\fIkern22\fR> +kernel for +.B gageKernel22 +.RI ( kernel\ specification ); +default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-sscp\fR <\fIpath\fR> +path (without trailing +.BR / ) +for where to read/write pre-blurred volumes for scale-space +.RI ( string ); +default: +.RB \(lq ./ \(rq +.TP +.B \-kssb\fR <\fIkernel\fR> +blurring kernel, to sample scale space +.RI ( kernel\ specification ); +default: +.RB \(lq ds:1,5 \(rq +.TP +.B \-kssr\fR <\fIkernel\fR> +kernel for reconstructing from scale space samples +.RI ( kernel\ specification ); +default: +.RB \(lq hermite \(rq +.TP +.B \-nssr\fR <\fI#\ scl\ smpls\fR> +if using +.RB \(lq \-ppv \(rq; +number of samples along scale axis for each spatial position +.RI ( unsigned\ int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-np\fR <\fI#\ points\fR> +number of points to start in system +.RI ( unsigned\ int ); +default: +.RB \(lq 1000 \(rq +.TP +.B \-halton +use Halton sequence initialization instead of uniform random +.TP +.B \-ppv\fR <\fI#\ p[nts/vox\fR> +number of points per voxel to start in simulation (need to have a seed +threshold volume, overrides +.RB \(lq \-np \(rq) +.RI ( int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ppvzr\fR <\fIz\ range\fR> +range of Z slices (1st num < 2nd num) to do +.B ppv +in, or, +.RB \(lq 1\ 0 \(rq) +for whole volume (2 \fIunsigned\ int\fRs); default: +.RB \(lq 1\ 0 \(rq +.TP +.B \-jit\fR <\fIjitter\fR> +amount of jittering to do with +.B ppv +.RI ( double ); +default: +.RB \(lq 0 \(rq +.TP +.B \-pi\fR <\fInpos\fR> +4-by-N array of positions to start at (overrides +.RB \(lq \-np \(rq +.RI ( nrrd ); +default: \(lq\(rq +.TP +.B \-step\fR <\fIstep\fR> +initial step size for gradient descent +.RI ( double ); +default: +.RB \(lq 1 \(rq +.TP +.B \-csm\fR <\fIstep\fR> +convergence criterion for constraint satisfaction +.RI ( double ); +default: +.RB \(lq 0.0001 \(rq +.TP +.B \-snap\fR <\fI#\ iters\fR> +if non-zero, # iters between saved snapshots +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-maxi\fR <\fI#\ iters\fR> +if non-zero, max # iterations to run whole system +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-stim\fR <\fI#\ iters\fR> +if non-zero, max # iterations to allow a particle to be stuck before nixing +.RI ( unsigned\ int ); +default: +.RB \(lq 5 \(rq +.TP +.B \-maxci\fR <\fI#\ iters\fR> +if non-zero, max # iterations for contraint enforcement +.RI ( unsigned\ int ); +default: +.RB \(lq 15 \(rq +.TP +.B \-irad\fR <\fIscale\fR> +particle radius in spatial domain +.RI ( double ); +default: +.RB \(lq 1 \(rq +.TP +.B \-srad\fR <\fIscale\fR> +particle radius in scale domain +.RI ( double ); +default: +.RB \(lq 1 \(rq +.TP +.B \-bws\fR <\fIbin\ width\fR> +spatial bin width as multiple of spatial radius +.RI ( double ); +default: +.RB \(lq 1.001 \(rq +.TP +.B \-alpha\fR <\fIalpha\fR> +blend between particle-image (\fIalpha\fR=\fB0\fR) and inter-particle +(\fIalpha\fR=\fB1\fR) energies +.RI ( double ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-beta\fR <\fIbeta\fR> +when using +.B Phi2 +energy, blend between pure space repulsion (\fIbeta\fR=\fB0\fR) and scale +attraction (\fIbeta\fR=\fB1\fR) +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-gamma\fR <\fIgamma\fR> +scaling factor on energy from strength +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-theta\fR <\fItheta\fR> +slope of increasing +.B livethresh +with respect to scale +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-wall\fR <\fIk\fR> +spring constant on walls +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-eip\fR <\fIk\fR> +amount by which it\(cqs okay for +.B per-particle +energy to increase during gradient descent process +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-ess\fR <\fIscl\fR> +when energy goes up instead of down, scale step size by this +.RI ( double ); +default: +.RB \(lq 0.5 \(rq +.TP +.B \-oss\fR <\fIscl\fR> +opportunistic scaling (hopefully up, >1) of step size on every iteration +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-edmin\fR <\fIfrac\fR> +convergence threshold: stop when fractional improvement (decrease) in energy +dips below this +.RI ( double ); +default: +.RB \(lq 0.0001 \(rq +.TP +.B \-edpcmin\fR <\fIfrac\fR> +population control is triggered when energy improvement goes below this +threshold +.RI ( double ); +default: +.RB \(lq 0.01 \(rq +.TP +.B \-fnnm\fR <\fIfrac\fR> +don\(cqt nix if this fraction (or more) of neighbors have been nixed +.RI ( double ); +default: +.RB \(lq 0.25 \(rq +.TP +.B \-pcp\fR <\fIperiod\fR> +# iters to wait between attempts at population control +.RI ( unsigned\ int ); +default: +.RB \(lq 20 \(rq +.TP +.B \-iad\fR <\fI#\ iters\fR> +# iters to run descent on tentative new points during PC +.RI ( unsigned\ int ); +default: +.RB \(lq 10 \(rq +.TP +.B \-icb\fR <\fI#\ iters\fR> +periodicity of calling rendering callback +.RI ( unsigned\ int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-ac3c\fR <\fIac3c\fR> +allow codimensions 3 constraints +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-sit\fR <\fIsit\fR> +scale is tau +.RI ( bool ); +default: +.RB \(lq false \(rq +.TP +.B \-rng\fR <\fIseed\fR> +base seed value for RNGs +.RI ( unsigned\ int ); +default: +.RB \(lq 42 \(rq +.TP +.B \-pbm\fR <\fImod\fR> +progress bin mod +.RI ( unsigned\ int ); +default: +.RB \(lq 50 \(rq +.TP +.B \-eiphl\fR <\fIhl\fR> +half-life of +.BR energyIncreasePermute (\(lq \-eip \(rq) +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-nt\fR <\fI#\ threads\fR> +number of threads hoover should use +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-nprob\fR <\fIprob\fR> +do full neighbor discovery with this probability +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-pprob\fR <\fIprob\fR> +probe local image values with this probability +.RI ( double ); +default: +.RB \(lq 1.0 \(rq +.TP +.B \-addlog\fR <\fIfname\fR> +name of file in which to log all particle additions +.RI ( string ); +default: \(lq\(rq +.TP +.B \-o\fR <\fInout\fR> +filename for saving computed positions +.RI ( string ); +default: +.RB \(lq \- \(rq +.TP +.B \-eob\fR <\fIbase\fR> +save extra info (besides position), and use this string as the base of the +filenames. +Not using this eans the extra info is not saved. +.RI ( string ); +default: \(lq\(rq +.SH NOTES +.P +Published research using this tool or the \(lqpull\(rq library should cite the +paper: +.in +4n +\fBGordon L. Kindlmann, Ra{\(rs\(aqu}l San Jos{\(rs\(aqe} Est{\(rs\(aqe}par, +Stephen M. Smith, Carl-Fredrik Westin. +Sampling and Visualizing Creases with Scale-Space Particles. +IEEE Trans. on Visualization and Computer Graphics, 15(6):1415-1424 (2009).\fR +.in +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR tend (1), +.BR unu (1), +.BR vprobe (1) diff --git a/teem.spec b/teem.spec index 2ebe7a6..b69288c 100644 --- a/teem.spec +++ b/teem.spec @@ -1,3 +1,7 @@ +# Writing man pages is a work in progress. We do not install them until we have +# a complete set. +%bcond_with man_pages + Name: teem Version: 1.11.0 %global so_version 1 @@ -16,8 +20,124 @@ License: LGPLv2+ # python/ctypes/pullDemo.py # python/ctypes/teem-gen.py # python/ctypes/teem.py -URL: https://teem.sourceforge.net +URL: http://teem.sourceforge.net Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... + +Source1: gprobe.1 +Source2: ilk.1 +Source3: miter.1 +Source4: mrender.1 +Source5: nrrdSanity.1 +Source6: overrgb.1 +Source7: puller.1 +Source8: tend.1 +Source9: unu.1 +Source10: vprobe.1 + +Source800: tend-about.1 +Source801: tend-grads.1 +Source802: tend-epireg.1 +Source803: tend-bmat.1 +Source804: tend-estim.1 +Source805: tend-sim.1 +Source806: tend-mfit.1 +Source807: tend-mconv.1 +Source808: tend-msim.1 +Source809: tend-make.1 +Source810: tend-avg.1 +#Source811: tend-helix.1 +#Source812: tend-sten.1 +#Source813: tend-glyph.1 +#Source814: tend-ellipse.1 +#Source815: tend-anplot.1 +#Source816: tend-anvol.1 +#Source817: tend-anscale.1 +#Source818: tend-anhist.1 +#Source819: tend-triple.1 +#Source820: tend-tconv.1 +#Source821: tend-point.1 +#Source822: tend-slice.1 +#Source823: tend-norm.1 +#Source824: tend-fiber.1 +#Source825: tend-eval.1 +#Source826: tend-evalpow.1 +#Source827: tend-evalclamp.1 +#Source828: tend-evaladd.1 +#Source829: tend-evalmul.1 +#Source830: tend-log.1 +#Source831: tend-exp.1 +#Source832: tend-evec.1 +#Source833: tend-evecrgb.1 +#Source834: tend-evq.1 +#Source835: tend-unmf.1 +#Source836: tend-expand.1 +#Source837: tend-shrink.1 +#Source838: tend-bfit.1 +#Source839: tend-satin.1 +# +#Source900: unu-about.1 +#Source901: unu-env.1 +#Source902: unu-i2w.1 +#Source903: unu-w2i.1 +#Source904: unu-make.1 +#Source905: unu-head.1 +#Source906: unu-data.1 +#Source907: unu-convert.1 +#Source908: unu-resample.1 +#Source909: unu-fft.1 +#Source910: unu-cmedian.1 +#Source911: unu-dist.1 +#Source912: unu-minmax.1 +#Source913: unu-cksum.1 +#Source914: unu-diff.1 +#Source915: unu-quantize.1 +#Source916: unu-unquantize.1 +#Source917: unu-project.1 +#Source918: unu-slice.1 +#Source919: unu-sselect.1 +#Source920: unu-dice.1 +#Source921: unu-splice.1 +#Source922: unu-join.1 +#Source923: unu-crop.1 +#Source924: unu-acrop.1 +#Source925: unu-inset.1 +#Source926: unu-pad.1 +#Source927: unu-reshape.1 +#Source928: unu-permute.1 +#Source929: unu-swap.1 +#Source930: unu-shuffle.1 +#Source931: unu-flip.1 +#Source932: unu-unorient.1 +#Source933: unu-axinfo.1 +#Source934: unu-axinsert.1 +#Source935: unu-axsplit.1 +#Source936: unu-axdelete.1 +#Source937: unu-axmerge.1 +#Source938: unu-tile.1 +#Source939: unu-untile.1 +#Source940: unu-histo.1 +#Source941: unu-dhisto.1 +#Source942: unu-jhisto.1 +#Source943: unu-histax.1 +#Source944: unu-heq.1 +#Source945: unu-gamma.1 +#Source946: unu-1op.1 +#Source947: unu-2op.1 +#Source948: unu-3op.1 +#Source949: unu-affine.1 +#Source950: unu-lut.1 +#Source951: unu-mlut.1 +#Source952: unu-subst.1 +#Source953: unu-rmap.1 +#Source954: unu-mrmap.1 +#Source955: unu-imap.1 +#Source956: unu-lut2.1 +#Source957: unu-ccfind.1 +#Source958: unu-ccadj.1 +#Source959: unu-ccmerge.1 +#Source960: unu-ccsettle.1 +#Source961: unu-save.1 + # Patch CMakeLists.txt to fix library install paths to match what Fedora # expects. It is not immediately obvious if this patch is suitable for # sending upstream or not. @@ -141,6 +261,34 @@ rm -rvf python %install %cmake3_install +%if %{with man_pages} +install -d %{buildroot}%{_mandir}/man1 +install -t %{buildroot}%{_mandir}/man1 -p -m 0644 \ + %{SOURCE1} %{SOURCE2} %{SOURCE3} %{SOURCE4} %{SOURCE5} %{SOURCE6} \ + %{SOURCE7} %{SOURCE8} %{SOURCE9} %{SOURCE10} \ + %{SOURCE800} %{SOURCE801} %{SOURCE802} %{SOURCE803} %{SOURCE804} \ + %{SOURCE805} %{SOURCE806} %{SOURCE807} %{SOURCE808} %{SOURCE809} \ + %{SOURCE810} %{SOURCE811} %{SOURCE812} %{SOURCE813} %{SOURCE814} \ + %{SOURCE815} %{SOURCE816} %{SOURCE817} %{SOURCE818} %{SOURCE819} \ + %{SOURCE820} %{SOURCE821} %{SOURCE822} %{SOURCE823} %{SOURCE824} \ + %{SOURCE825} %{SOURCE826} %{SOURCE827} %{SOURCE828} %{SOURCE829} \ + %{SOURCE830} %{SOURCE831} %{SOURCE832} %{SOURCE833} %{SOURCE834} \ + %{SOURCE835} %{SOURCE836} %{SOURCE837} %{SOURCE838} %{SOURCE839} \ + %{SOURCE900} %{SOURCE901} %{SOURCE902} %{SOURCE903} %{SOURCE904} \ + %{SOURCE905} %{SOURCE906} %{SOURCE907} %{SOURCE908} %{SOURCE909} \ + %{SOURCE910} %{SOURCE911} %{SOURCE912} %{SOURCE913} %{SOURCE914} \ + %{SOURCE915} %{SOURCE916} %{SOURCE917} %{SOURCE918} %{SOURCE919} \ + %{SOURCE920} %{SOURCE921} %{SOURCE922} %{SOURCE923} %{SOURCE924} \ + %{SOURCE925} %{SOURCE926} %{SOURCE927} %{SOURCE928} %{SOURCE929} \ + %{SOURCE930} %{SOURCE931} %{SOURCE932} %{SOURCE933} %{SOURCE934} \ + %{SOURCE935} %{SOURCE936} %{SOURCE937} %{SOURCE938} %{SOURCE939} \ + %{SOURCE940} %{SOURCE941} %{SOURCE942} %{SOURCE943} %{SOURCE944} \ + %{SOURCE945} %{SOURCE946} %{SOURCE947} %{SOURCE948} %{SOURCE949} \ + %{SOURCE950} %{SOURCE951} %{SOURCE952} %{SOURCE953} %{SOURCE954} \ + %{SOURCE955} %{SOURCE956} %{SOURCE957} %{SOURCE958} %{SOURCE959} \ + %{SOURCE960} %{SOURCE961} +%endif + %check # We must exclude probeSS_ctmr04 and probeSS_ctmr10 on certain architectures @@ -171,6 +319,21 @@ rm -rvf python %{_bindir}/unu %{_bindir}/vprobe +%if %{with man_pages} +%{_mandir}/man1/gprobe.1* +%{_mandir}/man1/ilk.1* +%{_mandir}/man1/miter.1* +%{_mandir}/man1/mrender.1* +%{_mandir}/man1/nrrdSanity.1* +%{_mandir}/man1/overrgb.1* +%{_mandir}/man1/puller.1* +%{_mandir}/man1/tend.1* +%{_mandir}/man1/tend-*.1* +%{_mandir}/man1/unu.1* +%{_mandir}/man1/unu-*.1* +%{_mandir}/man1/vprobe.1* +%endif + %files libs %license LICENSE.txt @@ -193,7 +356,7 @@ rm -rvf python %changelog * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch -- Update URLs from HTTP to HTTPS +- Update download URL from HTTP to HTTPS - Improved package summaries and descriptions - Adjust whitespace to personal preference - Fix stray line continuation backslash @@ -204,6 +367,7 @@ rm -rvf python to that subpackage; remove certain unused files with other licenses in %%prep - Require cmake-filesystem instead of all of CMake in -devel - More precisely skip overly-strict floating-point tests where required +- Start work on adding a complete set of man pages * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild diff --git a/tend-about.1 b/tend-about.1 new file mode 100644 index 0000000..21d8320 --- /dev/null +++ b/tend-about.1 @@ -0,0 +1,9 @@ +.TH TEND\-ABOUT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-about \- information about +.BR tend (1) +and its use +.SH SYNOPSIS +.B tend\ about +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-avg.1 b/tend-avg.1 new file mode 100644 index 0000000..8b67389 --- /dev/null +++ b/tend-avg.1 @@ -0,0 +1,32 @@ +.TH TEND\-AVG "1" "April 2021" "" "User Commands" +.SH NAME +tend\-avg \- average across tensor volumes +.SH SYNOPSIS +.B tend\ avg +.B \-i +.RI < nin1 \ nin2 \ ...> +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Average across tensor volumes. +The output is the same size as the any one of the inputs. +The individual tensors may be averaged in various ways. +.SH OPTIONS +.TP +.B \-i\fR <\fInin1\fR\ \fInin2\fR\ ...> +list of input diffusion tensor volumes (2 or more +.IR nrrd s) +.TP +.B \-t\fR <\fItype\fR> +averaging method; default: +.RB \(lq linear \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-bmat.1 b/tend-bmat.1 new file mode 100644 index 0000000..e0a8c3b --- /dev/null +++ b/tend-bmat.1 @@ -0,0 +1,43 @@ +.TH TEND\-BMAT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-bmat \- calculate B-matrix given gradient directions +.SH SYNOPSIS +.B tend\ bmat +.B \-i +.RI < grads > +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Calculate B-matrix given gradient directions, assuming no diffusion weighting +from the other imaging gradients. +The input is a 3-by-N array of floats or doubles, each row being one of the +gradient directions used for diffusion-weighted imaging. +A plain text file with one gradient per line, no punctuation, is an easy way to +specify this information. +The gradient vector coefficients are used as is, without normalization (since +different gradient strengths are sometimes desired). +The output has one row of the +B-matrix per line, with coefficient ordering +.BR Bxx , +.BR Bxy , +.BR Bxz , +.BR Byy , +.BR Byz , +.BR Bzz , +and with the off-diagonal elements NOT pre-multiplied by 2. +.SH OPTIONS +.TP +.B \-i\fR <\fIgrads\fR> +array of gradient directions +.TP +.B \-o\fR <\fInout\fR> +output B matrix +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-estim (1), +.BR tend\-msim (1), +.BR tend\-sim (1) diff --git a/tend-epireg.1 b/tend-epireg.1 new file mode 100644 index 0000000..cb45cb6 --- /dev/null +++ b/tend-epireg.1 @@ -0,0 +1,139 @@ +.TH TEND\-EPIREG "1" "April 2021" "" "User Commands" +.SH NAME +tend\-epireg \- register diffusion-weighted echo-planar images +.SH SYNOPSIS +.B tend\ epireg +.B \-i +.RI < dwi0\fR\ \fBdwi1 \ ...> +.B \-g +.RI < grads > +.RB [ \-r +.RI < reference >] +.RB [ \-nv ] +.RB [ \-p ] +.RB [ \-bw +.RI < x\fB,\fIy\fB\ blur >] +.RB [ \-t +.RI < DWI\ thresh >] +.RB [ \-ncc ] +.RB [ \-f +.RI < fit\ frac >] +.RB [ \-k +.RI < kernel >] +.RB [ \-s +.RI < start\ # >] +.RB [ \-o +.RI < output/prefix >] +.SH DESCRIPTION +.P +Register diffusion-weighted echo-planar images. +This registration corrects the shear, scale, and translate along the phase +encoding direction (assumed to be the Y (second) axis of the image) caused by +eddy currents from the diffusion-encoding gradients with echo-planar imaging. +The method is based on calculating moments of segmented images, where the +segmentation is a simple procedure based on blurring (optional), thresholding +and connected component analysis. +The registered DWIs are resampled with the chosen kernel, with the separate +DWIs stacked along axis 0. +.SH OPTIONS +.TP +.B \-i\fR <\fIdwi0\fR\ \fIdwi1\fR\ ...> +all the diffusion-weighted images (DWIs), as separate 3D +.IR nrrd s, +.BR OR : +one 4D +.I nrrd +of all DWIs stacked along axis 0 (1 or more +.IR nrrd s) +.TP +.B \-g\fR <\fIgrads\fR> +array of gradient directions, in the same order as the associated DWIs were +given to +.RB \(lq \-i \(rq, +.B OR +.RB \(lq \-g\ kvp \(rq +signifies that gradient directions should be read from the key/value pairs of +the DWI +.RI ( string ) +.TP +.B \-r\fR <\fIreference\fR> +which of the DW volumes (zero-based numbering) should be used as the standard, +to which all other images are transformed. +Using +.B \-1 +(the default) means that 9 intrinsic parameters governing the relationship +between the gradient direction and the resulting distortion are estimated and +fitted, ensuring good registration with the non-diffusion-weighted T2 image +(which is never explicitly used in registration). +Otherwise, by picking a specific DWI, no distortion parameter estimation is +done. +.RI ( int ); +default: +.RB \(lq \-1 \(rq +.TP +.B \-nv +turn OFF verbose mode, and have no idea what stage processing is at. +.TP +.B \-p +save out intermediate steps of processing +.TP +.B \-bw\fR <\fIx\fB,\fIy\ blur\fR> +standard deviations in X and Y directions of gaussian filter used to blur the +DWIs prior to doing segmentation. +This blurring does not effect the final resampling of registered DWIs. +Use +.RB \(lq 0.0\ 0.0 \(rq +to say \(lqno blurring\(rq (2 +.IR float s); +default: +.RB \(lq 1.0\ 2.0 \(rq +.TP +.B \-t\fR <\fIDWI\ thresh\fR> +Threshold value to use on DWIs, to do initial separation of brain and +non-brain. +By default, the threshold is determined automatically by histogram analysis. +.RI ( float ) +.TP +.B \-ncc +do +.B NOT +do connected component (CC) analysis, after thresholding and before moment +calculation. +Doing CC analysis usually gives better results because it converts the +thresholding output into something much closer to a real segmentation +.TP +.B \-f\fR <\fIfit\ frac\fR> +(only meaningful with +.RB \(lq \-r\ \-1 \(rq) +When doing linear fitting of the intrinsic distortion parameters, it is good to +ignore the slices for which the segmentation was poor. +A heuristic is used to rank the slices according to segmentation quality. +This option controls how many of the (best) slices contribute to the fitting. +Use +.RB \(lq 0 \(rq +to disable distortion parameter fitting. +.RI ( float ) +default: +.RB \(lq 0.70 \(rq +.TP +.B \-k\fR <\fIkernel\fR> +kernel for resampling DWIs along the phase-encoding direction during final +registration stage; default: +.RB \(lq cubic:0,0.5 \(rq +.TP +.B \-s\fR <\fIstart\ #\fR> +first number to use in numbered sequence of output files. +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-o\fR <\fIoutput/prefix\ #\fR> +For separate 3D DWI volume inputs: prefix for output filenames; will save out +one (registered) DWI for each input DWI, using the same type as the input. +.BR OR : +For single 4D DWI input: output file name. +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-estim.1 b/tend-estim.1 new file mode 100644 index 0000000..649a1e1 --- /dev/null +++ b/tend-estim.1 @@ -0,0 +1,196 @@ +.TH TEND\-ESTIM "1" "April 2021" "" "User Commands" +.SH NAME +tend\-estim \- estimate tensors from a set of DW images +.SH SYNOPSIS +.B tend\ estim +.RB [ \-old ] +.RB [ \-sigma +.RI < sigma >] +.RB [ \-v +.RI < verbose >] +.RB [ \-est +.RI < estimate\ method >] +.RB [ \-wlsi +.RI < WLS\ iters >] +.RB [ \-fixneg ] +.RB [ \-ee +.RI < filename >] +.RB [ \-eb +.RI < filename >] +.RB [ \-t +.RI < thresh >] +.RB [ \-soft +.RI < soft >] +.RB [ \-scale +.RI < scale >] +.RB [ \-mv +.RI < min\ val >] +.B \-B +.RI < B\-list > +.RB [ \-b +.RI < b >] +.B \-knownB0 +.RI < bool > +.RB [ \-i +.RI < dwi0\fR\ \fIdwi1\fR\ ...>] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Estimate tensors from a set of DW images. +The tensor coefficient weightings associated with each of the DWIs, the +B-matrix, is given either as a separate array, (see +.BR tend\-bmat (1) for +details), or by the key-value pairs in the DWI +.I nrrd +header. +A \(lqconfidence\(rq value is computed with the tensor, based on a soft +thresholding of the sum of all the DWIs, according to the threshold and +softness parameters. +.SH OPTIONS +.TP +.B \-old +instead of the new +.B tenEstimateContext +code, use the old +.B tenEstimateLinear +code +.TP +.B \-sigma\fR <\fIsigma\fR> +Rician noise parameter +.RI ( float ) +.TP +.B \-v\fR <\fIverbose\fR> +verbosity level +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-est\fR <\fIestimate\ method\fR> +estimation method to use. +.RB \(lq lls \(rq: +linear-least squares; default: +.RB \(lq lls \(rq +.TP +.B \-wlsi\fR <\fIWLS\ iters\fR> +when using weighted-least-squares +.RB (\(lq \-est\ wls \(rq), +how many iterations to do after the initial weighted fit. +.RI ( unsigned\ int ) +default: +.RB \(lq 1 \(rq +.TP +.B \-fixneg +after estimating the tensor, ensure that there are no negative eigenvalues by +adding (to all eigenvalues) the amount by which the smallest is negative +(corresponding to increasing the non-DWI image value). +.TP +.B \-ee\fR <\fIfilename\fR> +Giving a filename here allows you to save out the tensor estimation error: a +value which measures how much error there is between the tensor model and the +given diffusion weighted measurements for each sample. +By default, no such error calculation is saved. +.RI ( string ) +.TP +.B \-eb\fR <\fIfilename\fR> +In those cases where there is no B=0 reference image given +.RB (\(lq \-knownB0\ false \(rq), +giving a filename here allows you to save out the +.B B=0 +image which is estimated from the data. +By default, this image value is estimated but not saved. +.RI ( string ) +.TP +.B \-t\fR <\fIthresh\fR> +value at which to threshold the mean DWI value per pixel in order to generate +the \(lqconfidence\(rq mask. +By default, the threshold value is calculated automatically, based on histogram +analysis. +.RI ( double ) +.TP +.B \-soft\fR <\fIsoft\fR> +how fuzzy the confidence boundary should be. +By default, confidence boundary is perfectly sharp +.RI ( float ) +default: +.RB \(lq 0 \(rq +.TP +.B \-scale\fR <\fIscale\fR> +After estimating the tensor, scale all of its elements (but not the confidence +value) by this amount. +Can help with downstream numerical precision if values are very large or small. +.RI ( float ) +default: +.RB \(lq 1 \(rq +.TP +.B \-mv\fR <\fImin\ val\fR> +minimum plausible value (especially important for linear least squares +estimation) +.RI ( double ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-B\fR <\fIB\-list\fR> +6-by-N list of B-matrices characterizing the diffusion weighting for each +image. +.BR tend\-bmat (1) +is one source for such a matrix; see its usage info for specifics on how the +coefficients of the B-matrix are ordered. +An unadorned plain text file is a great way to specify the B-matrix. +.IP +.B OR +.IP +Can say just +.RB \(lq \-B\ kvp \(rq +to try to learn B matrices from key/value pair information in input images. +.IP +.RI ( string ) +.TP +.B \-b\fR <\fIb\fR> +\(lqb\(rq diffusion-weighting factor (units of sec/mm^2) +.RI ( double ) +.TP +.B \-knownB0\fR <\fIbool\fR> +Indicates if the +.B B=0 +non-diffusion-weighted reference image is known, or if it has to be estimated +along with the tensor elements +.RS +7n +.IP \(bu 2 +if +.RB \(lq true \(rq: +in the given list of diffusion gradients or B-matrices, there are one or more +with zero norm, which are simply averaged to find the +.B B=0 +reference image value +.IP \(bu 2 +if +.RB \(lq false \(rq: +there may or may not be diffusion-weighted images among the input; the +.B B=0 +image value is going to be estimated along with the diffusion model +.P +.RI ( bool ) +.RE +.TP +.B \-i\fR <\fIdwi0\fR\ \fIdwi1\fR\ ...> +all the diffusion-weighted images (DWIs), as separate 3D +.IR nrrd s, +.BR OR : +One 4D +.I nrrd +of all DWIs stacked along axis 0 (1 or more +.IR nrrd s); +default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output tensor volume +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) +.BR tend\-bmat (1), +.BR tend\-msim (1), +.BR tend\-sim (1) diff --git a/tend-grads.1 b/tend-grads.1 new file mode 100644 index 0000000..e92bc8f --- /dev/null +++ b/tend-grads.1 @@ -0,0 +1,162 @@ +.TH TEND\-GRADS "1" "April 2021" "" "User Commands" +.SH NAME +tend\-grads \- calculate balanced gradient directions for DWI acquisition +.SH SYNOPSIS +.B tend\ grads +.RB [ \-n +.RI < #\ dir >] +.RB [ \-i +.RI < grads >] +.RB [ \-seed +.RI < value >] +.RB [ \-step +.RI < step >] +.RB [ \-single ] +.RB [ \-snap +.RI < interval >] +.RB [ \-jitter +.RI < jitter >] +.RB [ \-miniter +.RI < #\ iters >] +.RB [ \-maxiter +.RI < #\ iters >] +.RB [ \-minvelo +.RI < vel >] +.RB [ \-exp +.RI < exponent >] +.RB [ \-dp +.RI < potential\ change >] +.RB [ \-minimprov +.RI < delta >] +.RB [ \-minmean +.RI < len >] +.RB [ \-izv +.RI < insert >] +.RB [ \-o +.RI < filename >] +.SH DESCRIPTION +.P +Composites an RGBA +.I nrrd +over a background color (or image), after doing gamma correction, then +quantizes to an 8-bit image. +Actually, the input +.I nrrd +can have more than 4 values per pixel, but only the first four are used. +If the RGBA +.I nrrd +s floating point, the values are taken at face value; if it is fixed point, the +values interpreted as having been quantized (so that 8-bit RGBA images will act +as you expect). +When compositing with a background image, the given background image does not +have to be the same size as the input image; it will be resampled (with linear +interpolation) to fit. +.SH OPTIONS +.TP +.B \-n\fR <\fI#\ dir\fR> +desired number of diffusion gradient directions +.RI ( int ) +default: +.RB \(lq 6 \(rq +.TP +.B \-i\fR <\fIgrads\fR> +initial gradient directions to start with, instead of default random initial +directions (overrides +.RB \(lq \-n \(rq); +default: \(lq\(rq +.TP +.B \-seed\fR <\fIvalue\fR> +seed value to used with +.B airSrandMT() +.RI ( unsigned\ int ) +default: +.RB \(lq 42 \(rq +.TP +.B \-step\fR <\fIstep\fR> +time increment in solver +.RI ( double ) +default: +.RB \(lq 1.0 \(rq +.TP +.B \-single +instead of the default behavior of tracking a pair of antipodal points +(appropriate for determining DWI gradients), use only single points +(appropriate for who knows what). +.TP +.B \-snap\fR <\fIinterval\fR> +specifies an interval between which snapshots of the point positions should be +saved out. +By default (not using this option), there is no such snapshot behavior +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-jitter\fR <\fIjitter\fR> +amount by which to perturb points when given an input +.I nrrd +.RI ( double ) +default: +.RB \(lq 0.1 \(rq +.TP +.B \-miniter\fR <\fI#\ iters\fR> +min number of iterations for which to run the simulation +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-maxiter\fR <\fI#\ iters\fR> +max number of iterations for which to run the simulation +.RI ( int ) +default: +.RB \(lq 1000000 \(rq +.TP +.B \-minvelo\fR <\fIvel\fR> +low threshold on mean velocity of repelling points, at which point repulsion +phase of algorithm terminates. +.RI ( double ) +default: +.RB \(lq 0.00001 \(rq +.TP +.B \-exp\fR <\fIexponent\fR> +the exponent n that determines the potential energy +.BR 1/r^n . +.RI ( double ) +default: +.RB \(lq 1 \(rq +.TP +.B \-dp\fR <\fIpotential\ change\fR> +low threshold on fractional change of potential at which point repulsion phase +of algorithm terminates. +.RI ( double ) +default: +.RB \(lq 0.000000001 \(rq +.TP +.B \-minimprov\fR <\fIdelta\fR> +in the second phase of the algorithm, when stochastically balancing the sign of +the gradients, the (small) improvement in length of mean gradient which +triggers termination (as further improvements are unlikely. +.RI ( double ) +default: +.RB \(lq 0.00005 \(rq +.TP +.B \-minmean\fR <\fIlen\fR> +if length of mean gradient falls below this, finish the balancing phase +.RI ( double ) +default: +.RB \(lq 0.0001 \(rq +.TP +.B \-izv\fR <\fIinsert\fR> +adding zero vector at beginning of grads +.RI ( bool ) +default: +.RB \(lq false \(rq +.TP +.B \-o\fR <\fIfilename\fR> +file to write output +.I nrrd +to +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-make.1 b/tend-make.1 new file mode 100644 index 0000000..c4b7b08 --- /dev/null +++ b/tend-make.1 @@ -0,0 +1,28 @@ +.TH TEND\-MAKE "1" "April 2021" "" "User Commands" +.SH NAME +tend\-make \- create DT volume from confidence and eigensystem +.SH SYNOPSIS +.B tend\ make +.B \-i +.RI < conf \ evals \ evecs > +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Create DT volume from confidence and eigensystem. +The input is in the form of three +.IR nrrd s, +one for confidence values (3D), one for eigenvalues (4D, three evals per +voxel), and one for eigenvectors (4D, nine evec components per voxel). +.SH OPTIONS +.TP +.B \-i\fR <\fIconf\fR\ \fIevals\fR\ \fIevecs\fR> +input diffusion tensor volume (3 +.IR nrrd s) +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-mconv.1 b/tend-mconv.1 new file mode 100644 index 0000000..54a6f07 --- /dev/null +++ b/tend-mconv.1 @@ -0,0 +1,39 @@ +.TH TEND\-MCONV "1" "April 2021" "" "User Commands" +.SH NAME +tend\-mconv \- convert from one model to another +.SH SYNOPSIS +.B tend\ mconv +.B \-mo +.RI < model > +.RB [ \-mi +.RI < model >] +.RB [ \-i +.RI < nin >] +.RB [ \-o +.RI < nout >] +.SH OPTIONS +.TP +.B \-mo\fR <\fImodel\fR> +which model to convert to +.RI ( string ) +.TP +.B \-mi\fR <\fImodel\fR> +model converting from; if not set, will try to determine from input +.I nrrd +.RI ( string ) +.TP +.B \-i\fR <\fInin\fR> +input +.I nrrd +of model parms; default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output +.I nrrd +of model parms +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-mfit.1 b/tend-mfit.1 new file mode 100644 index 0000000..fc220b4 --- /dev/null +++ b/tend-mfit.1 @@ -0,0 +1,129 @@ +.TH TEND\-MFIT "1" "April 2021" "" "User Commands" +.SH NAME +tend\-mfit \- estimate models from a set of DW images +.SH SYNOPSIS +.B tend\ mfit +.RB [ \-v +.RI < verbose >] +.B \-m +.RI < model > +.RB [ \-ns +.RI < #\ starts >] +.RB [ \-ml ] +.RB [ \-sigma +.RI < sigma >] +.RB [ \-eps +.RI < eps >] +.RB [ \-mini +.RI < min\ iters >] +.RB [ \-maxi +.RI < max\ iters >] +.B \-knownB0 +.RI < bool > +.RB [ \-t +.RI < type >] +.RB [ \-i +.RI < dwi >] +.RB [ \-o +.RI < nout >] +.RB [ \-eo +.RI < filename >] +.RB [ \-co +.RI < filename >] +.RB [ \-io +.RI < filename >] +.SH OPTIONS +.TP +.B \-v\fR <\fIverbose\fR> +verbosity level +.RI ( int ) +default: +.RB \(lq 0 \(rq +.TP +.B \-m\fR <\fImodel\fR> +which model to fit. +Use optional +.RB \(lq b0+ \(rq +prefix to indicate that the +.B B0 +image should also be saved (independent of whether it was known or had to be +estimated, according to +.RB \(lq \-knownB0 \(rq). +.RI ( string ) +.TP +.B \-ns\fR <\fI#\ starts\fR> +number of random starting points at which to initialize fitting +.RI ( unsigned\ int ) +default: +.RB \(lq 1 \(rq +.TP +.B \-ml +do ML fitting, rather than least-squares, which also requires setting +.RB \(lq \-sigma \(rq +.TP +.B \-sigma\fR <\fIsigma\fR> +Gaussian/Rician noise parameter +.RI ( double ) +.TP +.B \-eps\fR <\fIeps\fR> +convergence epsilon +.RI ( double ) +default: +.RB \(lq 0.01 \(rq +.TP +.B \-mini\fR <\fImin\ iters\fR> +minimum required # iterations for fitting. +.RI ( unsigned\ int ) +default: +.RB \(lq 3 \(rq +.TP +.B \-maxi\fR <\fImax\ iters\fR> +maximum allowable # iterations for fitting. +.RI ( unsigned\ int ) +default: +.RB \(lq 100 \(rq +.TP +.B \-knownB0\fR <\fIbool\fR> +Indicates if the +.B B=0 +non-diffusion-weighted reference image is known +.RB (\(lq true \(rq) +because it appears one or more times amongst the DWIs, or, if it has to be +estimated along with the other model parameters +.RB (\(lq false \(rq) +.RI ( bool ) +.TP +.B \-t\fR <\fItype\fR> +output type of model parameters; default: +.RB \(lq float \(rq +.TP +.B \-i\fR <\fIdwi\fR> +all the diffusion-weighted images in one 4D +.IR nrrd ; +default: +.RB \(lq \- \(rq +.TP +.B \-o\fR <\fInout\fR> +output parameter vector image +.RI ( string ) +default: +.RB \(lq \- \(rq +.TP +.B \-eo\fR <\fIfilename\fR> +Giving a filename here allows you to save out the per-sample fitting error. +By default, no such error is saved. +.RI ( string ) +.TP +.B \-co\fR <\fIfilename\fR> +Giving a filename here allows you to save out the per-sample convergence +fraction. +By default, no such error is saved. +.RI ( string ) +.TP +.B \-io\fR <\fIfilename\fR> +Giving a filename here allows you to save out the per-sample number of +iterations needed for fitting. +By default, no such error is saved. +.RI ( string ) +.SH "SEE\ ALSO" +.BR tend (1) diff --git a/tend-msim.1 b/tend-msim.1 new file mode 100644 index 0000000..2d0b76a --- /dev/null +++ b/tend-msim.1 @@ -0,0 +1,111 @@ +.TH TEND\-MSIM "1" "April 2021" "" "User Commands" +.SH NAME +tend\-msim \- simulate DW images from an image of models +.SH SYNOPSIS +.B tend\ msim +.RB [ \-sigma +.RI < sigma >] +.RB [ \-seed +.RI < seed >] +.B \-g +.RI < grad\ list > +.RB [ \-b0 +.RI < b0\ image >] +.RB [ \-i +.RI < model\ image >] +.B \-m +.RI < model > +.RB [ \-ib0 +.RI < bool >] +.RB [ \-b +.RI < b >] +.RB [ \-kvp +.RI < bool >] +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +Simulate DW images from an image of models. +The output will be in the same form as the input to +.BR tend\-estim (1). +The B-matrices +.RB (\(lq \-B \(rq) +can be the output from +.BR tend\-bmat (1), +or the gradients can be given directly +.RB (\(lq \-g \(rq); +one of these is required. +Note that the input tensor image +.RB (\(lq \-i \(rq) +is the basis of the output per-axis fields and image orientation. +.B NOTE: +this includes the measurement frame used in the input tensor image, which +implies that the given gradients or B-matrices are already expressed in that +measurement frame. +.SH OPTIONS +.TP +.B \-sigma\fR <\fIsigma\fR> +Gaussian/Rician noise parameter +.RI ( double ) +default: +.RB \(lq 0.0 \(rq +.TP +.B \-seed\fR <\fIseed\fR> +seed value for RNG which creates noise +.RI ( int ) +default: +.RB \(lq 42 \(rq +.TP +.B \-g\fR <\fIgrad\ list\fR> +gradient list, one row per diffusion-weighted image +.TP +.B \-b0\fR <\fIb0\ image\fR> +reference non-diffusion-weighted +.RB (\(lq B0 \(rq) +image, which may be needed if it isn't part of the given model parameter image +.TP +.B \-m\fR <\fImodel\fR> +model with which to simulate DWIs, which must be specified if it is not +indicated by the first axis in input model image. +.RB \(lq string \(rq +.TP +.B \-ib0\fR <\fIbool\fR> +insert a non-DW +.B B0 +image at the beginning of the experiment specification (useful if the given +gradient list doesn't already have one) and hence also insert a +.B B0 +image at the beginning of the output simulated DWIs +.RB \(lq bool \(rq +default: +.RB \(lq false \(rq +.TP +.B \-b\fR <\fIb\fR> +.B b +value for simulated scan +.RB \(lq double \(rq +default: +.RB \(lq 1000 \(rq +.TP +.B \-kvp\fR <\fIbool\fR> +generate key/value pairs in the NRRD header corresponding to the input +.BR b -value +and gradients. +.RB \(lq bool \(rq +default: +.RB \(lq true \(rq +.TP +.B \-t\fR <\fItype\fR> +output type of DWIs; default: +.RB \(lq float \(rq +.TP +.B \-o\fR <\fInout\fR> +output dwis +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-bmat (1), +.BR tend\-estim (1) diff --git a/tend-sim.1 b/tend-sim.1 new file mode 100644 index 0000000..3761398 --- /dev/null +++ b/tend-sim.1 @@ -0,0 +1,101 @@ +.TH TEND\-SIM "1" "April 2021" "" "User Commands" +.SH NAME +tend\-sim \- simulate DW images from a tensor field +.SH SYNOPSIS +.B tend\ sim +.RB [ \-old ] +.RB [ \-sigma +.RI < sigma >] +.RB [ \-seed +.RI < seed >] +.RB [ \-g +.RI < grad\ list >] +.RB [ \-B +.RI < B\ matrix >] +.B \-r +.RI < reference\ field > +.RB [ \-i +.RI < tensor\ field >] +.RB [ \-b +.RI < b >] +.RB [ \-kvp ] +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Simulate DW images from a tensor field. +The output will be in the same form as the input to +.BR tend\-estim (1). +The B-matrices +.RB (\(lq \-B \(rq) +can be the output from +.BR tend\-bmat (1), +or the gradients can be given directly +.RB (\(lq \-g \(rq); +one of these is required. +Note that the input tensor field +.RB (\(lq \-i \(rq) +is the basis of the output per-axis fields and image orientation. +.B NOTE: +this includes the measurement frame used in the input tensor field, which +implies that the given gradients or B-matrices are already expressed in that +measurement frame. +.SH OPTIONS +.TP +.B \-old +don't use the new +.B tenEstimateContext +functionality +.TP +.B \-sigma\fR <\fIsigma\fR> +Rician noise parameter +.RI ( float ) +default: +.RB \(lq 0.0 \(rq +.TP +.B \-seed\fR <\fIseed\fR> +seed value for RNG which creates noise +.RI ( int ) +default: +.RB \(lq 42 \(rq +.TP +.B \-g\fR <\fIgrad\ list\fR> +gradient list, one row per diffusion-weighted image +.TP +.B \-B\fR <\fIB\ matrix\fR> +B matrix, one row per diffusion-weighted image. +Using this overrides the gradient list input via +.RB \(lq \-g \(rq +.TP +.B \-r\fR <\fIreference\ field\fR> +reference anatomical scan, with no diffusion weighting +.TP +.B \-i\fR <\fItensor\ field\fR> +input diffusion tensor field +.TP +.B \-b\fR <\fIb\fR> +.B b +value for simulated scan +.RI ( float ) +default: +.RB \(lq 1000 \(rq +.TP +.B \-kvp +generate key/value pairs in the NRRD header corresponding to the input b-value +and gradients or B-matrices. +.TP +.B \-t\fR <\fItype\fR> +output type of DWIs; default: +.RB \(lq float \(rq +.TP +.B \-o\fR <\fInout\fR> +output image (floating point) +.RI ( string ) +default: +.RB \(lq \- \(rq +.SH "SEE\ ALSO" +.BR tend (1), +.BR tend\-bmat (1), +.BR tend\-estim (1) diff --git a/tend.1 b/tend.1 new file mode 100644 index 0000000..e61040a --- /dev/null +++ b/tend.1 @@ -0,0 +1,316 @@ +.TH TEND "1" "April 2021" "" "User Commands" +.SH NAME +tend \- diffusion image processing and analysis +.SH SYNOPSIS +.B tend +.I COMMAND +.RI [ OPTION ]... +.SH DESCRIPTION +.BR tend (1) +is a command-line interface to much of the functionality in \(lqten\(rq, a C +library for diffusion image processing. +Ten is one library in the \(lqTeem\(rq collection of libraries. +More information about Teem is at +.UR http://teem.sf.net +http://teem.sf.net +.UE . +A checkout of Teem source is available via: +.in +4n +.EX +.B svn co https://svn.code.sf.net/p/teem/code/teem/trunk teem +.EE +.in +.P +Long-term maintenance of this software depends on funding, and funding depends +on being able to document who is using it for what. +If +.BR tend (1) +or Ten has helped in your research, including for simple one-off experiments or +mundane data hacking, the developers of Teem would love to know. +There are multiple ways of communicating this. +In your publications, consider adding a line such as this in the +Acknowledgments: +.in +4n +Data processing performed with the tend tool, part of the Teem toolkit +available at +.UR http://teem.sf.net +http://teem.sf.net +.UE . +.in +Alternatively, please email +.MT glk(a)uchicago.edu +glk(a)uchicago.edu +.ME +and briefly describe how Teem software has helped in your work. +Please also consider joining the +.UR https://lists.sourceforge.net/lists/listinfo/teem-users +teem\-users mailing list +.UE . +This is the primary forum for feedback, questions, and feature requests. +.P +Like +.BR unu (1), +another Teem command-line binary, it is often useful to chain together invocations of +.BR tend (1) +with pipes, as in the following, which estimates tensors from DWIs, takes a +slice of the tensor volume, computes the standard RGB colormap of the principal +eigenvector, and then quantizes it to an 8-bit PNG: +.in +4n +.EX +\fBtend\ estim\ \-i\ dwi.nhdr\ \-B\ kvp\ \-knownB0\ true\ \(rs +\ |\ tend\ slice\ \-a\ 2\ \-p\ 30\ \(rs +\ |\ tend\ evecrgb\ \-c\ 0\ \-a\ cl2\ \-gam\ 1.2\ \(rs +\ |\ unu\ quantize\ \-b\ 8\ \-min\ 0\ \-max\ 1\ \-o\ z30\-rgb.png +.EE +.in +.SH OPTIONS +.SS tend\ about +Information about this program and its use +.P +See +.BR tend\-about (1). +.SS tend\ grads +Calculate balanced gradient directions for DWI acquisition +.P +See +.BR tend\-grads (1). +.SS tend\ epireg +Register diffusion-weighted echo-planar images +.P +See +.BR tend\-epireg (1). +.SS tend\ bmat +Calculate B-matrix given gradient directions +.P +See +.BR tend\-bmat (1). +.SS tend\ estim +Estimate tensors from a set of DW images +.P +See +.BR tend\-estim (1). +.SS tend\ sim +Simulate DW images from a tensor field +.P +See +.BR tend\-sim (1). +.SS tend\ mfit +Estimate models from a set of DW images +.P +See +.BR tend\-mfit (1). +.SS tend\ mconv +Convert from one model to another +.P +See +.BR tend\-mconv (1). +.SS tend\ msim +Simulate DW images from an image of models +.P +See +.BR tend\-msim (1). +.SS tend\ make +Create DT volume from confidence and eigensystem +.P +See +.BR tend\-make (1). +.SS tend\ avg +Average across tensor volumes +.P +See +.BR tend\-avg (1). +.SS tend\ helix +Generate twisting helical tensor field +.P +See +.BR tend\-helix (1). +.SS tend\ sten +Calculate structure tensors from a scalar field +.P +See +.BR tend\-sten (1). +.SS tend\ glyph +Generate postscript or ray-traced renderings of 3D glyphs +.P +See +.BR tend\-glyph (1). +.SS tend\ ellipse +Generate postscript renderings of 2D glyphs +.P +See +.BR tend\-ellipse (1). +.SS tend\ anplot +Graph anisotropy metric in barycentric coords +.P +See +.BR tend\-anplot (1). +.SS tend\ anvol +Apply an anisotropy metric to a DT volume +.P +See +.BR tend\-anvol (1). +.SS tend\ anscale +Scale the anisotropic component of the tensors +.P +See +.BR tend\-anscale (1). +.SS tend\ anhist +Generate barycentric histograms of anisotropy +.P +See +.BR tend\-anhist (1). +.SS tend\ triple +Compute volume of shape triples +.P +See +.BR tend\-triple (1). +.SS tend\ tconv +Convert between different shape triples +.P +See +.BR tend\-tconv (1). +.SS tend\ point +Describe everything about one sample in a DT volume +.P +See +.BR tend\-point (1). +.SS tend\ slice +Slice 3D tensors to get slab/image of 3D/2D tensors +.P +See +.BR tend\-slice (1). +.SS tend\ norm +Normalize tensor size +.P +See +.BR tend\-norm (1). +.SS tend\ fiber +Fiber tractography, from one or more seeds +.P +See +.BR tend\-fiber (1). +.SS tend\ eval +Calculate one or more eigenvalues in a DT volume +.P +See +.BR tend\-eval (1). +.SS tend\ evalpow +Modify shape by raising eigenvalues to some power +.P +See +.BR tend\-evalpow (1). +.SS tend\ evalclamp +Modify shape by clamping eigenvalues in some range +.P +See +.BR tend\-evalclamp (1). +.SS tend\ evaladd +Modify shape by adding a constant to all eigenvalues +.P +See +.BR tend\-evaladd (1). +.SS tend\ evalmul +Modify shape by multiplying eigenvalues by a constant +.P +See +.BR tend\-evalmul (1). +.SS tend\ log +Calculates logarithm of the tensor +.P +See +.BR tend\-log (1). +.SS tend\ exp +Calculates \fBexp()\fR of the tensor +.P +See +.BR tend\-exp (1). +.SS tend\ evec +Calculate one or more eigenvectors in a DT volume +.P +See +.BR tend\-evec (1). +.SS tend\ evecrgb +Make an RGB volume from an eigenvector and an anisotropy +.P +See +.BR tend\-evecrgb (1). +.SS tend\ evq +Quantize directions of diffusion +.P +See +.BR tend\-evq (1). +.SS tend\ unmf +Applies and removes the measurement frame +.P +See +.BR tend\-unmf (1). +.SS tend\ expand +Converts masked non-redundant tensor images to redundant +.P +See +.BR tend\-expand (1). +.SS tend\ shrink +Converts a 9-value DT volume to a 7-value DT volume +.P +See +.BR tend\-shrink (1). +.SS tend\ bfit +Non-linear least-squares fitting of b-value curves +.P +See +.BR tend\-bfit (1). +.SS tend\ satin +Generate a pretty synthetic DT volume +.P +See +.BR tend\-satin (1). +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR unu (1), +.BR vprobe (1), +.BR tend\-about (1), +.BR tend\-anhist (1), +.BR tend\-anplot (1), +.BR tend\-anscale (1), +.BR tend\-anvol (1), +.BR tend\-avg (1), +.BR tend\-bfit (1), +.BR tend\-bmat (1), +.BR tend\-ellipse (1), +.BR tend\-epireg (1), +.BR tend\-estim (1), +.BR tend\-eval (1), +.BR tend\-evaladd (1), +.BR tend\-evalclamp (1), +.BR tend\-evalmul (1), +.BR tend\-evalpow (1), +.BR tend\-evec (1), +.BR tend\-evecrgb (1), +.BR tend\-evq (1), +.BR tend\-exp (1), +.BR tend\-expand (1), +.BR tend\-fiber (1), +.BR tend\-glyph (1), +.BR tend\-grads (1), +.BR tend\-helix (1), +.BR tend\-log (1), +.BR tend\-make (1), +.BR tend\-mconv (1), +.BR tend\-mfit (1), +.BR tend\-msim (1), +.BR tend\-norm (1), +.BR tend\-point (1), +.BR tend\-satin (1), +.BR tend\-shrink (1), +.BR tend\-sim (1), +.BR tend\-slice (1), +.BR tend\-sten (1), +.BR tend\-tconv (1), +.BR tend\-triple (1), +.BR tend\-unmf (1) diff --git a/unu.1 b/unu.1 new file mode 100644 index 0000000..ef710be --- /dev/null +++ b/unu.1 @@ -0,0 +1,127 @@ +.TH UNU "1" "April 2021" "" "User Commands" +.SH NAME +unu \- Utah Nrrd Utilities command-line interface +.SH SYNOPSIS +.B unu +.I COMMAND +.RI [ OPTION ]... +.SH DESCRIPTION +.BR unu (1) +is a command-line interface to much of the functionality in \(lqnrrd\(rq, a C +library for raster data processing. +Nrrd is one library in the \(lqTeem\(rq collection of libraries. +More information about Teem is at +.UR http://teem.sf.net +http://teem.sf.net +.UE . +A checkout of Teem source is available via: +.in +4n +.EX +.B svn co https://svn.code.sf.net/p/teem/code/teem/trunk teem +.EE +.in +.P +Long-term maintenance of this software depends on funding, and funding depends +on being able to document who is using it for what. +If +.BR unu (1) +or Nrrd has helped in your research, including for simple one-off experiments +or mundane data hacking, the developers of Teem would love to know. +There are multiple ways of communicating this. +In your publications, consider adding a line such as this in the +Acknowledgments: +.in +4n +Data processing performed with the unu tool, part of the Teem toolkit available +at +.UR http://teem.sf.net +http://teem.sf.net +.UE . +.in +Alternatively, please email +.MT glk(a)uchicago.edu +glk(a)uchicago.edu +.ME +and briefly describe how Teem software has helped in your work. +Please also consider joining the +.UR https://lists.sourceforge.net/lists/listinfo/teem-users +teem\-users mailing list +.UE . +This is the primary forum for feedback, questions, and feature requests. +.P +A summary list of unu commands is generated by running simply +.RB \(lq unu \(rq. +Running a +.BR unu (1) +command without additional arguments (e.g. \(lq\fBunu\ slice\fR\(rq) +generates its description and usage information. +This includes information (marked with +.RB \(lq *\ Uses\ ... \(rq) +about the underling Nrrd library calls (e.g. \fBnrrdSlice()\fR) that implement +the basic functionality in that +.BR unu (1) +command. +.P +The utility of +.BR unu (1) +is mainly as a pre-processing tool for getting data into a type, encoding, +format, or dimensions best suited for some visualization or rendering task. +Also, slices and projections are effective ways to visually inspect the +contents of a dataset. +Especially useful + commands include +.BR make , +.BR resample , +.BR crop , +.BR slice , +.BR project , +.BR histo , +.BR dhisto , +.BR quantize , +and +.BR save . +.BR unu (1) +can process CT and MRI volume datasets, grayscale and color images, +time-varying volumes of vector fields (5-D arrays), and more. +Currently supported formats are plain text files (2-D float arrays), NRRD, VTK +structured points, and PNG and PNM images. +.RB \(lq unu\ make\ \-bs\ \-1 \(rq +can read from most DICOM files. +.RB \(lq unu\ save \(rq +can generate EPS files. +Supported encodings are raw, ascii, hex, gzip, and bzip2. +.P +Much of the functionality of +.BR unu (1) +derives from chaining multiple invocations together with pipes +.RB (\(lq | \(rq), +minimizing the need to save out intermediate files. +For example, if +.RB (\(lq data.raw.gz \(rq), +is a gzip\(cqed 256\ x\ 256\ x\ 80 volume of raw floats written from a PC, then +the following will save to +.RB (\(lq zsum.png \(rq) +a histogram equalized summation projection along the slowest axis: +.in +4n +.EX +\fBunu\ make\ \-i\ data.raw.gz\ \-t\ float\ \-s\ 256\ 256\ 80\ \-e\ gzip\ \-en\ little\ \(rs +\ |\ unu\ project\ \-a\ 2\ \-m\ sum\ \(rs +\ |\ unu\ heq\ \-b\ 2000\ \-s\ 1\ \(rs +\ |\ unu\ quantize\ \-b\ 8\ \-o\ zsum.png +.EE +.in +.P +Formats available: +.B nrrd pnm png vtk text eps +.P +Nrrd data encodings available: +.B raw ascii hex gz bz2 +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR mrender (1), +.BR miter (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR vprobe (1) diff --git a/vprobe.1 b/vprobe.1 new file mode 100644 index 0000000..bdee507 --- /dev/null +++ b/vprobe.1 @@ -0,0 +1,214 @@ +.TH VPROBE "1" "April 2021" "" "User Commands" +.SH NAME +vprobe \- shows off the functionality of the gage library +.SH SYNOPSIS +.B vprobe +.B \-i +.RI < nin > +.B \-k +.RI < kind > +.RB [ \-v +.RI < verbosity >] +.B \-q +.RI < query > +.RB [ \-s +.RI < sclX \ xclY \ sxlZ >] +.RB [ \-k00 +.RI < kern00 >] +.RB [ \-k11 +.RI < kern11 >] +.RB [ \-k22 +.RI < kern22 >] +.RB [ \-seed +.RI < N >] +.RB [ \-ssn +.RI < SS\ # >] +.RB [ \-ssr +.RI < scale\ range >] +.RB [ \-ssrf +.RI < SS\ read\ format >] +.RB [ \-sssf +.RI < SS\ save\ format >] +.RB [ \-ssw +.RI < SS\ pos >] +.RB [ \-kssb +.RI < kernel >] +.RB [ \-kssr +.RI < kernel >] +.RB [ \-ssu ] +.RB [ \-sso ] +.RB [ \-ssnd ] +.RB [ \-rn ] +.RB [ \-gmc +.RI < min\ gradmag >] +.RB [ \-ofs ] +.RB [ \-t +.RI < type >] +.RB [ \-o +.RI < nout >] +.SH DESCRIPTION +.P +Shows off the functionality of the gage library. +Uses gageProbe() to query various kinds of volumes to learn various measured or +derived quantities. +Can set environment variable +.B TEEM_VPROBE_HACK_ZI +to limit probing to a single z slice. +.SH OPTIONS +.TP +.B \-i\fR\ <\fInin\fR> +input volume +.TP +.B \-k\fR\ <\fIkind\fR> +\(lqkind\(rq of volume +.RB (\(lq scalar \(rq, +.RB \(lq vector \(rq, +.RB \(lq tensor \(rq, +or +.RB \(lq dwi \(rq) +.TP +.B \-v\fR\ <\fIverbosity\fR> +verbosity level +.RI ( int ); +default: +.RB \(lq 1 \(rq +.TP +.B \-q\fR\ <\fIquery\fR> +the quantity +.RB ( scalar , +.BR vector , +or +.BR matrix ) +to learn by probing +.RI ( string ) +.TP +.B \-s\fR\ <\fIsclX\fR\ \fIsclY\fR\ \fIsxlZ\fR> +scaling factor for resampling on each axis +.RB (> 1.0 : +supersampling); (3 +.IR double s); +default: +.RB \(lq 1.0\ 1.0\ 1.0 \(rq +.TP +.B \-k00\fR\ <\fIkern00\fR> +kernel for +.BR gageKernel00 ; +default: +.RB \(lq tent \(rq +.TP +.B \-k11\fR\ <\fIkern11\fR> +kernel for +.BR gageKernel11 ; +default: +.RB \(lq cubicd:1,0 \(rq +.TP +.B \-k22\fR\ <\fIkern22\fR> +kernel for +.BR gageKernel22 ; +default: +.RB \(lq cubicdd:1,0 \(rq +.TP +.B \-seed\fR\ <\fIN\fR> +RNG seed; mostly for debugging +.RI ( unsigned\ int ); +default: +.RB \(lq 42 \(rq +.TP +.B \-ssn\fR\ <\fISS\ #\fR> +how many scale-space samples to evaluate, or, +.B 0 +to turn-off all scale-space behavior +.RI ( unsigned\ int ); +default: +.RB \(lq 0 \(rq +.TP +.B \-ssr\fR\ <\fIscale\ range\fR> +range of scales in scale-space (2 +.IR double s); +default: +.RB \(lq nan\ nan \(rq +.TP +.B \-ssrf\fR\ <\fISS\ read\ format\fR> +.BR printf (3)\-style +format (including a +.RB \(lq %u \(rq) +for the filenames from which to +.I read +pre-blurred volumes computed for the stack +.RI ( string ); +default: \(lq\(rq +.TP +.B \-sssf\fR\ <\fISS\ save\ format\fR> +.BR printf (3)\-style +format (including a +.RB \(lq %u \(rq) +for the filenames from which to +.I save +pre-blurred volumes computed for the stack +.RI ( string ); +default: \(lq\(rq +.TP +.B \-ssw\fR\ <\fISS\ pos\fR> +\(lqworld\(rq)-space position (true sigma) at which to sample in scale-space +.RI ( double ); +default: +.RB \(lq 0 \(rq +.TP +.B \-kssb\fR\ <\fIkernel\fR> +blurring kernel, to sample scale space; default: +.RB \(lq dgauss:1,5 \(rq +.TP +.B \-kssr\fR\ <\fIkernel\fR> +kernel for reconstructing from scale space samples +.RB \(lq hermite \(rq +.TP +.B \-ssu +do uniform samples along sigma, and not (by default) samples according to the +effective diffusion scale +.TP +.B \-sso +if not using \(lq\-ssu\(rq, use pre-computed optimal sigmas when possible +.TP +.B \-ssnd +normalize derivatives by scale +.TP +.B \-rn +renormalize kernel weights at each new sample location. +\(lqAccurate\(rq kernels don\(cqt need this; doing it always makes things go +slower +.TP +.B \-gmc\fR\ <\fImin\ gradmag\fR> +For curvature-based queries, use zero when gradient magnitude is below this +.RI ( double ); +default: +.RB \(lq 0.0 \(rq +.TP +.B \-ofs +If only per-axis spacing is available, use that to contrive full orientation +info +.TP +.B \-t\fR\ <\fItype\fR> +type of output volume +.RI ( type ); +default: +.RB \(lq float \(rq +.TP +.B \-o\fR\ <\fInout\fR> +output volume +.RI ( string ); +default: +.RB \(lq \- \(rq +.SH ENVIRONMENT +.TP +.B TEEM_VPROBE_HACK_ZI +If set, probing is limited to a single z slice. +.SH "SEE\ ALSO" +.BR gprobe (1), +.BR ilk (1), +.BR miter (1), +.BR mrender (1), +.BR nrrdSanity (1), +.BR overrgb (1), +.BR puller (1), +.BR tend (1), +.BR unu (1) commit 593f4aa56a75b955f0a6b62a4a248954e702945d Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 12:41:10 2021 -0400 More precisely skip overly-strict floating-point tests where required diff --git a/teem.spec b/teem.spec index f97e08f..2ebe7a6 100644 --- a/teem.spec +++ b/teem.spec @@ -143,13 +143,15 @@ rm -rvf python %check -# tests fail on 32-bit arches -# seems that computation accuracy is arch-dependant -%global _smp_mflags -j1 -%ifarch x86_64 -%ctest3 +# We must exclude probeSS_ctmr04 and probeSS_ctmr10 on certain architectures +# due to overly-strict rounding requirements. +%ifarch %{arm64} ppc64le s390x +%global ctest_excludes --exclude-regex '^(probeSS_ctmr(04|10))$' %endif +# Tests are not parallel-safe +%ctest3 %{?ctest_excludes} -j1 + %if 0%{?epel} == 7 %ldconfig_scriptlets libs @@ -201,6 +203,7 @@ rm -rvf python - Add an -examples subpackage so the BSD and zlib licenses can be “contained” to that subpackage; remove certain unused files with other licenses in %%prep - Require cmake-filesystem instead of all of CMake in -devel +- More precisely skip overly-strict floating-point tests where required * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 23e9f5a00538ba4ca386c4cf3cb6384c16caa08a Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:49:36 2021 -0400 Add explicit BR on make (implied by cmake/cmake3) diff --git a/teem.spec b/teem.spec index d1fa1e0..f97e08f 100644 --- a/teem.spec +++ b/teem.spec @@ -25,6 +25,7 @@ Patch0: lib_install_dir.patch BuildRequires: gcc-c++ BuildRequires: cmake3 +BuildRequires: make BuildRequires: zlib-devel BuildRequires: libpng-devel commit db87fd2490d946f17a6d9fc4b18e47d37bebb4b3 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:43:41 2021 -0400 Require cmake-filesystem instead of all of CMake in -devel diff --git a/teem.spec b/teem.spec index d4c3d79..d1fa1e0 100644 --- a/teem.spec +++ b/teem.spec @@ -92,7 +92,7 @@ applications that use Teem. %package devel Summary: Development files for %{name} Requires: %{name}-libs%{?_isa} = %{version}-%{release} -Requires: cmake%{?_isa} +Requires: cmake-filesystem %description devel %{common_description} @@ -199,6 +199,7 @@ rm -rvf python - Use stricter file globs, including specifying the so-version - Add an -examples subpackage so the BSD and zlib licenses can be “contained” to that subpackage; remove certain unused files with other licenses in %%prep +- Require cmake-filesystem instead of all of CMake in -devel * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit e6982c7d45b51e73e424b3235560d9c3d6314908 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:42:16 2021 -0400 Add an -examples subpackage so the BSD and zlib licenses can be “contained” to that subpackage; remove certain unused files with other licenses in %%prep diff --git a/teem.spec b/teem.spec index b3f50d4..d4c3d79 100644 --- a/teem.spec +++ b/teem.spec @@ -4,7 +4,18 @@ Version: 1.11.0 Release: 15%{?dist} Summary: Libraries for processing and visualizing scientific raster data +# The entire source is LGPLv2+, except files noted at the License fields of certain subpackages. License: LGPLv2+ +# Additionally, the following are removed in %%prep to assert that they do not +# contribute to the built package: +# +# zlib: +# arch/win32/include/zlib.h +# MIT: +# python/ctypes/Nrrd.py +# python/ctypes/pullDemo.py +# python/ctypes/teem-gen.py +# python/ctypes/teem.py URL: https://teem.sourceforge.net Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... # Patch CMakeLists.txt to fix library install paths to match what Fedora @@ -89,9 +100,33 @@ The %{name}-devel package contains libraries and header files for developing applications that use Teem. +%package examples +Summary: Examples for developing with for %{name} +# The entire contents of this subpackage are LGPLv2+, except: +# +# zlib: +# UseTeemCMakeDemo/sanity.c +# BSD: +# Examples/sanity/sanity.c +License: LGPLv2+ and zlib and BSD +BuildArch: noarch + +%description examples %{common_description} + +The %{name}-examples package contains examples for developing applications that +use Teem. + + %prep %autosetup -n %{name}-%{version}-src -p1 +# Remove files that, while they have acceptable licenses, we want to assert do +# not contribute to the built RPMs: +# - Not applicable to this platform +rm -rvf arch/win32 +# - Nothing here appears suitable for packaging: +rm -rvf python + %build %cmake3 \ @@ -141,12 +176,17 @@ applications that use Teem. %files devel -%doc Examples/sanity/ %{_includedir}/teem/ %{_libdir}/libteem.so %{_libdir}/cmake/Teem-%{version}/ +%files examples +%license LICENSE.txt +%doc Examples +%doc UseTeemCMakeDemo + + %changelog * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch @@ -156,6 +196,9 @@ applications that use Teem. - Fix stray line continuation backslash - Support EPEL7 - Build with “levmar” support enabled +- Use stricter file globs, including specifying the so-version +- Add an -examples subpackage so the BSD and zlib licenses can be “contained” + to that subpackage; remove certain unused files with other licenses in %%prep * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit f879b4ba5748261a4e94736d94a9aecf9e63a24b Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:22:50 2021 -0400 Use stricter file globs, including specifying the so-version diff --git a/teem.spec b/teem.spec index be5871f..b3f50d4 100644 --- a/teem.spec +++ b/teem.spec @@ -1,5 +1,6 @@ Name: teem Version: 1.11.0 +%global so_version 1 Release: 15%{?dist} Summary: Libraries for processing and visualizing scientific raster data @@ -121,12 +122,22 @@ applications that use Teem. %files %doc README.txt -%{_bindir}/* +%{_bindir}/gprobe +%{_bindir}/ilk +%{_bindir}/miter +%{_bindir}/mrender +%{_bindir}/nrrdSanity +%{_bindir}/overrgb +%{_bindir}/puller +%{_bindir}/tend +%{_bindir}/unu +%{_bindir}/vprobe %files libs %license LICENSE.txt -%{_libdir}/libteem.so.* +%{_libdir}/libteem.so.%{so_version} +%{_libdir}/libteem.so.%{so_version}.* %files devel commit 8e9d83ec6f4083e2e472511cf71e6a4cb303f6f6 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:19:43 2021 -0400 Build with “levmar” support enabled diff --git a/teem.spec b/teem.spec index 5f11edb..be5871f 100644 --- a/teem.spec +++ b/teem.spec @@ -18,6 +18,7 @@ BuildRequires: zlib-devel BuildRequires: libpng-devel BuildRequires: bzip2-devel BuildRequires: fftw-devel +BuildRequires: levmar-devel %global common_description %{expand: What Is Teem? @@ -95,7 +96,8 @@ applications that use Teem. %cmake3 \ -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR=ON \ - -DTeem_FFTW3=ON + -DTeem_FFTW3=ON \ + -DTeem_LEVMAR=ON %cmake3_build @@ -142,6 +144,7 @@ applications that use Teem. - Adjust whitespace to personal preference - Fix stray line continuation backslash - Support EPEL7 +- Build with “levmar” support enabled * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 3d52b904785970205228eea38b1f59eab1e5f7e8 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:18:27 2021 -0400 Rearrange BR’s, and drop gcc (implied by gcc-c++) diff --git a/teem.spec b/teem.spec index 31cd485..5f11edb 100644 --- a/teem.spec +++ b/teem.spec @@ -12,12 +12,12 @@ Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/% Patch0: lib_install_dir.patch BuildRequires: gcc-c++ -BuildRequires: gcc BuildRequires: cmake3 + +BuildRequires: zlib-devel +BuildRequires: libpng-devel BuildRequires: bzip2-devel BuildRequires: fftw-devel -BuildRequires: libpng-devel -BuildRequires: zlib-devel %global common_description %{expand: What Is Teem? commit b4222b2431c0b4975ed3ddbc8bf009cd7af182b3 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:15:50 2021 -0400 Support EPEL7 diff --git a/teem.spec b/teem.spec index a6f7829..31cd485 100644 --- a/teem.spec +++ b/teem.spec @@ -13,7 +13,7 @@ Patch0: lib_install_dir.patch BuildRequires: gcc-c++ BuildRequires: gcc -BuildRequires: cmake +BuildRequires: cmake3 BuildRequires: bzip2-devel BuildRequires: fftw-devel BuildRequires: libpng-devel @@ -92,15 +92,15 @@ applications that use Teem. %build -%cmake \ +%cmake3 \ -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR=ON \ -DTeem_FFTW3=ON -%cmake_build +%cmake3_build %install -%cmake_install +%cmake3_install %check @@ -108,11 +108,13 @@ applications that use Teem. # seems that computation accuracy is arch-dependant %global _smp_mflags -j1 %ifarch x86_64 -%ctest +%ctest3 %endif +%if 0%{?epel} == 7 %ldconfig_scriptlets libs +%endif %files @@ -139,6 +141,7 @@ applications that use Teem. - Improved package summaries and descriptions - Adjust whitespace to personal preference - Fix stray line continuation backslash +- Support EPEL7 * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 59bc546adcb1c818b1406486ff585c265ec7d975 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:06:20 2021 -0400 Fix stray line continuation backslash diff --git a/teem.spec b/teem.spec index 96ea77c..a6f7829 100644 --- a/teem.spec +++ b/teem.spec @@ -95,7 +95,7 @@ applications that use Teem. %cmake \ -DCMAKE_SKIP_INSTALL_RPATH=ON \ -DTeem_USE_LIB_INSTALL_SUBDIR=ON \ - -DTeem_FFTW3=ON \ + -DTeem_FFTW3=ON %cmake_build @@ -138,6 +138,7 @@ applications that use Teem. - Update URLs from HTTP to HTTPS - Improved package summaries and descriptions - Adjust whitespace to personal preference +- Fix stray line continuation backslash * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 1a749c45beb6a651404240b06296b5561d55e673 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:01:56 2021 -0400 Adjust whitespace to personal preference diff --git a/teem.spec b/teem.spec index 8f24e62..96ea77c 100644 --- a/teem.spec +++ b/teem.spec @@ -1,23 +1,23 @@ -Name: teem -Version: 1.11.0 -Release: 15%{?dist} -Summary: Libraries for processing and visualizing scientific raster data - -License: LGPLv2+ -URL: https://teem.sourceforge.net -Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... +Name: teem +Version: 1.11.0 +Release: 15%{?dist} +Summary: Libraries for processing and visualizing scientific raster data + +License: LGPLv2+ +URL: https://teem.sourceforge.net +Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... # Patch CMakeLists.txt to fix library install paths to match what Fedora # expects. It is not immediately obvious if this patch is suitable for # sending upstream or not. -Patch0: lib_install_dir.patch +Patch0: lib_install_dir.patch BuildRequires: gcc-c++ -BuildRequires: gcc -BuildRequires: cmake -BuildRequires: bzip2-devel -BuildRequires: fftw-devel -BuildRequires: libpng-devel -BuildRequires: zlib-devel +BuildRequires: gcc +BuildRequires: cmake +BuildRequires: bzip2-devel +BuildRequires: fftw-devel +BuildRequires: libpng-devel +BuildRequires: zlib-devel %global common_description %{expand: What Is Teem? @@ -66,6 +66,7 @@ Strengths of Teem The %{name} package contains the command-line tools included with Teem. + %package libs Summary: Libraries files for %{name} @@ -74,10 +75,11 @@ Summary: Libraries files for %{name} The %{name}-libs package contains libraries that may be required at runtime by applications that use Teem. + %package devel Summary: Development files for %{name} -Requires: %{name}-libs%{?_isa} = %{version}-%{release} -Requires: cmake%{?_isa} +Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: cmake%{?_isa} %description devel %{common_description} @@ -100,6 +102,7 @@ applications that use Teem. %install %cmake_install + %check # tests fail on 32-bit arches # seems that computation accuracy is arch-dependant @@ -108,16 +111,20 @@ applications that use Teem. %ctest %endif + %ldconfig_scriptlets libs + %files %doc README.txt %{_bindir}/* + %files libs %license LICENSE.txt %{_libdir}/libteem.so.* + %files devel %doc Examples/sanity/ %{_includedir}/teem/ @@ -130,6 +137,7 @@ applications that use Teem. - Fix typo in lib_install_dir.patch - Update URLs from HTTP to HTTPS - Improved package summaries and descriptions +- Adjust whitespace to personal preference * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 68faf7af85f2054b1476dc60655e208092e76cac Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 09:00:17 2021 -0400 Improved package summaries and descriptions diff --git a/teem.spec b/teem.spec index 04a9438..8f24e62 100644 --- a/teem.spec +++ b/teem.spec @@ -1,7 +1,7 @@ Name: teem Version: 1.11.0 Release: 15%{?dist} -Summary: Libraries for scientific raster data processing and visualizing +Summary: Libraries for processing and visualizing scientific raster data License: LGPLv2+ URL: https://teem.sourceforge.net @@ -19,41 +19,70 @@ BuildRequires: fftw-devel BuildRequires: libpng-devel BuildRequires: zlib-devel -%description -Teem is a coordinated group of libraries for representing, processing, -and visualizing scientific raster data. Teem includes command-line tools -that permit the library functions to be quickly applied to files and streams, -without having to write any code. The most important and useful libraries -in Teem are: - -- Nrrd (and the unu command-line tool on top of it) supports a range - of operations for transforming N-dimensional raster data (resample, crop, - slice, project, histogram, etc.), as well as the NRRD file format - for storing arrays and their meta-information. -- Gage: fast convolution-based measurements at arbitrary point locations - in volume datasets (scalar, vector, tensor, etc.) -- Mite: a multi-threaded ray-casting volume render with transfer functions - based on any quantity Gage can measure -- Ten: for estimating, processing, and visualizing diffusion tensor fields, - including fiber tractography methods. - +%global common_description %{expand: +What Is Teem? + +Teem is a coordinated group of libraries for representing, processing, and +visualizing scientific raster data. Teem includes command-line tools that +permit the library functions to be quickly applied to files and streams, +without having to write any code. The most important and useful libraries in +Teem are: + + • Nrrd (and the unu command-line tool on top of it) supports a range of + operations for transforming N-dimensional raster data (resample, crop, + slice, project, histogram, etc.), as well as the NRRD file format for + storing arrays and their meta-information. + • Gage: fast convolution-based measurements at arbitrary point locations in + volume datasets (scalar, vector, tensor, etc.) + • Mite: a multi-threaded ray-casting volume render with transfer functions + based on any quantity Gage can measure + • Ten: for estimating, processing, and visualizing diffusion tensor fields, + including fiber tractography methods. + +Strengths of Teem + + • Teem works: Its purpose is to enable research in visualization and image + processing, and research is enabled when simple things are simple to do. + Teem’s functionality and its ease of use have allowed it to become a + component of larger research software projects, such as SCIRun and 3D + Slicer. + • Teem is light-weight: The libraries are written with an eye towards + minimizing the annoyance of getting data in an out, by using the simplest + possible constructs for the job, and by supporting combinations of operations + that arise in common practice. + • Teem is coherent: There is a consistent logic to how information is + represented, and uniformity in the APIs across libraries. + • Teem is portable: All the code is written in plain ANSI C, so it compiles + everywhere, including Windows, using either CMake or GNU Make. A Dashboard + is used to monitor compiler errors and warnings. + • Teem is growing: Some Teem libraries were created years ago and have + remained stable, but new libraries and new functionality are continually + being added. + • Teem is open source: Anyone can use it, and contributions are welcome. Teem + is licensed under the GNU Lesser General Public License, plus exceptions + which facilitate linking Teem into binary-only applications.} + +%description %{common_description} + +The %{name} package contains the command-line tools included with Teem. %package libs -Summary: Libraries for scientific raster data processing and visualizing +Summary: Libraries files for %{name} + +%description libs %{common_description} -%description libs -Teem is a coordinated group of libraries for representing, processing, -and visualizing scientific raster data. +The %{name}-libs package contains libraries that may be required at runtime by +applications that use Teem. %package devel -Summary: Libraries for scientific raster data processing and visualizing +Summary: Development files for %{name} Requires: %{name}-libs%{?_isa} = %{version}-%{release} Requires: cmake%{?_isa} -%description devel -Teem is a coordinated group of libraries for representing, processing, -and visualizing scientific raster data. This package contains development -files. +%description devel %{common_description} + +The %{name}-devel package contains libraries and header files for developing +applications that use Teem. %prep @@ -100,6 +129,7 @@ files. * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch - Update URLs from HTTP to HTTPS +- Improved package summaries and descriptions * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 45277db33360db4931556c3c678c8df5a42d11f9 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 08:50:07 2021 -0400 Update hash in sources file from MD5 to SHA-512 diff --git a/sources b/sources index f09a911..4a5f2e5 100644 --- a/sources +++ b/sources @@ -1 +1 @@ -6b9737e8b7640e18eaf281e830fe59d1 teem-1.11.0-src.tar.gz +SHA512 (teem-1.11.0-src.tar.gz) = 48b171a12db0f02dcfdaa87aa84464c651d661fa66201dc966b3cd5a8134c5bad1dad8987ffcc5d7c21c5d14c2eb617d48200410a1bda19008ef743c093ed575 commit ea786f8048639405a91a5ebb7ef9ed932b514674 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 08:48:37 2021 -0400 Update URLs from HTTP to HTTPS diff --git a/teem.spec b/teem.spec index 272c4b9..04a9438 100644 --- a/teem.spec +++ b/teem.spec @@ -4,8 +4,8 @@ Release: 15%{?dist} Summary: Libraries for scientific raster data processing and visualizing License: LGPLv2+ -URL: http://teem.sourceforge.net -Source0: http://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{v... +URL: https://teem.sourceforge.net +Source0: https://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{... # Patch CMakeLists.txt to fix library install paths to match what Fedora # expects. It is not immediately obvious if this patch is suitable for # sending upstream or not. @@ -99,6 +99,7 @@ files. %changelog * Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 - Fix typo in lib_install_dir.patch +- Update URLs from HTTP to HTTPS * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 5e008cd008b4422253f4aa2edc846e49efcb41cb Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 08:48:27 2021 -0400 Add a comment about lib_install_dir.patch diff --git a/teem.spec b/teem.spec index 6c490a4..272c4b9 100644 --- a/teem.spec +++ b/teem.spec @@ -6,6 +6,9 @@ Summary: Libraries for scientific raster data processing and visualizing License: LGPLv2+ URL: http://teem.sourceforge.net Source0: http://downloads.sourceforge.net/project/teem/teem/%{version}/%{name}-%{v... +# Patch CMakeLists.txt to fix library install paths to match what Fedora +# expects. It is not immediately obvious if this patch is suitable for +# sending upstream or not. Patch0: lib_install_dir.patch BuildRequires: gcc-c++ commit 427091f9585922ee66a43470d65ea1a17726f334 Author: Benjamin A. Beasley <code(a)musicinmybrain.net> Date: Sat Apr 3 08:35:58 2021 -0400 Fix typo in lib_install_dir.patch diff --git a/lib_install_dir.patch b/lib_install_dir.patch index ba4a5be..c39fed0 100644 --- a/lib_install_dir.patch +++ b/lib_install_dir.patch @@ -6,7 +6,7 @@ Index: teem-1.11.0-src/CMakeLists.txt # RPATH stuff, and mac will ingore the INSTALL_RPATH. Make sure for # macs to set BUILD_WITH_INSTALL_RPATH OFF and set INSTALL_NAME_DIR. # I belive INSTALL_NAME_DIR will be ignored on linux. -+SET(LIB_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib CACHE PATH "Lirary installation directory.") ++SET(LIB_INSTALL_DIR ${CMAKE_INSTALL_PREFIX}/lib CACHE PATH "Library installation directory.") SET_TARGET_PROPERTIES(teem PROPERTIES BUILD_WITH_INSTALL_RPATH OFF - INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib diff --git a/teem.spec b/teem.spec index 77f8aa7..6c490a4 100644 --- a/teem.spec +++ b/teem.spec @@ -1,6 +1,6 @@ Name: teem Version: 1.11.0 -Release: 14%{?dist} +Release: 15%{?dist} Summary: Libraries for scientific raster data processing and visualizing License: LGPLv2+ @@ -94,6 +94,9 @@ files. %changelog +* Sat Apr 03 2021 Benjamin A. Beasley <code(a)musicinmybrain.net> - 1.11.0-15 +- Fix typo in lib_install_dir.patch + * Wed Jan 27 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.11.0-14 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild

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zola ExclusiveArch: %{rust_arches}

2 years, 9 months

1
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0 / 0

Architecture specific change in rpms/libreoffice.git

by githook-noreply＠fedoraproject.org

The package rpms/libreoffice.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/libreoffice.git/commit/?id=d6ec43.... Change: -%ifnarch s390x Thanks. Full change: ============ commit 60006c173f8ef1039af9495a62a3ed268418b3f6 Merge: 7c788fc 58cb95c Author: Caolán McNamara <caolanm(a)redhat.com> Date: Fri Aug 20 16:47:37 2021 +0100 Merge branch 'rawhide' into f35 commit 58cb95c86542a20f5855a17396cd1910c556db92 Author: Caolán McNamara <caolanm(a)redhat.com> Date: Fri Aug 20 16:40:33 2021 +0100 try SMP_MFLAGS=2 instead of 3 diff --git a/libreoffice.spec b/libreoffice.spec index e0a9811..a9cdf14 100644 --- a/libreoffice.spec +++ b/libreoffice.spec @@ -1068,7 +1068,7 @@ SMP_MFLAGS=%{?_smp_mflags} SMP_MFLAGS=$[${SMP_MFLAGS/-j/}] %ifarch armv7hl -SMP_MFLAGS=3 +SMP_MFLAGS=2 %endif %if 0%{?flatpak} commit 41762c9f1e3e8e404b7cd33c0613b5b7a9026aa0 Author: Caolán McNamara <caolanm(a)redhat.com> Date: Fri Aug 20 16:38:14 2021 +0100 s390x firebird is available again diff --git a/libreoffice.spec b/libreoffice.spec index cbbfc91..e0a9811 100644 --- a/libreoffice.spec +++ b/libreoffice.spec @@ -50,7 +50,7 @@ Summary: Free Software Productivity Suite Name: libreoffice Epoch: 1 Version: %{libo_version}.4 -Release: 1%{?libo_prerelease}%{?dist} +Release: 2%{?libo_prerelease}%{?dist} License: (MPLv1.1 or LGPLv3+) and LGPLv3 and LGPLv2+ and BSD and (MPLv1.1 or GPLv2 or LGPLv2 or Netscape) and Public Domain and ASL 2.0 and MPLv2.0 and CC0 URL: http://www.libreoffice.org/ @@ -2248,6 +2248,9 @@ gtk-update-icon-cache -q %{_datadir}/icons/hicolor &>/dev/null || : %{_includedir}/LibreOfficeKit %changelog +* Fri Aug 20 2021 Caolán McNamara <caolanm(a)redhat.com> - 1:7.2.0.4-2 +- s390x firebird is available again + * Mon Aug 16 2021 Caolán McNamara <caolanm(a)redhat.com> - 1:7.2.0.4-1 - upgrade to 7.2.0 commit d6ec438d90bd22106aa791b5936b3dfd8a1448cf Author: Caolán McNamara <caolanm(a)redhat.com> Date: Fri Aug 20 11:21:08 2021 +0100 Related: rhbz#1969393 can now renable firebird support on s390x diff --git a/libreoffice.spec b/libreoffice.spec index d765b04..cbbfc91 100644 --- a/libreoffice.spec +++ b/libreoffice.spec @@ -126,10 +126,8 @@ BuildRequires: boost-devel BuildRequires: cups-devel BuildRequires: fontpackages-devel %if 0%{?fedora} -%ifnarch s390x BuildRequires: firebird-devel %endif -%endif BuildRequires: glm-devel BuildRequires: hyphen-devel BuildRequires: libjpeg-turbo-devel @@ -333,10 +331,8 @@ to be written in python. %package base Summary: Database front-end for LibreOffice %if 0%{?fedora} -%ifnarch s390x Requires: firebird %endif -%endif Requires: pentaho-reporting-flow-engine Requires: postgresql-jdbc Requires: %{name}-core%{?_isa} = %{epoch}:%{version}-%{release} @@ -1058,12 +1054,8 @@ export CXXFLAGS=$ARCH_FLAGS %define distrooptions --disable-eot --disable-scripting-beanshell --disable-scripting-javascript --disable-firebird-sdbc %else # fedora -%ifarch s390x -%define distrooptions --enable-eot --enable-kf5 --disable-firebird-sdbc -%else %define distrooptions --enable-eot --enable-kf5 %endif -%endif %if %{with langpacks} %define with_lang --with-lang='%{langpack_langs}' @@ -1865,10 +1857,8 @@ rm -f %{buildroot}%{baseinstdir}/program/classes/smoketest.jar %{baseinstdir}/program/libabplo.so %{baseinstdir}/program/libdbplo.so %if 0%{?fedora} -%ifnarch s390x %{baseinstdir}/program/libfirebird_sdbclo.so %endif -%endif %{baseinstdir}/program/libhsqldb.so %{baseinstdir}/program/librptlo.so %{baseinstdir}/program/librptuilo.so

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Architecture specific change in rpms/pcl.git

by githook-noreply＠fedoraproject.org

The package rpms/pcl.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/pcl.git/commit/?id=bc37e95042b961.... Change: -%ifarch %{arm} Thanks. Full change: ============ commit d115054c29fb244c1ad0d161c1fb3f6e60677a84 Author: Björn Esser <besser82(a)fedoraproject.org> Date: Fri Aug 20 17:02:24 2021 +0200 Disable fat-lto-objects to reduce memory usage Doing so will not hurt as we are not shipping any static libraries diff --git a/pcl.spec b/pcl.spec index a05375e..193093e 100644 --- a/pcl.spec +++ b/pcl.spec @@ -104,7 +104,7 @@ sed -i 's|@PCL_SOURCE_DIR@/build|@PCL_SOURCE_DIR@/%{_vpath_builddir}|' doc/doxyg %build # try to reduce memory usage of compile process (can cause OOM errors # esp. on ARM builders) -%global optflags %(echo %{optflags} | sed -e 's/-g /-g1 /' -e 's/-pipe //') +%global optflags %(echo %{optflags} | sed -e 's/-g /-g1 /' -e 's/-pipe //' -e's/-ffat-lto-objects/-fno-fat-lto-objects/') %cmake \ -DCMAKE_BUILD_TYPE=None \ @@ -191,7 +191,11 @@ mv $RPM_BUILD_ROOT%{_datadir}/%{name}-*/Modules $RPM_BUILD_ROOT%{_libdir}/cmake/ %doc %{_vpath_builddir}/doc/advanced/advanced %changelog -* Mon Aug 17 2021 Rich Mattes <richmattes(a)gmail.com> - 1.12.0-1 +* Fri Aug 20 2021 Björn Esser <besser82(a)fedoraproject.org> - 1.12.0-1 +- Disable fat-lto-objects to reduce memory usage + Doing so will not hurt as we are not shipping any static libraries + +* Tue Aug 17 2021 Rich Mattes <richmattes(a)gmail.com> - 1.12.0-1 - Drop "oom" patch to resolve multiple definition error and fix FTBFS (rhbz#1992893) - Enable LTO and add library versions in files section commit bc37e95042b961dbb194fb0e2bd9f187eea4e589 Author: Björn Esser <besser82(a)fedoraproject.org> Date: Fri Aug 20 17:01:36 2021 +0200 Revert "Limit to 3 cpus on arm to try to prevent memory issues" This reverts commit fcbd73e2a8805f79814cac3e72340a6edcead49b. diff --git a/pcl.spec b/pcl.spec index a95c5c5..a05375e 100644 --- a/pcl.spec +++ b/pcl.spec @@ -105,10 +105,6 @@ sed -i 's|@PCL_SOURCE_DIR@/build|@PCL_SOURCE_DIR@/%{_vpath_builddir}|' doc/doxyg # try to reduce memory usage of compile process (can cause OOM errors # esp. on ARM builders) %global optflags %(echo %{optflags} | sed -e 's/-g /-g1 /' -e 's/-pipe //') -%ifarch %{arm} -# Likely running out of memory during build -%global _smp_ncpus_max 3 -%endif %cmake \ -DCMAKE_BUILD_TYPE=None \ @@ -195,10 +191,7 @@ mv $RPM_BUILD_ROOT%{_datadir}/%{name}-*/Modules $RPM_BUILD_ROOT%{_libdir}/cmake/ %doc %{_vpath_builddir}/doc/advanced/advanced %changelog -* Fri Aug 20 2021 Björn Esser <besser82(a)fedoraproject.org> - 1.12.0-1 -- Limit to 3 cpus on arm to try to prevent memory issues - -* Tue Aug 17 2021 Rich Mattes <richmattes(a)gmail.com> - 1.12.0-1 +* Mon Aug 17 2021 Rich Mattes <richmattes(a)gmail.com> - 1.12.0-1 - Drop "oom" patch to resolve multiple definition error and fix FTBFS (rhbz#1992893) - Enable LTO and add library versions in files section

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Architecture specific change in rpms/pcl.git

by githook-noreply＠fedoraproject.org

The package rpms/pcl.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/pcl.git/commit/?id=fcbd73e2a8805f.... Change: +%ifarch %{arm} Thanks. Full change: ============ commit fcbd73e2a8805f79814cac3e72340a6edcead49b Author: Björn Esser <besser82(a)fedoraproject.org> Date: Fri Aug 20 15:21:49 2021 +0200 Limit to 3 cpus on arm to try to prevent memory issues diff --git a/pcl.spec b/pcl.spec index a05375e..a95c5c5 100644 --- a/pcl.spec +++ b/pcl.spec @@ -105,6 +105,10 @@ sed -i 's|@PCL_SOURCE_DIR@/build|@PCL_SOURCE_DIR@/%{_vpath_builddir}|' doc/doxyg # try to reduce memory usage of compile process (can cause OOM errors # esp. on ARM builders) %global optflags %(echo %{optflags} | sed -e 's/-g /-g1 /' -e 's/-pipe //') +%ifarch %{arm} +# Likely running out of memory during build +%global _smp_ncpus_max 3 +%endif %cmake \ -DCMAKE_BUILD_TYPE=None \ @@ -191,7 +195,10 @@ mv $RPM_BUILD_ROOT%{_datadir}/%{name}-*/Modules $RPM_BUILD_ROOT%{_libdir}/cmake/ %doc %{_vpath_builddir}/doc/advanced/advanced %changelog -* Mon Aug 17 2021 Rich Mattes <richmattes(a)gmail.com> - 1.12.0-1 +* Fri Aug 20 2021 Björn Esser <besser82(a)fedoraproject.org> - 1.12.0-1 +- Limit to 3 cpus on arm to try to prevent memory issues + +* Tue Aug 17 2021 Rich Mattes <richmattes(a)gmail.com> - 1.12.0-1 - Drop "oom" patch to resolve multiple definition error and fix FTBFS (rhbz#1992893) - Enable LTO and add library versions in files section

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Architecture specific change in rpms/pacemaker.git

by githook-noreply＠fedoraproject.org

The package rpms/pacemaker.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/pacemaker.git/commit/?id=15ac1a3c.... Change: +ExclusiveArch: aarch64 i686 ppc64le s390x x86_64 Thanks. Full change: ============ commit eb015df7012a1ef2358394807b49a82021dd4c7f Merge: e103b00 a74f8cf Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri Aug 20 14:16:02 2021 +0200 Merge branch 'rawhide' into f33 commit a74f8cfffa01425166cf6793858b614b09280026 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri Aug 20 01:22:00 2021 +0200 * Thu Aug 19 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.5.rc3 - Fix malformed xml in fence_watchdog metadata diff --git a/0007-Fix-fence_watchdog-fix-malformed-xml-in-metadata.patch b/0007-Fix-fence_watchdog-fix-malformed-xml-in-metadata.patch new file mode 100644 index 0000000..0d2c32e --- /dev/null +++ b/0007-Fix-fence_watchdog-fix-malformed-xml-in-metadata.patch @@ -0,0 +1,25 @@ +From 46dd1118cae948649e000b2159e8e92623520ad9 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Thu, 19 Aug 2021 09:28:54 +0200 +Subject: [PATCH] Fix: fence_watchdog: fix malformed xml in metadata + +--- + daemons/fenced/fence_watchdog.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/daemons/fenced/fence_watchdog.in b/daemons/fenced/fence_watchdog.in +index 700065e..eefa739 100755 +--- a/daemons/fenced/fence_watchdog.in ++++ b/daemons/fenced/fence_watchdog.in +@@ -124,7 +124,7 @@ def metadata(avail_opt, options): + for option, dummy in sorted_options(avail_opt): + if "shortdesc" in ALL_OPT[option]: + print(' <parameter name="' + option + +- 'required="' + ALL_OPT[option]["required"] + '">') ++ '" required="' + ALL_OPT[option]["required"] + '">') + + default = "" + default_name_arg = "-" + ALL_OPT[option]["getopt"][:-1] +-- +1.8.3.1 + diff --git a/pacemaker.spec b/pacemaker.spec index 2cd4aab..92eafb3 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -32,7 +32,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.1 -%global specversion 0.4.rc3 +%global specversion 0.5.rc3 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build %global commit c6a4f6e6cdcedf08e0bfd81248b86812c2a571b2 @@ -221,6 +221,7 @@ Patch2: 0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch Patch3: 0004-Build-rpm-package-fence_watchdog-in-base-package.patch Patch4: 0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch Patch5: 0006-Build-manpages-using-help2man-check-exit-code-of-too.patch +Patch6: 0007-Fix-fence_watchdog-fix-malformed-xml-in-metadata.patch # upstream commits @@ -829,6 +830,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Thu Aug 19 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.5.rc3 +- Fix malformed xml in fence_watchdog metadata + * Tue Aug 17 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.4.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc3, for full details, see included ChangeLog file or commit b2569f82a6db1b7ddd4c28fc4e317f96fa3f5518 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Tue Aug 17 09:42:18 2021 +0200 * Tue Aug 17 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.4.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc3, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc3 - Make tools exit-codes consistent for --version - Check exit-codes of tools prior to manpage-generation diff --git a/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch b/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch deleted file mode 100644 index 3e64b25..0000000 --- a/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch +++ /dev/null @@ -1,122 +0,0 @@ -From ee7eba6a7a05bdf0a12d60ebabb334d8ee021101 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 9 Aug 2021 14:48:57 -0500 -Subject: [PATCH] Fix: controller: ensure lost node's transient attributes are - cleared without DC - -Previously, peer_update_callback() cleared a lost node's transient attributes -if either the local node is DC, or there is no DC. - -However, that left the possibility of the DC being lost at the same time as -another node -- the local node would still have fsa_our_dc set while processing -the leave notifications, so no node would clear the attributes for the non-DC -node. - -Now, the controller has its own CPG configuration change callback, which sets a -global boolean before calling the usual one, so that peer_update_callback() can -know when the DC has been lost. ---- - daemons/controld/controld_callbacks.c | 4 ++- - daemons/controld/controld_corosync.c | 57 ++++++++++++++++++++++++++++++++++- - 2 files changed, 59 insertions(+), 2 deletions(-) - -diff --git a/daemons/controld/controld_callbacks.c b/daemons/controld/controld_callbacks.c -index af24856..e564b3d 100644 ---- a/daemons/controld/controld_callbacks.c -+++ b/daemons/controld/controld_callbacks.c -@@ -99,6 +99,8 @@ node_alive(const crm_node_t *node) - - #define state_text(state) ((state)? (const char *)(state) : "in unknown state") - -+bool controld_dc_left = false; -+ - void - peer_update_callback(enum crm_status_type type, crm_node_t * node, const void *data) - { -@@ -217,7 +219,7 @@ peer_update_callback(enum crm_status_type type, crm_node_t * node, const void *d - cib_scope_local); - } - -- } else if (AM_I_DC || (fsa_our_dc == NULL)) { -+ } else if (AM_I_DC || controld_dc_left || (fsa_our_dc == NULL)) { - /* This only needs to be done once, so normally the DC should do - * it. However if there is no DC, every node must do it, since - * there is no other way to ensure some one node does it. -diff --git a/daemons/controld/controld_corosync.c b/daemons/controld/controld_corosync.c -index db99630..c5ab658 100644 ---- a/daemons/controld/controld_corosync.c -+++ b/daemons/controld/controld_corosync.c -@@ -87,6 +87,61 @@ crmd_cs_destroy(gpointer user_data) - } - } - -+extern bool controld_dc_left; -+ -+/*! -+ * \brief Handle a Corosync notification of a CPG configuration change -+ * -+ * \param[in] handle CPG connection -+ * \param[in] cpg_name CPG group name -+ * \param[in] member_list List of current CPG members -+ * \param[in] member_list_entries Number of entries in \p member_list -+ * \param[in] left_list List of CPG members that left -+ * \param[in] left_list_entries Number of entries in \p left_list -+ * \param[in] joined_list List of CPG members that joined -+ * \param[in] joined_list_entries Number of entries in \p joined_list -+ */ -+static void -+cpg_membership_callback(cpg_handle_t handle, const struct cpg_name *cpg_name, -+ const struct cpg_address *member_list, -+ size_t member_list_entries, -+ const struct cpg_address *left_list, -+ size_t left_list_entries, -+ const struct cpg_address *joined_list, -+ size_t joined_list_entries) -+{ -+ /* When nodes leave CPG, the DC clears their transient node attributes. -+ * -+ * However if there is no DC, or the DC is among the nodes that left, each -+ * remaining node needs to do the clearing, to ensure it gets done. -+ * Otherwise, the attributes would persist when the nodes rejoin, which -+ * could have serious consequences for unfencing, agents that use attributes -+ * for internal logic, etc. -+ * -+ * Here, we set a global boolean if the DC is among the nodes that left, for -+ * use by the peer callback. -+ */ -+ if (fsa_our_dc != NULL) { -+ crm_node_t *peer = pcmk__search_cluster_node_cache(0, fsa_our_dc); -+ -+ if (peer != NULL) { -+ for (int i = 0; i < left_list_entries; ++i) { -+ if (left_list[i].nodeid == peer->id) { -+ controld_dc_left = true; -+ break; -+ } -+ } -+ } -+ } -+ -+ // Process the change normally, which will call the peer callback as needed -+ pcmk_cpg_membership(handle, cpg_name, member_list, member_list_entries, -+ left_list, left_list_entries, -+ joined_list, joined_list_entries); -+ -+ controld_dc_left = false; -+} -+ - extern gboolean crm_connect_corosync(crm_cluster_t * cluster); - - gboolean -@@ -95,7 +150,7 @@ crm_connect_corosync(crm_cluster_t * cluster) - if (is_corosync_cluster()) { - crm_set_status_callback(&peer_update_callback); - cluster->cpg.cpg_deliver_fn = crmd_cs_dispatch; -- cluster->cpg.cpg_confchg_fn = pcmk_cpg_membership; -+ cluster->cpg.cpg_confchg_fn = cpg_membership_callback; - cluster->destroy = crmd_cs_destroy; - - if (crm_cluster_connect(cluster)) { --- -1.8.3.1 - diff --git a/0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch b/0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch new file mode 100644 index 0000000..f72774f --- /dev/null +++ b/0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch @@ -0,0 +1,82 @@ +From b34570ecaeb4fb0106dd0aa5a8776a5417a07f90 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Mon, 16 Aug 2021 16:41:18 +0200 +Subject: [PATCH] Fix: tools: make exit-code stdout/stderr consistent with + --version + +--- + tools/crm_attribute.c | 2 +- + tools/crm_diff.c | 2 +- + tools/crm_error.c | 2 +- + tools/crm_node.c | 2 +- + tools/crm_rule.c | 2 +- + 5 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/tools/crm_attribute.c b/tools/crm_attribute.c +index 6bd4e2a..faf4aae 100644 +--- a/tools/crm_attribute.c ++++ b/tools/crm_attribute.c +@@ -326,7 +326,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_attribute is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + if (options.promotion_score && options.attr_name == NULL) { +diff --git a/tools/crm_diff.c b/tools/crm_diff.c +index 9890c10..18f5d48 100644 +--- a/tools/crm_diff.c ++++ b/tools/crm_diff.c +@@ -322,7 +322,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_diff is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + if (options.apply && options.no_version) { +diff --git a/tools/crm_error.c b/tools/crm_error.c +index 923f393..f26efe7 100644 +--- a/tools/crm_error.c ++++ b/tools/crm_error.c +@@ -93,7 +93,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_error is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + if (options.do_list) { +diff --git a/tools/crm_node.c b/tools/crm_node.c +index 25da978..489a39a 100644 +--- a/tools/crm_node.c ++++ b/tools/crm_node.c +@@ -549,7 +549,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_node is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + if (options.command == 0) { +diff --git a/tools/crm_rule.c b/tools/crm_rule.c +index 30c5155..0880415 100644 +--- a/tools/crm_rule.c ++++ b/tools/crm_rule.c +@@ -252,7 +252,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_rule is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + /* Check command line arguments before opening a connection to +-- +1.8.3.1 + diff --git a/0006-Build-manpages-using-help2man-check-exit-code-of-too.patch b/0006-Build-manpages-using-help2man-check-exit-code-of-too.patch new file mode 100644 index 0000000..7c408b8 --- /dev/null +++ b/0006-Build-manpages-using-help2man-check-exit-code-of-too.patch @@ -0,0 +1,29 @@ +From 2e0ac6390327e387e9b94e50080d13fd95f545d6 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Mon, 16 Aug 2021 16:42:51 +0200 +Subject: [PATCH] Build: manpages: using help2man check exit-code of tools + +--- + mk/common.mk | 6 ++++++ + 1 file changed, 6 insertions(+) + +diff --git a/mk/common.mk b/mk/common.mk +index aa59feb..c3d1993 100644 +--- a/mk/common.mk ++++ b/mk/common.mk +@@ -68,6 +68,12 @@ HELP2MAN_ARGS = -N --section 8 --name "Part of the Pacemaker cluster resource ma + # and all wrappers to C code. + %.8: % $(MAN8DEPS) + $(AM_V_at)chmod a+x $(abs_builddir)/$< ++ PATH=$(abs_builddir):$$PATH $(abs_builddir)/$< --version >/dev/null ++ if [ -f $(abs_srcdir)/$@.inc ]; then \ ++ PATH=$(abs_builddir):$$PATH $(abs_builddir)/$< --help-all >/dev/null; \ ++ else \ ++ PATH=$(abs_builddir):$$PATH $(abs_builddir)/$< --help >/dev/null; \ ++ fi + $(AM_V_MAN)if [ -f $(abs_srcdir)/$@.inc ]; then \ + PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ + -h --help-all \ +-- +1.8.3.1 + diff --git a/pacemaker.spec b/pacemaker.spec index a138e31..2cd4aab 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -32,10 +32,10 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.1 -%global specversion 0.3.rc2 +%global specversion 0.4.rc3 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build -%global commit a64ad221abe9cdd968ceacd35c23832ce0fcd189 +%global commit c6a4f6e6cdcedf08e0bfd81248b86812c2a571b2 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. @@ -219,7 +219,8 @@ Patch0: 0001-feature-watchdog-fencing-allow-restriction-to-certai.patch Patch1: 0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch Patch2: 0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch Patch3: 0004-Build-rpm-package-fence_watchdog-in-base-package.patch -Patch4: 0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch +Patch4: 0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch +Patch5: 0006-Build-manpages-using-help2man-check-exit-code-of-too.patch # upstream commits @@ -828,6 +829,13 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Tue Aug 17 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.4.rc3 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc3, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc3 +- Make tools exit-codes consistent for --version +- Check exit-codes of tools prior to manpage-generation + * Wed Aug 11 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.3.rc2 - package fence_watchdog in base-package instead if cli-subpackage - fix version output of fence_watchdog as needed for help2man diff --git a/sources b/sources index 2ccc4d0..edc4941 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-a64ad221a.tar.gz) = ee954bd8efd135965290f9958b65680cbf101e14e2fd22d326e53a250281a7e5b6b6ec979c7f76072514dbf4d29868e99931842dbcc99bab5e5ba5e4bbc4ef0a +SHA512 (pacemaker-c6a4f6e6c.tar.gz) = 28a313c016add4f95ec2b546c468826c8234bafdc1a7a7d26b785733ee10ec209dc0dbf3f107df57604990b5f89b2d05831684b5d3adfd45479706d9c6d5654f commit 7889c6669e78faaef3ce77ff149430c179bb6792 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Wed Aug 11 11:48:10 2021 +0200 * Wed Aug 11 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.3.rc2 - package fence_watchdog in base-package instead if cli-subpackage - fix version output of fence_watchdog as needed for help2man - ensure transient attributes of lost nodes are cleared reliably diff --git a/0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch b/0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch new file mode 100644 index 0000000..8245e4f --- /dev/null +++ b/0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch @@ -0,0 +1,24 @@ +From 88e75d5b98df197fa731e7642434951a24a67095 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Tue, 10 Aug 2021 09:10:23 +0200 +Subject: [PATCH] Fix: fence_watchdog: fix version output needed for help2man + +--- + daemons/fenced/fence_watchdog.in | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/daemons/fenced/fence_watchdog.in b/daemons/fenced/fence_watchdog.in +index c83304f..700065e 100755 +--- a/daemons/fenced/fence_watchdog.in ++++ b/daemons/fenced/fence_watchdog.in +@@ -12,6 +12,7 @@ import sys + import atexit + import getopt + ++AGENT_VERSION = "1.0.0" + SHORT_DESC = "Dummy watchdog fence agent" + LONG_DESC = """fence_watchdog just provides + meta-data - actual fencing is done by the pacemaker internal watchdog agent.""" +-- +1.8.3.1 + diff --git a/0004-Build-rpm-package-fence_watchdog-in-base-package.patch b/0004-Build-rpm-package-fence_watchdog-in-base-package.patch new file mode 100644 index 0000000..d112c40 --- /dev/null +++ b/0004-Build-rpm-package-fence_watchdog-in-base-package.patch @@ -0,0 +1,32 @@ +From 61eb9c240004d1dbd0b5973e2fecda3686bb4c53 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Tue, 10 Aug 2021 09:06:55 +0200 +Subject: [PATCH] Build: rpm: package fence_watchdog in base-package + +--- + rpm/pacemaker.spec.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/rpm/pacemaker.spec.in b/rpm/pacemaker.spec.in +index f58357a..0c569b9 100644 +--- a/rpm/pacemaker.spec.in ++++ b/rpm/pacemaker.spec.in +@@ -734,6 +734,7 @@ exit 0 + %{_sbindir}/crm_attribute + %{_sbindir}/crm_master + %{_sbindir}/fence_legacy ++%{_sbindir}/fence_watchdog + + %doc %{_mandir}/man7/pacemaker-controld.* + %doc %{_mandir}/man7/pacemaker-schedulerd.* +@@ -797,7 +798,6 @@ exit 0 + %{_sbindir}/crm_simulate + %{_sbindir}/crm_report + %{_sbindir}/crm_ticket +-%{_sbindir}/fence_watchdog + %{_sbindir}/stonith_admin + # "dirname" is owned by -schemas, which is a prerequisite + %{_datadir}/pacemaker/report.collector +-- +1.8.3.1 + diff --git a/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch b/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch new file mode 100644 index 0000000..3e64b25 --- /dev/null +++ b/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch @@ -0,0 +1,122 @@ +From ee7eba6a7a05bdf0a12d60ebabb334d8ee021101 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 9 Aug 2021 14:48:57 -0500 +Subject: [PATCH] Fix: controller: ensure lost node's transient attributes are + cleared without DC + +Previously, peer_update_callback() cleared a lost node's transient attributes +if either the local node is DC, or there is no DC. + +However, that left the possibility of the DC being lost at the same time as +another node -- the local node would still have fsa_our_dc set while processing +the leave notifications, so no node would clear the attributes for the non-DC +node. + +Now, the controller has its own CPG configuration change callback, which sets a +global boolean before calling the usual one, so that peer_update_callback() can +know when the DC has been lost. +--- + daemons/controld/controld_callbacks.c | 4 ++- + daemons/controld/controld_corosync.c | 57 ++++++++++++++++++++++++++++++++++- + 2 files changed, 59 insertions(+), 2 deletions(-) + +diff --git a/daemons/controld/controld_callbacks.c b/daemons/controld/controld_callbacks.c +index af24856..e564b3d 100644 +--- a/daemons/controld/controld_callbacks.c ++++ b/daemons/controld/controld_callbacks.c +@@ -99,6 +99,8 @@ node_alive(const crm_node_t *node) + + #define state_text(state) ((state)? (const char *)(state) : "in unknown state") + ++bool controld_dc_left = false; ++ + void + peer_update_callback(enum crm_status_type type, crm_node_t * node, const void *data) + { +@@ -217,7 +219,7 @@ peer_update_callback(enum crm_status_type type, crm_node_t * node, const void *d + cib_scope_local); + } + +- } else if (AM_I_DC || (fsa_our_dc == NULL)) { ++ } else if (AM_I_DC || controld_dc_left || (fsa_our_dc == NULL)) { + /* This only needs to be done once, so normally the DC should do + * it. However if there is no DC, every node must do it, since + * there is no other way to ensure some one node does it. +diff --git a/daemons/controld/controld_corosync.c b/daemons/controld/controld_corosync.c +index db99630..c5ab658 100644 +--- a/daemons/controld/controld_corosync.c ++++ b/daemons/controld/controld_corosync.c +@@ -87,6 +87,61 @@ crmd_cs_destroy(gpointer user_data) + } + } + ++extern bool controld_dc_left; ++ ++/*! ++ * \brief Handle a Corosync notification of a CPG configuration change ++ * ++ * \param[in] handle CPG connection ++ * \param[in] cpg_name CPG group name ++ * \param[in] member_list List of current CPG members ++ * \param[in] member_list_entries Number of entries in \p member_list ++ * \param[in] left_list List of CPG members that left ++ * \param[in] left_list_entries Number of entries in \p left_list ++ * \param[in] joined_list List of CPG members that joined ++ * \param[in] joined_list_entries Number of entries in \p joined_list ++ */ ++static void ++cpg_membership_callback(cpg_handle_t handle, const struct cpg_name *cpg_name, ++ const struct cpg_address *member_list, ++ size_t member_list_entries, ++ const struct cpg_address *left_list, ++ size_t left_list_entries, ++ const struct cpg_address *joined_list, ++ size_t joined_list_entries) ++{ ++ /* When nodes leave CPG, the DC clears their transient node attributes. ++ * ++ * However if there is no DC, or the DC is among the nodes that left, each ++ * remaining node needs to do the clearing, to ensure it gets done. ++ * Otherwise, the attributes would persist when the nodes rejoin, which ++ * could have serious consequences for unfencing, agents that use attributes ++ * for internal logic, etc. ++ * ++ * Here, we set a global boolean if the DC is among the nodes that left, for ++ * use by the peer callback. ++ */ ++ if (fsa_our_dc != NULL) { ++ crm_node_t *peer = pcmk__search_cluster_node_cache(0, fsa_our_dc); ++ ++ if (peer != NULL) { ++ for (int i = 0; i < left_list_entries; ++i) { ++ if (left_list[i].nodeid == peer->id) { ++ controld_dc_left = true; ++ break; ++ } ++ } ++ } ++ } ++ ++ // Process the change normally, which will call the peer callback as needed ++ pcmk_cpg_membership(handle, cpg_name, member_list, member_list_entries, ++ left_list, left_list_entries, ++ joined_list, joined_list_entries); ++ ++ controld_dc_left = false; ++} ++ + extern gboolean crm_connect_corosync(crm_cluster_t * cluster); + + gboolean +@@ -95,7 +150,7 @@ crm_connect_corosync(crm_cluster_t * cluster) + if (is_corosync_cluster()) { + crm_set_status_callback(&peer_update_callback); + cluster->cpg.cpg_deliver_fn = crmd_cs_dispatch; +- cluster->cpg.cpg_confchg_fn = pcmk_cpg_membership; ++ cluster->cpg.cpg_confchg_fn = cpg_membership_callback; + cluster->destroy = crmd_cs_destroy; + + if (crm_cluster_connect(cluster)) { +-- +1.8.3.1 + diff --git a/pacemaker.spec b/pacemaker.spec index a8f1d51..a138e31 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -32,7 +32,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.1 -%global specversion 0.2.rc2 +%global specversion 0.3.rc2 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build %global commit a64ad221abe9cdd968ceacd35c23832ce0fcd189 @@ -217,6 +217,9 @@ Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{arch Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... Patch0: 0001-feature-watchdog-fencing-allow-restriction-to-certai.patch Patch1: 0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch +Patch2: 0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch +Patch3: 0004-Build-rpm-package-fence_watchdog-in-base-package.patch +Patch4: 0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch # upstream commits @@ -660,6 +663,7 @@ exit 0 %{_sbindir}/crm_attribute %{_sbindir}/crm_master +%{_sbindir}/fence_watchdog %doc %{_mandir}/man7/pacemaker-controld.* %doc %{_mandir}/man7/pacemaker-schedulerd.* @@ -709,7 +713,6 @@ exit 0 %{_sbindir}/crm_simulate %{_sbindir}/crm_report %{_sbindir}/crm_ticket -%{_sbindir}/fence_watchdog %{_sbindir}/stonith_admin # "dirname" is owned by -schemas, which is a prerequisite %{_datadir}/pacemaker/report.collector @@ -825,6 +828,11 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Wed Aug 11 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.3.rc2 +- package fence_watchdog in base-package instead if cli-subpackage +- fix version output of fence_watchdog as needed for help2man +- ensure transient attributes of lost nodes are cleared reliably + * Mon Aug 9 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.2.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc2, for full details, see included ChangeLog file or commit e8f53e7d76dd1680d55e0436757380baf9abdc38 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Aug 9 17:50:26 2021 +0200 * Mon Aug 9 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.2.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc2, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc2 - Added feature patch that allows to explicitly specify nodes that should do watchdog-fencing diff --git a/0001-feature-watchdog-fencing-allow-restriction-to-certai.patch b/0001-feature-watchdog-fencing-allow-restriction-to-certai.patch new file mode 100644 index 0000000..97e6071 --- /dev/null +++ b/0001-feature-watchdog-fencing-allow-restriction-to-certai.patch @@ -0,0 +1,1119 @@ +From 5dd1e4459335764e0adf5fa78d81c875ae2332e9 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Fri, 30 Jul 2021 18:15:10 +0200 +Subject: [PATCH] feature: watchdog-fencing: allow restriction to certain nodes + +Bump CRM_FEATURE_SET to 3.11.0 to encourage cluster being +fully upgraded to a version that supports the feature +before explicitly adding a watchdog-fence-device. +--- + configure.ac | 1 + + daemons/controld/controld_control.c | 2 +- + daemons/controld/controld_fencing.c | 14 ++ + daemons/controld/controld_fencing.h | 1 + + daemons/fenced/Makefile.am | 2 +- + daemons/fenced/fence_watchdog.in | 283 ++++++++++++++++++++++++++++++++++++ + daemons/fenced/fenced_commands.c | 141 ++++++++++++++---- + daemons/fenced/fenced_remote.c | 71 ++++++--- + daemons/fenced/pacemaker-fenced.c | 131 ++++++++++++----- + daemons/fenced/pacemaker-fenced.h | 5 +- + include/crm/crm.h | 2 +- + include/crm/fencing/internal.h | 8 +- + lib/fencing/st_client.c | 61 ++++++++ + lib/lrmd/lrmd_client.c | 6 +- + rpm/pacemaker.spec.in | 3 + + 16 files changed, 635 insertions(+), 97 deletions(-) + create mode 100755 daemons/fenced/fence_watchdog.in + +diff --git a/configure.ac b/configure.ac +index 436100c..013562e 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -1972,6 +1972,7 @@ CONFIG_FILES_EXEC([cts/cts-cli], + [cts/support/fence_dummy], + [cts/support/pacemaker-cts-dummyd], + [daemons/fenced/fence_legacy], ++ [daemons/fenced/fence_watchdog], + [doc/abi-check], + [extra/resources/ClusterMon], + [extra/resources/HealthSMART], +diff --git a/daemons/controld/controld_control.c b/daemons/controld/controld_control.c +index 45a70bb..b5da6a4 100644 +--- a/daemons/controld/controld_control.c ++++ b/daemons/controld/controld_control.c +@@ -615,7 +615,7 @@ static pcmk__cluster_option_t crmd_opts[] = { + }, + { + "stonith-watchdog-timeout", NULL, "time", NULL, +- "0", pcmk__valid_sbd_timeout, ++ "0", controld_verify_stonith_watchdog_timeout, + "How long to wait before we can assume nodes are safely down " + "when watchdog-based self-fencing via SBD is in use", + "If nonzero, along with `have-watchdog=true` automatically set by the " +diff --git a/daemons/controld/controld_fencing.c b/daemons/controld/controld_fencing.c +index 0fba661..6c2a6c5 100644 +--- a/daemons/controld/controld_fencing.c ++++ b/daemons/controld/controld_fencing.c +@@ -11,6 +11,7 @@ + #include <crm/crm.h> + #include <crm/msg_xml.h> + #include <crm/common/xml.h> ++#include <crm/stonith-ng.h> + #include <crm/fencing/internal.h> + + #include <pacemaker-controld.h> +@@ -886,6 +887,19 @@ te_fence_node(crm_graph_t *graph, crm_action_t *action) + return TRUE; + } + ++bool ++controld_verify_stonith_watchdog_timeout(const char *value) ++{ ++ gboolean rv = TRUE; ++ ++ if (stonith_api && (stonith_api->state != stonith_disconnected) && ++ stonith__watchdog_fencing_enabled_for_node_api(stonith_api, ++ fsa_our_uname)) { ++ rv = pcmk__valid_sbd_timeout(value); ++ } ++ return rv; ++} ++ + /* end stonith API client functions */ + + +diff --git a/daemons/controld/controld_fencing.h b/daemons/controld/controld_fencing.h +index d0ecc82..ef68a0c 100644 +--- a/daemons/controld/controld_fencing.h ++++ b/daemons/controld/controld_fencing.h +@@ -24,6 +24,7 @@ void update_stonith_max_attempts(const char* value); + void controld_trigger_fencer_connect(void); + void controld_disconnect_fencer(bool destroy); + gboolean te_fence_node(crm_graph_t *graph, crm_action_t *action); ++bool controld_verify_stonith_watchdog_timeout(const char *value); + + // stonith cleanup list + void add_stonith_cleanup(const char *target); +diff --git a/daemons/fenced/Makefile.am b/daemons/fenced/Makefile.am +index 43413e1..2923d7c 100644 +--- a/daemons/fenced/Makefile.am ++++ b/daemons/fenced/Makefile.am +@@ -15,7 +15,7 @@ halibdir = $(CRM_DAEMON_DIR) + + halib_PROGRAMS = pacemaker-fenced cts-fence-helper + +-sbin_SCRIPTS = fence_legacy ++sbin_SCRIPTS = fence_legacy fence_watchdog + + noinst_HEADERS = pacemaker-fenced.h + +diff --git a/daemons/fenced/fence_watchdog.in b/daemons/fenced/fence_watchdog.in +new file mode 100755 +index 0000000..c83304f +--- /dev/null ++++ b/daemons/fenced/fence_watchdog.in +@@ -0,0 +1,283 @@ ++#!@PYTHON@ ++"""Dummy watchdog fence agent for providing meta-data for the pacemaker internal agent ++""" ++ ++__copyright__ = "Copyright 2012-2021 the Pacemaker project contributors" ++__license__ = "GNU General Public License version 2 or later (GPLv2+) WITHOUT ANY WARRANTY" ++ ++import io ++import os ++import re ++import sys ++import atexit ++import getopt ++ ++SHORT_DESC = "Dummy watchdog fence agent" ++LONG_DESC = """fence_watchdog just provides ++meta-data - actual fencing is done by the pacemaker internal watchdog agent.""" ++ ++ALL_OPT = { ++ "version" : { ++ "getopt" : "V", ++ "longopt" : "version", ++ "help" : "-V, --version Display version information and exit", ++ "required" : "0", ++ "shortdesc" : "Display version information and exit", ++ "order" : 53 ++ }, ++ "help" : { ++ "getopt" : "h", ++ "longopt" : "help", ++ "help" : "-h, --help Display this help and exit", ++ "required" : "0", ++ "shortdesc" : "Display help and exit", ++ "order" : 54 ++ }, ++ "action" : { ++ "getopt" : "o:", ++ "longopt" : "action", ++ "help" : "-o, --action=[action] Action: metadata", ++ "required" : "1", ++ "shortdesc" : "Fencing Action", ++ "default" : "metadata", ++ "order" : 1 ++ }, ++ "nodename" : { ++ "getopt" : "N:", ++ "longopt" : "nodename", ++ "help" : "-N, --nodename Node name of fence victim (ignored)", ++ "required" : "0", ++ "shortdesc" : "Ignored", ++ "order" : 2 ++ }, ++ "plug" : { ++ "getopt" : "n:", ++ "longopt" : "plug", ++ "help" : "-n, --plug=[id] Physical plug number on device (ignored)", ++ "required" : "1", ++ "shortdesc" : "Ignored", ++ "order" : 4 ++ } ++} ++ ++ ++def agent(): ++ """ Return name this file was run as. """ ++ ++ return os.path.basename(sys.argv[0]) ++ ++ ++def fail_usage(message): ++ """ Print a usage message and exit. """ ++ ++ sys.exit("%s\nPlease use '-h' for usage" % message) ++ ++ ++def show_docs(options): ++ """ Handle informational options (display info and exit). """ ++ ++ device_opt = options["device_opt"] ++ ++ if "-h" in options: ++ usage(device_opt) ++ sys.exit(0) ++ ++ if "-o" in options and options["-o"].lower() == "metadata": ++ metadata(device_opt, options) ++ sys.exit(0) ++ ++ if "-V" in options: ++ print(AGENT_VERSION) ++ sys.exit(0) ++ ++ ++def sorted_options(avail_opt): ++ """ Return a list of all options, in their internally specified order. """ ++ ++ sorted_list = [(key, ALL_OPT[key]) for key in avail_opt] ++ sorted_list.sort(key=lambda x: x[1]["order"]) ++ return sorted_list ++ ++ ++def usage(avail_opt): ++ """ Print a usage message. """ ++ print(LONG_DESC) ++ print() ++ print("Usage:") ++ print("\t" + agent() + " [options]") ++ print("Options:") ++ ++ for dummy, value in sorted_options(avail_opt): ++ if len(value["help"]) != 0: ++ print(" " + value["help"]) ++ ++ ++def metadata(avail_opt, options): ++ """ Print agent metadata. """ ++ ++ print("""<?xml version="1.0" ?> ++<resource-agent name="%s" shortdesc="%s"> ++<longdesc>%s</longdesc> ++<parameters>""" % (agent(), SHORT_DESC, LONG_DESC)) ++ ++ for option, dummy in sorted_options(avail_opt): ++ if "shortdesc" in ALL_OPT[option]: ++ print(' <parameter name="' + option + ++ 'required="' + ALL_OPT[option]["required"] + '">') ++ ++ default = "" ++ default_name_arg = "-" + ALL_OPT[option]["getopt"][:-1] ++ default_name_no_arg = "-" + ALL_OPT[option]["getopt"] ++ ++ if "default" in ALL_OPT[option]: ++ default = 'default="%s"' % str(ALL_OPT[option]["default"]) ++ elif default_name_arg in options: ++ if options[default_name_arg]: ++ try: ++ default = 'default="%s"' % options[default_name_arg] ++ except TypeError: ++ ## @todo/@note: Currently there is no clean way how to handle lists ++ ## we can create a string from it but we can't set it on command line ++ default = 'default="%s"' % str(options[default_name_arg]) ++ elif default_name_no_arg in options: ++ default = 'default="true"' ++ ++ mixed = ALL_OPT[option]["help"] ++ ## split it between option and help text ++ res = re.compile(r"^(.*--\S+)\s+", re.IGNORECASE | re.S).search(mixed) ++ if None != res: ++ mixed = res.group(1) ++ mixed = mixed.replace("<", "<").replace(">", ">") ++ print(' <getopt mixed="' + mixed + '" />') ++ ++ if ALL_OPT[option]["getopt"].count(":") > 0: ++ print(' <content type="string" ' + default + ' />') ++ else: ++ print(' <content type="boolean" ' + default + ' />') ++ ++ print(' <shortdesc lang="en">' + ALL_OPT[option]["shortdesc"] + '</shortdesc>') ++ print(' </parameter>') ++ ++ print(' </parameters>\n <actions>') ++ print(' <action name="on" />') ++ print(' <action name="off" />') ++ print(' <action name="reboot" />') ++ print(' <action name="monitor" />') ++ print(' <action name="list" />') ++ print(' <action name="metadata" />') ++ print(' </actions>') ++ print('</resource-agent>') ++ ++ ++def option_longopt(option): ++ """ Return the getopt-compatible long-option name of the given option. """ ++ ++ if ALL_OPT[option]["getopt"].endswith(":"): ++ return ALL_OPT[option]["longopt"] + "=" ++ else: ++ return ALL_OPT[option]["longopt"] ++ ++ ++def opts_from_command_line(argv, avail_opt): ++ """ Read options from command-line arguments. """ ++ ++ # Prepare list of options for getopt ++ getopt_string = "" ++ longopt_list = [] ++ for k in avail_opt: ++ if k in ALL_OPT: ++ getopt_string += ALL_OPT[k]["getopt"] ++ else: ++ fail_usage("Parse error: unknown option '" + k + "'") ++ ++ if k in ALL_OPT and "longopt" in ALL_OPT[k]: ++ longopt_list.append(option_longopt(k)) ++ ++ try: ++ opt, dummy = getopt.gnu_getopt(argv, getopt_string, longopt_list) ++ except getopt.GetoptError as error: ++ fail_usage("Parse error: " + error.msg) ++ ++ # Transform longopt to short one which are used in fencing agents ++ old_opt = opt ++ opt = {} ++ for old_option in dict(old_opt).keys(): ++ if old_option.startswith("--"): ++ for option in ALL_OPT.keys(): ++ if "longopt" in ALL_OPT[option] and "--" + ALL_OPT[option]["longopt"] == old_option: ++ opt["-" + ALL_OPT[option]["getopt"].rstrip(":")] = dict(old_opt)[old_option] ++ else: ++ opt[old_option] = dict(old_opt)[old_option] ++ ++ return opt ++ ++ ++def opts_from_stdin(avail_opt): ++ """ Read options from standard input. """ ++ ++ opt = {} ++ name = "" ++ for line in sys.stdin.readlines(): ++ line = line.strip() ++ if line.startswith("#") or (len(line) == 0): ++ continue ++ ++ (name, value) = (line + "=").split("=", 1) ++ value = value[:-1] ++ ++ if name not in avail_opt: ++ print("Parse error: Ignoring unknown option '%s'" % line, ++ file=sys.stderr) ++ continue ++ ++ if ALL_OPT[name]["getopt"].endswith(":"): ++ opt["-"+ALL_OPT[name]["getopt"].rstrip(":")] = value ++ elif value.lower() in ["1", "yes", "on", "true"]: ++ opt["-"+ALL_OPT[name]["getopt"]] = "1" ++ ++ return opt ++ ++ ++def process_input(avail_opt): ++ """ Set standard environment variables, and parse all options. """ ++ ++ # Set standard environment ++ os.putenv("LANG", "C") ++ os.putenv("LC_ALL", "C") ++ ++ # Read options from command line or standard input ++ if len(sys.argv) > 1: ++ return opts_from_command_line(sys.argv[1:], avail_opt) ++ else: ++ return opts_from_stdin(avail_opt) ++ ++ ++def atexit_handler(): ++ """ Close stdout on exit. """ ++ ++ try: ++ sys.stdout.close() ++ os.close(1) ++ except IOError: ++ sys.exit("%s failed to close standard output" % agent()) ++ ++ ++def main(): ++ """ Make it so! """ ++ ++ device_opt = ALL_OPT.keys() ++ ++ ## Defaults for fence agent ++ atexit.register(atexit_handler) ++ options = process_input(device_opt) ++ options["device_opt"] = device_opt ++ show_docs(options) ++ ++ print("Watchdog fencing may be initiated only by the cluster, not this agent.", ++ file=sys.stderr) ++ ++ sys.exit(1) ++ ++ ++if __name__ == "__main__": ++ main() +diff --git a/daemons/fenced/fenced_commands.c b/daemons/fenced/fenced_commands.c +index cd9968f..9470ea2 100644 +--- a/daemons/fenced/fenced_commands.c ++++ b/daemons/fenced/fenced_commands.c +@@ -397,15 +397,13 @@ stonith_device_execute(stonith_device_t * device) + return TRUE; + } + +- if(pcmk__str_eq(device->agent, STONITH_WATCHDOG_AGENT, pcmk__str_casei)) { +- if(pcmk__str_eq(cmd->action, "reboot", pcmk__str_casei)) { +- pcmk__panic(__func__); +- goto done; +- +- } else if(pcmk__str_eq(cmd->action, "off", pcmk__str_casei)) { +- pcmk__panic(__func__); +- goto done; +- ++ if (pcmk__str_any_of(device->agent, STONITH_WATCHDOG_AGENT, ++ STONITH_WATCHDOG_AGENT_INTERNAL, NULL)) { ++ if (pcmk__strcase_any_of(cmd->action, "reboot", "off", NULL)) { ++ if (node_does_watchdog_fencing(stonith_our_uname)) { ++ pcmk__panic(__func__); ++ goto done; ++ } + } else { + crm_info("Faking success for %s watchdog operation", cmd->action); + cmd->done_cb(0, 0, NULL, cmd); +@@ -716,7 +714,7 @@ get_agent_metadata(const char *agent, xmlNode ** metadata) + return EINVAL; + } + *metadata = NULL; +- if (pcmk__str_eq(agent, STONITH_WATCHDOG_AGENT, pcmk__str_none)) { ++ if (pcmk__str_eq(agent, STONITH_WATCHDOG_AGENT_INTERNAL, pcmk__str_none)) { + return pcmk_rc_ok; + } + init_metadata_cache(); +@@ -1050,24 +1048,6 @@ schedule_internal_command(const char *origin, + schedule_stonith_command(cmd, device); + } + +-gboolean +-string_in_list(GList *list, const char *item) +-{ +- int lpc = 0; +- int max = g_list_length(list); +- +- for (lpc = 0; lpc < max; lpc++) { +- const char *value = g_list_nth_data(list, lpc); +- +- if (pcmk__str_eq(item, value, pcmk__str_casei)) { +- return TRUE; +- } else { +- crm_trace("%d: '%s' != '%s'", lpc, item, value); +- } +- } +- return FALSE; +-} +- + static void + status_search_cb(GPid pid, int rc, const char *output, gpointer user_data) + { +@@ -1144,7 +1124,7 @@ dynamic_list_search_cb(GPid pid, int rc, const char *output, gpointer user_data) + if (!alias) { + alias = search->host; + } +- if (string_in_list(dev->targets, alias)) { ++ if (pcmk__str_in_list(dev->targets, alias, pcmk__str_casei)) { + can_fence = TRUE; + } + } +@@ -1215,9 +1195,62 @@ stonith_device_register(xmlNode * msg, const char **desc, gboolean from_cib) + stonith_device_t *dup = NULL; + stonith_device_t *device = build_device_from_xml(msg); + guint ndevices = 0; ++ int rv = pcmk_ok; + + CRM_CHECK(device != NULL, return -ENOMEM); + ++ /* do we have a watchdog-device? */ ++ if (pcmk__str_eq(device->id, STONITH_WATCHDOG_ID, pcmk__str_none) || ++ pcmk__str_any_of(device->agent, STONITH_WATCHDOG_AGENT, ++ STONITH_WATCHDOG_AGENT_INTERNAL, NULL)) do { ++ if (stonith_watchdog_timeout_ms <= 0) { ++ crm_err("Ignoring watchdog fence device without " ++ "stonith-watchdog-timeout set."); ++ rv = -ENODEV; ++ /* fall through to cleanup & return */ ++ } else if (!pcmk__str_any_of(device->agent, STONITH_WATCHDOG_AGENT, ++ STONITH_WATCHDOG_AGENT_INTERNAL, NULL)) { ++ crm_err("Ignoring watchdog fence device with unknown " ++ "agent '%s' unequal '" STONITH_WATCHDOG_AGENT "'.", ++ device->agent?device->agent:""); ++ rv = -ENODEV; ++ /* fall through to cleanup & return */ ++ } else if (!pcmk__str_eq(device->id, STONITH_WATCHDOG_ID, ++ pcmk__str_none)) { ++ crm_err("Ignoring watchdog fence device " ++ "named %s !='"STONITH_WATCHDOG_ID"'.", ++ device->id?device->id:""); ++ rv = -ENODEV; ++ /* fall through to cleanup & return */ ++ } else { ++ if (pcmk__str_eq(device->agent, STONITH_WATCHDOG_AGENT, ++ pcmk__str_none)) { ++ /* this either has an empty list or the targets ++ configured for watchdog-fencing ++ */ ++ g_list_free_full(stonith_watchdog_targets, free); ++ stonith_watchdog_targets = device->targets; ++ device->targets = NULL; ++ } ++ if (node_does_watchdog_fencing(stonith_our_uname)) { ++ g_list_free_full(device->targets, free); ++ device->targets = stonith__parse_targets(stonith_our_uname); ++ g_hash_table_replace(device->params, ++ strdup(PCMK_STONITH_HOST_LIST), ++ strdup(stonith_our_uname)); ++ /* proceed as with any other stonith-device */ ++ break; ++ } ++ ++ crm_debug("Skip registration of watchdog fence device on node not in host-list."); ++ /* cleanup and fall through to more cleanup and return */ ++ device->targets = NULL; ++ stonith_device_remove(device->id, from_cib); ++ } ++ free_device(device); ++ return rv; ++ } while (0); ++ + dup = device_has_duplicate(device); + if (dup) { + ndevices = g_hash_table_size(device_list); +@@ -1598,6 +1631,39 @@ stonith_level_remove(xmlNode *msg, char **desc) + * (CIB registration is not sufficient), because monitor should not be + * possible unless the device is "started" (API registered). + */ ++ ++static char * ++list_to_string(GList *list, const char *delim, gboolean terminate_with_delim) ++{ ++ int max = g_list_length(list); ++ size_t delim_len = delim?strlen(delim):0; ++ size_t alloc_size = 1 + (max?((max-1+(terminate_with_delim?1:0))*delim_len):0); ++ char *rv; ++ GList *gIter; ++ ++ for (gIter = list; gIter != NULL; gIter = gIter->next) { ++ const char *value = (const char *) gIter->data; ++ ++ alloc_size += strlen(value); ++ } ++ rv = calloc(alloc_size, sizeof(char)); ++ if (rv) { ++ char *pos = rv; ++ const char *lead_delim = ""; ++ ++ for (gIter = list; gIter != NULL; gIter = gIter->next) { ++ const char *value = (const char *) gIter->data; ++ ++ pos = &pos[sprintf(pos, "%s%s", lead_delim, value)]; ++ lead_delim = delim; ++ } ++ if (max && terminate_with_delim) { ++ sprintf(pos, "%s", delim); ++ } ++ } ++ return rv; ++} ++ + static int + stonith_device_action(xmlNode * msg, char **output) + { +@@ -1615,6 +1681,19 @@ stonith_device_action(xmlNode * msg, char **output) + return -EPROTO; + } + ++ if (pcmk__str_eq(id, STONITH_WATCHDOG_ID, pcmk__str_none)) { ++ if (stonith_watchdog_timeout_ms <= 0) { ++ return -ENODEV; ++ } else { ++ if (pcmk__str_eq(action, "list", pcmk__str_casei)) { ++ *output = list_to_string(stonith_watchdog_targets, "\n", TRUE); ++ return pcmk_ok; ++ } else if (pcmk__str_eq(action, "monitor", pcmk__str_casei)) { ++ return pcmk_ok; ++ } ++ } ++ } ++ + device = g_hash_table_lookup(device_list, id); + if ((device == NULL) + || (!device->api_registered && !strcmp(action, "monitor"))) { +@@ -1742,7 +1821,7 @@ can_fence_host_with_device(stonith_device_t * dev, struct device_search_s *searc + * Only use if all hosts on which the device can be active can always fence all listed hosts + */ + +- if (string_in_list(dev->targets, host)) { ++ if (pcmk__str_in_list(dev->targets, host, pcmk__str_casei)) { + can = TRUE; + } else if (g_hash_table_lookup(dev->params, PCMK_STONITH_HOST_MAP) + && g_hash_table_lookup(dev->aliases, host)) { +@@ -1763,7 +1842,7 @@ can_fence_host_with_device(stonith_device_t * dev, struct device_search_s *searc + return; + } + +- if (string_in_list(dev->targets, alias)) { ++ if (pcmk__str_in_list(dev->targets, alias, pcmk__str_casei)) { + can = TRUE; + } + +diff --git a/daemons/fenced/fenced_remote.c b/daemons/fenced/fenced_remote.c +index cf91aca..224f2ba 100644 +--- a/daemons/fenced/fenced_remote.c ++++ b/daemons/fenced/fenced_remote.c +@@ -1522,6 +1522,25 @@ advance_topology_device_in_level(remote_fencing_op_t *op, const char *device, + } + } + ++static gboolean ++check_watchdog_fencing_and_wait(remote_fencing_op_t * op) ++{ ++ if (node_does_watchdog_fencing(op->target)) { ++ ++ crm_notice("Waiting %lds for %s to self-fence (%s) for " ++ "client %s " CRM_XS " id=%.8s", ++ (stonith_watchdog_timeout_ms / 1000), ++ op->target, op->action, op->client_name, op->id); ++ op->op_timer_one = g_timeout_add(stonith_watchdog_timeout_ms, ++ remote_op_watchdog_done, op); ++ return TRUE; ++ } else { ++ crm_debug("Skipping fallback to watchdog-fencing as %s is " ++ "not in host-list", op->target); ++ } ++ return FALSE; ++} ++ + void + call_remote_stonith(remote_fencing_op_t * op, st_query_result_t * peer, int rc) + { +@@ -1592,26 +1611,33 @@ call_remote_stonith(remote_fencing_op_t * op, st_query_result_t * peer, int rc) + g_source_remove(op->op_timer_one); + } + +- if(stonith_watchdog_timeout_ms > 0 && device && pcmk__str_eq(device, "watchdog", pcmk__str_casei)) { +- crm_notice("Waiting %lds for %s to self-fence (%s) for client %s " +- CRM_XS " id=%.8s", (stonith_watchdog_timeout_ms / 1000), +- op->target, op->action, op->client_name, op->id); +- op->op_timer_one = g_timeout_add(stonith_watchdog_timeout_ms, remote_op_watchdog_done, op); +- +- /* TODO check devices to verify watchdog will be in use */ +- } else if(stonith_watchdog_timeout_ms > 0 +- && pcmk__str_eq(peer->host, op->target, pcmk__str_casei) +- && !pcmk__str_eq(op->action, "on", pcmk__str_casei)) { +- crm_notice("Waiting %lds for %s to self-fence (%s) for client %s " +- CRM_XS " id=%.8s", (stonith_watchdog_timeout_ms / 1000), +- op->target, op->action, op->client_name, op->id); +- op->op_timer_one = g_timeout_add(stonith_watchdog_timeout_ms, remote_op_watchdog_done, op); +- +- } else { ++ if (!(stonith_watchdog_timeout_ms > 0 && ( ++ (pcmk__str_eq(device, STONITH_WATCHDOG_ID, ++ pcmk__str_none)) || ++ (pcmk__str_eq(peer->host, op->target, pcmk__str_casei) ++ && !pcmk__str_eq(op->action, "on", pcmk__str_casei))) && ++ check_watchdog_fencing_and_wait(op))) { ++ ++ /* Some thoughts about self-fencing cases reaching this point: ++ - Actually check in check_watchdog_fencing_and_wait ++ shouldn't fail if STONITH_WATCHDOG_ID is ++ chosen as fencing-device and it being present implies ++ watchdog-fencing is enabled anyway ++ - If watchdog-fencing is disabled either in general or for ++ a specific target - detected in check_watchdog_fencing_and_wait - ++ for some other kind of self-fencing we can't expect ++ a success answer but timeout is fine if the node doesn't ++ come back in between ++ - Delicate might be the case where we have watchdog-fencing ++ enabled for a node but the watchdog-fencing-device isn't ++ explicitly chosen for suicide. Local pe-execution in sbd ++ may detect the node as unclean and lead to timely suicide. ++ Otherwise the selection of stonith-watchdog-timeout at ++ least is questionable. ++ */ + op->op_timer_one = g_timeout_add((1000 * timeout_one), remote_op_timeout_one, op); + } + +- + send_cluster_message(crm_get_peer(0, peer->host), crm_msg_stonith_ng, remote_op, FALSE); + peer->tried = TRUE; + free_xml(remote_op); +@@ -1645,12 +1671,11 @@ call_remote_stonith(remote_fencing_op_t * op, st_query_result_t * peer, int rc) + * but we have all the expected replies, then no devices + * are available to execute the fencing operation. */ + +- if(stonith_watchdog_timeout_ms && pcmk__str_eq(device, "watchdog", pcmk__str_null_matches | pcmk__str_casei)) { +- crm_notice("Waiting %lds for %s to self-fence (%s) for client %s " +- CRM_XS " id=%.8s", (stonith_watchdog_timeout_ms / 1000), +- op->target, op->action, op->client_name, op->id); +- op->op_timer_one = g_timeout_add(stonith_watchdog_timeout_ms, remote_op_watchdog_done, op); +- return; ++ if(stonith_watchdog_timeout_ms > 0 && pcmk__str_eq(device, ++ STONITH_WATCHDOG_ID, pcmk__str_null_matches)) { ++ if (check_watchdog_fencing_and_wait(op)) { ++ return; ++ } + } + + if (op->state == st_query) { +diff --git a/daemons/fenced/pacemaker-fenced.c b/daemons/fenced/pacemaker-fenced.c +index 39738d8..7f8b427 100644 +--- a/daemons/fenced/pacemaker-fenced.c ++++ b/daemons/fenced/pacemaker-fenced.c +@@ -42,6 +42,7 @@ + + char *stonith_our_uname = NULL; + long stonith_watchdog_timeout_ms = 0; ++GList *stonith_watchdog_targets = NULL; + + static GMainLoop *mainloop = NULL; + +@@ -578,7 +579,44 @@ our_node_allowed_for(pe_resource_t *rsc) + } + + static void +-watchdog_device_update(xmlNode *cib) ++watchdog_device_update(void) ++{ ++ if (stonith_watchdog_timeout_ms > 0) { ++ if (!g_hash_table_lookup(device_list, STONITH_WATCHDOG_ID) && ++ !stonith_watchdog_targets) { ++ /* getting here watchdog-fencing enabled, no device there yet ++ and reason isn't stonith_watchdog_targets preventing that ++ */ ++ int rc; ++ xmlNode *xml; ++ ++ xml = create_device_registration_xml( ++ STONITH_WATCHDOG_ID, ++ st_namespace_internal, ++ STONITH_WATCHDOG_AGENT, ++ NULL, /* stonith_device_register will add our ++ own name as PCMK_STONITH_HOST_LIST param ++ so we can skip that here ++ */ ++ NULL); ++ rc = stonith_device_register(xml, NULL, TRUE); ++ free_xml(xml); ++ if (rc != pcmk_ok) { ++ crm_crit("Cannot register watchdog pseudo fence agent"); ++ crm_exit(CRM_EX_FATAL); ++ } ++ } ++ ++ } else { ++ /* be silent if no device - todo parameter to stonith_device_remove */ ++ if (g_hash_table_lookup(device_list, STONITH_WATCHDOG_ID)) { ++ stonith_device_remove(STONITH_WATCHDOG_ID, TRUE); ++ } ++ } ++} ++ ++static void ++update_stonith_watchdog_timeout_ms(xmlNode *cib) + { + xmlNode *stonith_enabled_xml = NULL; + const char *stonith_enabled_s = NULL; +@@ -608,33 +646,7 @@ watchdog_device_update(xmlNode *cib) + } + } + +- if (timeout_ms != stonith_watchdog_timeout_ms) { +- crm_notice("New watchdog timeout %lds (was %lds)", timeout_ms/1000, stonith_watchdog_timeout_ms/1000); +- stonith_watchdog_timeout_ms = timeout_ms; +- +- if (stonith_watchdog_timeout_ms > 0) { +- int rc; +- xmlNode *xml; +- stonith_key_value_t *params = NULL; +- +- params = stonith_key_value_add(params, PCMK_STONITH_HOST_LIST, +- stonith_our_uname); +- +- xml = create_device_registration_xml("watchdog", st_namespace_internal, +- STONITH_WATCHDOG_AGENT, params, +- NULL); +- stonith_key_value_freeall(params, 1, 1); +- rc = stonith_device_register(xml, NULL, FALSE); +- free_xml(xml); +- if (rc != pcmk_ok) { +- crm_crit("Cannot register watchdog pseudo fence agent"); +- crm_exit(CRM_EX_FATAL); +- } +- +- } else { +- stonith_device_remove("watchdog", FALSE); +- } +- } ++ stonith_watchdog_timeout_ms = timeout_ms; + } + + /*! +@@ -677,6 +689,16 @@ static void cib_device_update(pe_resource_t *rsc, pe_working_set_t *data_set) + return; + } + ++ /* if watchdog-fencing is disabled handle any watchdog-fence ++ resource as if it was disabled ++ */ ++ if ((stonith_watchdog_timeout_ms <= 0) && ++ pcmk__str_eq(rsc->id, STONITH_WATCHDOG_ID, pcmk__str_none)) { ++ crm_info("Watchdog-fencing disabled thus handling " ++ "device %s as disabled", rsc->id); ++ return; ++ } ++ + /* Check whether our node is allowed for this resource (and its parent if in a group) */ + node = our_node_allowed_for(rsc); + if (rsc->parent && (rsc->parent->variant == pe_group)) { +@@ -772,6 +794,12 @@ cib_devices_update(void) + } + } + ++ /* have list repopulated if cib has a watchdog-fencing-resource ++ TODO: keep a cached list for queries happening while we are refreshing ++ */ ++ g_list_free_full(stonith_watchdog_targets, free); ++ stonith_watchdog_targets = NULL; ++ + for (gIter = fenced_data_set->resources; gIter != NULL; gIter = gIter->next) { + cib_device_update(gIter->data, fenced_data_set); + } +@@ -825,6 +853,8 @@ update_cib_stonith_devices_v2(const char *event, xmlNode * msg) + if (search != NULL) { + *search = 0; + stonith_device_remove(rsc_id, TRUE); ++ /* watchdog_device_update called afterwards ++ to fall back to implicit definition if needed */ + } else { + crm_warn("Ignoring malformed CIB update (resource deletion)"); + } +@@ -968,6 +998,24 @@ node_has_attr(const char *node, const char *name, const char *value) + return (match != NULL); + } + ++/*! ++ * \internal ++ * \brief Check whether a node does watchdog-fencing ++ * ++ * \param[in] node Name of node to check ++ * ++ * \return TRUE if node found in stonith_watchdog_targets ++ * or stonith_watchdog_targets is empty indicating ++ * all nodes are doing watchdog-fencing ++ */ ++gboolean ++node_does_watchdog_fencing(const char *node) ++{ ++ return ((stonith_watchdog_targets == NULL) || ++ pcmk__str_in_list(stonith_watchdog_targets, node, pcmk__str_casei)); ++} ++ ++ + static void + update_fencing_topology(const char *event, xmlNode * msg) + { +@@ -1073,6 +1121,8 @@ update_cib_cache_cb(const char *event, xmlNode * msg) + xmlNode *stonith_enabled_xml = NULL; + const char *stonith_enabled_s = NULL; + static gboolean stonith_enabled_saved = TRUE; ++ long timeout_ms_saved = stonith_watchdog_timeout_ms; ++ gboolean need_full_refresh = FALSE; + + if(!have_cib_devices) { + crm_trace("Skipping updates until we get a full dump"); +@@ -1127,6 +1177,7 @@ update_cib_cache_cb(const char *event, xmlNode * msg) + } + + pcmk__refresh_node_caches_from_cib(local_cib); ++ update_stonith_watchdog_timeout_ms(local_cib); + + stonith_enabled_xml = get_xpath_object("//nvpair[@name='stonith-enabled']", + local_cib, LOG_NEVER); +@@ -1134,23 +1185,30 @@ update_cib_cache_cb(const char *event, xmlNode * msg) + stonith_enabled_s = crm_element_value(stonith_enabled_xml, XML_NVPAIR_ATTR_VALUE); + } + +- watchdog_device_update(local_cib); +- + if (stonith_enabled_s && crm_is_true(stonith_enabled_s) == FALSE) { + crm_trace("Ignoring CIB updates while fencing is disabled"); + stonith_enabled_saved = FALSE; +- return; + + } else if (stonith_enabled_saved == FALSE) { + crm_info("Updating fencing device and topology lists " + "now that fencing is enabled"); + stonith_enabled_saved = TRUE; +- fencing_topology_init(); +- cib_devices_update(); ++ need_full_refresh = TRUE; + + } else { +- update_fencing_topology(event, msg); +- update_cib_stonith_devices(event, msg); ++ if (timeout_ms_saved != stonith_watchdog_timeout_ms) { ++ need_full_refresh = TRUE; ++ } else { ++ update_fencing_topology(event, msg); ++ update_cib_stonith_devices(event, msg); ++ watchdog_device_update(); ++ } ++ } ++ ++ if (need_full_refresh) { ++ fencing_topology_init(); ++ cib_devices_update(); ++ watchdog_device_update(); + } + } + +@@ -1162,10 +1220,11 @@ init_cib_cache_cb(xmlNode * msg, int call_id, int rc, xmlNode * output, void *us + local_cib = copy_xml(output); + + pcmk__refresh_node_caches_from_cib(local_cib); ++ update_stonith_watchdog_timeout_ms(local_cib); + + fencing_topology_init(); +- watchdog_device_update(local_cib); + cib_devices_update(); ++ watchdog_device_update(); + } + + static void +diff --git a/daemons/fenced/pacemaker-fenced.h b/daemons/fenced/pacemaker-fenced.h +index d330fda..14e085e 100644 +--- a/daemons/fenced/pacemaker-fenced.h ++++ b/daemons/fenced/pacemaker-fenced.h +@@ -260,14 +260,15 @@ bool fencing_peer_active(crm_node_t *peer); + + int stonith_manual_ack(xmlNode * msg, remote_fencing_op_t * op); + +-gboolean string_in_list(GList *list, const char *item); +- + gboolean node_has_attr(const char *node, const char *name, const char *value); + ++gboolean node_does_watchdog_fencing(const char *node); ++ + extern char *stonith_our_uname; + extern gboolean stand_alone; + extern GHashTable *device_list; + extern GHashTable *topology; + extern long stonith_watchdog_timeout_ms; ++extern GList *stonith_watchdog_targets; + + extern GHashTable *stonith_remote_op_list; +diff --git a/include/crm/crm.h b/include/crm/crm.h +index ee52c36..7861c16 100644 +--- a/include/crm/crm.h ++++ b/include/crm/crm.h +@@ -66,7 +66,7 @@ extern "C" { + * >=3.0.13: Fail counts include operation name and interval + * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED + */ +-# define CRM_FEATURE_SET "3.10.2" ++# define CRM_FEATURE_SET "3.11.0" + + /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and + * recipient of a CPG message. This imposes an arbitrary limit on cluster node +diff --git a/include/crm/fencing/internal.h b/include/crm/fencing/internal.h +index 8bcb544..f222edb 100644 +--- a/include/crm/fencing/internal.h ++++ b/include/crm/fencing/internal.h +@@ -164,7 +164,10 @@ void stonith__device_parameter_flags(uint32_t *device_flags, + # define STONITH_OP_LEVEL_ADD "st_level_add" + # define STONITH_OP_LEVEL_DEL "st_level_remove" + +-# define STONITH_WATCHDOG_AGENT "#watchdog" ++# define STONITH_WATCHDOG_AGENT "fence_watchdog" ++/* Don't change 2 below as it would break rolling upgrade */ ++# define STONITH_WATCHDOG_AGENT_INTERNAL "#watchdog" ++# define STONITH_WATCHDOG_ID "watchdog" + + # ifdef HAVE_STONITH_STONITH_H + // utilities from st_lha.c +@@ -211,4 +214,7 @@ stonith__op_state_pending(enum op_state state) + return state != st_failed && state != st_done; + } + ++gboolean stonith__watchdog_fencing_enabled_for_node(const char *node); ++gboolean stonith__watchdog_fencing_enabled_for_node_api(stonith_t *st, const char *node); ++ + #endif +diff --git a/lib/fencing/st_client.c b/lib/fencing/st_client.c +index e285f51..0ff9815 100644 +--- a/lib/fencing/st_client.c ++++ b/lib/fencing/st_client.c +@@ -195,6 +195,67 @@ stonith_get_namespace(const char *agent, const char *namespace_s) + return st_namespace_invalid; + } + ++gboolean ++stonith__watchdog_fencing_enabled_for_node_api(stonith_t *st, const char *node) ++{ ++ gboolean rv = FALSE; ++ stonith_t *stonith_api = st?st:stonith_api_new(); ++ char *list = NULL; ++ ++ if(stonith_api) { ++ if (stonith_api->state == stonith_disconnected) { ++ int rc = stonith_api->cmds->connect(stonith_api, "stonith-api", NULL); ++ ++ if (rc != pcmk_ok) { ++ crm_err("Failed connecting to Stonith-API for watchdog-fencing-query."); ++ } ++ } ++ ++ if (stonith_api->state != stonith_disconnected) { ++ /* caveat!!! ++ * this might fail when when stonithd is just updating the device-list ++ * probably something we should fix as well for other api-calls */ ++ int rc = stonith_api->cmds->list(stonith_api, st_opt_sync_call, STONITH_WATCHDOG_ID, &list, 0); ++ if ((rc != pcmk_ok) || (list == NULL)) { ++ /* due to the race described above it can happen that ++ * we drop in here - so as not to make remote nodes ++ * panic on that answer ++ */ ++ crm_warn("watchdog-fencing-query failed"); ++ } else if (list[0] == '\0') { ++ crm_warn("watchdog-fencing-query returned an empty list - any node"); ++ rv = TRUE; ++ } else { ++ GList *targets = stonith__parse_targets(list); ++ rv = pcmk__str_in_list(targets, node, pcmk__str_casei); ++ g_list_free_full(targets, free); ++ } ++ free(list); ++ if (!st) { ++ /* if we're provided the api we still might have done the ++ * connection - but let's assume the caller won't bother ++ */ ++ stonith_api->cmds->disconnect(stonith_api); ++ } ++ } ++ ++ if (!st) { ++ stonith_api_delete(stonith_api); ++ } ++ } else { ++ crm_err("Stonith-API for watchdog-fencing-query couldn't be created."); ++ } ++ crm_trace("Pacemaker assumes node %s %sto do watchdog-fencing.", ++ node, rv?"":"not "); ++ return rv; ++} ++ ++gboolean ++stonith__watchdog_fencing_enabled_for_node(const char *node) ++{ ++ return stonith__watchdog_fencing_enabled_for_node_api(NULL, node); ++} ++ + static void + log_action(stonith_action_t *action, pid_t pid) + { +diff --git a/lib/lrmd/lrmd_client.c b/lib/lrmd/lrmd_client.c +index 87d050e..bf4bceb 100644 +--- a/lib/lrmd/lrmd_client.c ++++ b/lib/lrmd/lrmd_client.c +@@ -34,6 +34,7 @@ + #include <crm/msg_xml.h> + + #include <crm/stonith-ng.h> ++#include <crm/fencing/internal.h> + + #ifdef HAVE_GNUTLS_GNUTLS_H + # undef KEYFILE +@@ -934,7 +935,10 @@ lrmd__validate_remote_settings(lrmd_t *lrmd, GHashTable *hash) + crm_xml_add(data, F_LRMD_ORIGIN, __func__); + + value = g_hash_table_lookup(hash, "stonith-watchdog-timeout"); +- crm_xml_add(data, F_LRMD_WATCHDOG, value); ++ if ((value) && ++ (stonith__watchdog_fencing_enabled_for_node(native->remote_nodename))) { ++ crm_xml_add(data, F_LRMD_WATCHDOG, value); ++ } + + rc = lrmd_send_command(lrmd, LRMD_OP_CHECK, data, NULL, 0, 0, + (native->type == pcmk__client_ipc)); +diff --git a/rpm/pacemaker.spec.in b/rpm/pacemaker.spec.in +index 79e78ed..f58357a 100644 +--- a/rpm/pacemaker.spec.in ++++ b/rpm/pacemaker.spec.in +@@ -744,6 +744,7 @@ exit 0 + %doc %{_mandir}/man8/crm_attribute.* + %doc %{_mandir}/man8/crm_master.* + %doc %{_mandir}/man8/fence_legacy.* ++%doc %{_mandir}/man8/fence_watchdog.* + %doc %{_mandir}/man8/pacemakerd.* + + %doc %{_datadir}/pacemaker/alerts +@@ -796,6 +797,7 @@ exit 0 + %{_sbindir}/crm_simulate + %{_sbindir}/crm_report + %{_sbindir}/crm_ticket ++%{_sbindir}/fence_watchdog + %{_sbindir}/stonith_admin + # "dirname" is owned by -schemas, which is a prerequisite + %{_datadir}/pacemaker/report.collector +@@ -822,6 +824,7 @@ exit 0 + %exclude %{_mandir}/man8/crm_attribute.* + %exclude %{_mandir}/man8/crm_master.* + %exclude %{_mandir}/man8/fence_legacy.* ++%exclude %{_mandir}/man8/fence_watchdog.* + %exclude %{_mandir}/man8/pacemakerd.* + %exclude %{_mandir}/man8/pacemaker-remoted.* + +-- +1.8.3.1 + diff --git a/0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch b/0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch new file mode 100644 index 0000000..ccfbccc --- /dev/null +++ b/0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch @@ -0,0 +1,25 @@ +From 53dd360f096e5f005e3221e8d44d82d3654b5172 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Wed, 4 Aug 2021 15:57:23 +0200 +Subject: [PATCH] Fix: watchdog-fencing: Silence warning without node + restriction + +--- + lib/fencing/st_client.c | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/lib/fencing/st_client.c b/lib/fencing/st_client.c +index 0ff9815..14fa7b2 100644 +--- a/lib/fencing/st_client.c ++++ b/lib/fencing/st_client.c +@@ -223,7 +223,6 @@ stonith__watchdog_fencing_enabled_for_node_api(stonith_t *st, const char *node) + */ + crm_warn("watchdog-fencing-query failed"); + } else if (list[0] == '\0') { +- crm_warn("watchdog-fencing-query returned an empty list - any node"); + rv = TRUE; + } else { + GList *targets = stonith__parse_targets(list); +-- +1.8.3.1 + diff --git a/pacemaker.spec b/pacemaker.spec index b3f962b..a8f1d51 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -32,10 +32,10 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.1 -%global specversion 0.1.rc1 +%global specversion 0.2.rc2 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build -%global commit 9e3a841a33c3125034922ec061f6516d307f20d1 +%global commit a64ad221abe9cdd968ceacd35c23832ce0fcd189 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. @@ -215,6 +215,8 @@ Url: https://www.clusterlabs.org/ # You can use "spectool -s 0 pacemaker.spec" (rpmdevtools) to show final URL. Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{archive_gith... Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... +Patch0: 0001-feature-watchdog-fencing-allow-restriction-to-certai.patch +Patch1: 0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch # upstream commits @@ -240,9 +242,19 @@ Requires: libqb >= 0.17.0 BuildRequires: libqb-devel >= 0.17.0 # Required basic build tools -BuildRequires: coreutils findutils grep sed -BuildRequires: autoconf automake gcc make pkgconfig -BuildRequires: libtool %{?pkgname_libtool_devel} +BuildRequires: autoconf +BuildRequires: automake +BuildRequires: coreutils +BuildRequires: findutils +BuildRequires: gcc +BuildRequires: grep +BuildRequires: libtool +BuildRequires: make +%if %{defined pkgname_libtool_devel} +BuildRequires: %{?pkgname_libtool_devel} +%endif +BuildRequires: pkgconfig +BuildRequires: sed # Required for core functionality BuildRequires: pkgconfig(glib-2.0) >= 2.42 @@ -250,8 +262,12 @@ BuildRequires: libxml2-devel libxslt-devel libuuid-devel BuildRequires: %{pkgname_bzip2_devel} # Enables optional functionality -BuildRequires: ncurses-devel %{pkgname_docbook_xsl} -BuildRequires: help2man %{pkgname_gnutls_devel} pam-devel pkgconfig(dbus-1) +BuildRequires: pkgconfig(dbus-1) +BuildRequires: %{pkgname_docbook_xsl} +BuildRequires: %{pkgname_gnutls_devel} +BuildRequires: help2man +BuildRequires: ncurses-devel +BuildRequires: pam-devel BuildRequires: pkgconfig(systemd) @@ -266,7 +282,9 @@ BuildRequires: %{pkgname_glue_libs}-devel %endif %if %{with doc} -BuildRequires: asciidoc inkscape %{python_name}-sphinx +BuildRequires: asciidoc +BuildRequires: inkscape +BuildRequires: %{python_name}-sphinx %endif Provides: pcmk-cluster-manager = %{version}-%{release} @@ -368,11 +386,16 @@ License: GPLv2+ and LGPLv2+ Summary: Pacemaker development package Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Requires: %{name}-cluster-libs%{?_isa} = %{version}-%{release} -Requires: %{?pkgname_libtool_devel_arch} libuuid-devel%{?_isa} -Requires: libxml2-devel%{?_isa} libxslt-devel%{?_isa} -Requires: %{pkgname_bzip2_devel}%{?_isa} glib2-devel%{?_isa} +Requires: %{pkgname_bzip2_devel}%{?_isa} +Requires: corosync-devel >= 2.0.0 +Requires: glib2-devel%{?_isa} Requires: libqb-devel%{?_isa} -Requires: corosync-devel%{?_isa} >= 2.0.0 +%if %{defined pkgname_libtool_devel_arch} +Requires: %{?pkgname_libtool_devel_arch} +%endif +Requires: libuuid-devel%{?_isa} +Requires: libxml2-devel%{?_isa} +Requires: libxslt-devel%{?_isa} %description -n %{pkgname_pcmk_libs}-devel Pacemaker is an advanced, scalable High-Availability cluster resource @@ -645,6 +668,7 @@ exit 0 %doc %{_mandir}/man7/ocf_pacemaker_remote.* %doc %{_mandir}/man8/crm_attribute.* %doc %{_mandir}/man8/crm_master.* +%doc %{_mandir}/man8/fence_watchdog.* %doc %{_mandir}/man8/pacemakerd.* %doc %{_datadir}/pacemaker/alerts @@ -685,6 +709,7 @@ exit 0 %{_sbindir}/crm_simulate %{_sbindir}/crm_report %{_sbindir}/crm_ticket +%{_sbindir}/fence_watchdog %{_sbindir}/stonith_admin # "dirname" is owned by -schemas, which is a prerequisite %{_datadir}/pacemaker/report.collector @@ -711,6 +736,7 @@ exit 0 %exclude %{_mandir}/man8/crm_attribute.* %exclude %{_mandir}/man8/crm_master.* %exclude %{_mandir}/man8/fence_legacy.* +%exclude %{_mandir}/man8/fence_watchdog.* %exclude %{_mandir}/man8/pacemakerd.* %exclude %{_mandir}/man8/pacemaker-remoted.* @@ -799,6 +825,13 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Aug 9 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.2.rc2 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc2, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc2 +- Added feature patch that allows to explicitly specify nodes that + should do watchdog-fencing + * Wed Jul 28 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc1, for full details, see included ChangeLog file or diff --git a/sources b/sources index b933127..2ccc4d0 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-9e3a841a3.tar.gz) = 26745ba0d9f6730de13ad106fe57beaff9d49c7df1ec528f0689c2faa872608408fb04401a4d49d73deec5422bd7665496a964b1fcbe69866a5983ac2306b6be +SHA512 (pacemaker-a64ad221a.tar.gz) = ee954bd8efd135965290f9958b65680cbf101e14e2fd22d326e53a250281a7e5b6b6ec979c7f76072514dbf4d29868e99931842dbcc99bab5e5ba5e4bbc4ef0a commit 6fcc0b8f5b6f278f33126c445552ad30336e5380 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Wed Jul 28 14:28:47 2021 +0200 * Wed Jul 28 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc1, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc1 diff --git a/001-ping-agent.patch b/001-ping-agent.patch deleted file mode 100644 index 89fe41a..0000000 --- a/001-ping-agent.patch +++ /dev/null @@ -1,225 +0,0 @@ -From c6ee0973522268ed7b3241cf0ec2e06398444114 Mon Sep 17 00:00:00 2001 -From: Grace Chin <gchin(a)redhat.com> -Date: Tue, 4 May 2021 12:02:17 -0400 -Subject: [PATCH 1/4] Remove deprecated attrd_options - ---- - extra/resources/ping | 11 +++-------- - 1 file changed, 3 insertions(+), 8 deletions(-) - -diff --git a/extra/resources/ping b/extra/resources/ping -index 3cf8dfe..2e93f22 100755 ---- a/extra/resources/ping -+++ b/extra/resources/ping -@@ -178,7 +178,7 @@ ping_stop() { - - rm -f "${OCF_RESKEY_pidfile}" - -- attrd_updater -D -n "$OCF_RESKEY_name" -d "$OCF_RESKEY_dampen" $attrd_options -+ attrd_updater -D -n "$OCF_RESKEY_name" -d "$OCF_RESKEY_dampen" - - return $OCF_SUCCESS - } -@@ -302,9 +302,9 @@ ping_update() { - - score=$(expr $active \* $OCF_RESKEY_multiplier) - if [ "$__OCF_ACTION" = "start" ] ; then -- attrd_updater -n "$OCF_RESKEY_name" -B "$score" -d "$OCF_RESKEY_dampen" $attrd_options -+ attrd_updater -n "$OCF_RESKEY_name" -B "$score" -d "$OCF_RESKEY_dampen" - else -- attrd_updater -n "$OCF_RESKEY_name" -v "$score" -d "$OCF_RESKEY_dampen" $attrd_options -+ attrd_updater -n "$OCF_RESKEY_name" -v "$score" -d "$OCF_RESKEY_dampen" - fi - rc=$? - case $rc in -@@ -396,11 +396,6 @@ case "${OCF_RESKEY_debug}" in - ;; - esac - --attrd_options='-q' --if [ "${OCF_RESKEY_debug}" = "true" ]; then -- attrd_options='' --fi -- - case "$__OCF_ACTION" in - meta-data) meta_data - exit $OCF_SUCCESS --- -1.8.3.1 - - -From 6d6c4691cf0970059689856c354daf9e098b4451 Mon Sep 17 00:00:00 2001 -From: Grace Chin <gchin(a)redhat.com> -Date: Tue, 4 May 2021 14:50:37 -0400 -Subject: [PATCH 2/4] Replace debug values, true and false, with 0 and 1 - ---- - extra/resources/ping | 8 ++++---- - 1 file changed, 4 insertions(+), 4 deletions(-) - -diff --git a/extra/resources/ping b/extra/resources/ping -index 2e93f22..fee019b 100755 ---- a/extra/resources/ping -+++ b/extra/resources/ping -@@ -24,7 +24,7 @@ - : ${OCF_RESKEY_dampen:="5s"} - : ${OCF_RESKEY_attempts:="3"} - : ${OCF_RESKEY_multiplier:="1"} --: ${OCF_RESKEY_debug:="false"} -+: ${OCF_RESKEY_debug:="0"} - : ${OCF_RESKEY_failure_score:="0"} - : ${OCF_RESKEY_use_fping:="1"} - : ${OCF_RESKEY_host_list:=""} -@@ -152,7 +152,7 @@ END - - ping_conditional_log() { - level="$1"; shift -- if [ "${OCF_RESKEY_debug}" = "true" ]; then -+ if [ $OCF_RESKEY_debug -gt 0 ]; then - ocf_log "$level" "$*" - fi - } -@@ -388,8 +388,8 @@ fi - - # Check the debug option - case "${OCF_RESKEY_debug}" in -- true|True|TRUE|1) OCF_RESKEY_debug=true;; -- false|False|FALSE|0) OCF_RESKEY_debug=false;; -+ true|True|TRUE|1) OCF_RESKEY_debug=0;; -+ false|False|FALSE|0) OCF_RESKEY_debug=1;; - *) - ocf_log warn "Value for 'debug' is incorrect. Please specify 'true' or 'false' not: ${OCF_RESKEY_debug}" - OCF_RESKEY_debug=false --- -1.8.3.1 - - -From a886a31056b6aca764c6911f5432af2c5ebf51df Mon Sep 17 00:00:00 2001 -From: Grace Chin <gchin(a)redhat.com> -Date: Tue, 11 May 2021 11:04:50 -0400 -Subject: [PATCH 3/4] Add verbose debug mode which logs ping and fping output - when set - ---- - extra/resources/ping | 19 ++++++++++++++----- - 1 file changed, 14 insertions(+), 5 deletions(-) - -diff --git a/extra/resources/ping b/extra/resources/ping -index fee019b..cc796af 100755 ---- a/extra/resources/ping -+++ b/extra/resources/ping -@@ -249,10 +249,13 @@ fping_check() { - - case $rc in - 0) -+ if [ $OCF_RESKEY_debug -gt 1 ]; then -+ ping_conditional_log info "$output" -+ fi - ;; - 1) - for h in $(echo "$output" | grep "is unreachable" | awk '{print $1}'); do -- ping_conditional_log warn "$h is inactive" -+ ping_conditional_log warn "$h is inactive: $output" - done - ;; - *) -@@ -282,7 +285,12 @@ ping_check() { - p_out=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? - - case $rc in -- 0) active=$(expr $active + 1);; -+ 0) -+ active=$(expr $active + 1) -+ if [ $OCF_RESKEY_debug -gt 1 ]; then -+ ping_conditional_log info "$p_out" -+ fi -+ ;; - 1) ping_conditional_log warn "$host is inactive: $p_out";; - *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $p_out";; - esac -@@ -388,10 +396,11 @@ fi - - # Check the debug option - case "${OCF_RESKEY_debug}" in -- true|True|TRUE|1) OCF_RESKEY_debug=0;; -- false|False|FALSE|0) OCF_RESKEY_debug=1;; -+ true|True|TRUE|1) OCF_RESKEY_debug=1;; -+ false|False|FALSE|0) OCF_RESKEY_debug=0;; -+ verbose|Verbose|VERBOSE|2) OCF_RESKEY_debug=2;; - *) -- ocf_log warn "Value for 'debug' is incorrect. Please specify 'true' or 'false' not: ${OCF_RESKEY_debug}" -+ ocf_log warn "Value for 'debug' is incorrect. Please specify 'true', 'false', or 'verbose', not: ${OCF_RESKEY_debug}" - OCF_RESKEY_debug=false - ;; - esac --- -1.8.3.1 - - -From 460043f133ced80e923b1290af70502a72deb7f8 Mon Sep 17 00:00:00 2001 -From: Grace Chin <gchin(a)redhat.com> -Date: Tue, 11 May 2021 11:07:05 -0400 -Subject: [PATCH 4/4] Improve variable names - ---- - extra/resources/ping | 20 ++++++++++---------- - 1 file changed, 10 insertions(+), 10 deletions(-) - -diff --git a/extra/resources/ping b/extra/resources/ping -index cc796af..9763b60 100755 ---- a/extra/resources/ping -+++ b/extra/resources/ping -@@ -244,22 +244,22 @@ fping_check() { - timeout=$(expr $OCF_RESKEY_timeout \* 1000 / $OCF_RESKEY_attempts) - - cmd="$p_exe -r $OCF_RESKEY_attempts -t $timeout -B 1.0 $OCF_RESKEY_options $OCF_RESKEY_host_list" -- output=$($cmd 2>&1); rc=$? -- active=$(echo "$output" | grep "is alive" | wc -l) -+ fping_output=$($cmd 2>&1); rc=$? -+ active=$(echo "$fping_output" | grep "is alive" | wc -l) - - case $rc in - 0) - if [ $OCF_RESKEY_debug -gt 1 ]; then -- ping_conditional_log info "$output" -+ ping_conditional_log info "$fping_output" - fi - ;; - 1) -- for h in $(echo "$output" | grep "is unreachable" | awk '{print $1}'); do -- ping_conditional_log warn "$h is inactive: $output" -+ for h in $(echo "$fping_output" | grep "is unreachable" | awk '{print $1}'); do -+ ping_conditional_log warn "$h is inactive: $fping_output" - done - ;; - *) -- ocf_log err "Unexpected result for '$cmd' $rc: $(echo "$output" | tr '\n' ';')" -+ ocf_log err "Unexpected result for '$cmd' $rc: $(echo "$fping_output" | tr '\n' ';')" - ;; - esac - -@@ -282,17 +282,17 @@ ping_check() { - *:*) p_exe=ping6 - esac - -- p_out=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? -+ ping_output=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? - - case $rc in - 0) - active=$(expr $active + 1) - if [ $OCF_RESKEY_debug -gt 1 ]; then -- ping_conditional_log info "$p_out" -+ ping_conditional_log info "$ping_output" - fi - ;; -- 1) ping_conditional_log warn "$host is inactive: $p_out";; -- *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $p_out";; -+ 1) ping_conditional_log warn "$host is inactive: $ping_output";; -+ *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $ping_output";; - esac - done - return $active --- -1.8.3.1 - diff --git a/002-pacemakerd-options.patch b/002-pacemakerd-options.patch deleted file mode 100644 index 56941ec..0000000 --- a/002-pacemakerd-options.patch +++ /dev/null @@ -1,451 +0,0 @@ -From 0d40ebf10b1794ece2c5c9768ea7222d3834d3b3 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 13 May 2021 11:42:18 -0400 -Subject: [PATCH 1/4] Build: Use a different variable to find man page - includes. - -With other programs outside of the tools directory being converted to -use glib for command line handling, their includes are not going to be -in tools/. So we need to use a different autoconf variable to find -them. ---- - mk/common.mk | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/mk/common.mk b/mk/common.mk -index b247670..aa59feb 100644 ---- a/mk/common.mk -+++ b/mk/common.mk -@@ -1,5 +1,5 @@ - # --# Copyright 2014-2020 the Pacemaker project contributors -+# Copyright 2014-2021 the Pacemaker project contributors - # - # The version control history for this file may have further details. - # -@@ -68,11 +68,11 @@ HELP2MAN_ARGS = -N --section 8 --name "Part of the Pacemaker cluster resource ma - # and all wrappers to C code. - %.8: % $(MAN8DEPS) - $(AM_V_at)chmod a+x $(abs_builddir)/$< -- $(AM_V_MAN)if [ -f $(top_srcdir)/tools/$@.inc ]; then \ -+ $(AM_V_MAN)if [ -f $(abs_srcdir)/$@.inc ]; then \ - PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ - -h --help-all \ - --no-discard-stderr \ -- -i $(top_srcdir)/tools/$@.inc $(abs_builddir)/$< \ -+ -i $(abs_srcdir)/$@.inc $(abs_builddir)/$< \ - | sed -f $(top_srcdir)/tools/fix-manpages > $@ ; \ - else \ - PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ --- -1.8.3.1 - - -From c7ab1d901bcbbf0137277e783e072777ca2f82d9 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 13 May 2021 11:44:16 -0400 -Subject: [PATCH 2/4] Refactor: daemons: Remove the pid_file variable from - pacemakerd. - -It's never used anywhere. ---- - daemons/pacemakerd/pacemakerd.c | 3 --- - 1 file changed, 3 deletions(-) - -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index 8ec9708..03d688e 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -27,8 +27,7 @@ - - static crm_trigger_t *shutdown_trigger = NULL; - static crm_trigger_t *startup_trigger = NULL; --static const char *pid_file = PCMK_RUN_DIR "/pacemaker.pid"; - - /* state we report when asked via pacemakerd-api status-ping */ - static const char *pacemakerd_state = XML_PING_ATTR_PACEMAKERDSTATE_INIT; - static gboolean running_with_sbd = FALSE; /* local copy */ -@@ -224,7 +222,6 @@ main(int argc, char **argv) - /* Legacy */ - break; - case 'p': -- pid_file = optarg; - break; - case 's': - pcmk__set_env_option("node_start_state", "standby"); --- -1.8.3.1 - - -From 98990eed9f6a5dbde7c8a5aa0783e93d5479295b Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 13 May 2021 13:14:38 -0400 -Subject: [PATCH 3/4] Refactor: daemons: Use glib for command line handling in - pacemakerd. - ---- - daemons/pacemakerd/Makefile.am | 2 + - daemons/pacemakerd/pacemakerd.8.inc | 5 + - daemons/pacemakerd/pacemakerd.c | 195 ++++++++++++++++++------------------ - 3 files changed, 102 insertions(+), 100 deletions(-) - create mode 100644 daemons/pacemakerd/pacemakerd.8.inc - -diff --git a/daemons/pacemakerd/Makefile.am b/daemons/pacemakerd/Makefile.am -index cc657f5..84517a3 100644 ---- a/daemons/pacemakerd/Makefile.am -+++ b/daemons/pacemakerd/Makefile.am -@@ -15,6 +15,8 @@ if BUILD_SYSTEMD - systemdsystemunit_DATA = pacemaker.service - endif - -+EXTRA_DIST = pacemakerd.8.inc -+ - ## SOURCES - - noinst_HEADERS = pacemakerd.h -diff --git a/daemons/pacemakerd/pacemakerd.8.inc b/daemons/pacemakerd/pacemakerd.8.inc -new file mode 100644 -index 0000000..902af4e ---- /dev/null -+++ b/daemons/pacemakerd/pacemakerd.8.inc -@@ -0,0 +1,5 @@ -+[synopsis] -+pacemakerd [options] -+ -+/subsidiary Pacemaker daemons/ -+.SH OPTIONS -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index 03d688e..ce194bf 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -23,12 +23,54 @@ - #include <crm/msg_xml.h> - #include <crm/common/ipc_internal.h> - #include <crm/common/mainloop.h> -+#include <crm/common/cmdline_internal.h> - #include <crm/cluster/internal.h> - #include <crm/cluster.h> - - #include <dirent.h> - #include <ctype.h> - -+#define SUMMARY "pacemakerd - primary Pacemaker daemon that launches and monitors all subsidiary Pacemaker daemons" -+ -+struct { -+ gboolean features; -+ gboolean foreground; -+ gboolean shutdown; -+ gboolean standby; -+} options; -+ -+static gboolean -+pid_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { -+ return TRUE; -+} -+ -+static gboolean -+standby_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { -+ options.standby = TRUE; -+ pcmk__set_env_option("node_start_state", "standby"); -+ return TRUE; -+} -+ -+static GOptionEntry entries[] = { -+ { "features", 'F', 0, G_OPTION_ARG_NONE, &options.features, -+ "Display full version and list of features Pacemaker was built with", -+ NULL }, -+ { "foreground", 'f', 0, G_OPTION_ARG_NONE, &options.foreground, -+ "(Ignored) Pacemaker always runs in the foreground", -+ NULL }, -+ { "pid-file", 'p', 0, G_OPTION_ARG_CALLBACK, pid_cb, -+ "(Ignored) Daemon pid file location", -+ "FILE" }, -+ { "shutdown", 'S', 0, G_OPTION_ARG_NONE, &options.shutdown, -+ "Instruct Pacemaker to shutdown on this machine", -+ NULL }, -+ { "standby", 's', G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, standby_cb, -+ "Start node in standby state", -+ NULL }, -+ -+ { NULL } -+}; -+ - static gboolean fatal_error = FALSE; - static GMainLoop *mainloop = NULL; - static bool global_keep_tracking = false; -@@ -642,49 +685,6 @@ pcmk_sigquit(int nsig) - .connection_destroyed = pcmk_ipc_destroy - }; - --static pcmk__cli_option_t long_options[] = { -- // long option, argument type, storage, short option, description, flags -- { -- "help", no_argument, NULL, '?', -- "\tThis text", pcmk__option_default -- }, -- { -- "version", no_argument, NULL, '$', -- "\tVersion information", pcmk__option_default -- }, -- { -- "verbose", no_argument, NULL, 'V', -- "\tIncrease debug output", pcmk__option_default -- }, -- { -- "shutdown", no_argument, NULL, 'S', -- "\tInstruct Pacemaker to shutdown on this machine", pcmk__option_default -- }, -- { -- "features", no_argument, NULL, 'F', -- "\tDisplay full version and list of features Pacemaker was built with", -- pcmk__option_default -- }, -- { -- "-spacer-", no_argument, NULL, '-', -- "\nAdditional Options:", pcmk__option_default -- }, -- { -- "foreground", no_argument, NULL, 'f', -- "\t(Ignored) Pacemaker always runs in the foreground", -- pcmk__option_default -- }, -- { -- "pid-file", required_argument, NULL, 'p', -- "\t(Ignored) Daemon pid file location", pcmk__option_default -- }, -- { -- "standby", no_argument, NULL, 's', -- "\tStart node in standby state", pcmk__option_default -- }, -- { 0, 0, 0, 0 } --}; -- - static void - mcp_chown(const char *path, uid_t uid, gid_t gid) - { -@@ -1168,83 +1211,66 @@ request_shutdown(crm_ipc_t *ipc) - return status; - } - -+static GOptionContext * -+build_arg_context(pcmk__common_args_t *args) { -+ GOptionContext *context = NULL; -+ -+ context = pcmk__build_arg_context(args, NULL, NULL, NULL); -+ pcmk__add_main_args(context, entries); -+ return context; -+} -+ - int - main(int argc, char **argv) - { -- int flag; -- int argerr = 0; -+ crm_exit_t exit_code = CRM_EX_OK; -+ -+ GError *error = NULL; -+ -+ pcmk__common_args_t *args = pcmk__new_common_args(SUMMARY); -+ gchar **processed_args = pcmk__cmdline_preproc(argv, "p"); -+ GOptionContext *context = build_arg_context(args); - -- int option_index = 0; - bool old_instance_connected = false; -- gboolean shutdown = FALSE; - - crm_ipc_t *old_instance = NULL; - qb_ipcs_service_t *ipcs = NULL; - - crm_log_preinit(NULL, argc, argv); -- pcmk__set_cli_options(NULL, "[options]", long_options, -- "primary Pacemaker daemon that launches and " -- "monitors all subsidiary Pacemaker daemons"); - mainloop_add_signal(SIGHUP, pcmk_ignore); - mainloop_add_signal(SIGQUIT, pcmk_sigquit); - -- while (1) { -- flag = pcmk__next_cli_option(argc, argv, &option_index, NULL); -- if (flag == -1) -- break; -- -- switch (flag) { -- case 'V': -- crm_bump_log_level(argc, argv); -- break; -- case 'f': -- /* Legacy */ -- break; -- case 'p': -- break; -- case 's': -- pcmk__set_env_option("node_start_state", "standby"); -- break; -- case '$': -- case '?': -- pcmk__cli_help(flag, CRM_EX_OK); -- break; -- case 'S': -- shutdown = TRUE; -- break; -- case 'F': -- printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, -- CRM_FEATURE_SET, CRM_FEATURES); -- crm_exit(CRM_EX_OK); -- default: -- printf("Argument code 0%o (%c) is not (?yet?) supported\n", flag, flag); -- ++argerr; -- break; -- } -+ if (!g_option_context_parse_strv(context, &processed_args, &error)) { -+ exit_code = CRM_EX_USAGE; -+ goto done; - } - -- if (optind < argc) { -- printf("non-option ARGV-elements: "); -- while (optind < argc) -- printf("%s ", argv[optind++]); -- printf("\n"); -- } -- if (argerr) { -- pcmk__cli_help('?', CRM_EX_USAGE); -+ if (options.features) { -+ printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, -+ CRM_FEATURE_SET, CRM_FEATURES); -+ exit_code = CRM_EX_OK; -+ goto done; - } - -+ if (args->version) { -+ g_strfreev(processed_args); -+ pcmk__free_arg_context(context); -+ /* FIXME: When pacemakerd is converted to use formatted output, this can go. */ -+ pcmk__cli_help('v', CRM_EX_USAGE); -+ } - - setenv("LC_ALL", "C", 1); - - pcmk__set_env_option("mcp", "true"); - -+ pcmk__cli_init_logging("pacemakerd", args->verbosity); - crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); - - crm_debug("Checking for existing Pacemaker instance"); - old_instance = crm_ipc_new(CRM_SYSTEM_MCP, 0); - old_instance_connected = crm_ipc_connect(old_instance); - -- if (shutdown) { -+ if (options.shutdown) { - if (old_instance_connected) { - crm_exit(request_shutdown(old_instance)); - } else { -@@ -1253,22 +1279,25 @@ main(int argc, char **argv) - "Pacemaker instance: %s", strerror(errno)); - crm_ipc_close(old_instance); - crm_ipc_destroy(old_instance); -- crm_exit(CRM_EX_DISCONNECT); -+ exit_code = CRM_EX_DISCONNECT; -+ goto done; - } - - } else if (old_instance_connected) { - crm_ipc_close(old_instance); - crm_ipc_destroy(old_instance); - crm_err("Aborting start-up because active Pacemaker instance found"); -- crm_exit(CRM_EX_FATAL); -+ exit_code = CRM_EX_FATAL; -+ goto done; - } - - crm_ipc_close(old_instance); - crm_ipc_destroy(old_instance); - - #ifdef SUPPORT_COROSYNC - if (mcp_read_config() == FALSE) { -- crm_exit(CRM_EX_UNAVAILABLE); -+ exit_code = CRM_EX_UNAVAILABLE; -+ goto done; - } - #endif - -@@ -1292,7 +1321,8 @@ main(int argc, char **argv) - #ifdef SUPPORT_COROSYNC - /* Allows us to block shutdown */ - if (!cluster_connect_cfg()) { -- crm_exit(CRM_EX_PROTOCOL); -+ exit_code = CRM_EX_PROTOCOL; -+ goto done; - } - #endif - -@@ -1307,9 +1337,11 @@ main(int argc, char **argv) - case pcmk_rc_ok: - break; - case pcmk_rc_ipc_unauthorized: -- crm_exit(CRM_EX_CANTCREAT); -+ exit_code = CRM_EX_CANTCREAT; -+ goto done; - default: -- crm_exit(CRM_EX_FATAL); -+ exit_code = CRM_EX_FATAL; -+ goto done; - }; - - mainloop_add_signal(SIGTERM, pcmk_shutdown); -@@ -1342,5 +1374,11 @@ main(int argc, char **argv) - #ifdef SUPPORT_COROSYNC - cluster_disconnect_cfg(); - #endif -- crm_exit(CRM_EX_OK); -+ -+done: -+ g_strfreev(processed_args); -+ pcmk__free_arg_context(context); -+ -+ pcmk__output_and_clear_error(error, NULL); -+ crm_exit(exit_code); - } --- -1.8.3.1 - - -From 8f7924fbb2a012bedcad59335b7bebc5020b26e3 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 13 May 2021 13:27:13 -0400 -Subject: [PATCH 4/4] Low: pacemaker.service: Don't start pacemakerd with -f. - -This option is completely ignored by pacemakerd. ---- - daemons/pacemakerd/pacemaker.service.in | 2 +- - doc/sphinx/Clusters_from_Scratch/verification.rst | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/daemons/pacemakerd/pacemaker.service.in b/daemons/pacemakerd/pacemaker.service.in -index b128ddc..0363a22 100644 ---- a/daemons/pacemakerd/pacemaker.service.in -+++ b/daemons/pacemakerd/pacemaker.service.in -@@ -44,7 +44,7 @@ EnvironmentFile=-@CONFIGDIR@/pacemaker - EnvironmentFile=-@CONFIGDIR@/sbd - SuccessExitStatus=100 - --ExecStart=@sbindir@/pacemakerd -f -+ExecStart=@sbindir@/pacemakerd - - # Systemd v227 and above can limit the number of processes spawned by a - # service. That is a bad idea for an HA cluster resource manager, so disable it -diff --git a/doc/sphinx/Clusters_from_Scratch/verification.rst b/doc/sphinx/Clusters_from_Scratch/verification.rst -index 9d647f8..b7fa20e 100644 ---- a/doc/sphinx/Clusters_from_Scratch/verification.rst -+++ b/doc/sphinx/Clusters_from_Scratch/verification.rst -@@ -103,7 +103,7 @@ the necessary processes are running: - 2 ? S 0:00 [kthreadd] - ...lots of processes... - 17121 ? SLsl 0:01 /usr/sbin/corosync -f -- 17133 ? Ss 0:00 /usr/sbin/pacemakerd -f -+ 17133 ? Ss 0:00 /usr/sbin/pacemakerd - 17134 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-based - 17135 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-fenced - 17136 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-execd --- -1.8.3.1 - diff --git a/003-pacemakerd-output.patch b/003-pacemakerd-output.patch deleted file mode 100644 index 167e22b..0000000 --- a/003-pacemakerd-output.patch +++ /dev/null @@ -1,343 +0,0 @@ -From 7c35387a9896cb968cf4087b5cbed94af44e1ea5 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 14 May 2021 12:03:46 -0400 -Subject: [PATCH 1/5] Feature: daemons: Convert pacemakerd to formatted output. - -The main purpose of this is to finish getting pacemakerd moved off the -existing command line handling code (pcmk__cli_help in particular) so -that code can eventually be deprecated or removed. pacemakerd itself -does fairly little printing. ---- - daemons/pacemakerd/pacemakerd.c | 58 ++++++++++++++++++++++++++++++----------- - 1 file changed, 43 insertions(+), 15 deletions(-) - -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index ce194bf..bd59729 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -25,6 +25,7 @@ - #include <crm/common/ipc_internal.h> - #include <crm/common/mainloop.h> - #include <crm/common/cmdline_internal.h> -+#include <crm/common/output_internal.h> - #include <crm/cluster/internal.h> - #include <crm/cluster.h> - -@@ -37,6 +38,14 @@ struct { - gboolean standby; - } options; - -+static pcmk__output_t *out = NULL; -+ -+static pcmk__supported_format_t formats[] = { -+ PCMK__SUPPORTED_FORMAT_NONE, -+ PCMK__SUPPORTED_FORMAT_TEXT, -+ { NULL, NULL, NULL } -+}; -+ - static gboolean - pid_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { - return TRUE; -@@ -1167,10 +1176,10 @@ pacemakerd_event_cb(pcmk_ipc_api_t *pacemakerd_api, - } - - static GOptionContext * --build_arg_context(pcmk__common_args_t *args) { -+build_arg_context(pcmk__common_args_t *args, GOptionGroup **group) { - GOptionContext *context = NULL; - -- context = pcmk__build_arg_context(args, NULL, NULL, NULL); -+ context = pcmk__build_arg_context(args, "text", group, NULL); - pcmk__add_main_args(context, entries); - return context; - } -@@ -1182,9 +1191,11 @@ main(int argc, char **argv) - - GError *error = NULL; - -+ int rc = pcmk_rc_ok; -+ GOptionGroup *output_group = NULL; - pcmk__common_args_t *args = pcmk__new_common_args(SUMMARY); - gchar **processed_args = pcmk__cmdline_preproc(argv, "p"); -- GOptionContext *context = build_arg_context(args); -+ GOptionContext *context = build_arg_context(args, &output_group); - - bool old_instance_connected = false; - -@@ -1195,23 +1205,30 @@ main(int argc, char **argv) - mainloop_add_signal(SIGHUP, pcmk_ignore); - mainloop_add_signal(SIGQUIT, pcmk_sigquit); - -+ pcmk__register_formats(output_group, formats); - if (!g_option_context_parse_strv(context, &processed_args, &error)) { - exit_code = CRM_EX_USAGE; - goto done; - } - -+ rc = pcmk__output_new(&out, args->output_ty, args->output_dest, argv); -+ if (rc != pcmk_rc_ok) { -+ exit_code = CRM_EX_ERROR; -+ g_set_error(&error, PCMK__EXITC_ERROR, exit_code, "Error creating output format %s: %s", -+ args->output_ty, pcmk_rc_str(rc)); -+ goto done; -+ } -+ - if (options.features) { -- printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, -- CRM_FEATURE_SET, CRM_FEATURES); -+ out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, -+ BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); - exit_code = CRM_EX_OK; - goto done; - } - - if (args->version) { -- g_strfreev(processed_args); -- pcmk__free_arg_context(context); -- /* FIXME: When pacemakerd is converted to use formatted output, this can go. */ -- pcmk__cli_help('v', CRM_EX_USAGE); -+ out->version(out, false); -+ goto done; - } - - setenv("LC_ALL", "C", 1); -@@ -1248,6 +1265,13 @@ main(int argc, char **argv) - crm_ipc_close(old_instance); - crm_ipc_destroy(old_instance); - -+ /* Don't allow any accidental output after this point. */ -+ if (out != NULL) { -+ out->finish(out, exit_code, true, NULL); -+ pcmk__output_free(out); -+ out = NULL; -+ } -+ - #ifdef SUPPORT_COROSYNC - if (mcp_read_config() == FALSE) { - exit_code = CRM_EX_UNAVAILABLE; -@@ -1333,6 +1357,11 @@ done: - g_strfreev(processed_args); - pcmk__free_arg_context(context); - -- pcmk__output_and_clear_error(error, NULL); -+ pcmk__output_and_clear_error(error, out); -+ -+ if (out != NULL) { -+ out->finish(out, exit_code, true, NULL); -+ pcmk__output_free(out); -+ } - crm_exit(exit_code); - } --- -1.8.3.1 - - -From 35e6da64381fcb092d81ce16835cc28670b077cb Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 17 May 2021 10:04:04 -0400 -Subject: [PATCH 2/5] Features: daemons: Output the pacemakerd feature list in - XML. - ---- - daemons/pacemakerd/pacemakerd.c | 45 ++++++++++++++++++++++++++++++++++++++--- - 1 file changed, 42 insertions(+), 3 deletions(-) - -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index bd59729..93cf743 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -43,6 +43,42 @@ static pcmk__output_t *out = NULL; - static pcmk__supported_format_t formats[] = { - PCMK__SUPPORTED_FORMAT_NONE, - PCMK__SUPPORTED_FORMAT_TEXT, -+ PCMK__SUPPORTED_FORMAT_XML, -+ { NULL, NULL, NULL } -+}; -+ -+static int -+pacemakerd_features(pcmk__output_t *out, va_list args) { -+ out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, -+ BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); -+ return pcmk_rc_ok; -+} -+ -+static int -+pacemakerd_features_xml(pcmk__output_t *out, va_list args) { -+ gchar **feature_list = g_strsplit(CRM_FEATURES, " ", 0); -+ -+ pcmk__output_xml_create_parent(out, "pacemakerd", -+ "version", PACEMAKER_VERSION, -+ "build", BUILD_VERSION, -+ "feature_set", CRM_FEATURE_SET, -+ NULL); -+ out->begin_list(out, NULL, NULL, "features"); -+ -+ for (char **s = feature_list; *s != NULL; s++) { -+ pcmk__output_create_xml_text_node(out, "feature", *s); -+ } -+ -+ out->end_list(out); -+ -+ g_strfreev(feature_list); -+ return pcmk_rc_ok; -+} -+ -+static pcmk__message_entry_t fmt_functions[] = { -+ { "features", "default", pacemakerd_features }, -+ { "features", "xml", pacemakerd_features_xml }, -+ - { NULL, NULL, NULL } - }; - -@@ -200,7 +236,7 @@ static GOptionContext * - build_arg_context(pcmk__common_args_t *args, GOptionGroup **group) { - GOptionContext *context = NULL; - -- context = pcmk__build_arg_context(args, "text", group, NULL); -+ context = pcmk__build_arg_context(args, "text (default), xml", group, NULL); - pcmk__add_main_args(context, entries); - return context; - } -@@ -241,9 +277,12 @@ main(int argc, char **argv) - goto done; - } - -+ pcmk__force_args(context, &error, "%s --xml-simple-list", g_get_prgname()); -+ -+ pcmk__register_messages(out, fmt_functions); -+ - if (options.features) { -- out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, -- BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); -+ out->message(out, "features"); - exit_code = CRM_EX_OK; - goto done; - } --- -1.8.3.1 - - -From 5b7f5eb35b025b59805cf3c7c3dcb6a3cf4b71b3 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 17 May 2021 11:09:53 -0400 -Subject: [PATCH 3/5] Low: daemons: Conditionally enable logging in pacemakerd. - -If we're doing an interactive command-line call, use -pcmk__cli_init_logging. At the moment, all command line calls except -for --shutdown do their work before logging would even come up, so we -really only need to do this for --shutdown. - -If we're doing a daemon call, use crm_log_init. ---- - daemons/pacemakerd/pacemakerd.c | 7 +++++-- - 1 file changed, 5 insertions(+), 2 deletions(-) - -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index 93cf743..c20bde7 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -296,8 +296,11 @@ main(int argc, char **argv) - - pcmk__set_env_option("mcp", "true"); - -- pcmk__cli_init_logging("pacemakerd", args->verbosity); -- crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); -+ if (options.shutdown) { -+ pcmk__cli_init_logging("pacemakerd", args->verbosity); -+ } else { -+ crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); -+ } - - crm_debug("Checking for existing Pacemaker instance"); - old_instance = crm_ipc_new(CRM_SYSTEM_MCP, 0); --- -1.8.3.1 - - -From 2393362bb7489e86d937ed46a1c5cfb93d9bf3ab Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 17 May 2021 11:58:06 -0400 -Subject: [PATCH 4/5] Fix: include: Bump CRM_FEATURE_SET for new pacemakerd - args. - ---- - include/crm/crm.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/include/crm/crm.h b/include/crm/crm.h -index fdfc825..92a98fa 100644 ---- a/include/crm/crm.h -+++ b/include/crm/crm.h -@@ -66,7 +66,7 @@ extern "C" { - * >=3.0.13: Fail counts include operation name and interval - * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED - */ --# define CRM_FEATURE_SET "3.10.0" -+# define CRM_FEATURE_SET "3.10.1" - - /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and - * recipient of a CPG message. This imposes an arbitrary limit on cluster node --- -1.8.3.1 - - -From 3ad8edbd91631b87ef5f53fa2d68f0c8bbb9ee2b Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 17 May 2021 11:57:09 -0400 -Subject: [PATCH 5/5] Feature: xml: Add schema for pacemakerd. - ---- - xml/Makefile.am | 1 + - xml/api/pacemakerd-2.10.rng | 28 ++++++++++++++++++++++++++++ - 2 files changed, 29 insertions(+) - create mode 100644 xml/api/pacemakerd-2.10.rng - -diff --git a/xml/Makefile.am b/xml/Makefile.am -index 12a51c5..b9448d4 100644 ---- a/xml/Makefile.am -+++ b/xml/Makefile.am -@@ -56,6 +56,7 @@ API_request_base = command-output \ - crm_simulate \ - crmadmin \ - digests \ -+ pacemakerd \ - stonith_admin \ - version - -diff --git a/xml/api/pacemakerd-2.10.rng b/xml/api/pacemakerd-2.10.rng -new file mode 100644 -index 0000000..41a11e7 ---- /dev/null -+++ b/xml/api/pacemakerd-2.10.rng -@@ -0,0 +1,28 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="element-pacemakerd"/> -+ </start> -+ -+ <define name="element-pacemakerd"> -+ <element name="pacemakerd"> -+ <attribute name="version"> <text /> </attribute> -+ <attribute name="build"> <text /> </attribute> -+ <attribute name="feature_set"> <text /> </attribute> -+ -+ <optional> -+ <ref name="feature-list" /> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="feature-list"> -+ <element name="features"> -+ <oneOrMore> -+ <element name="feature"> <text/> </element> -+ </oneOrMore> -+ </element> -+ </define> -+</grammar> --- -1.8.3.1 - diff --git a/004-check-level.patch b/004-check-level.patch deleted file mode 100644 index f2abb5f..0000000 --- a/004-check-level.patch +++ /dev/null @@ -1,199 +0,0 @@ -From 3905e7eac11298fc20efd567a773666f948edf61 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 3 May 2021 11:19:04 -0400 -Subject: [PATCH 1/2] Feature: tools: Add OCF_CHECK_LEVEL to crm_resource - environment. - -If --validate= or --force-check= are given with a level, pass that along -as OCF_CHECK_LEVEL. This argument is optional, and if no value is given -then the environment variable will not be set and whatever's the default -on the resource agent will be used. - -See: rhbz#1955792. ---- - tools/crm_resource.c | 29 +++++++++++++++++++++-------- - tools/crm_resource.h | 4 ++-- - tools/crm_resource_runtime.c | 13 ++++++++++--- - 3 files changed, 33 insertions(+), 13 deletions(-) - -diff --git a/tools/crm_resource.c b/tools/crm_resource.c -index 45db2b2..6ca96f8 100644 ---- a/tools/crm_resource.c -+++ b/tools/crm_resource.c -@@ -100,6 +100,7 @@ struct { - int timeout_ms; // Parsed from --timeout value - char *agent_spec; // Standard and/or provider and/or agent - gchar *xml_file; // Value of (deprecated) --xml-file -+ int check_level; // Optional value of --validate or --force-check - - // Resource configuration specified via command-line arguments - gboolean cmdline_config; // Resource configuration was via arguments -@@ -113,6 +114,7 @@ struct { - GHashTable *override_params; // Resource parameter values that override config - } options = { - .attr_set_type = XML_TAG_ATTR_SETS, -+ .check_level = -1, - .cib_options = cib_sync_call, - .require_cib = TRUE, - .require_dataset = TRUE, -@@ -402,14 +404,15 @@ static GOptionEntry query_entries[] = { - }; - - static GOptionEntry command_entries[] = { -- { "validate", 0, G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, -+ { "validate", 0, G_OPTION_FLAG_OPTIONAL_ARG, G_OPTION_ARG_CALLBACK, - validate_or_force_cb, - "Validate resource configuration by calling agent's validate-all\n" - INDENT "action. The configuration may be specified either by giving an\n" - INDENT "existing resource name with -r, or by specifying --class,\n" - INDENT "--agent, and --provider arguments, along with any number of\n" -- INDENT "--option arguments.", -- NULL }, -+ INDENT "--option arguments. An optional LEVEL argument can be given\n" -+ INDENT "to control the level of checking performed.", -+ "LEVEL" }, - { "cleanup", 'C', G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, cleanup_refresh_cb, - "If resource has any past failures, clear its history and fail\n" - INDENT "count. Optionally filtered by --resource, --node, --operation\n" -@@ -546,11 +549,12 @@ static GOptionEntry advanced_entries[] = { - INDENT "the cluster believes the resource is a clone instance already\n" - INDENT "running on the local node.", - NULL }, -- { "force-check", 0, G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, -+ { "force-check", 0, G_OPTION_FLAG_OPTIONAL_ARG, G_OPTION_ARG_CALLBACK, - validate_or_force_cb, - "(Advanced) Bypass the cluster and check the state of a resource on\n" -- INDENT "the local node", -- NULL }, -+ INDENT "the local node. An optional LEVEL argument can be given\n" -+ INDENT "to control the level of checking performed.", -+ "LEVEL" }, - - { NULL } - }; -@@ -910,6 +914,15 @@ validate_or_force_cb(const gchar *option_name, const gchar *optarg, - if (options.override_params == NULL) { - options.override_params = pcmk__strkey_table(free, free); - } -+ -+ if (optarg != NULL) { -+ if (pcmk__scan_min_int(optarg, &options.check_level, 0) != pcmk_rc_ok) { -+ g_set_error(error, G_OPTION_ERROR, CRM_EX_INVALID_PARAM, -+ "Invalid check level setting: %s", optarg); -+ return FALSE; -+ } -+ } -+ - return TRUE; - } - -@@ -1826,12 +1839,12 @@ main(int argc, char **argv) - options.v_class, options.v_provider, options.v_agent, - "validate-all", options.cmdline_params, - options.override_params, options.timeout_ms, -- args->verbosity, options.force); -+ args->verbosity, options.force, options.check_level); - } else { - exit_code = cli_resource_execute(rsc, options.rsc_id, - options.operation, options.override_params, - options.timeout_ms, cib_conn, data_set, -- args->verbosity, options.force); -+ args->verbosity, options.force, options.check_level); - } - goto done; - -diff --git a/tools/crm_resource.h b/tools/crm_resource.h -index 3560377..5ab10d6 100644 ---- a/tools/crm_resource.h -+++ b/tools/crm_resource.h -@@ -88,11 +88,11 @@ crm_exit_t cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc - const char *rsc_type, const char *rsc_action, - GHashTable *params, GHashTable *override_hash, - int timeout_ms, int resource_verbose, -- gboolean force); -+ gboolean force, int check_level); - crm_exit_t cli_resource_execute(pe_resource_t *rsc, const char *requested_name, - const char *rsc_action, GHashTable *override_hash, - int timeout_ms, cib_t *cib, pe_working_set_t *data_set, -- int resource_verbose, gboolean force); -+ int resource_verbose, gboolean force, int check_level); - - int cli_resource_update_attribute(pe_resource_t *rsc, const char *requested_name, - const char *attr_set, const char *attr_set_type, -diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c -index fe0ec98..bde83b6 100644 ---- a/tools/crm_resource_runtime.c -+++ b/tools/crm_resource_runtime.c -@@ -1679,7 +1679,8 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, - const char *rsc_class, const char *rsc_prov, - const char *rsc_type, const char *action, - GHashTable *params, GHashTable *override_hash, -- int timeout_ms, int resource_verbose, gboolean force) -+ int timeout_ms, int resource_verbose, gboolean force, -+ int check_level) - { - GHashTable *params_copy = NULL; - crm_exit_t exit_code = CRM_EX_OK; -@@ -1703,6 +1704,12 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, - /* add crm_feature_set env needed by some resource agents */ - g_hash_table_insert(params, strdup(XML_ATTR_CRM_VERSION), strdup(CRM_FEATURE_SET)); - -+ if (check_level >= 0) { -+ char *level = crm_strdup_printf("%d", check_level); -+ setenv("OCF_CHECK_LEVEL", level, 1); -+ free(level); -+ } -+ - /* resources_action_create frees the params hash table it's passed, but we - * may need to reuse it in a second call to resources_action_create. Thus - * we'll make a copy here so that gets freed and the original remains for -@@ -1790,7 +1797,7 @@ crm_exit_t - cli_resource_execute(pe_resource_t *rsc, const char *requested_name, - const char *rsc_action, GHashTable *override_hash, - int timeout_ms, cib_t * cib, pe_working_set_t *data_set, -- int resource_verbose, gboolean force) -+ int resource_verbose, gboolean force, int check_level) - { - pcmk__output_t *out = data_set->priv; - crm_exit_t exit_code = CRM_EX_OK; -@@ -1856,7 +1863,7 @@ cli_resource_execute(pe_resource_t *rsc, const char *requested_name, - - exit_code = cli_resource_execute_from_params(out, rid, rclass, rprov, rtype, action, - params, override_hash, timeout_ms, -- resource_verbose, force); -+ resource_verbose, force, check_level); - return exit_code; - } - --- -1.8.3.1 - - -From d13ba4bd6defe0dd81fdf8ab39ae5b889513c0c0 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 20 May 2021 10:59:23 -0400 -Subject: [PATCH 2/2] Fix: include: Bump feature set to 3.10.2. - -This is for the OCF_CHECK_LEVEL environment variable. - -See: rhbz#1955792. ---- - include/crm/crm.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/include/crm/crm.h b/include/crm/crm.h -index 92a98fa..ee52c36 100644 ---- a/include/crm/crm.h -+++ b/include/crm/crm.h -@@ -66,7 +66,7 @@ extern "C" { - * >=3.0.13: Fail counts include operation name and interval - * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED - */ --# define CRM_FEATURE_SET "3.10.1" -+# define CRM_FEATURE_SET "3.10.2" - - /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and - * recipient of a CPG message. This imposes an arbitrary limit on cluster node --- -1.8.3.1 - diff --git a/005-crm_resource.patch b/005-crm_resource.patch deleted file mode 100644 index 1683026..0000000 --- a/005-crm_resource.patch +++ /dev/null @@ -1,866 +0,0 @@ -From a5a507d4e1abf242903472719a19977811e6f164 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 20 May 2021 11:59:36 -0400 -Subject: [PATCH 01/10] Feature: libcrmcommon: Add OCF_OUTPUT_FORMAT to - crm_resource environment. - -See: rhbz#1644628 ---- - lib/common/output.c | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/lib/common/output.c b/lib/common/output.c -index 6cb49b5..58872e0 100644 ---- a/lib/common/output.c -+++ b/lib/common/output.c -@@ -71,6 +71,8 @@ pcmk__output_new(pcmk__output_t **out, const char *fmt_name, const char *filenam - return ENOMEM; - } - -+ setenv("OCF_OUTPUT_FORMAT", (*out)->fmt_name, 1); -+ - return pcmk_rc_ok; - } - --- -1.8.3.1 - - -From acc6ecdbfb797d69794e68f75a734d6252434e01 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 21 May 2021 14:20:30 -0400 -Subject: [PATCH 02/10] Feature: schemas: Copy crm_resource schema in - preparation for changes. - -See: rhbz#1644628 ---- - xml/api/crm_resource-2.11.rng | 238 ++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 238 insertions(+) - create mode 100644 xml/api/crm_resource-2.11.rng - -diff --git a/xml/api/crm_resource-2.11.rng b/xml/api/crm_resource-2.11.rng -new file mode 100644 -index 0000000..8e386db ---- /dev/null -+++ b/xml/api/crm_resource-2.11.rng -@@ -0,0 +1,238 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="element-crm-resource"/> -+ </start> -+ -+ <define name="element-crm-resource"> -+ <choice> -+ <ref name="agents-list" /> -+ <ref name="alternatives-list" /> -+ <ref name="constraints-list" /> -+ <externalRef href="generic-list-2.4.rng"/> -+ <element name="metadata"> <text/> </element> -+ <ref name="locate-list" /> -+ <ref name="operations-list" /> -+ <ref name="providers-list" /> -+ <ref name="reasons-list" /> -+ <ref name="resource-check" /> -+ <ref name="resource-config" /> -+ <ref name="resources-list" /> -+ </choice> -+ </define> -+ -+ <define name="agents-list"> -+ <element name="agents"> -+ <attribute name="standard"> <text/> </attribute> -+ <optional> -+ <attribute name="provider"> <text/> </attribute> -+ </optional> -+ <zeroOrMore> -+ <element name="agent"> <text/> </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="alternatives-list"> -+ <element name="providers"> -+ <attribute name="for"> <text/> </attribute> -+ <zeroOrMore> -+ <element name="provider"> <text/> </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="constraints-list"> -+ <element name="constraints"> -+ <interleave> -+ <zeroOrMore> -+ <ref name="rsc-location" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="rsc-colocation" /> -+ </zeroOrMore> -+ </interleave> -+ </element> -+ </define> -+ -+ <define name="locate-list"> -+ <element name="nodes"> -+ <attribute name="resource"> <text/> </attribute> -+ <zeroOrMore> -+ <element name="node"> -+ <optional> -+ <attribute name="state"><value>promoted</value></attribute> -+ </optional> -+ <text/> -+ </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="rsc-location"> -+ <element name="rsc_location"> -+ <attribute name="node"> <text/> </attribute> -+ <attribute name="rsc"> <text/> </attribute> -+ <attribute name="id"> <text/> </attribute> -+ <externalRef href="../score.rng"/> -+ </element> -+ </define> -+ -+ <define name="operations-list"> -+ <element name="operations"> -+ <oneOrMore> -+ <ref name="element-operation-list" /> -+ </oneOrMore> -+ </element> -+ </define> -+ -+ <define name="providers-list"> -+ <element name="providers"> -+ <attribute name="standard"> <value>ocf</value> </attribute> -+ <optional> -+ <attribute name="agent"> <text/> </attribute> -+ </optional> -+ <zeroOrMore> -+ <element name="provider"> <text/> </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="reasons-list"> -+ <choice> -+ <ref name="no-resource-or-uname"/> -+ <ref name="resource-and-uname"/> -+ <ref name="no-resource-but-uname"/> -+ <ref name="resource-but-no-uname"/> -+ </choice> -+ </define> -+ -+ <define name="no-resource-or-uname"> -+ <element name="reason"> -+ <element name="resources"> -+ <zeroOrMore> -+ <element name="resource"> -+ <attribute name="id"> <text/> </attribute> -+ <attribute name="running"> <data type="boolean"/> </attribute> -+ <ref name="resource-check"/> -+ </element> -+ </zeroOrMore> -+ </element> -+ </element> -+ </define> -+ -+ <define name="resource-and-uname"> -+ <element name="reason"> -+ <attribute name="running_on"> <text/> </attribute> -+ <ref name="resource-check"/> -+ </element> -+ </define> -+ -+ <define name="no-resource-but-uname"> -+ <element name="reason"> -+ <element name="resources"> -+ <zeroOrMore> -+ <element name="resource"> -+ <attribute name="id"> <text/> </attribute> -+ <attribute name="running"> <data type="boolean"/> </attribute> -+ <attribute name="host"> <text/> </attribute> -+ <ref name="resource-check"/> -+ </element> -+ </zeroOrMore> -+ </element> -+ </element> -+ </define> -+ -+ <define name="resource-but-no-uname"> -+ <element name="reason"> -+ <attribute name="running"> <data type="boolean"/> </attribute> -+ <ref name="resource-check"/> -+ </element> -+ </define> -+ -+ <define name="resource-config"> -+ <element name="resource_config"> -+ <externalRef href="resources-2.4.rng" /> -+ <element name="xml"> <text/> </element> -+ </element> -+ </define> -+ -+ <define name="resource-check"> -+ <element name="check"> -+ <attribute name="id"> <text/> </attribute> -+ <optional> -+ <choice> -+ <attribute name="remain_stopped"><value>true</value></attribute> -+ <attribute name="promotable"><value>false</value></attribute> -+ </choice> -+ </optional> -+ <optional> -+ <attribute name="unmanaged"><value>true</value></attribute> -+ </optional> -+ <optional> -+ <attribute name="locked-to"> <text/> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="resources-list"> -+ <element name="resources"> -+ <zeroOrMore> -+ <externalRef href="resources-2.4.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="rsc-colocation"> -+ <element name="rsc_colocation"> -+ <attribute name="id"> <text/> </attribute> -+ <attribute name="rsc"> <text/> </attribute> -+ <attribute name="with-rsc"> <text/> </attribute> -+ <externalRef href="../score.rng"/> -+ <optional> -+ <attribute name="node-attribute"> <text/> </attribute> -+ </optional> -+ <optional> -+ <attribute name="rsc-role"> -+ <ref name="attribute-roles"/> -+ </attribute> -+ </optional> -+ <optional> -+ <attribute name="with-rsc-role"> -+ <ref name="attribute-roles"/> -+ </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-operation-list"> -+ <element name="operation"> -+ <optional> -+ <group> -+ <attribute name="rsc"> <text/> </attribute> -+ <attribute name="agent"> <text/> </attribute> -+ </group> -+ </optional> -+ <attribute name="op"> <text/> </attribute> -+ <attribute name="node"> <text/> </attribute> -+ <attribute name="call"> <data type="integer" /> </attribute> -+ <attribute name="rc"> <data type="nonNegativeInteger" /> </attribute> -+ <optional> -+ <attribute name="last-rc-change"> <text/> </attribute> -+ <attribute name="exec-time"> <data type="nonNegativeInteger" /> </attribute> -+ </optional> -+ <attribute name="status"> <text/> </attribute> -+ </element> -+ </define> -+ -+ <define name="attribute-roles"> -+ <choice> -+ <value>Stopped</value> -+ <value>Started</value> -+ <value>Master</value> -+ <value>Slave</value> -+ </choice> -+ </define> -+</grammar> --- -1.8.3.1 - - -From 1bbdf2149a111e9e19c388834f82001e0d31c427 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 24 May 2021 12:23:55 -0400 -Subject: [PATCH 03/10] Feature: xml: Update the crm_resource schema for XML - output. - -See: rhbz#1644628 ---- - xml/api/crm_resource-2.11.rng | 50 +++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 50 insertions(+) - -diff --git a/xml/api/crm_resource-2.11.rng b/xml/api/crm_resource-2.11.rng -index 8e386db..aaa54d6 100644 ---- a/xml/api/crm_resource-2.11.rng -+++ b/xml/api/crm_resource-2.11.rng -@@ -20,6 +20,7 @@ - <ref name="resource-check" /> - <ref name="resource-config" /> - <ref name="resources-list" /> -+ <ref name="resource-agent-action" /> - </choice> - </define> - -@@ -227,6 +228,55 @@ - </element> - </define> - -+ <define name="resource-agent-action"> -+ <element name="resource-agent-action"> -+ <attribute name="action"> <text/> </attribute> -+ <optional> -+ <attribute name="rsc"> <text/> </attribute> -+ </optional> -+ <attribute name="class"> <text/> </attribute> -+ <attribute name="type"> <text/> </attribute> -+ <optional> -+ <attribute name="provider"> <text/> </attribute> -+ </optional> -+ <optional> -+ <ref name="overrides-list"/> -+ </optional> -+ <ref name="agent-status"/> -+ <optional> -+ <choice> -+ <element name="command"> -+ <text /> -+ </element> -+ <externalRef href="command-output-1.0.rng"/> -+ </choice> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="overrides-list"> -+ <element name="overrides"> -+ <zeroOrMore> -+ <element name="override"> -+ <optional> -+ <attribute name="rsc"> <text/> </attribute> -+ </optional> -+ <attribute name="name"> <text/> </attribute> -+ <attribute name="value"> <text/> </attribute> -+ </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="agent-status"> -+ <element name="agent-status"> -+ <attribute name="code"> <data type="integer" /> </attribute> -+ <optional> -+ <attribute name="message"> <text/> </attribute> -+ </optional> -+ </element> -+ </define> -+ - <define name="attribute-roles"> - <choice> - <value>Stopped</value> --- -1.8.3.1 - - -From d89f5bc7fec856fdcd32fa14edbd0019507d5d15 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Tue, 1 Jun 2021 15:26:58 -0400 -Subject: [PATCH 04/10] Low: libcrmcommon: Increase PCMK__API_VERSION for new - crm_resource output. - -See: rhbz#1644628 ---- - include/crm/common/output_internal.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/include/crm/common/output_internal.h b/include/crm/common/output_internal.h -index 10b315b..0436cde 100644 ---- a/include/crm/common/output_internal.h -+++ b/include/crm/common/output_internal.h -@@ -27,7 +27,7 @@ extern "C" { - # include <glib.h> - # include <crm/common/results.h> - --# define PCMK__API_VERSION "2.9" -+# define PCMK__API_VERSION "2.11" - - #if defined(PCMK__WITH_ATTRIBUTE_OUTPUT_ARGS) - # define PCMK__OUTPUT_ARGS(ARGS...) __attribute__((output_args(ARGS))) --- -1.8.3.1 - - -From 30bd2ddf43ee2a911681e51f40ed9ba20ec250b0 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 27 May 2021 13:57:12 -0400 -Subject: [PATCH 05/10] Low: tools: Pass NULL to - cli_resource_execute_from_params... - -if no resource name is given. This happens if we are validating based -on the --class/--agent/--provider command line options instead. ---- - tools/crm_resource.c | 2 +- - tools/crm_resource_runtime.c | 8 ++++---- - 2 files changed, 5 insertions(+), 5 deletions(-) - -diff --git a/tools/crm_resource.c b/tools/crm_resource.c -index 24f1121..37a0bb0 100644 ---- a/tools/crm_resource.c -+++ b/tools/crm_resource.c -@@ -1840,7 +1840,7 @@ main(int argc, char **argv) - - case cmd_execute_agent: - if (options.cmdline_config) { -- exit_code = cli_resource_execute_from_params(out, "test", -+ exit_code = cli_resource_execute_from_params(out, NULL, - options.v_class, options.v_provider, options.v_agent, - "validate-all", options.cmdline_params, - options.override_params, options.timeout_ms, -diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c -index 48a4b40..ebf48bb 100644 ---- a/tools/crm_resource_runtime.c -+++ b/tools/crm_resource_runtime.c -@@ -1717,14 +1717,14 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, - */ - params_copy = pcmk__str_table_dup(params); - -- op = resources_action_create(rsc_name, rsc_class, rsc_prov, rsc_type, action, 0, -- timeout_ms, params_copy, 0); -+ op = resources_action_create(rsc_name ? rsc_name : "test", rsc_class, rsc_prov, -+ rsc_type, action, 0, timeout_ms, params_copy, 0); - if (op == NULL) { - /* Re-run with stderr enabled so we can display a sane error message */ - crm_enable_stderr(TRUE); - params_copy = pcmk__str_table_dup(params); -- op = resources_action_create(rsc_name, rsc_class, rsc_prov, rsc_type, action, 0, -- timeout_ms, params_copy, 0); -+ op = resources_action_create(rsc_name ? rsc_name : "test", rsc_class, rsc_prov, -+ rsc_type, action, 0, timeout_ms, params_copy, 0); - - /* Callers of cli_resource_execute expect that the params hash table will - * be freed. That function uses this one, so for that reason and for --- -1.8.3.1 - - -From ee56efd53d14cfc4f902769540b72b3bb6096a73 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 24 May 2021 12:08:52 -0400 -Subject: [PATCH 06/10] Feature: tools: Add an agent-status message for - crm_resource. - -This moves what was previously only done in an out->info call to its own -output message, which means it will appear in XML output as well. Also, -note that if --class/--agent/--provider are given, the resource name -will be set to "test". In that case, do not display the resource name -in the output. - -This message will be used for --validate and the --force-* command line -options to crm_resource. - -See: rhbz#1644628 ---- - tools/crm_resource_print.c | 53 ++++++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 53 insertions(+) - -diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c -index 9d82cf8..88d5878 100644 ---- a/tools/crm_resource_print.c -+++ b/tools/crm_resource_print.c -@@ -152,6 +152,57 @@ attribute_list_default(pcmk__output_t *out, va_list args) { - return pcmk_rc_ok; - } - -+PCMK__OUTPUT_ARGS("agent-status", "int", "const char *", "const char *", "const char *", -+ "const char *", "const char *", "int") -+static int -+agent_status_default(pcmk__output_t *out, va_list args) { -+ int status = va_arg(args, int); -+ const char *action = va_arg(args, const char *); -+ const char *name = va_arg(args, const char *); -+ const char *class = va_arg(args, const char *); -+ const char *provider = va_arg(args, const char *); -+ const char *type = va_arg(args, const char *); -+ int rc = va_arg(args, int); -+ -+ if (status == PCMK_LRM_OP_DONE) { -+ out->info(out, "Operation %s%s%s (%s%s%s:%s) returned: '%s' (%d)", -+ action, name ? " for " : "", name ? name : "", -+ class, provider ? ":" : "", provider ? provider : "", type, -+ services_ocf_exitcode_str(rc), rc); -+ } else { -+ out->err(out, "Operation %s%s%s (%s%s%s:%s) failed: '%s' (%d)", -+ action, name ? " for " : "", name ? name : "", -+ class, provider ? ":" : "", provider ? provider : "", type, -+ services_lrm_status_str(status), status); -+ } -+ -+ return pcmk_rc_ok; -+} -+ -+PCMK__OUTPUT_ARGS("agent-status", "int", "const char *", "const char *", "const char *", -+ "const char *", "const char *", "int") -+static int -+agent_status_xml(pcmk__output_t *out, va_list args) { -+ int status G_GNUC_UNUSED = va_arg(args, int); -+ const char *action G_GNUC_UNUSED = va_arg(args, const char *); -+ const char *name G_GNUC_UNUSED = va_arg(args, const char *); -+ const char *class G_GNUC_UNUSED = va_arg(args, const char *); -+ const char *provider G_GNUC_UNUSED = va_arg(args, const char *); -+ const char *type G_GNUC_UNUSED = va_arg(args, const char *); -+ int rc = va_arg(args, int); -+ -+ char *status_str = pcmk__itoa(rc); -+ -+ pcmk__output_create_xml_node(out, "agent-status", -+ "code", status_str, -+ "message", services_ocf_exitcode_str(rc), -+ NULL); -+ -+ free(status_str); -+ -+ return pcmk_rc_ok; -+} -+ - PCMK__OUTPUT_ARGS("attribute-list", "pe_resource_t *", "char *", "GHashTable *") - static int - attribute_list_text(pcmk__output_t *out, va_list args) { -@@ -562,6 +613,8 @@ resource_names(pcmk__output_t *out, va_list args) { - } - - static pcmk__message_entry_t fmt_functions[] = { -+ { "agent-status", "default", agent_status_default }, -+ { "agent-status", "xml", agent_status_xml }, - { "attribute-list", "default", attribute_list_default }, - { "attribute-list", "text", attribute_list_text }, - { "property-list", "default", property_list_default }, --- -1.8.3.1 - - -From 85cb6b6bff96b18c5174d11e4de4d49cbfb20bb7 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Tue, 1 Jun 2021 14:47:30 -0400 -Subject: [PATCH 07/10] Feature: tools: Add an overridden params output - message. - -This also replaces what was previously being done in an out->info call -with an output message. This means it shows up in XML output as well. -Also, note that if --class/--agent/--provider are given, the resource -name will be set to "test". In that case, do not display the resource -name in the output. - -See: rhbz#1644628 ---- - tools/crm_resource_print.c | 39 +++++++++++++++++++++++++++++++++++++++ - 1 file changed, 39 insertions(+) - -diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c -index 88d5878..119d83f 100644 ---- a/tools/crm_resource_print.c -+++ b/tools/crm_resource_print.c -@@ -224,6 +224,43 @@ attribute_list_text(pcmk__output_t *out, va_list args) { - return pcmk_rc_ok; - } - -+PCMK__OUTPUT_ARGS("override", "const char *", "const char *", "const char *") -+static int -+override_default(pcmk__output_t *out, va_list args) { -+ const char *rsc_name = va_arg(args, const char *); -+ const char *name = va_arg(args, const char *); -+ const char *value = va_arg(args, const char *); -+ -+ if (rsc_name == NULL) { -+ out->list_item(out, NULL, "Overriding the cluster configuration with '%s' = '%s'", -+ name, value); -+ } else { -+ out->list_item(out, NULL, "Overriding the cluster configuration for '%s' with '%s' = '%s'", -+ rsc_name, name, value); -+ } -+ -+ return pcmk_rc_ok; -+} -+ -+PCMK__OUTPUT_ARGS("override", "const char *", "const char *", "const char *") -+static int -+override_xml(pcmk__output_t *out, va_list args) { -+ const char *rsc_name = va_arg(args, const char *); -+ const char *name = va_arg(args, const char *); -+ const char *value = va_arg(args, const char *); -+ -+ xmlNodePtr node = pcmk__output_create_xml_node(out, "override", -+ "name", name, -+ "value", value, -+ NULL); -+ -+ if (rsc_name != NULL) { -+ crm_xml_add(node, "rsc", rsc_name); -+ } -+ -+ return pcmk_rc_ok; -+} -+ - PCMK__OUTPUT_ARGS("property-list", "pe_resource_t *", "char *") - static int - property_list_default(pcmk__output_t *out, va_list args) { -@@ -617,6 +654,8 @@ static pcmk__message_entry_t fmt_functions[] = { - { "agent-status", "xml", agent_status_xml }, - { "attribute-list", "default", attribute_list_default }, - { "attribute-list", "text", attribute_list_text }, -+ { "override", "default", override_default }, -+ { "override", "xml", override_xml }, - { "property-list", "default", property_list_default }, - { "property-list", "text", property_list_text }, - { "resource-check-list", "default", resource_check_list_default }, --- -1.8.3.1 - - -From e5e24592c7c3231c619fb5253e7925ffbc634a99 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 4 Jun 2021 10:24:51 -0400 -Subject: [PATCH 08/10] Low: tools: Use simple XML lists for resource actions - as well. - -See: rhbz#1644628 ---- - tools/crm_resource.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/tools/crm_resource.c b/tools/crm_resource.c -index 37a0bb0..e957011 100644 ---- a/tools/crm_resource.c -+++ b/tools/crm_resource.c -@@ -1643,6 +1643,7 @@ main(int argc, char **argv) - * saves from having to write custom messages to build the lists around all these things - */ - switch (options.rsc_cmd) { -+ case cmd_execute_agent: - case cmd_list_resources: - case cmd_query_xml: - case cmd_query_raw_xml: --- -1.8.3.1 - - -From 3e75174d0bc31b261adb1994214a5878b79da85b Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 4 Jun 2021 10:30:10 -0400 -Subject: [PATCH 09/10] Feature: tools: Add an output message for resource - actions. - -This wraps up the override and agent-status messages into a single -message, along with any stdout/stderr from the resource action. This -message should be called after taking the action. - -This also implements handling XML output from resource actions. Check -to see if the validate-all action returns XML. If so, output it as a -CDATA block under a "command" element. If not, treat it as plain text -and output it as stdout/stderr from a command. - -See: rhbz#1644628 ---- - tools/crm_resource_print.c | 122 +++++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 122 insertions(+) - -diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c -index 119d83f..19a366d 100644 ---- a/tools/crm_resource_print.c -+++ b/tools/crm_resource_print.c -@@ -293,6 +293,126 @@ property_list_text(pcmk__output_t *out, va_list args) { - return pcmk_rc_ok; - } - -+PCMK__OUTPUT_ARGS("resource-agent-action", "int", "const char *", "const char *", -+ "const char *", "const char *", "const char *", "GHashTable *", -+ "int", "int", "char *", "char *") -+static int -+resource_agent_action_default(pcmk__output_t *out, va_list args) { -+ int verbose = va_arg(args, int); -+ -+ const char *class = va_arg(args, const char *); -+ const char *provider = va_arg(args, const char *); -+ const char *type = va_arg(args, const char *); -+ const char *rsc_name = va_arg(args, const char *); -+ const char *action = va_arg(args, const char *); -+ GHashTable *overrides = va_arg(args, GHashTable *); -+ int rc = va_arg(args, int); -+ int status = va_arg(args, int); -+ char *stdout_data = va_arg(args, char *); -+ char *stderr_data = va_arg(args, char *); -+ -+ if (overrides) { -+ GHashTableIter iter; -+ char *name = NULL; -+ char *value = NULL; -+ -+ out->begin_list(out, NULL, NULL, "overrides"); -+ -+ g_hash_table_iter_init(&iter, overrides); -+ while (g_hash_table_iter_next(&iter, (gpointer *) &name, (gpointer *) &value)) { -+ out->message(out, "override", rsc_name, name, value); -+ } -+ -+ out->end_list(out); -+ } -+ -+ out->message(out, "agent-status", status, action, rsc_name, class, provider, -+ type, rc); -+ -+ /* hide output for validate-all if not in verbose */ -+ if (verbose == 0 && pcmk__str_eq(action, "validate-all", pcmk__str_casei)) { -+ return pcmk_rc_ok; -+ } -+ -+ if (stdout_data || stderr_data) { -+ xmlNodePtr doc = string2xml(stdout_data); -+ -+ if (doc != NULL) { -+ out->output_xml(out, "command", stdout_data); -+ xmlFreeNode(doc); -+ } else { -+ out->subprocess_output(out, rc, stdout_data, stderr_data); -+ } -+ } -+ -+ return pcmk_rc_ok; -+} -+ -+PCMK__OUTPUT_ARGS("resource-agent-action", "int", "const char *", "const char *", -+ "const char *", "const char *", "const char *", "GHashTable *", -+ "int", "int", "char *", "char *") -+static int -+resource_agent_action_xml(pcmk__output_t *out, va_list args) { -+ int verbose G_GNUC_UNUSED = va_arg(args, int); -+ -+ const char *class = va_arg(args, const char *); -+ const char *provider = va_arg(args, const char *); -+ const char *type = va_arg(args, const char *); -+ const char *rsc_name = va_arg(args, const char *); -+ const char *action = va_arg(args, const char *); -+ GHashTable *overrides = va_arg(args, GHashTable *); -+ int rc = va_arg(args, int); -+ int status = va_arg(args, int); -+ char *stdout_data = va_arg(args, char *); -+ char *stderr_data = va_arg(args, char *); -+ -+ xmlNodePtr node = pcmk__output_xml_create_parent(out, "resource-agent-action", -+ "action", action, -+ "class", class, -+ "type", type, -+ NULL); -+ -+ if (rsc_name) { -+ crm_xml_add(node, "rsc", rsc_name); -+ } -+ -+ if (provider) { -+ crm_xml_add(node, "provider", provider); -+ } -+ -+ if (overrides) { -+ GHashTableIter iter; -+ char *name = NULL; -+ char *value = NULL; -+ -+ out->begin_list(out, NULL, NULL, "overrides"); -+ -+ g_hash_table_iter_init(&iter, overrides); -+ while (g_hash_table_iter_next(&iter, (gpointer *) &name, (gpointer *) &value)) { -+ out->message(out, "override", rsc_name, name, value); -+ } -+ -+ out->end_list(out); -+ } -+ -+ out->message(out, "agent-status", status, action, rsc_name, class, provider, -+ type, rc); -+ -+ if (stdout_data || stderr_data) { -+ xmlNodePtr doc = string2xml(stdout_data); -+ -+ if (doc != NULL) { -+ out->output_xml(out, "command", stdout_data); -+ xmlFreeNode(doc); -+ } else { -+ out->subprocess_output(out, rc, stdout_data, stderr_data); -+ } -+ } -+ -+ pcmk__output_xml_pop_parent(out); -+ return pcmk_rc_ok; -+} -+ - PCMK__OUTPUT_ARGS("resource-check-list", "resource_checks_t *") - static int - resource_check_list_default(pcmk__output_t *out, va_list args) { -@@ -658,6 +778,8 @@ static pcmk__message_entry_t fmt_functions[] = { - { "override", "xml", override_xml }, - { "property-list", "default", property_list_default }, - { "property-list", "text", property_list_text }, -+ { "resource-agent-action", "default", resource_agent_action_default }, -+ { "resource-agent-action", "xml", resource_agent_action_xml }, - { "resource-check-list", "default", resource_check_list_default }, - { "resource-check-list", "xml", resource_check_list_xml }, - { "resource-search-list", "default", resource_search_list_default }, --- -1.8.3.1 - - -From b50b2418e1e997b42f5370b4672a3f105d74634f Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 4 Jun 2021 10:40:16 -0400 -Subject: [PATCH 10/10] Feature: tools: Use the new resource-agent-action - message. - -See: rhbz#1644628 ---- - tools/crm_resource_runtime.c | 21 +++------------------ - 1 file changed, 3 insertions(+), 18 deletions(-) - -diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c -index ebf48bb..755be9f 100644 ---- a/tools/crm_resource_runtime.c -+++ b/tools/crm_resource_runtime.c -@@ -1765,28 +1765,13 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, - if (services_action_sync(op)) { - exit_code = op->rc; - -- if (op->status == PCMK_LRM_OP_DONE) { -- out->info(out, "Operation %s for %s (%s:%s:%s) returned: '%s' (%d)", -- action, rsc_name, rsc_class, rsc_prov ? rsc_prov : "", rsc_type, -- services_ocf_exitcode_str(op->rc), op->rc); -- } else { -- out->err(out, "Operation %s for %s (%s:%s:%s) failed: '%s' (%d)", -- action, rsc_name, rsc_class, rsc_prov ? rsc_prov : "", rsc_type, -- services_lrm_status_str(op->status), op->status); -- } -- -- /* hide output for validate-all if not in verbose */ -- if (resource_verbose == 0 && pcmk__str_eq(action, "validate-all", pcmk__str_casei)) -- goto done; -- -- if (op->stdout_data || op->stderr_data) { -- out->subprocess_output(out, op->rc, op->stdout_data, op->stderr_data); -- } -+ out->message(out, "resource-agent-action", resource_verbose, rsc_class, -+ rsc_prov, rsc_type, rsc_name, action, override_hash, op->rc, -+ op->status, op->stdout_data, op->stderr_data); - } else { - exit_code = op->rc == 0 ? CRM_EX_ERROR : op->rc; - } - --done: - services_action_free(op); - /* See comment above about why we free params here. */ - g_hash_table_destroy(params); --- -1.8.3.1 - diff --git a/006-crm_simulate.patch b/006-crm_simulate.patch deleted file mode 100644 index c8d4e3f..0000000 --- a/006-crm_simulate.patch +++ /dev/null @@ -1,896 +0,0 @@ -From 97571e6ccc9b7fa339a7e27d9b0b9ab782ff3003 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Wed, 16 Jun 2021 13:54:10 -0400 -Subject: [PATCH 1/5] Low: schemas: Copy crm_mon.rng in preparation for - changes. - ---- - xml/api/crm_mon-2.12.rng | 243 +++++++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 243 insertions(+) - create mode 100644 xml/api/crm_mon-2.12.rng - -diff --git a/xml/api/crm_mon-2.12.rng b/xml/api/crm_mon-2.12.rng -new file mode 100644 -index 0000000..ffec923 ---- /dev/null -+++ b/xml/api/crm_mon-2.12.rng -@@ -0,0 +1,243 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="element-crm-mon"/> -+ </start> -+ -+ <define name="element-crm-mon"> -+ <optional> -+ <ref name="element-summary" /> -+ </optional> -+ <optional> -+ <ref name="nodes-list" /> -+ </optional> -+ <optional> -+ <ref name="resources-list" /> -+ </optional> -+ <optional> -+ <ref name="node-attributes-list" /> -+ </optional> -+ <optional> -+ <ref name="node-history-list" /> -+ </optional> -+ <optional> -+ <ref name="failures-list" /> -+ </optional> -+ <optional> -+ <ref name="fence-event-list" /> -+ </optional> -+ <optional> -+ <ref name="tickets-list" /> -+ </optional> -+ <optional> -+ <ref name="bans-list" /> -+ </optional> -+ </define> -+ -+ <define name="element-summary"> -+ <element name="summary"> -+ <optional> -+ <element name="stack"> -+ <attribute name="type"> <text /> </attribute> -+ </element> -+ </optional> -+ <optional> -+ <element name="current_dc"> -+ <attribute name="present"> <data type="boolean" /> </attribute> -+ <optional> -+ <group> -+ <attribute name="version"> <text /> </attribute> -+ <attribute name="name"> <text /> </attribute> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="with_quorum"> <data type="boolean" /> </attribute> -+ </group> -+ </optional> -+ </element> -+ </optional> -+ <optional> -+ <element name="last_update"> -+ <attribute name="time"> <text /> </attribute> -+ </element> -+ <element name="last_change"> -+ <attribute name="time"> <text /> </attribute> -+ <attribute name="user"> <text /> </attribute> -+ <attribute name="client"> <text /> </attribute> -+ <attribute name="origin"> <text /> </attribute> -+ </element> -+ </optional> -+ <optional> -+ <element name="nodes_configured"> -+ <attribute name="number"> <data type="nonNegativeInteger" /> </attribute> -+ </element> -+ <element name="resources_configured"> -+ <attribute name="number"> <data type="nonNegativeInteger" /> </attribute> -+ <attribute name="disabled"> <data type="nonNegativeInteger" /> </attribute> -+ <attribute name="blocked"> <data type="nonNegativeInteger" /> </attribute> -+ </element> -+ </optional> -+ <optional> -+ <element name="cluster_options"> -+ <attribute name="stonith-enabled"> <data type="boolean" /> </attribute> -+ <attribute name="symmetric-cluster"> <data type="boolean" /> </attribute> -+ <attribute name="no-quorum-policy"> <text /> </attribute> -+ <attribute name="maintenance-mode"> <data type="boolean" /> </attribute> -+ <attribute name="stop-all-resources"> <data type="boolean" /> </attribute> -+ </element> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="resources-list"> -+ <element name="resources"> -+ <zeroOrMore> -+ <externalRef href="resources-2.4.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="nodes-list"> -+ <element name="nodes"> -+ <zeroOrMore> -+ <externalRef href="nodes-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="node-attributes-list"> -+ <element name="node_attributes"> -+ <zeroOrMore> -+ <externalRef href="node-attrs-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="node-history-list"> -+ <element name="node_history"> -+ <zeroOrMore> -+ <ref name="element-node-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="failures-list"> -+ <element name="failures"> -+ <zeroOrMore> -+ <externalRef href="failure-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="fence-event-list"> -+ <element name="fence_history"> -+ <optional> -+ <attribute name="status"> <data type="integer" /> </attribute> -+ </optional> -+ <zeroOrMore> -+ <externalRef href="fence-event-2.0.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="tickets-list"> -+ <element name="tickets"> -+ <zeroOrMore> -+ <ref name="element-ticket" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="bans-list"> -+ <element name="bans"> -+ <zeroOrMore> -+ <ref name="element-ban" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-node-history"> -+ <element name="node"> -+ <attribute name="name"> <text /> </attribute> -+ <zeroOrMore> -+ <ref name="element-resource-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-resource-history"> -+ <element name="resource_history"> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="orphan"> <data type="boolean" /> </attribute> -+ <optional> -+ <group> -+ <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> -+ <optional> -+ <attribute name="fail-count"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-failure"> <text /> </attribute> -+ </optional> -+ </group> -+ </optional> -+ <zeroOrMore> -+ <ref name="element-operation-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-operation-history"> -+ <element name="operation_history"> -+ <attribute name="call"> <text /> </attribute> -+ <attribute name="task"> <text /> </attribute> -+ <optional> -+ <attribute name="interval"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-rc-change"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-run"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="exec-time"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="queue-time"> <text /> </attribute> -+ </optional> -+ <attribute name="rc"> <data type="integer" /> </attribute> -+ <attribute name="rc_text"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-ticket"> -+ <element name="ticket"> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="status"> -+ <choice> -+ <value>granted</value> -+ <value>revoked</value> -+ </choice> -+ </attribute> -+ <attribute name="standby"> <data type="boolean" /> </attribute> -+ <optional> -+ <attribute name="last-granted"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-ban"> -+ <element name="ban"> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="resource"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="weight"> <data type="integer" /> </attribute> -+ <attribute name="promoted-only"> <data type="boolean" /> </attribute> -+  -+ <attribute name="master_only"> <data type="boolean" /> </attribute> -+ </element> -+ </define> -+</grammar> --- -1.8.3.1 - - -From da394983f106f974274ddd94675a04c85086010e Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 18 Jun 2021 15:06:34 -0400 -Subject: [PATCH 2/5] Refactor: Split node history out into its own XML schema. - -This allows for sharing it between crm_mon and crm_simulate. ---- - xml/Makefile.am | 2 +- - xml/api/crm_mon-2.12.rng | 64 +-------------------------------------- - xml/api/node-history-2.12.rng | 70 +++++++++++++++++++++++++++++++++++++++++++ - 3 files changed, 72 insertions(+), 64 deletions(-) - create mode 100644 xml/api/node-history-2.12.rng - -diff --git a/xml/Makefile.am b/xml/Makefile.am -index b9448d4..8e7b6d3 100644 ---- a/xml/Makefile.am -+++ b/xml/Makefile.am -@@ -64,7 +64,7 @@ API_request_base = command-output \ - CIB_cfg_base = options nodes resources constraints fencing acls tags alerts - - # Names of all schemas (including top level and those included by others) --API_base = $(API_request_base) fence-event failure generic-list item node-attrs nodes resources status -+API_base = $(API_request_base) fence-event failure generic-list item node-attrs node-history nodes resources status - CIB_base = cib $(CIB_cfg_base) status score rule nvset - - # Static schema files and transforms (only CIB has transforms) -diff --git a/xml/api/crm_mon-2.12.rng b/xml/api/crm_mon-2.12.rng -index ffec923..be14412 100644 ---- a/xml/api/crm_mon-2.12.rng -+++ b/xml/api/crm_mon-2.12.rng -@@ -20,7 +20,7 @@ - <ref name="node-attributes-list" /> - </optional> - <optional> -- <ref name="node-history-list" /> -+ <externalRef href="node-history-2.12.rng"/> - </optional> - <optional> - <ref name="failures-list" /> -@@ -113,14 +113,6 @@ - </element> - </define> - -- <define name="node-history-list"> -- <element name="node_history"> -- <zeroOrMore> -- <ref name="element-node-history" /> -- </zeroOrMore> -- </element> -- </define> -- - <define name="failures-list"> - <element name="failures"> - <zeroOrMore> -@@ -156,60 +148,6 @@ - </element> - </define> - -- <define name="element-node-history"> -- <element name="node"> -- <attribute name="name"> <text /> </attribute> -- <zeroOrMore> -- <ref name="element-resource-history" /> -- </zeroOrMore> -- </element> -- </define> -- -- <define name="element-resource-history"> -- <element name="resource_history"> -- <attribute name="id"> <text /> </attribute> -- <attribute name="orphan"> <data type="boolean" /> </attribute> -- <optional> -- <group> -- <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> -- <optional> -- <attribute name="fail-count"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="last-failure"> <text /> </attribute> -- </optional> -- </group> -- </optional> -- <zeroOrMore> -- <ref name="element-operation-history" /> -- </zeroOrMore> -- </element> -- </define> -- -- <define name="element-operation-history"> -- <element name="operation_history"> -- <attribute name="call"> <text /> </attribute> -- <attribute name="task"> <text /> </attribute> -- <optional> -- <attribute name="interval"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="last-rc-change"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="last-run"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="exec-time"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="queue-time"> <text /> </attribute> -- </optional> -- <attribute name="rc"> <data type="integer" /> </attribute> -- <attribute name="rc_text"> <text /> </attribute> -- </element> -- </define> -- - <define name="element-ticket"> - <element name="ticket"> - <attribute name="id"> <text /> </attribute> -diff --git a/xml/api/node-history-2.12.rng b/xml/api/node-history-2.12.rng -new file mode 100644 -index 0000000..9628000 ---- /dev/null -+++ b/xml/api/node-history-2.12.rng -@@ -0,0 +1,70 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="node-history-list" /> -+ </start> -+ -+ <define name="node-history-list"> -+ <element name="node_history"> -+ <zeroOrMore> -+ <ref name="element-node-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-node-history"> -+ <element name="node"> -+ <attribute name="name"> <text /> </attribute> -+ <zeroOrMore> -+ <ref name="element-resource-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-resource-history"> -+ <element name="resource_history"> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="orphan"> <data type="boolean" /> </attribute> -+ <optional> -+ <group> -+ <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> -+ <optional> -+ <attribute name="fail-count"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-failure"> <text /> </attribute> -+ </optional> -+ </group> -+ </optional> -+ <zeroOrMore> -+ <ref name="element-operation-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-operation-history"> -+ <element name="operation_history"> -+ <attribute name="call"> <text /> </attribute> -+ <attribute name="task"> <text /> </attribute> -+ <optional> -+ <attribute name="interval"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-rc-change"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-run"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="exec-time"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="queue-time"> <text /> </attribute> -+ </optional> -+ <attribute name="rc"> <data type="integer" /> </attribute> -+ <attribute name="rc_text"> <text /> </attribute> -+ </element> -+ </define> -+</grammar> --- -1.8.3.1 - - -From bf72b2615630eef7876e443d60b34d5a316de847 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Wed, 16 Jun 2021 14:09:31 -0400 -Subject: [PATCH 3/5] Low: schemas: Copy crm_simulate.rng in preparation for - changes. - ---- - xml/api/crm_simulate-2.12.rng | 335 ++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 335 insertions(+) - create mode 100644 xml/api/crm_simulate-2.12.rng - -diff --git a/xml/api/crm_simulate-2.12.rng b/xml/api/crm_simulate-2.12.rng -new file mode 100644 -index 0000000..9a7612d ---- /dev/null -+++ b/xml/api/crm_simulate-2.12.rng -@@ -0,0 +1,335 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="element-crm-simulate"/> -+ </start> -+ -+ <define name="element-crm-simulate"> -+ <choice> -+ <ref name="timings-list" /> -+ <group> -+ <ref name="cluster-status" /> -+ <optional> -+ <ref name="modifications-list" /> -+ </optional> -+ <optional> -+ <ref name="allocations-utilizations-list" /> -+ </optional> -+ <optional> -+ <ref name="action-list" /> -+ </optional> -+ <optional> -+ <ref name="cluster-injected-actions-list" /> -+ <ref name="revised-cluster-status" /> -+ </optional> -+ </group> -+ </choice> -+ </define> -+ -+ <define name="allocations-utilizations-list"> -+ <choice> -+ <element name="allocations"> -+ <zeroOrMore> -+ <choice> -+ <ref name="element-allocation" /> -+ <ref name="element-promotion" /> -+ </choice> -+ </zeroOrMore> -+ </element> -+ <element name="utilizations"> -+ <zeroOrMore> -+ <choice> -+ <ref name="element-capacity" /> -+ <ref name="element-utilization" /> -+ </choice> -+ </zeroOrMore> -+ </element> -+ <element name="allocations_utilizations"> -+ <zeroOrMore> -+ <choice> -+ <ref name="element-allocation" /> -+ <ref name="element-promotion" /> -+ <ref name="element-capacity" /> -+ <ref name="element-utilization" /> -+ </choice> -+ </zeroOrMore> -+ </element> -+ </choice> -+ </define> -+ -+ <define name="cluster-status"> -+ <element name="cluster_status"> -+ <ref name="nodes-list" /> -+ <ref name="resources-list" /> -+ <optional> -+ <ref name="node-attributes-list" /> -+ </optional> -+ <optional> -+ <ref name="failures-list" /> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="modifications-list"> -+ <element name="modifications"> -+ <optional> -+ <attribute name="quorum"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="watchdog"> <text /> </attribute> -+ </optional> -+ <zeroOrMore> -+ <ref name="element-inject-modify-node" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="element-inject-modify-ticket" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="element-inject-spec" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="element-inject-attr" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="revised-cluster-status"> -+ <element name="revised_cluster_status"> -+ <ref name="nodes-list" /> -+ <ref name="resources-list" /> -+ <optional> -+ <ref name="node-attributes-list" /> -+ </optional> -+ <optional> -+ <ref name="failures-list" /> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-inject-attr"> -+ <element name="inject_attr"> -+ <attribute name="cib_node"> <text /> </attribute> -+ <attribute name="name"> <text /> </attribute> -+ <attribute name="node_path"> <text /> </attribute> -+ <attribute name="value"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-inject-modify-node"> -+ <element name="modify_node"> -+ <attribute name="action"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-inject-spec"> -+ <element name="inject_spec"> -+ <attribute name="spec"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-inject-modify-ticket"> -+ <element name="modify_ticket"> -+ <attribute name="action"> <text /> </attribute> -+ <attribute name="ticket"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="cluster-injected-actions-list"> -+ <element name="transition"> -+ <zeroOrMore> -+ <ref name="element-injected-actions" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="node-attributes-list"> -+ <element name="node_attributes"> -+ <zeroOrMore> -+ <externalRef href="node-attrs-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="failures-list"> -+ <element name="failures"> -+ <zeroOrMore> -+ <externalRef href="failure-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="nodes-list"> -+ <element name="nodes"> -+ <zeroOrMore> -+ <externalRef href="nodes-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="resources-list"> -+ <element name="resources"> -+ <zeroOrMore> -+ <externalRef href="resources-2.4.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="timings-list"> -+ <element name="timings"> -+ <zeroOrMore> -+ <ref name="element-timing" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="action-list"> -+ <element name="actions"> -+ <zeroOrMore> -+ <ref name="element-node-action" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="element-rsc-action" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-allocation"> -+ <element name="node_weight"> -+ <attribute name="function"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ <externalRef href="../score.rng" /> -+ <optional> -+ <attribute name="id"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-capacity"> -+ <element name="capacity"> -+ <attribute name="comment"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ <zeroOrMore> -+ <element> -+ <anyName /> -+ <text /> -+ </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-inject-cluster-action"> -+ <element name="cluster_action"> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="task"> <text /> </attribute> -+ <optional> -+ <attribute name="id"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-injected-actions"> -+ <choice> -+ <ref name="element-inject-cluster-action" /> -+ <ref name="element-inject-fencing-action" /> -+ <ref name="element-inject-pseudo-action" /> -+ <ref name="element-inject-rsc-action" /> -+ </choice> -+ </define> -+ -+ <define name="element-inject-fencing-action"> -+ <element name="fencing_action"> -+ <attribute name="op"> <text /> </attribute> -+ <attribute name="target"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-node-action"> -+ <element name="node_action"> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="reason"> <text /> </attribute> -+ <attribute name="task"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-promotion"> -+ <element name="promotion_score"> -+ <attribute name="id"> <text /> </attribute> -+ <externalRef href="../score.rng" /> -+ <optional> -+ <attribute name="node"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-inject-pseudo-action"> -+ <element name="pseudo_action"> -+ <attribute name="task"> <text /> </attribute> -+ <optional> -+ <attribute name="node"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-inject-rsc-action"> -+ <element name="rsc_action"> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="op"> <text /> </attribute> -+ <attribute name="resource"> <text /> </attribute> -+ <optional> -+ <attribute name="interval"> <data type="integer" /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-timing"> -+ <element name="timing"> -+ <attribute name="file"> <text /> </attribute> -+ <attribute name="duration"> <data type="double" /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-rsc-action"> -+ <element name="rsc_action"> -+ <attribute name="action"> <text /> </attribute> -+ <attribute name="resource"> <text /> </attribute> -+ <optional> -+ <attribute name="blocked"> <data type="boolean" /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="dest"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="next-role"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="node"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="reason"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="role"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="source"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-utilization"> -+ <element name="utilization"> -+ <attribute name="function"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="resource"> <text /> </attribute> -+ <zeroOrMore> -+ <element> -+ <anyName /> -+ <text /> -+ </element> -+ </zeroOrMore> -+ </element> -+ </define> -+</grammar> --- -1.8.3.1 - - -From c46e07788788acf5669e3f89b9344190a91c7331 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 18 Jun 2021 15:10:19 -0400 -Subject: [PATCH 4/5] Feature: tools: Add the node-summary to crm_simulate - output. - -If --show-failcounts is given to crm_simulate, it should also display -the node-summary message. - -See: rhbz#1686426 ---- - tools/crm_simulate.c | 7 +++++-- - xml/api/crm_simulate-2.12.rng | 3 +++ - 2 files changed, 8 insertions(+), 2 deletions(-) - -diff --git a/tools/crm_simulate.c b/tools/crm_simulate.c -index b4aa9d1..2ea292c 100644 ---- a/tools/crm_simulate.c -+++ b/tools/crm_simulate.c -@@ -409,11 +409,14 @@ print_cluster_status(pe_working_set_t * data_set, unsigned int print_opts) - FALSE, FALSE, all, all, FALSE); - - if (options.show_attrs) { -- out->message(out, "node-attribute-list", data_set, -- 0, rc == pcmk_rc_ok, FALSE, FALSE, FALSE, all, all); -+ rc = out->message(out, "node-attribute-list", data_set, -+ 0, rc == pcmk_rc_ok, FALSE, FALSE, FALSE, all, all); - } - - if (options.show_failcounts) { -+ rc = out->message(out, "node-summary", data_set, all, all, -+ 0, print_opts, FALSE, FALSE, FALSE, FALSE, rc == pcmk_rc_ok); -+ - out->message(out, "failed-action-list", data_set, all, all, - rc == pcmk_rc_ok); - } -diff --git a/xml/api/crm_simulate-2.12.rng b/xml/api/crm_simulate-2.12.rng -index 9a7612d..f90bd36 100644 ---- a/xml/api/crm_simulate-2.12.rng -+++ b/xml/api/crm_simulate-2.12.rng -@@ -67,6 +67,9 @@ - <ref name="node-attributes-list" /> - </optional> - <optional> -+ <externalRef href="node-history-2.12.rng" /> -+ </optional> -+ <optional> - <ref name="failures-list" /> - </optional> - </element> --- -1.8.3.1 - - -From bac50336e0264604716e5997b87ee7e65311b982 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 18 Jun 2021 15:21:52 -0400 -Subject: [PATCH 5/5] Low: libcrmcommon: Increase PCMK__API_VERSION for new - crm_resource output. - -See: rhbz#1686426 ---- - include/crm/common/output_internal.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/include/crm/common/output_internal.h b/include/crm/common/output_internal.h -index 0436cde..ba9c423 100644 ---- a/include/crm/common/output_internal.h -+++ b/include/crm/common/output_internal.h -@@ -27,7 +27,7 @@ extern "C" { - # include <glib.h> - # include <crm/common/results.h> - --# define PCMK__API_VERSION "2.11" -+# define PCMK__API_VERSION "2.12" - - #if defined(PCMK__WITH_ATTRIBUTE_OUTPUT_ARGS) - # define PCMK__OUTPUT_ARGS(ARGS...) __attribute__((output_args(ARGS))) --- -1.8.3.1 - diff --git a/007-unfencing-loop.patch b/007-unfencing-loop.patch deleted file mode 100644 index d4950c8..0000000 --- a/007-unfencing-loop.patch +++ /dev/null @@ -1,733 +0,0 @@ -From 6dcd6b51d7d3993bc483588d6ed75077518ed600 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 4 Jun 2021 16:30:55 -0500 -Subject: [PATCH 01/11] Low: controller: check whether unfenced node was remote - node - -... so the controller can indicate the node is remote (if known at that point, -which is not guaranteed) when setting unfencing-related node attributes. ---- - daemons/controld/controld_fencing.c | 21 ++++++++++++++++++--- - 1 file changed, 18 insertions(+), 3 deletions(-) - -diff --git a/daemons/controld/controld_fencing.c b/daemons/controld/controld_fencing.c -index 23dff28..0fba661 100644 ---- a/daemons/controld/controld_fencing.c -+++ b/daemons/controld/controld_fencing.c -@@ -757,15 +757,30 @@ tengine_stonith_callback(stonith_t *stonith, stonith_callback_data_t *data) - if (pcmk__str_eq("on", op, pcmk__str_casei)) { - const char *value = NULL; - char *now = pcmk__ttoa(time(NULL)); -+ gboolean is_remote_node = FALSE; -+ -+ /* This check is not 100% reliable, since this node is not -+ * guaranteed to have the remote node cached. However, it -+ * doesn't have to be reliable, since the attribute manager can -+ * learn a node's "remoteness" by other means sooner or later. -+ * This allows it to learn more quickly if this node does have -+ * the information. -+ */ -+ if (g_hash_table_lookup(crm_remote_peer_cache, uuid) != NULL) { -+ is_remote_node = TRUE; -+ } - -- update_attrd(target, CRM_ATTR_UNFENCED, now, NULL, FALSE); -+ update_attrd(target, CRM_ATTR_UNFENCED, now, NULL, -+ is_remote_node); - free(now); - - value = crm_meta_value(action->params, XML_OP_ATTR_DIGESTS_ALL); -- update_attrd(target, CRM_ATTR_DIGESTS_ALL, value, NULL, FALSE); -+ update_attrd(target, CRM_ATTR_DIGESTS_ALL, value, NULL, -+ is_remote_node); - - value = crm_meta_value(action->params, XML_OP_ATTR_DIGESTS_SECURE); -- update_attrd(target, CRM_ATTR_DIGESTS_SECURE, value, NULL, FALSE); -+ update_attrd(target, CRM_ATTR_DIGESTS_SECURE, value, NULL, -+ is_remote_node); - - } else if (action->sent_update == FALSE) { - send_stonith_update(action, target, uuid); --- -1.8.3.1 - - -From 3ef6d9403f68ab8559c45cc99f5a8da05ca6420b Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 10:50:36 -0500 -Subject: [PATCH 02/11] Refactor: pacemaker-attrd: functionize adding remote - node to cache - -... for future reuse ---- - daemons/attrd/attrd_commands.c | 34 +++++++++++++++++++++++----------- - 1 file changed, 23 insertions(+), 11 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 731c243..93a165b 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -102,6 +102,28 @@ free_attribute(gpointer data) - } - } - -+/*! -+ * \internal -+ * \brief Ensure a Pacemaker Remote node is in the correct peer cache -+ * -+ * \param[in] -+ */ -+static void -+cache_remote_node(const char *node_name) -+{ -+ /* If we previously assumed this node was an unseen cluster node, -+ * remove its entry from the cluster peer cache. -+ */ -+ crm_node_t *dup = pcmk__search_cluster_node_cache(0, node_name); -+ -+ if (dup && (dup->uuid == NULL)) { -+ reap_crm_member(0, node_name); -+ } -+ -+ // Ensure node is in the remote peer cache -+ CRM_ASSERT(crm_remote_peer_get(node_name) != NULL); -+} -+ - static xmlNode * - build_attribute_xml( - xmlNode *parent, const char *name, const char *set, const char *uuid, unsigned int timeout_ms, const char *user, -@@ -709,17 +731,7 @@ attrd_lookup_or_create_value(GHashTable *values, const char *host, xmlNode *xml) - - crm_element_value_int(xml, PCMK__XA_ATTR_IS_REMOTE, &is_remote); - if (is_remote) { -- /* If we previously assumed this node was an unseen cluster node, -- * remove its entry from the cluster peer cache. -- */ -- crm_node_t *dup = pcmk__search_cluster_node_cache(0, host); -- -- if (dup && (dup->uuid == NULL)) { -- reap_crm_member(0, host); -- } -- -- /* Ensure this host is in the remote peer cache */ -- CRM_ASSERT(crm_remote_peer_get(host) != NULL); -+ cache_remote_node(host); - } - - if (v == NULL) { --- -1.8.3.1 - - -From 6fac2c71bc2c56870ac828d7cd7b7c799279c47e Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 10:39:34 -0500 -Subject: [PATCH 03/11] Refactor: pacemaker-attrd: don't try to remove votes - for remote nodes - -Remote nodes never vote. - -This has no effect in practice since the removal would simply do nothing, -but we might as well not waste time trying. ---- - daemons/attrd/attrd_commands.c | 11 ++++++----- - 1 file changed, 6 insertions(+), 5 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 93a165b..dbe777e 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -976,7 +976,8 @@ attrd_election_cb(gpointer user_data) - void - attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *data) - { -- bool remove_voter = FALSE; -+ bool gone = false; -+ bool is_remote = pcmk_is_set(peer->flags, crm_remote_node); - - switch (kind) { - case crm_status_uname: -@@ -984,7 +985,7 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da - - case crm_status_processes: - if (!pcmk_is_set(peer->processes, crm_get_cluster_proc())) { -- remove_voter = TRUE; -+ gone = true; - } - break; - -@@ -1000,13 +1001,13 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da - } else { - // Remove all attribute values associated with lost nodes - attrd_peer_remove(peer->uname, FALSE, "loss"); -- remove_voter = TRUE; -+ gone = true; - } - break; - } - -- // In case an election is in progress, remove any vote by the node -- if (remove_voter) { -+ // Remove votes from cluster nodes that leave, in case election in progress -+ if (gone && !is_remote) { - attrd_remove_voter(peer); - } - } --- -1.8.3.1 - - -From 54089fc663d6aaf10ca164c6c94b3b17237788de Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 10:40:06 -0500 -Subject: [PATCH 04/11] Low: pacemaker-attrd: check for remote nodes in peer - update callback - -If a remote node was started before the local cluster node joined the cluster, -the cluster node will assume its node attributes are for a cluster node until -it learns otherwise. Check for remoteness in the peer update callback, to have -another way we can learn it. ---- - daemons/attrd/attrd_commands.c | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index dbe777e..5f6a754 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -1009,6 +1009,10 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da - // Remove votes from cluster nodes that leave, in case election in progress - if (gone && !is_remote) { - attrd_remove_voter(peer); -+ -+ // Ensure remote nodes that come up are in the remote node cache -+ } else if (!gone && is_remote) { -+ cache_remote_node(peer->uname); - } - } - --- -1.8.3.1 - - -From 8c048df0312d0d9c857d87b570a352429a710928 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 11:29:12 -0500 -Subject: [PATCH 05/11] Log: pacemaker-attrd: log peer status changes - ---- - daemons/attrd/attrd_commands.c | 9 +++++++++ - 1 file changed, 9 insertions(+) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 5f6a754..d6d179b 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -972,6 +972,7 @@ attrd_election_cb(gpointer user_data) - return FALSE; - } - -+#define state_text(state) ((state)? (const char *)(state) : "in unknown state") - - void - attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *data) -@@ -981,15 +982,23 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da - - switch (kind) { - case crm_status_uname: -+ crm_debug("%s node %s is now %s", -+ (is_remote? "Remote" : "Cluster"), -+ peer->uname, state_text(peer->state)); - break; - - case crm_status_processes: - if (!pcmk_is_set(peer->processes, crm_get_cluster_proc())) { - gone = true; - } -+ crm_debug("Node %s is %s a peer", -+ peer->uname, (gone? "no longer" : "now")); - break; - - case crm_status_nstate: -+ crm_debug("%s node %s is now %s (was %s)", -+ (is_remote? "Remote" : "Cluster"), -+ peer->uname, state_text(peer->state), state_text(data)); - if (pcmk__str_eq(peer->state, CRM_NODE_MEMBER, pcmk__str_casei)) { - /* If we're the writer, send new peers a list of all attributes - * (unless it's a remote node, which doesn't run its own attrd) --- -1.8.3.1 - - -From 1dcc8dee4990cf0dbdec0e14db6d9a3ad67a41d5 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 11:13:53 -0500 -Subject: [PATCH 06/11] Low: pacemaker-attrd: ensure node ID is only set for - attributes when known - -In most cases, attribute updates contained the node ID, and the node ID was -used by other code, only if known (i.e. positive). However a couple places did -not check this, so add that. - -I am unsure whether the missing check caused problems in practice, but there -appears to be the possibility that a remote node would wrongly be added to the -cluster node cache. ---- - daemons/attrd/attrd_commands.c | 6 ++++-- - 1 file changed, 4 insertions(+), 2 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index d6d179b..b3f441c 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -136,7 +136,9 @@ build_attribute_xml( - crm_xml_add(xml, PCMK__XA_ATTR_UUID, uuid); - crm_xml_add(xml, PCMK__XA_ATTR_USER, user); - crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, peer); -- crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); -+ if (peerid > 0) { -+ crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); -+ } - crm_xml_add(xml, PCMK__XA_ATTR_VALUE, value); - crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, timeout_ms/1000); - crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, is_private); -@@ -937,7 +939,7 @@ attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) - /* If this is a cluster node whose node ID we are learning, remember it */ - if ((v->nodeid == 0) && (v->is_remote == FALSE) - && (crm_element_value_int(xml, PCMK__XA_ATTR_NODE_ID, -- (int*)&v->nodeid) == 0)) { -+ (int*)&v->nodeid) == 0) && (v->nodeid > 0)) { - - crm_node_t *known_peer = crm_get_peer(v->nodeid, host); - --- -1.8.3.1 - - -From 8d12490e88b558d01db37a38f7d35175c6d2d69a Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Thu, 10 Jun 2021 17:25:57 -0500 -Subject: [PATCH 07/11] Refactor: pacemaker-attrd: functionize processing a - sync response - -... for code isolation, and because we need to add more to it ---- - daemons/attrd/attrd_commands.c | 59 ++++++++++++++++++++++++++++-------------- - 1 file changed, 39 insertions(+), 20 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index b3f441c..d02d3e6 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -572,6 +572,43 @@ attrd_peer_clear_failure(crm_node_t *peer, xmlNode *xml) - } - - /*! -+ * \internal -+ * \brief Load attributes from a peer sync response -+ * -+ * \param[in] peer Peer that sent clear request -+ * \param[in] peer_won Whether peer is the attribute writer -+ * \param[in] xml Request XML -+ */ -+static void -+process_peer_sync_response(crm_node_t *peer, bool peer_won, xmlNode *xml) -+{ -+ crm_info("Processing " PCMK__ATTRD_CMD_SYNC_RESPONSE " from %s", -+ peer->uname); -+ -+ if (peer_won) { -+ /* Initialize the "seen" flag for all attributes to cleared, so we can -+ * detect attributes that local node has but the writer doesn't. -+ */ -+ clear_attribute_value_seen(); -+ } -+ -+ // Process each attribute update in the sync response -+ for (xmlNode *child = pcmk__xml_first_child(xml); child != NULL; -+ child = pcmk__xml_next(child)) { -+ attrd_peer_update(peer, child, -+ crm_element_value(child, PCMK__XA_ATTR_NODE_NAME), -+ TRUE); -+ } -+ -+ if (peer_won) { -+ /* If any attributes are still not marked as seen, the writer doesn't -+ * know about them, so send all peers an update with them. -+ */ -+ attrd_current_only_attribute_update(peer, xml); -+ } -+} -+ -+/*! - \internal - \brief Broadcast private attribute for local node with protocol version - */ -@@ -596,7 +633,7 @@ attrd_peer_message(crm_node_t *peer, xmlNode *xml) - const char *op = crm_element_value(xml, PCMK__XA_TASK); - const char *election_op = crm_element_value(xml, F_CRM_TASK); - const char *host = crm_element_value(xml, PCMK__XA_ATTR_NODE_NAME); -- bool peer_won = FALSE; -+ bool peer_won = false; - - if (election_op) { - attrd_handle_election_op(peer, xml); -@@ -631,25 +668,7 @@ attrd_peer_message(crm_node_t *peer, xmlNode *xml) - - } else if (pcmk__str_eq(op, PCMK__ATTRD_CMD_SYNC_RESPONSE, pcmk__str_casei) - && !pcmk__str_eq(peer->uname, attrd_cluster->uname, pcmk__str_casei)) { -- xmlNode *child = NULL; -- -- crm_info("Processing %s from %s", op, peer->uname); -- -- /* Clear the seen flag for attribute processing held only in the own node. */ -- if (peer_won) { -- clear_attribute_value_seen(); -- } -- -- for (child = pcmk__xml_first_child(xml); child != NULL; -- child = pcmk__xml_next(child)) { -- host = crm_element_value(child, PCMK__XA_ATTR_NODE_NAME); -- attrd_peer_update(peer, child, host, TRUE); -- } -- -- if (peer_won) { -- /* Synchronize if there is an attribute held only by own node that Writer does not have. */ -- attrd_current_only_attribute_update(peer, xml); -- } -+ process_peer_sync_response(peer, peer_won, xml); - - } else if (pcmk__str_eq(op, PCMK__ATTRD_CMD_FLUSH, pcmk__str_casei)) { - /* Ignore. The flush command was removed in 2.0.0 but may be --- -1.8.3.1 - - -From a890a0e5bbbcabf907f51ed0460868035f72464d Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 11 Jun 2021 14:40:39 -0500 -Subject: [PATCH 08/11] Refactor: pacemaker-attrd: functionize broadcasting - local override - -... for code isolation ---- - daemons/attrd/attrd_commands.c | 42 +++++++++++++++++++++++++++++------------- - 1 file changed, 29 insertions(+), 13 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index d02d3e6..4783427 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -804,6 +804,34 @@ attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml) - free_xml(sync); - } - -+/*! -+ * \internal -+ * \brief Override an attribute sync with a local value -+ * -+ * Broadcast the local node's value for an attribute that's different from the -+ * value provided in a peer's attribute synchronization response. This ensures a -+ * node's values for itself take precedence and all peers are kept in sync. -+ * -+ * \param[in] a Attribute entry to override -+ * -+ * \return Local instance of attribute value -+ */ -+static attribute_value_t * -+broadcast_local_value(attribute_t *a) -+{ -+ attribute_value_t *v = g_hash_table_lookup(a->values, attrd_cluster->uname); -+ xmlNode *sync = create_xml_node(NULL, __func__); -+ -+ crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -+ build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, -+ a->user, a->is_private, v->nodename, v->nodeid, -+ v->current, FALSE); -+ attrd_xml_add_writer(sync); -+ send_attrd_message(NULL, sync); -+ free_xml(sync); -+ return v; -+} -+ - void - attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) - { -@@ -899,21 +927,9 @@ attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) - if (filter && !pcmk__str_eq(v->current, value, pcmk__str_casei) - && pcmk__str_eq(host, attrd_cluster->uname, pcmk__str_casei)) { - -- xmlNode *sync = create_xml_node(NULL, __func__); -- - crm_notice("%s[%s]: local value '%s' takes priority over '%s' from %s", - attr, host, v->current, value, peer->uname); -- -- crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -- v = g_hash_table_lookup(a->values, host); -- build_attribute_xml(sync, attr, a->set, a->uuid, a->timeout_ms, a->user, -- a->is_private, v->nodename, v->nodeid, v->current, FALSE); -- -- attrd_xml_add_writer(sync); -- -- /* Broadcast in case any other nodes had the inconsistent value */ -- send_attrd_message(NULL, sync); -- free_xml(sync); -+ v = broadcast_local_value(a); - - } else if (!pcmk__str_eq(v->current, value, pcmk__str_casei)) { - crm_notice("Setting %s[%s]: %s -> %s " CRM_XS " from %s", --- -1.8.3.1 - - -From f6f65e3dab070f1bbdf6d1383f4d6173a8840bc9 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 11 Jun 2021 14:50:29 -0500 -Subject: [PATCH 09/11] Log: pacemaker-attrd: improve messages when - broadcasting local-only values - -The traces aren't necessary since build_attribute_xml() already logs the same -info at debug. Also, rename function for clarity, and make static. ---- - daemons/attrd/attrd_commands.c | 35 ++++++++++++++++------------------- - 1 file changed, 16 insertions(+), 19 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 4783427..356defb 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -51,11 +51,12 @@ GHashTable *attributes = NULL; - - void write_attribute(attribute_t *a, bool ignore_delay); - void write_or_elect_attribute(attribute_t *a); --void attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml); - void attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter); - void attrd_peer_sync(crm_node_t *peer, xmlNode *xml); - void attrd_peer_remove(const char *host, gboolean uncache, const char *source); - -+static void broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml); -+ - static gboolean - send_attrd_message(crm_node_t * node, xmlNode * data) - { -@@ -604,7 +605,7 @@ process_peer_sync_response(crm_node_t *peer, bool peer_won, xmlNode *xml) - /* If any attributes are still not marked as seen, the writer doesn't - * know about them, so send all peers an update with them. - */ -- attrd_current_only_attribute_update(peer, xml); -+ broadcast_unseen_local_values(peer, xml); - } - } - -@@ -768,40 +769,36 @@ attrd_lookup_or_create_value(GHashTable *values, const char *host, xmlNode *xml) - return(v); - } - --void --attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml) -+void -+broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml) - { - GHashTableIter aIter; - GHashTableIter vIter; -- attribute_t *a; -+ attribute_t *a = NULL; - attribute_value_t *v = NULL; -- xmlNode *sync = create_xml_node(NULL, __func__); -- gboolean build = FALSE; -- -- crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -+ xmlNode *sync = NULL; - - g_hash_table_iter_init(&aIter, attributes); - while (g_hash_table_iter_next(&aIter, NULL, (gpointer *) & a)) { - g_hash_table_iter_init(&vIter, a->values); - while (g_hash_table_iter_next(&vIter, NULL, (gpointer *) & v)) { -- if (pcmk__str_eq(v->nodename, attrd_cluster->uname, pcmk__str_casei) && v->seen == FALSE) { -- crm_trace("Syncing %s[%s] = %s to everyone.(from local only attributes)", a->id, v->nodename, v->current); -- -- build = TRUE; -+ if (!(v->seen) && pcmk__str_eq(v->nodename, attrd_cluster->uname, -+ pcmk__str_casei)) { -+ if (sync == NULL) { -+ sync = create_xml_node(NULL, __func__); -+ crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -+ } - build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, - v->nodename, v->nodeid, v->current, (a->timeout_ms && a->timer ? TRUE : FALSE)); -- } else { -- crm_trace("Local attribute(%s[%s] = %s) was ignore.(another host) : [%s]", a->id, v->nodename, v->current, attrd_cluster->uname); -- continue; - } - } - } - -- if (build) { -- crm_debug("Syncing values to everyone.(from local only attributes)"); -+ if (sync != NULL) { -+ crm_debug("Broadcasting local-only values"); - send_attrd_message(NULL, sync); -+ free_xml(sync); - } -- free_xml(sync); - } - - /*! --- -1.8.3.1 - - -From ab90ffb785ea018556f216b8f540f8c3429a3947 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 11 Jun 2021 15:04:20 -0500 -Subject: [PATCH 10/11] Refactor: pacemaker-attrd: simplify attribute XML - creation function - -... and rename for clarity ---- - daemons/attrd/attrd_commands.c | 48 ++++++++++++++++++++++++------------------ - 1 file changed, 27 insertions(+), 21 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 356defb..5b32a77 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -125,25 +125,35 @@ cache_remote_node(const char *node_name) - CRM_ASSERT(crm_remote_peer_get(node_name) != NULL); - } - -+/*! -+ * \internal -+ * \brief Create an XML representation of an attribute for use in peer messages -+ * -+ * \param[in] parent Create attribute XML as child element of this element -+ * \param[in] a Attribute to represent -+ * \param[in] v Attribute value to represent -+ * \param[in] force_write If true, value should be written even if unchanged -+ * -+ * \return XML representation of attribute -+ */ - static xmlNode * --build_attribute_xml( -- xmlNode *parent, const char *name, const char *set, const char *uuid, unsigned int timeout_ms, const char *user, -- gboolean is_private, const char *peer, uint32_t peerid, const char *value, gboolean is_force_write) -+add_attribute_value_xml(xmlNode *parent, attribute_t *a, attribute_value_t *v, -+ bool force_write) - { - xmlNode *xml = create_xml_node(parent, __func__); - -- crm_xml_add(xml, PCMK__XA_ATTR_NAME, name); -- crm_xml_add(xml, PCMK__XA_ATTR_SET, set); -- crm_xml_add(xml, PCMK__XA_ATTR_UUID, uuid); -- crm_xml_add(xml, PCMK__XA_ATTR_USER, user); -- crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, peer); -- if (peerid > 0) { -- crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); -+ crm_xml_add(xml, PCMK__XA_ATTR_NAME, a->id); -+ crm_xml_add(xml, PCMK__XA_ATTR_SET, a->set); -+ crm_xml_add(xml, PCMK__XA_ATTR_UUID, a->uuid); -+ crm_xml_add(xml, PCMK__XA_ATTR_USER, a->user); -+ crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, v->nodename); -+ if (v->nodeid > 0) { -+ crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, v->nodeid); - } -- crm_xml_add(xml, PCMK__XA_ATTR_VALUE, value); -- crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, timeout_ms/1000); -- crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, is_private); -- crm_xml_add_int(xml, PCMK__XA_ATTR_FORCE, is_force_write); -+ crm_xml_add(xml, PCMK__XA_ATTR_VALUE, v->current); -+ crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, a->timeout_ms / 1000); -+ crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, a->is_private); -+ crm_xml_add_int(xml, PCMK__XA_ATTR_FORCE, force_write); - - return xml; - } -@@ -695,8 +705,7 @@ attrd_peer_sync(crm_node_t *peer, xmlNode *xml) - g_hash_table_iter_init(&vIter, a->values); - while (g_hash_table_iter_next(&vIter, NULL, (gpointer *) & v)) { - crm_debug("Syncing %s[%s] = %s to %s", a->id, v->nodename, v->current, peer?peer->uname:"everyone"); -- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, -- v->nodename, v->nodeid, v->current, FALSE); -+ add_attribute_value_xml(sync, a, v, false); - } - } - -@@ -788,8 +797,7 @@ broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml) - sync = create_xml_node(NULL, __func__); - crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); - } -- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, -- v->nodename, v->nodeid, v->current, (a->timeout_ms && a->timer ? TRUE : FALSE)); -+ add_attribute_value_xml(sync, a, v, a->timeout_ms && a->timer); - } - } - } -@@ -820,9 +828,7 @@ broadcast_local_value(attribute_t *a) - xmlNode *sync = create_xml_node(NULL, __func__); - - crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, -- a->user, a->is_private, v->nodename, v->nodeid, -- v->current, FALSE); -+ add_attribute_value_xml(sync, a, v, false); - attrd_xml_add_writer(sync); - send_attrd_message(NULL, sync); - free_xml(sync); --- -1.8.3.1 - - -From 540d74130c5c8d9c626d6c50475e4dc4f64234e7 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 4 Jun 2021 16:34:26 -0500 -Subject: [PATCH 11/11] Fix: pacemaker-attrd: avoid repeated unfencing of - remote nodes - -The attribute manager can't record a remote node's attributes to the CIB until -it knows the node is remote. Normally, this is learned when the remote node -starts, because the controller clears the CRM_OP_PROBED attribute and indicates -that it is for a remote node. - -However, if a cluster node is down when a remote node starts, and later comes -up, it learns the remote node's existing attributes as part of the attribute -sync. Previously, this did not include whether each value is for a cluster or -remote node, so the newly joined attribute manager couldn't write out remote -nodes' attributes until it learned that via some other event -- which might not -happen before the node becomes DC, in which case its scheduler will not see any -unfencing-related node attributes and may wrongly schedule unfencing. - -The sync response handling already calls attrd_lookup_or_create_value(), which -checks PCMK__XA_ATTR_IS_REMOTE, so all we need to do is add that to the sync -response. ---- - daemons/attrd/attrd_commands.c | 6 +++++- - 1 file changed, 5 insertions(+), 1 deletion(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 5b32a77..0142383 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -43,8 +43,9 @@ - * 1 1.1.15 PCMK__ATTRD_CMD_UPDATE_BOTH, - * PCMK__ATTRD_CMD_UPDATE_DELAY - * 2 1.1.17 PCMK__ATTRD_CMD_CLEAR_FAILURE -+ * 3 2.1.1 PCMK__ATTRD_CMD_SYNC_RESPONSE indicates remote nodes - */ --#define ATTRD_PROTOCOL_VERSION "2" -+#define ATTRD_PROTOCOL_VERSION "3" - - int last_cib_op_done = 0; - GHashTable *attributes = NULL; -@@ -150,6 +151,9 @@ add_attribute_value_xml(xmlNode *parent, attribute_t *a, attribute_value_t *v, - if (v->nodeid > 0) { - crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, v->nodeid); - } -+ if (v->is_remote != 0) { -+ crm_xml_add_int(xml, PCMK__XA_ATTR_IS_REMOTE, 1); -+ } - crm_xml_add(xml, PCMK__XA_ATTR_VALUE, v->current); - crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, a->timeout_ms / 1000); - crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, a->is_private); --- -1.8.3.1 - diff --git a/pacemaker.spec b/pacemaker.spec index a2a1dfb..b3f962b 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -31,11 +31,11 @@ ## Upstream pacemaker version, and its package version (specversion ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) -%global pcmkversion 2.1.0 -%global specversion 6 +%global pcmkversion 2.1.1 +%global specversion 0.1.rc1 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build -%global commit 7c3f660707a495a1331716ad32cd3ac9d9f8ff58 +%global commit 9e3a841a33c3125034922ec061f6516d307f20d1 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. @@ -80,7 +80,7 @@ ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) -%bcond_with pre_release +%bcond_without pre_release ## NOTE: skip --with upstart_job @@ -201,7 +201,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org/ @@ -217,13 +217,6 @@ Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{arch Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... # upstream commits -Patch1: 001-ping-agent.patch -Patch2: 002-pacemakerd-options.patch -Patch3: 003-pacemakerd-output.patch -Patch4: 004-check-level.patch -Patch5: 005-crm_resource.patch -Patch6: 006-crm_simulate.patch -Patch7: 007-unfencing-loop.patch Requires: resource-agents Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} @@ -806,6 +799,11 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Wed Jul 28 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.1.rc1 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc1, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc1 + * Thu Jul 22 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 2.1.0-6.1 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild diff --git a/sources b/sources index 2ab7f32..b933127 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-7c3f66070.tar.gz) = e1c53d019c965395affc1bd78358927617c9bc8572c405ee884737a8213455c5e85102e6f58bb5239ab23ebe5aa794f72c9cc0746900b7a6cc14fd3cf1879064 +SHA512 (pacemaker-9e3a841a3.tar.gz) = 26745ba0d9f6730de13ad106fe57beaff9d49c7df1ec528f0689c2faa872608408fb04401a4d49d73deec5422bd7665496a964b1fcbe69866a5983ac2306b6be commit 084488a3ae7b0d9112cb80ef1f9b0f7064fbcd72 Author: Fedora Release Engineering <releng(a)fedoraproject.org> Date: Thu Jul 22 17:33:56 2021 +0000 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering <releng(a)fedoraproject.org> diff --git a/pacemaker.spec b/pacemaker.spec index 48b6a44..a2a1dfb 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -201,7 +201,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist} +Release: %{pcmk_release}%{?dist}.1 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org/ @@ -806,6 +806,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Thu Jul 22 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 2.1.0-6.1 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Mon Jul 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-6 - synced/merged with CS9 spec-file for current 2.1.0-release build commit 15ac1a3c342218687bbddb1cdb2fc0edc968d5ac Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Jul 5 18:38:43 2021 +0200 * Mon Jul 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-6 - synced/merged with CS9 spec-file for current 2.1.0-release build * Tue Jun 8 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.5.rc3 - silence f33 s390x build complaining about possible format-trucation diff --git a/001-ping-agent.patch b/001-ping-agent.patch new file mode 100644 index 0000000..89fe41a --- /dev/null +++ b/001-ping-agent.patch @@ -0,0 +1,225 @@ +From c6ee0973522268ed7b3241cf0ec2e06398444114 Mon Sep 17 00:00:00 2001 +From: Grace Chin <gchin(a)redhat.com> +Date: Tue, 4 May 2021 12:02:17 -0400 +Subject: [PATCH 1/4] Remove deprecated attrd_options + +--- + extra/resources/ping | 11 +++-------- + 1 file changed, 3 insertions(+), 8 deletions(-) + +diff --git a/extra/resources/ping b/extra/resources/ping +index 3cf8dfe..2e93f22 100755 +--- a/extra/resources/ping ++++ b/extra/resources/ping +@@ -178,7 +178,7 @@ ping_stop() { + + rm -f "${OCF_RESKEY_pidfile}" + +- attrd_updater -D -n "$OCF_RESKEY_name" -d "$OCF_RESKEY_dampen" $attrd_options ++ attrd_updater -D -n "$OCF_RESKEY_name" -d "$OCF_RESKEY_dampen" + + return $OCF_SUCCESS + } +@@ -302,9 +302,9 @@ ping_update() { + + score=$(expr $active \* $OCF_RESKEY_multiplier) + if [ "$__OCF_ACTION" = "start" ] ; then +- attrd_updater -n "$OCF_RESKEY_name" -B "$score" -d "$OCF_RESKEY_dampen" $attrd_options ++ attrd_updater -n "$OCF_RESKEY_name" -B "$score" -d "$OCF_RESKEY_dampen" + else +- attrd_updater -n "$OCF_RESKEY_name" -v "$score" -d "$OCF_RESKEY_dampen" $attrd_options ++ attrd_updater -n "$OCF_RESKEY_name" -v "$score" -d "$OCF_RESKEY_dampen" + fi + rc=$? + case $rc in +@@ -396,11 +396,6 @@ case "${OCF_RESKEY_debug}" in + ;; + esac + +-attrd_options='-q' +-if [ "${OCF_RESKEY_debug}" = "true" ]; then +- attrd_options='' +-fi +- + case "$__OCF_ACTION" in + meta-data) meta_data + exit $OCF_SUCCESS +-- +1.8.3.1 + + +From 6d6c4691cf0970059689856c354daf9e098b4451 Mon Sep 17 00:00:00 2001 +From: Grace Chin <gchin(a)redhat.com> +Date: Tue, 4 May 2021 14:50:37 -0400 +Subject: [PATCH 2/4] Replace debug values, true and false, with 0 and 1 + +--- + extra/resources/ping | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/extra/resources/ping b/extra/resources/ping +index 2e93f22..fee019b 100755 +--- a/extra/resources/ping ++++ b/extra/resources/ping +@@ -24,7 +24,7 @@ + : ${OCF_RESKEY_dampen:="5s"} + : ${OCF_RESKEY_attempts:="3"} + : ${OCF_RESKEY_multiplier:="1"} +-: ${OCF_RESKEY_debug:="false"} ++: ${OCF_RESKEY_debug:="0"} + : ${OCF_RESKEY_failure_score:="0"} + : ${OCF_RESKEY_use_fping:="1"} + : ${OCF_RESKEY_host_list:=""} +@@ -152,7 +152,7 @@ END + + ping_conditional_log() { + level="$1"; shift +- if [ "${OCF_RESKEY_debug}" = "true" ]; then ++ if [ $OCF_RESKEY_debug -gt 0 ]; then + ocf_log "$level" "$*" + fi + } +@@ -388,8 +388,8 @@ fi + + # Check the debug option + case "${OCF_RESKEY_debug}" in +- true|True|TRUE|1) OCF_RESKEY_debug=true;; +- false|False|FALSE|0) OCF_RESKEY_debug=false;; ++ true|True|TRUE|1) OCF_RESKEY_debug=0;; ++ false|False|FALSE|0) OCF_RESKEY_debug=1;; + *) + ocf_log warn "Value for 'debug' is incorrect. Please specify 'true' or 'false' not: ${OCF_RESKEY_debug}" + OCF_RESKEY_debug=false +-- +1.8.3.1 + + +From a886a31056b6aca764c6911f5432af2c5ebf51df Mon Sep 17 00:00:00 2001 +From: Grace Chin <gchin(a)redhat.com> +Date: Tue, 11 May 2021 11:04:50 -0400 +Subject: [PATCH 3/4] Add verbose debug mode which logs ping and fping output + when set + +--- + extra/resources/ping | 19 ++++++++++++++----- + 1 file changed, 14 insertions(+), 5 deletions(-) + +diff --git a/extra/resources/ping b/extra/resources/ping +index fee019b..cc796af 100755 +--- a/extra/resources/ping ++++ b/extra/resources/ping +@@ -249,10 +249,13 @@ fping_check() { + + case $rc in + 0) ++ if [ $OCF_RESKEY_debug -gt 1 ]; then ++ ping_conditional_log info "$output" ++ fi + ;; + 1) + for h in $(echo "$output" | grep "is unreachable" | awk '{print $1}'); do +- ping_conditional_log warn "$h is inactive" ++ ping_conditional_log warn "$h is inactive: $output" + done + ;; + *) +@@ -282,7 +285,12 @@ ping_check() { + p_out=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? + + case $rc in +- 0) active=$(expr $active + 1);; ++ 0) ++ active=$(expr $active + 1) ++ if [ $OCF_RESKEY_debug -gt 1 ]; then ++ ping_conditional_log info "$p_out" ++ fi ++ ;; + 1) ping_conditional_log warn "$host is inactive: $p_out";; + *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $p_out";; + esac +@@ -388,10 +396,11 @@ fi + + # Check the debug option + case "${OCF_RESKEY_debug}" in +- true|True|TRUE|1) OCF_RESKEY_debug=0;; +- false|False|FALSE|0) OCF_RESKEY_debug=1;; ++ true|True|TRUE|1) OCF_RESKEY_debug=1;; ++ false|False|FALSE|0) OCF_RESKEY_debug=0;; ++ verbose|Verbose|VERBOSE|2) OCF_RESKEY_debug=2;; + *) +- ocf_log warn "Value for 'debug' is incorrect. Please specify 'true' or 'false' not: ${OCF_RESKEY_debug}" ++ ocf_log warn "Value for 'debug' is incorrect. Please specify 'true', 'false', or 'verbose', not: ${OCF_RESKEY_debug}" + OCF_RESKEY_debug=false + ;; + esac +-- +1.8.3.1 + + +From 460043f133ced80e923b1290af70502a72deb7f8 Mon Sep 17 00:00:00 2001 +From: Grace Chin <gchin(a)redhat.com> +Date: Tue, 11 May 2021 11:07:05 -0400 +Subject: [PATCH 4/4] Improve variable names + +--- + extra/resources/ping | 20 ++++++++++---------- + 1 file changed, 10 insertions(+), 10 deletions(-) + +diff --git a/extra/resources/ping b/extra/resources/ping +index cc796af..9763b60 100755 +--- a/extra/resources/ping ++++ b/extra/resources/ping +@@ -244,22 +244,22 @@ fping_check() { + timeout=$(expr $OCF_RESKEY_timeout \* 1000 / $OCF_RESKEY_attempts) + + cmd="$p_exe -r $OCF_RESKEY_attempts -t $timeout -B 1.0 $OCF_RESKEY_options $OCF_RESKEY_host_list" +- output=$($cmd 2>&1); rc=$? +- active=$(echo "$output" | grep "is alive" | wc -l) ++ fping_output=$($cmd 2>&1); rc=$? ++ active=$(echo "$fping_output" | grep "is alive" | wc -l) + + case $rc in + 0) + if [ $OCF_RESKEY_debug -gt 1 ]; then +- ping_conditional_log info "$output" ++ ping_conditional_log info "$fping_output" + fi + ;; + 1) +- for h in $(echo "$output" | grep "is unreachable" | awk '{print $1}'); do +- ping_conditional_log warn "$h is inactive: $output" ++ for h in $(echo "$fping_output" | grep "is unreachable" | awk '{print $1}'); do ++ ping_conditional_log warn "$h is inactive: $fping_output" + done + ;; + *) +- ocf_log err "Unexpected result for '$cmd' $rc: $(echo "$output" | tr '\n' ';')" ++ ocf_log err "Unexpected result for '$cmd' $rc: $(echo "$fping_output" | tr '\n' ';')" + ;; + esac + +@@ -282,17 +282,17 @@ ping_check() { + *:*) p_exe=ping6 + esac + +- p_out=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? ++ ping_output=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? + + case $rc in + 0) + active=$(expr $active + 1) + if [ $OCF_RESKEY_debug -gt 1 ]; then +- ping_conditional_log info "$p_out" ++ ping_conditional_log info "$ping_output" + fi + ;; +- 1) ping_conditional_log warn "$host is inactive: $p_out";; +- *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $p_out";; ++ 1) ping_conditional_log warn "$host is inactive: $ping_output";; ++ *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $ping_output";; + esac + done + return $active +-- +1.8.3.1 + diff --git a/002-pacemakerd-options.patch b/002-pacemakerd-options.patch new file mode 100644 index 0000000..56941ec --- /dev/null +++ b/002-pacemakerd-options.patch @@ -0,0 +1,451 @@ +From 0d40ebf10b1794ece2c5c9768ea7222d3834d3b3 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 13 May 2021 11:42:18 -0400 +Subject: [PATCH 1/4] Build: Use a different variable to find man page + includes. + +With other programs outside of the tools directory being converted to +use glib for command line handling, their includes are not going to be +in tools/. So we need to use a different autoconf variable to find +them. +--- + mk/common.mk | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/mk/common.mk b/mk/common.mk +index b247670..aa59feb 100644 +--- a/mk/common.mk ++++ b/mk/common.mk +@@ -1,5 +1,5 @@ + # +-# Copyright 2014-2020 the Pacemaker project contributors ++# Copyright 2014-2021 the Pacemaker project contributors + # + # The version control history for this file may have further details. + # +@@ -68,11 +68,11 @@ HELP2MAN_ARGS = -N --section 8 --name "Part of the Pacemaker cluster resource ma + # and all wrappers to C code. + %.8: % $(MAN8DEPS) + $(AM_V_at)chmod a+x $(abs_builddir)/$< +- $(AM_V_MAN)if [ -f $(top_srcdir)/tools/$@.inc ]; then \ ++ $(AM_V_MAN)if [ -f $(abs_srcdir)/$@.inc ]; then \ + PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ + -h --help-all \ + --no-discard-stderr \ +- -i $(top_srcdir)/tools/$@.inc $(abs_builddir)/$< \ ++ -i $(abs_srcdir)/$@.inc $(abs_builddir)/$< \ + | sed -f $(top_srcdir)/tools/fix-manpages > $@ ; \ + else \ + PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ +-- +1.8.3.1 + + +From c7ab1d901bcbbf0137277e783e072777ca2f82d9 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 13 May 2021 11:44:16 -0400 +Subject: [PATCH 2/4] Refactor: daemons: Remove the pid_file variable from + pacemakerd. + +It's never used anywhere. +--- + daemons/pacemakerd/pacemakerd.c | 3 --- + 1 file changed, 3 deletions(-) + +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index 8ec9708..03d688e 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -27,8 +27,7 @@ + + static crm_trigger_t *shutdown_trigger = NULL; + static crm_trigger_t *startup_trigger = NULL; +-static const char *pid_file = PCMK_RUN_DIR "/pacemaker.pid"; + + /* state we report when asked via pacemakerd-api status-ping */ + static const char *pacemakerd_state = XML_PING_ATTR_PACEMAKERDSTATE_INIT; + static gboolean running_with_sbd = FALSE; /* local copy */ +@@ -224,7 +222,6 @@ main(int argc, char **argv) + /* Legacy */ + break; + case 'p': +- pid_file = optarg; + break; + case 's': + pcmk__set_env_option("node_start_state", "standby"); +-- +1.8.3.1 + + +From 98990eed9f6a5dbde7c8a5aa0783e93d5479295b Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 13 May 2021 13:14:38 -0400 +Subject: [PATCH 3/4] Refactor: daemons: Use glib for command line handling in + pacemakerd. + +--- + daemons/pacemakerd/Makefile.am | 2 + + daemons/pacemakerd/pacemakerd.8.inc | 5 + + daemons/pacemakerd/pacemakerd.c | 195 ++++++++++++++++++------------------ + 3 files changed, 102 insertions(+), 100 deletions(-) + create mode 100644 daemons/pacemakerd/pacemakerd.8.inc + +diff --git a/daemons/pacemakerd/Makefile.am b/daemons/pacemakerd/Makefile.am +index cc657f5..84517a3 100644 +--- a/daemons/pacemakerd/Makefile.am ++++ b/daemons/pacemakerd/Makefile.am +@@ -15,6 +15,8 @@ if BUILD_SYSTEMD + systemdsystemunit_DATA = pacemaker.service + endif + ++EXTRA_DIST = pacemakerd.8.inc ++ + ## SOURCES + + noinst_HEADERS = pacemakerd.h +diff --git a/daemons/pacemakerd/pacemakerd.8.inc b/daemons/pacemakerd/pacemakerd.8.inc +new file mode 100644 +index 0000000..902af4e +--- /dev/null ++++ b/daemons/pacemakerd/pacemakerd.8.inc +@@ -0,0 +1,5 @@ ++[synopsis] ++pacemakerd [options] ++ ++/subsidiary Pacemaker daemons/ ++.SH OPTIONS +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index 03d688e..ce194bf 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -23,12 +23,54 @@ + #include <crm/msg_xml.h> + #include <crm/common/ipc_internal.h> + #include <crm/common/mainloop.h> ++#include <crm/common/cmdline_internal.h> + #include <crm/cluster/internal.h> + #include <crm/cluster.h> + + #include <dirent.h> + #include <ctype.h> + ++#define SUMMARY "pacemakerd - primary Pacemaker daemon that launches and monitors all subsidiary Pacemaker daemons" ++ ++struct { ++ gboolean features; ++ gboolean foreground; ++ gboolean shutdown; ++ gboolean standby; ++} options; ++ ++static gboolean ++pid_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { ++ return TRUE; ++} ++ ++static gboolean ++standby_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { ++ options.standby = TRUE; ++ pcmk__set_env_option("node_start_state", "standby"); ++ return TRUE; ++} ++ ++static GOptionEntry entries[] = { ++ { "features", 'F', 0, G_OPTION_ARG_NONE, &options.features, ++ "Display full version and list of features Pacemaker was built with", ++ NULL }, ++ { "foreground", 'f', 0, G_OPTION_ARG_NONE, &options.foreground, ++ "(Ignored) Pacemaker always runs in the foreground", ++ NULL }, ++ { "pid-file", 'p', 0, G_OPTION_ARG_CALLBACK, pid_cb, ++ "(Ignored) Daemon pid file location", ++ "FILE" }, ++ { "shutdown", 'S', 0, G_OPTION_ARG_NONE, &options.shutdown, ++ "Instruct Pacemaker to shutdown on this machine", ++ NULL }, ++ { "standby", 's', G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, standby_cb, ++ "Start node in standby state", ++ NULL }, ++ ++ { NULL } ++}; ++ + static gboolean fatal_error = FALSE; + static GMainLoop *mainloop = NULL; + static bool global_keep_tracking = false; +@@ -642,49 +685,6 @@ pcmk_sigquit(int nsig) + .connection_destroyed = pcmk_ipc_destroy + }; + +-static pcmk__cli_option_t long_options[] = { +- // long option, argument type, storage, short option, description, flags +- { +- "help", no_argument, NULL, '?', +- "\tThis text", pcmk__option_default +- }, +- { +- "version", no_argument, NULL, '$', +- "\tVersion information", pcmk__option_default +- }, +- { +- "verbose", no_argument, NULL, 'V', +- "\tIncrease debug output", pcmk__option_default +- }, +- { +- "shutdown", no_argument, NULL, 'S', +- "\tInstruct Pacemaker to shutdown on this machine", pcmk__option_default +- }, +- { +- "features", no_argument, NULL, 'F', +- "\tDisplay full version and list of features Pacemaker was built with", +- pcmk__option_default +- }, +- { +- "-spacer-", no_argument, NULL, '-', +- "\nAdditional Options:", pcmk__option_default +- }, +- { +- "foreground", no_argument, NULL, 'f', +- "\t(Ignored) Pacemaker always runs in the foreground", +- pcmk__option_default +- }, +- { +- "pid-file", required_argument, NULL, 'p', +- "\t(Ignored) Daemon pid file location", pcmk__option_default +- }, +- { +- "standby", no_argument, NULL, 's', +- "\tStart node in standby state", pcmk__option_default +- }, +- { 0, 0, 0, 0 } +-}; +- + static void + mcp_chown(const char *path, uid_t uid, gid_t gid) + { +@@ -1168,83 +1211,66 @@ request_shutdown(crm_ipc_t *ipc) + return status; + } + ++static GOptionContext * ++build_arg_context(pcmk__common_args_t *args) { ++ GOptionContext *context = NULL; ++ ++ context = pcmk__build_arg_context(args, NULL, NULL, NULL); ++ pcmk__add_main_args(context, entries); ++ return context; ++} ++ + int + main(int argc, char **argv) + { +- int flag; +- int argerr = 0; ++ crm_exit_t exit_code = CRM_EX_OK; ++ ++ GError *error = NULL; ++ ++ pcmk__common_args_t *args = pcmk__new_common_args(SUMMARY); ++ gchar **processed_args = pcmk__cmdline_preproc(argv, "p"); ++ GOptionContext *context = build_arg_context(args); + +- int option_index = 0; + bool old_instance_connected = false; +- gboolean shutdown = FALSE; + + crm_ipc_t *old_instance = NULL; + qb_ipcs_service_t *ipcs = NULL; + + crm_log_preinit(NULL, argc, argv); +- pcmk__set_cli_options(NULL, "[options]", long_options, +- "primary Pacemaker daemon that launches and " +- "monitors all subsidiary Pacemaker daemons"); + mainloop_add_signal(SIGHUP, pcmk_ignore); + mainloop_add_signal(SIGQUIT, pcmk_sigquit); + +- while (1) { +- flag = pcmk__next_cli_option(argc, argv, &option_index, NULL); +- if (flag == -1) +- break; +- +- switch (flag) { +- case 'V': +- crm_bump_log_level(argc, argv); +- break; +- case 'f': +- /* Legacy */ +- break; +- case 'p': +- break; +- case 's': +- pcmk__set_env_option("node_start_state", "standby"); +- break; +- case '$': +- case '?': +- pcmk__cli_help(flag, CRM_EX_OK); +- break; +- case 'S': +- shutdown = TRUE; +- break; +- case 'F': +- printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, +- CRM_FEATURE_SET, CRM_FEATURES); +- crm_exit(CRM_EX_OK); +- default: +- printf("Argument code 0%o (%c) is not (?yet?) supported\n", flag, flag); +- ++argerr; +- break; +- } ++ if (!g_option_context_parse_strv(context, &processed_args, &error)) { ++ exit_code = CRM_EX_USAGE; ++ goto done; + } + +- if (optind < argc) { +- printf("non-option ARGV-elements: "); +- while (optind < argc) +- printf("%s ", argv[optind++]); +- printf("\n"); +- } +- if (argerr) { +- pcmk__cli_help('?', CRM_EX_USAGE); ++ if (options.features) { ++ printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, ++ CRM_FEATURE_SET, CRM_FEATURES); ++ exit_code = CRM_EX_OK; ++ goto done; + } + ++ if (args->version) { ++ g_strfreev(processed_args); ++ pcmk__free_arg_context(context); ++ /* FIXME: When pacemakerd is converted to use formatted output, this can go. */ ++ pcmk__cli_help('v', CRM_EX_USAGE); ++ } + + setenv("LC_ALL", "C", 1); + + pcmk__set_env_option("mcp", "true"); + ++ pcmk__cli_init_logging("pacemakerd", args->verbosity); + crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); + + crm_debug("Checking for existing Pacemaker instance"); + old_instance = crm_ipc_new(CRM_SYSTEM_MCP, 0); + old_instance_connected = crm_ipc_connect(old_instance); + +- if (shutdown) { ++ if (options.shutdown) { + if (old_instance_connected) { + crm_exit(request_shutdown(old_instance)); + } else { +@@ -1253,22 +1279,25 @@ main(int argc, char **argv) + "Pacemaker instance: %s", strerror(errno)); + crm_ipc_close(old_instance); + crm_ipc_destroy(old_instance); +- crm_exit(CRM_EX_DISCONNECT); ++ exit_code = CRM_EX_DISCONNECT; ++ goto done; + } + + } else if (old_instance_connected) { + crm_ipc_close(old_instance); + crm_ipc_destroy(old_instance); + crm_err("Aborting start-up because active Pacemaker instance found"); +- crm_exit(CRM_EX_FATAL); ++ exit_code = CRM_EX_FATAL; ++ goto done; + } + + crm_ipc_close(old_instance); + crm_ipc_destroy(old_instance); + + #ifdef SUPPORT_COROSYNC + if (mcp_read_config() == FALSE) { +- crm_exit(CRM_EX_UNAVAILABLE); ++ exit_code = CRM_EX_UNAVAILABLE; ++ goto done; + } + #endif + +@@ -1292,7 +1321,8 @@ main(int argc, char **argv) + #ifdef SUPPORT_COROSYNC + /* Allows us to block shutdown */ + if (!cluster_connect_cfg()) { +- crm_exit(CRM_EX_PROTOCOL); ++ exit_code = CRM_EX_PROTOCOL; ++ goto done; + } + #endif + +@@ -1307,9 +1337,11 @@ main(int argc, char **argv) + case pcmk_rc_ok: + break; + case pcmk_rc_ipc_unauthorized: +- crm_exit(CRM_EX_CANTCREAT); ++ exit_code = CRM_EX_CANTCREAT; ++ goto done; + default: +- crm_exit(CRM_EX_FATAL); ++ exit_code = CRM_EX_FATAL; ++ goto done; + }; + + mainloop_add_signal(SIGTERM, pcmk_shutdown); +@@ -1342,5 +1374,11 @@ main(int argc, char **argv) + #ifdef SUPPORT_COROSYNC + cluster_disconnect_cfg(); + #endif +- crm_exit(CRM_EX_OK); ++ ++done: ++ g_strfreev(processed_args); ++ pcmk__free_arg_context(context); ++ ++ pcmk__output_and_clear_error(error, NULL); ++ crm_exit(exit_code); + } +-- +1.8.3.1 + + +From 8f7924fbb2a012bedcad59335b7bebc5020b26e3 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 13 May 2021 13:27:13 -0400 +Subject: [PATCH 4/4] Low: pacemaker.service: Don't start pacemakerd with -f. + +This option is completely ignored by pacemakerd. +--- + daemons/pacemakerd/pacemaker.service.in | 2 +- + doc/sphinx/Clusters_from_Scratch/verification.rst | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/daemons/pacemakerd/pacemaker.service.in b/daemons/pacemakerd/pacemaker.service.in +index b128ddc..0363a22 100644 +--- a/daemons/pacemakerd/pacemaker.service.in ++++ b/daemons/pacemakerd/pacemaker.service.in +@@ -44,7 +44,7 @@ EnvironmentFile=-@CONFIGDIR@/pacemaker + EnvironmentFile=-@CONFIGDIR@/sbd + SuccessExitStatus=100 + +-ExecStart=@sbindir@/pacemakerd -f ++ExecStart=@sbindir@/pacemakerd + + # Systemd v227 and above can limit the number of processes spawned by a + # service. That is a bad idea for an HA cluster resource manager, so disable it +diff --git a/doc/sphinx/Clusters_from_Scratch/verification.rst b/doc/sphinx/Clusters_from_Scratch/verification.rst +index 9d647f8..b7fa20e 100644 +--- a/doc/sphinx/Clusters_from_Scratch/verification.rst ++++ b/doc/sphinx/Clusters_from_Scratch/verification.rst +@@ -103,7 +103,7 @@ the necessary processes are running: + 2 ? S 0:00 [kthreadd] + ...lots of processes... + 17121 ? SLsl 0:01 /usr/sbin/corosync -f +- 17133 ? Ss 0:00 /usr/sbin/pacemakerd -f ++ 17133 ? Ss 0:00 /usr/sbin/pacemakerd + 17134 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-based + 17135 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-fenced + 17136 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-execd +-- +1.8.3.1 + diff --git a/003-pacemakerd-output.patch b/003-pacemakerd-output.patch new file mode 100644 index 0000000..167e22b --- /dev/null +++ b/003-pacemakerd-output.patch @@ -0,0 +1,343 @@ +From 7c35387a9896cb968cf4087b5cbed94af44e1ea5 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 14 May 2021 12:03:46 -0400 +Subject: [PATCH 1/5] Feature: daemons: Convert pacemakerd to formatted output. + +The main purpose of this is to finish getting pacemakerd moved off the +existing command line handling code (pcmk__cli_help in particular) so +that code can eventually be deprecated or removed. pacemakerd itself +does fairly little printing. +--- + daemons/pacemakerd/pacemakerd.c | 58 ++++++++++++++++++++++++++++++----------- + 1 file changed, 43 insertions(+), 15 deletions(-) + +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index ce194bf..bd59729 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -25,6 +25,7 @@ + #include <crm/common/ipc_internal.h> + #include <crm/common/mainloop.h> + #include <crm/common/cmdline_internal.h> ++#include <crm/common/output_internal.h> + #include <crm/cluster/internal.h> + #include <crm/cluster.h> + +@@ -37,6 +38,14 @@ struct { + gboolean standby; + } options; + ++static pcmk__output_t *out = NULL; ++ ++static pcmk__supported_format_t formats[] = { ++ PCMK__SUPPORTED_FORMAT_NONE, ++ PCMK__SUPPORTED_FORMAT_TEXT, ++ { NULL, NULL, NULL } ++}; ++ + static gboolean + pid_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { + return TRUE; +@@ -1167,10 +1176,10 @@ pacemakerd_event_cb(pcmk_ipc_api_t *pacemakerd_api, + } + + static GOptionContext * +-build_arg_context(pcmk__common_args_t *args) { ++build_arg_context(pcmk__common_args_t *args, GOptionGroup **group) { + GOptionContext *context = NULL; + +- context = pcmk__build_arg_context(args, NULL, NULL, NULL); ++ context = pcmk__build_arg_context(args, "text", group, NULL); + pcmk__add_main_args(context, entries); + return context; + } +@@ -1182,9 +1191,11 @@ main(int argc, char **argv) + + GError *error = NULL; + ++ int rc = pcmk_rc_ok; ++ GOptionGroup *output_group = NULL; + pcmk__common_args_t *args = pcmk__new_common_args(SUMMARY); + gchar **processed_args = pcmk__cmdline_preproc(argv, "p"); +- GOptionContext *context = build_arg_context(args); ++ GOptionContext *context = build_arg_context(args, &output_group); + + bool old_instance_connected = false; + +@@ -1195,23 +1205,30 @@ main(int argc, char **argv) + mainloop_add_signal(SIGHUP, pcmk_ignore); + mainloop_add_signal(SIGQUIT, pcmk_sigquit); + ++ pcmk__register_formats(output_group, formats); + if (!g_option_context_parse_strv(context, &processed_args, &error)) { + exit_code = CRM_EX_USAGE; + goto done; + } + ++ rc = pcmk__output_new(&out, args->output_ty, args->output_dest, argv); ++ if (rc != pcmk_rc_ok) { ++ exit_code = CRM_EX_ERROR; ++ g_set_error(&error, PCMK__EXITC_ERROR, exit_code, "Error creating output format %s: %s", ++ args->output_ty, pcmk_rc_str(rc)); ++ goto done; ++ } ++ + if (options.features) { +- printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, +- CRM_FEATURE_SET, CRM_FEATURES); ++ out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, ++ BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); + exit_code = CRM_EX_OK; + goto done; + } + + if (args->version) { +- g_strfreev(processed_args); +- pcmk__free_arg_context(context); +- /* FIXME: When pacemakerd is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ out->version(out, false); ++ goto done; + } + + setenv("LC_ALL", "C", 1); +@@ -1248,6 +1265,13 @@ main(int argc, char **argv) + crm_ipc_close(old_instance); + crm_ipc_destroy(old_instance); + ++ /* Don't allow any accidental output after this point. */ ++ if (out != NULL) { ++ out->finish(out, exit_code, true, NULL); ++ pcmk__output_free(out); ++ out = NULL; ++ } ++ + #ifdef SUPPORT_COROSYNC + if (mcp_read_config() == FALSE) { + exit_code = CRM_EX_UNAVAILABLE; +@@ -1333,6 +1357,11 @@ done: + g_strfreev(processed_args); + pcmk__free_arg_context(context); + +- pcmk__output_and_clear_error(error, NULL); ++ pcmk__output_and_clear_error(error, out); ++ ++ if (out != NULL) { ++ out->finish(out, exit_code, true, NULL); ++ pcmk__output_free(out); ++ } + crm_exit(exit_code); + } +-- +1.8.3.1 + + +From 35e6da64381fcb092d81ce16835cc28670b077cb Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 17 May 2021 10:04:04 -0400 +Subject: [PATCH 2/5] Features: daemons: Output the pacemakerd feature list in + XML. + +--- + daemons/pacemakerd/pacemakerd.c | 45 ++++++++++++++++++++++++++++++++++++++--- + 1 file changed, 42 insertions(+), 3 deletions(-) + +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index bd59729..93cf743 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -43,6 +43,42 @@ static pcmk__output_t *out = NULL; + static pcmk__supported_format_t formats[] = { + PCMK__SUPPORTED_FORMAT_NONE, + PCMK__SUPPORTED_FORMAT_TEXT, ++ PCMK__SUPPORTED_FORMAT_XML, ++ { NULL, NULL, NULL } ++}; ++ ++static int ++pacemakerd_features(pcmk__output_t *out, va_list args) { ++ out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, ++ BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); ++ return pcmk_rc_ok; ++} ++ ++static int ++pacemakerd_features_xml(pcmk__output_t *out, va_list args) { ++ gchar **feature_list = g_strsplit(CRM_FEATURES, " ", 0); ++ ++ pcmk__output_xml_create_parent(out, "pacemakerd", ++ "version", PACEMAKER_VERSION, ++ "build", BUILD_VERSION, ++ "feature_set", CRM_FEATURE_SET, ++ NULL); ++ out->begin_list(out, NULL, NULL, "features"); ++ ++ for (char **s = feature_list; *s != NULL; s++) { ++ pcmk__output_create_xml_text_node(out, "feature", *s); ++ } ++ ++ out->end_list(out); ++ ++ g_strfreev(feature_list); ++ return pcmk_rc_ok; ++} ++ ++static pcmk__message_entry_t fmt_functions[] = { ++ { "features", "default", pacemakerd_features }, ++ { "features", "xml", pacemakerd_features_xml }, ++ + { NULL, NULL, NULL } + }; + +@@ -200,7 +236,7 @@ static GOptionContext * + build_arg_context(pcmk__common_args_t *args, GOptionGroup **group) { + GOptionContext *context = NULL; + +- context = pcmk__build_arg_context(args, "text", group, NULL); ++ context = pcmk__build_arg_context(args, "text (default), xml", group, NULL); + pcmk__add_main_args(context, entries); + return context; + } +@@ -241,9 +277,12 @@ main(int argc, char **argv) + goto done; + } + ++ pcmk__force_args(context, &error, "%s --xml-simple-list", g_get_prgname()); ++ ++ pcmk__register_messages(out, fmt_functions); ++ + if (options.features) { +- out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, +- BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); ++ out->message(out, "features"); + exit_code = CRM_EX_OK; + goto done; + } +-- +1.8.3.1 + + +From 5b7f5eb35b025b59805cf3c7c3dcb6a3cf4b71b3 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 17 May 2021 11:09:53 -0400 +Subject: [PATCH 3/5] Low: daemons: Conditionally enable logging in pacemakerd. + +If we're doing an interactive command-line call, use +pcmk__cli_init_logging. At the moment, all command line calls except +for --shutdown do their work before logging would even come up, so we +really only need to do this for --shutdown. + +If we're doing a daemon call, use crm_log_init. +--- + daemons/pacemakerd/pacemakerd.c | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index 93cf743..c20bde7 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -296,8 +296,11 @@ main(int argc, char **argv) + + pcmk__set_env_option("mcp", "true"); + +- pcmk__cli_init_logging("pacemakerd", args->verbosity); +- crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); ++ if (options.shutdown) { ++ pcmk__cli_init_logging("pacemakerd", args->verbosity); ++ } else { ++ crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); ++ } + + crm_debug("Checking for existing Pacemaker instance"); + old_instance = crm_ipc_new(CRM_SYSTEM_MCP, 0); +-- +1.8.3.1 + + +From 2393362bb7489e86d937ed46a1c5cfb93d9bf3ab Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 17 May 2021 11:58:06 -0400 +Subject: [PATCH 4/5] Fix: include: Bump CRM_FEATURE_SET for new pacemakerd + args. + +--- + include/crm/crm.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/crm/crm.h b/include/crm/crm.h +index fdfc825..92a98fa 100644 +--- a/include/crm/crm.h ++++ b/include/crm/crm.h +@@ -66,7 +66,7 @@ extern "C" { + * >=3.0.13: Fail counts include operation name and interval + * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED + */ +-# define CRM_FEATURE_SET "3.10.0" ++# define CRM_FEATURE_SET "3.10.1" + + /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and + * recipient of a CPG message. This imposes an arbitrary limit on cluster node +-- +1.8.3.1 + + +From 3ad8edbd91631b87ef5f53fa2d68f0c8bbb9ee2b Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 17 May 2021 11:57:09 -0400 +Subject: [PATCH 5/5] Feature: xml: Add schema for pacemakerd. + +--- + xml/Makefile.am | 1 + + xml/api/pacemakerd-2.10.rng | 28 ++++++++++++++++++++++++++++ + 2 files changed, 29 insertions(+) + create mode 100644 xml/api/pacemakerd-2.10.rng + +diff --git a/xml/Makefile.am b/xml/Makefile.am +index 12a51c5..b9448d4 100644 +--- a/xml/Makefile.am ++++ b/xml/Makefile.am +@@ -56,6 +56,7 @@ API_request_base = command-output \ + crm_simulate \ + crmadmin \ + digests \ ++ pacemakerd \ + stonith_admin \ + version + +diff --git a/xml/api/pacemakerd-2.10.rng b/xml/api/pacemakerd-2.10.rng +new file mode 100644 +index 0000000..41a11e7 +--- /dev/null ++++ b/xml/api/pacemakerd-2.10.rng +@@ -0,0 +1,28 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="element-pacemakerd"/> ++ </start> ++ ++ <define name="element-pacemakerd"> ++ <element name="pacemakerd"> ++ <attribute name="version"> <text /> </attribute> ++ <attribute name="build"> <text /> </attribute> ++ <attribute name="feature_set"> <text /> </attribute> ++ ++ <optional> ++ <ref name="feature-list" /> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="feature-list"> ++ <element name="features"> ++ <oneOrMore> ++ <element name="feature"> <text/> </element> ++ </oneOrMore> ++ </element> ++ </define> ++</grammar> +-- +1.8.3.1 + diff --git a/004-check-level.patch b/004-check-level.patch new file mode 100644 index 0000000..f2abb5f --- /dev/null +++ b/004-check-level.patch @@ -0,0 +1,199 @@ +From 3905e7eac11298fc20efd567a773666f948edf61 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 3 May 2021 11:19:04 -0400 +Subject: [PATCH 1/2] Feature: tools: Add OCF_CHECK_LEVEL to crm_resource + environment. + +If --validate= or --force-check= are given with a level, pass that along +as OCF_CHECK_LEVEL. This argument is optional, and if no value is given +then the environment variable will not be set and whatever's the default +on the resource agent will be used. + +See: rhbz#1955792. +--- + tools/crm_resource.c | 29 +++++++++++++++++++++-------- + tools/crm_resource.h | 4 ++-- + tools/crm_resource_runtime.c | 13 ++++++++++--- + 3 files changed, 33 insertions(+), 13 deletions(-) + +diff --git a/tools/crm_resource.c b/tools/crm_resource.c +index 45db2b2..6ca96f8 100644 +--- a/tools/crm_resource.c ++++ b/tools/crm_resource.c +@@ -100,6 +100,7 @@ struct { + int timeout_ms; // Parsed from --timeout value + char *agent_spec; // Standard and/or provider and/or agent + gchar *xml_file; // Value of (deprecated) --xml-file ++ int check_level; // Optional value of --validate or --force-check + + // Resource configuration specified via command-line arguments + gboolean cmdline_config; // Resource configuration was via arguments +@@ -113,6 +114,7 @@ struct { + GHashTable *override_params; // Resource parameter values that override config + } options = { + .attr_set_type = XML_TAG_ATTR_SETS, ++ .check_level = -1, + .cib_options = cib_sync_call, + .require_cib = TRUE, + .require_dataset = TRUE, +@@ -402,14 +404,15 @@ static GOptionEntry query_entries[] = { + }; + + static GOptionEntry command_entries[] = { +- { "validate", 0, G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, ++ { "validate", 0, G_OPTION_FLAG_OPTIONAL_ARG, G_OPTION_ARG_CALLBACK, + validate_or_force_cb, + "Validate resource configuration by calling agent's validate-all\n" + INDENT "action. The configuration may be specified either by giving an\n" + INDENT "existing resource name with -r, or by specifying --class,\n" + INDENT "--agent, and --provider arguments, along with any number of\n" +- INDENT "--option arguments.", +- NULL }, ++ INDENT "--option arguments. An optional LEVEL argument can be given\n" ++ INDENT "to control the level of checking performed.", ++ "LEVEL" }, + { "cleanup", 'C', G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, cleanup_refresh_cb, + "If resource has any past failures, clear its history and fail\n" + INDENT "count. Optionally filtered by --resource, --node, --operation\n" +@@ -546,11 +549,12 @@ static GOptionEntry advanced_entries[] = { + INDENT "the cluster believes the resource is a clone instance already\n" + INDENT "running on the local node.", + NULL }, +- { "force-check", 0, G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, ++ { "force-check", 0, G_OPTION_FLAG_OPTIONAL_ARG, G_OPTION_ARG_CALLBACK, + validate_or_force_cb, + "(Advanced) Bypass the cluster and check the state of a resource on\n" +- INDENT "the local node", +- NULL }, ++ INDENT "the local node. An optional LEVEL argument can be given\n" ++ INDENT "to control the level of checking performed.", ++ "LEVEL" }, + + { NULL } + }; +@@ -910,6 +914,15 @@ validate_or_force_cb(const gchar *option_name, const gchar *optarg, + if (options.override_params == NULL) { + options.override_params = pcmk__strkey_table(free, free); + } ++ ++ if (optarg != NULL) { ++ if (pcmk__scan_min_int(optarg, &options.check_level, 0) != pcmk_rc_ok) { ++ g_set_error(error, G_OPTION_ERROR, CRM_EX_INVALID_PARAM, ++ "Invalid check level setting: %s", optarg); ++ return FALSE; ++ } ++ } ++ + return TRUE; + } + +@@ -1826,12 +1839,12 @@ main(int argc, char **argv) + options.v_class, options.v_provider, options.v_agent, + "validate-all", options.cmdline_params, + options.override_params, options.timeout_ms, +- args->verbosity, options.force); ++ args->verbosity, options.force, options.check_level); + } else { + exit_code = cli_resource_execute(rsc, options.rsc_id, + options.operation, options.override_params, + options.timeout_ms, cib_conn, data_set, +- args->verbosity, options.force); ++ args->verbosity, options.force, options.check_level); + } + goto done; + +diff --git a/tools/crm_resource.h b/tools/crm_resource.h +index 3560377..5ab10d6 100644 +--- a/tools/crm_resource.h ++++ b/tools/crm_resource.h +@@ -88,11 +88,11 @@ crm_exit_t cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc + const char *rsc_type, const char *rsc_action, + GHashTable *params, GHashTable *override_hash, + int timeout_ms, int resource_verbose, +- gboolean force); ++ gboolean force, int check_level); + crm_exit_t cli_resource_execute(pe_resource_t *rsc, const char *requested_name, + const char *rsc_action, GHashTable *override_hash, + int timeout_ms, cib_t *cib, pe_working_set_t *data_set, +- int resource_verbose, gboolean force); ++ int resource_verbose, gboolean force, int check_level); + + int cli_resource_update_attribute(pe_resource_t *rsc, const char *requested_name, + const char *attr_set, const char *attr_set_type, +diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c +index fe0ec98..bde83b6 100644 +--- a/tools/crm_resource_runtime.c ++++ b/tools/crm_resource_runtime.c +@@ -1679,7 +1679,8 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, + const char *rsc_class, const char *rsc_prov, + const char *rsc_type, const char *action, + GHashTable *params, GHashTable *override_hash, +- int timeout_ms, int resource_verbose, gboolean force) ++ int timeout_ms, int resource_verbose, gboolean force, ++ int check_level) + { + GHashTable *params_copy = NULL; + crm_exit_t exit_code = CRM_EX_OK; +@@ -1703,6 +1704,12 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, + /* add crm_feature_set env needed by some resource agents */ + g_hash_table_insert(params, strdup(XML_ATTR_CRM_VERSION), strdup(CRM_FEATURE_SET)); + ++ if (check_level >= 0) { ++ char *level = crm_strdup_printf("%d", check_level); ++ setenv("OCF_CHECK_LEVEL", level, 1); ++ free(level); ++ } ++ + /* resources_action_create frees the params hash table it's passed, but we + * may need to reuse it in a second call to resources_action_create. Thus + * we'll make a copy here so that gets freed and the original remains for +@@ -1790,7 +1797,7 @@ crm_exit_t + cli_resource_execute(pe_resource_t *rsc, const char *requested_name, + const char *rsc_action, GHashTable *override_hash, + int timeout_ms, cib_t * cib, pe_working_set_t *data_set, +- int resource_verbose, gboolean force) ++ int resource_verbose, gboolean force, int check_level) + { + pcmk__output_t *out = data_set->priv; + crm_exit_t exit_code = CRM_EX_OK; +@@ -1856,7 +1863,7 @@ cli_resource_execute(pe_resource_t *rsc, const char *requested_name, + + exit_code = cli_resource_execute_from_params(out, rid, rclass, rprov, rtype, action, + params, override_hash, timeout_ms, +- resource_verbose, force); ++ resource_verbose, force, check_level); + return exit_code; + } + +-- +1.8.3.1 + + +From d13ba4bd6defe0dd81fdf8ab39ae5b889513c0c0 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 20 May 2021 10:59:23 -0400 +Subject: [PATCH 2/2] Fix: include: Bump feature set to 3.10.2. + +This is for the OCF_CHECK_LEVEL environment variable. + +See: rhbz#1955792. +--- + include/crm/crm.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/crm/crm.h b/include/crm/crm.h +index 92a98fa..ee52c36 100644 +--- a/include/crm/crm.h ++++ b/include/crm/crm.h +@@ -66,7 +66,7 @@ extern "C" { + * >=3.0.13: Fail counts include operation name and interval + * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED + */ +-# define CRM_FEATURE_SET "3.10.1" ++# define CRM_FEATURE_SET "3.10.2" + + /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and + * recipient of a CPG message. This imposes an arbitrary limit on cluster node +-- +1.8.3.1 + diff --git a/005-crm_resource.patch b/005-crm_resource.patch new file mode 100644 index 0000000..1683026 --- /dev/null +++ b/005-crm_resource.patch @@ -0,0 +1,866 @@ +From a5a507d4e1abf242903472719a19977811e6f164 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 20 May 2021 11:59:36 -0400 +Subject: [PATCH 01/10] Feature: libcrmcommon: Add OCF_OUTPUT_FORMAT to + crm_resource environment. + +See: rhbz#1644628 +--- + lib/common/output.c | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/lib/common/output.c b/lib/common/output.c +index 6cb49b5..58872e0 100644 +--- a/lib/common/output.c ++++ b/lib/common/output.c +@@ -71,6 +71,8 @@ pcmk__output_new(pcmk__output_t **out, const char *fmt_name, const char *filenam + return ENOMEM; + } + ++ setenv("OCF_OUTPUT_FORMAT", (*out)->fmt_name, 1); ++ + return pcmk_rc_ok; + } + +-- +1.8.3.1 + + +From acc6ecdbfb797d69794e68f75a734d6252434e01 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 21 May 2021 14:20:30 -0400 +Subject: [PATCH 02/10] Feature: schemas: Copy crm_resource schema in + preparation for changes. + +See: rhbz#1644628 +--- + xml/api/crm_resource-2.11.rng | 238 ++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 238 insertions(+) + create mode 100644 xml/api/crm_resource-2.11.rng + +diff --git a/xml/api/crm_resource-2.11.rng b/xml/api/crm_resource-2.11.rng +new file mode 100644 +index 0000000..8e386db +--- /dev/null ++++ b/xml/api/crm_resource-2.11.rng +@@ -0,0 +1,238 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="element-crm-resource"/> ++ </start> ++ ++ <define name="element-crm-resource"> ++ <choice> ++ <ref name="agents-list" /> ++ <ref name="alternatives-list" /> ++ <ref name="constraints-list" /> ++ <externalRef href="generic-list-2.4.rng"/> ++ <element name="metadata"> <text/> </element> ++ <ref name="locate-list" /> ++ <ref name="operations-list" /> ++ <ref name="providers-list" /> ++ <ref name="reasons-list" /> ++ <ref name="resource-check" /> ++ <ref name="resource-config" /> ++ <ref name="resources-list" /> ++ </choice> ++ </define> ++ ++ <define name="agents-list"> ++ <element name="agents"> ++ <attribute name="standard"> <text/> </attribute> ++ <optional> ++ <attribute name="provider"> <text/> </attribute> ++ </optional> ++ <zeroOrMore> ++ <element name="agent"> <text/> </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="alternatives-list"> ++ <element name="providers"> ++ <attribute name="for"> <text/> </attribute> ++ <zeroOrMore> ++ <element name="provider"> <text/> </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="constraints-list"> ++ <element name="constraints"> ++ <interleave> ++ <zeroOrMore> ++ <ref name="rsc-location" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="rsc-colocation" /> ++ </zeroOrMore> ++ </interleave> ++ </element> ++ </define> ++ ++ <define name="locate-list"> ++ <element name="nodes"> ++ <attribute name="resource"> <text/> </attribute> ++ <zeroOrMore> ++ <element name="node"> ++ <optional> ++ <attribute name="state"><value>promoted</value></attribute> ++ </optional> ++ <text/> ++ </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="rsc-location"> ++ <element name="rsc_location"> ++ <attribute name="node"> <text/> </attribute> ++ <attribute name="rsc"> <text/> </attribute> ++ <attribute name="id"> <text/> </attribute> ++ <externalRef href="../score.rng"/> ++ </element> ++ </define> ++ ++ <define name="operations-list"> ++ <element name="operations"> ++ <oneOrMore> ++ <ref name="element-operation-list" /> ++ </oneOrMore> ++ </element> ++ </define> ++ ++ <define name="providers-list"> ++ <element name="providers"> ++ <attribute name="standard"> <value>ocf</value> </attribute> ++ <optional> ++ <attribute name="agent"> <text/> </attribute> ++ </optional> ++ <zeroOrMore> ++ <element name="provider"> <text/> </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="reasons-list"> ++ <choice> ++ <ref name="no-resource-or-uname"/> ++ <ref name="resource-and-uname"/> ++ <ref name="no-resource-but-uname"/> ++ <ref name="resource-but-no-uname"/> ++ </choice> ++ </define> ++ ++ <define name="no-resource-or-uname"> ++ <element name="reason"> ++ <element name="resources"> ++ <zeroOrMore> ++ <element name="resource"> ++ <attribute name="id"> <text/> </attribute> ++ <attribute name="running"> <data type="boolean"/> </attribute> ++ <ref name="resource-check"/> ++ </element> ++ </zeroOrMore> ++ </element> ++ </element> ++ </define> ++ ++ <define name="resource-and-uname"> ++ <element name="reason"> ++ <attribute name="running_on"> <text/> </attribute> ++ <ref name="resource-check"/> ++ </element> ++ </define> ++ ++ <define name="no-resource-but-uname"> ++ <element name="reason"> ++ <element name="resources"> ++ <zeroOrMore> ++ <element name="resource"> ++ <attribute name="id"> <text/> </attribute> ++ <attribute name="running"> <data type="boolean"/> </attribute> ++ <attribute name="host"> <text/> </attribute> ++ <ref name="resource-check"/> ++ </element> ++ </zeroOrMore> ++ </element> ++ </element> ++ </define> ++ ++ <define name="resource-but-no-uname"> ++ <element name="reason"> ++ <attribute name="running"> <data type="boolean"/> </attribute> ++ <ref name="resource-check"/> ++ </element> ++ </define> ++ ++ <define name="resource-config"> ++ <element name="resource_config"> ++ <externalRef href="resources-2.4.rng" /> ++ <element name="xml"> <text/> </element> ++ </element> ++ </define> ++ ++ <define name="resource-check"> ++ <element name="check"> ++ <attribute name="id"> <text/> </attribute> ++ <optional> ++ <choice> ++ <attribute name="remain_stopped"><value>true</value></attribute> ++ <attribute name="promotable"><value>false</value></attribute> ++ </choice> ++ </optional> ++ <optional> ++ <attribute name="unmanaged"><value>true</value></attribute> ++ </optional> ++ <optional> ++ <attribute name="locked-to"> <text/> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="resources-list"> ++ <element name="resources"> ++ <zeroOrMore> ++ <externalRef href="resources-2.4.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="rsc-colocation"> ++ <element name="rsc_colocation"> ++ <attribute name="id"> <text/> </attribute> ++ <attribute name="rsc"> <text/> </attribute> ++ <attribute name="with-rsc"> <text/> </attribute> ++ <externalRef href="../score.rng"/> ++ <optional> ++ <attribute name="node-attribute"> <text/> </attribute> ++ </optional> ++ <optional> ++ <attribute name="rsc-role"> ++ <ref name="attribute-roles"/> ++ </attribute> ++ </optional> ++ <optional> ++ <attribute name="with-rsc-role"> ++ <ref name="attribute-roles"/> ++ </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-operation-list"> ++ <element name="operation"> ++ <optional> ++ <group> ++ <attribute name="rsc"> <text/> </attribute> ++ <attribute name="agent"> <text/> </attribute> ++ </group> ++ </optional> ++ <attribute name="op"> <text/> </attribute> ++ <attribute name="node"> <text/> </attribute> ++ <attribute name="call"> <data type="integer" /> </attribute> ++ <attribute name="rc"> <data type="nonNegativeInteger" /> </attribute> ++ <optional> ++ <attribute name="last-rc-change"> <text/> </attribute> ++ <attribute name="exec-time"> <data type="nonNegativeInteger" /> </attribute> ++ </optional> ++ <attribute name="status"> <text/> </attribute> ++ </element> ++ </define> ++ ++ <define name="attribute-roles"> ++ <choice> ++ <value>Stopped</value> ++ <value>Started</value> ++ <value>Master</value> ++ <value>Slave</value> ++ </choice> ++ </define> ++</grammar> +-- +1.8.3.1 + + +From 1bbdf2149a111e9e19c388834f82001e0d31c427 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 24 May 2021 12:23:55 -0400 +Subject: [PATCH 03/10] Feature: xml: Update the crm_resource schema for XML + output. + +See: rhbz#1644628 +--- + xml/api/crm_resource-2.11.rng | 50 +++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 50 insertions(+) + +diff --git a/xml/api/crm_resource-2.11.rng b/xml/api/crm_resource-2.11.rng +index 8e386db..aaa54d6 100644 +--- a/xml/api/crm_resource-2.11.rng ++++ b/xml/api/crm_resource-2.11.rng +@@ -20,6 +20,7 @@ + <ref name="resource-check" /> + <ref name="resource-config" /> + <ref name="resources-list" /> ++ <ref name="resource-agent-action" /> + </choice> + </define> + +@@ -227,6 +228,55 @@ + </element> + </define> + ++ <define name="resource-agent-action"> ++ <element name="resource-agent-action"> ++ <attribute name="action"> <text/> </attribute> ++ <optional> ++ <attribute name="rsc"> <text/> </attribute> ++ </optional> ++ <attribute name="class"> <text/> </attribute> ++ <attribute name="type"> <text/> </attribute> ++ <optional> ++ <attribute name="provider"> <text/> </attribute> ++ </optional> ++ <optional> ++ <ref name="overrides-list"/> ++ </optional> ++ <ref name="agent-status"/> ++ <optional> ++ <choice> ++ <element name="command"> ++ <text /> ++ </element> ++ <externalRef href="command-output-1.0.rng"/> ++ </choice> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="overrides-list"> ++ <element name="overrides"> ++ <zeroOrMore> ++ <element name="override"> ++ <optional> ++ <attribute name="rsc"> <text/> </attribute> ++ </optional> ++ <attribute name="name"> <text/> </attribute> ++ <attribute name="value"> <text/> </attribute> ++ </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="agent-status"> ++ <element name="agent-status"> ++ <attribute name="code"> <data type="integer" /> </attribute> ++ <optional> ++ <attribute name="message"> <text/> </attribute> ++ </optional> ++ </element> ++ </define> ++ + <define name="attribute-roles"> + <choice> + <value>Stopped</value> +-- +1.8.3.1 + + +From d89f5bc7fec856fdcd32fa14edbd0019507d5d15 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Tue, 1 Jun 2021 15:26:58 -0400 +Subject: [PATCH 04/10] Low: libcrmcommon: Increase PCMK__API_VERSION for new + crm_resource output. + +See: rhbz#1644628 +--- + include/crm/common/output_internal.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/crm/common/output_internal.h b/include/crm/common/output_internal.h +index 10b315b..0436cde 100644 +--- a/include/crm/common/output_internal.h ++++ b/include/crm/common/output_internal.h +@@ -27,7 +27,7 @@ extern "C" { + # include <glib.h> + # include <crm/common/results.h> + +-# define PCMK__API_VERSION "2.9" ++# define PCMK__API_VERSION "2.11" + + #if defined(PCMK__WITH_ATTRIBUTE_OUTPUT_ARGS) + # define PCMK__OUTPUT_ARGS(ARGS...) __attribute__((output_args(ARGS))) +-- +1.8.3.1 + + +From 30bd2ddf43ee2a911681e51f40ed9ba20ec250b0 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 27 May 2021 13:57:12 -0400 +Subject: [PATCH 05/10] Low: tools: Pass NULL to + cli_resource_execute_from_params... + +if no resource name is given. This happens if we are validating based +on the --class/--agent/--provider command line options instead. +--- + tools/crm_resource.c | 2 +- + tools/crm_resource_runtime.c | 8 ++++---- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/tools/crm_resource.c b/tools/crm_resource.c +index 24f1121..37a0bb0 100644 +--- a/tools/crm_resource.c ++++ b/tools/crm_resource.c +@@ -1840,7 +1840,7 @@ main(int argc, char **argv) + + case cmd_execute_agent: + if (options.cmdline_config) { +- exit_code = cli_resource_execute_from_params(out, "test", ++ exit_code = cli_resource_execute_from_params(out, NULL, + options.v_class, options.v_provider, options.v_agent, + "validate-all", options.cmdline_params, + options.override_params, options.timeout_ms, +diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c +index 48a4b40..ebf48bb 100644 +--- a/tools/crm_resource_runtime.c ++++ b/tools/crm_resource_runtime.c +@@ -1717,14 +1717,14 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, + */ + params_copy = pcmk__str_table_dup(params); + +- op = resources_action_create(rsc_name, rsc_class, rsc_prov, rsc_type, action, 0, +- timeout_ms, params_copy, 0); ++ op = resources_action_create(rsc_name ? rsc_name : "test", rsc_class, rsc_prov, ++ rsc_type, action, 0, timeout_ms, params_copy, 0); + if (op == NULL) { + /* Re-run with stderr enabled so we can display a sane error message */ + crm_enable_stderr(TRUE); + params_copy = pcmk__str_table_dup(params); +- op = resources_action_create(rsc_name, rsc_class, rsc_prov, rsc_type, action, 0, +- timeout_ms, params_copy, 0); ++ op = resources_action_create(rsc_name ? rsc_name : "test", rsc_class, rsc_prov, ++ rsc_type, action, 0, timeout_ms, params_copy, 0); + + /* Callers of cli_resource_execute expect that the params hash table will + * be freed. That function uses this one, so for that reason and for +-- +1.8.3.1 + + +From ee56efd53d14cfc4f902769540b72b3bb6096a73 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 24 May 2021 12:08:52 -0400 +Subject: [PATCH 06/10] Feature: tools: Add an agent-status message for + crm_resource. + +This moves what was previously only done in an out->info call to its own +output message, which means it will appear in XML output as well. Also, +note that if --class/--agent/--provider are given, the resource name +will be set to "test". In that case, do not display the resource name +in the output. + +This message will be used for --validate and the --force-* command line +options to crm_resource. + +See: rhbz#1644628 +--- + tools/crm_resource_print.c | 53 ++++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 53 insertions(+) + +diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c +index 9d82cf8..88d5878 100644 +--- a/tools/crm_resource_print.c ++++ b/tools/crm_resource_print.c +@@ -152,6 +152,57 @@ attribute_list_default(pcmk__output_t *out, va_list args) { + return pcmk_rc_ok; + } + ++PCMK__OUTPUT_ARGS("agent-status", "int", "const char *", "const char *", "const char *", ++ "const char *", "const char *", "int") ++static int ++agent_status_default(pcmk__output_t *out, va_list args) { ++ int status = va_arg(args, int); ++ const char *action = va_arg(args, const char *); ++ const char *name = va_arg(args, const char *); ++ const char *class = va_arg(args, const char *); ++ const char *provider = va_arg(args, const char *); ++ const char *type = va_arg(args, const char *); ++ int rc = va_arg(args, int); ++ ++ if (status == PCMK_LRM_OP_DONE) { ++ out->info(out, "Operation %s%s%s (%s%s%s:%s) returned: '%s' (%d)", ++ action, name ? " for " : "", name ? name : "", ++ class, provider ? ":" : "", provider ? provider : "", type, ++ services_ocf_exitcode_str(rc), rc); ++ } else { ++ out->err(out, "Operation %s%s%s (%s%s%s:%s) failed: '%s' (%d)", ++ action, name ? " for " : "", name ? name : "", ++ class, provider ? ":" : "", provider ? provider : "", type, ++ services_lrm_status_str(status), status); ++ } ++ ++ return pcmk_rc_ok; ++} ++ ++PCMK__OUTPUT_ARGS("agent-status", "int", "const char *", "const char *", "const char *", ++ "const char *", "const char *", "int") ++static int ++agent_status_xml(pcmk__output_t *out, va_list args) { ++ int status G_GNUC_UNUSED = va_arg(args, int); ++ const char *action G_GNUC_UNUSED = va_arg(args, const char *); ++ const char *name G_GNUC_UNUSED = va_arg(args, const char *); ++ const char *class G_GNUC_UNUSED = va_arg(args, const char *); ++ const char *provider G_GNUC_UNUSED = va_arg(args, const char *); ++ const char *type G_GNUC_UNUSED = va_arg(args, const char *); ++ int rc = va_arg(args, int); ++ ++ char *status_str = pcmk__itoa(rc); ++ ++ pcmk__output_create_xml_node(out, "agent-status", ++ "code", status_str, ++ "message", services_ocf_exitcode_str(rc), ++ NULL); ++ ++ free(status_str); ++ ++ return pcmk_rc_ok; ++} ++ + PCMK__OUTPUT_ARGS("attribute-list", "pe_resource_t *", "char *", "GHashTable *") + static int + attribute_list_text(pcmk__output_t *out, va_list args) { +@@ -562,6 +613,8 @@ resource_names(pcmk__output_t *out, va_list args) { + } + + static pcmk__message_entry_t fmt_functions[] = { ++ { "agent-status", "default", agent_status_default }, ++ { "agent-status", "xml", agent_status_xml }, + { "attribute-list", "default", attribute_list_default }, + { "attribute-list", "text", attribute_list_text }, + { "property-list", "default", property_list_default }, +-- +1.8.3.1 + + +From 85cb6b6bff96b18c5174d11e4de4d49cbfb20bb7 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Tue, 1 Jun 2021 14:47:30 -0400 +Subject: [PATCH 07/10] Feature: tools: Add an overridden params output + message. + +This also replaces what was previously being done in an out->info call +with an output message. This means it shows up in XML output as well. +Also, note that if --class/--agent/--provider are given, the resource +name will be set to "test". In that case, do not display the resource +name in the output. + +See: rhbz#1644628 +--- + tools/crm_resource_print.c | 39 +++++++++++++++++++++++++++++++++++++++ + 1 file changed, 39 insertions(+) + +diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c +index 88d5878..119d83f 100644 +--- a/tools/crm_resource_print.c ++++ b/tools/crm_resource_print.c +@@ -224,6 +224,43 @@ attribute_list_text(pcmk__output_t *out, va_list args) { + return pcmk_rc_ok; + } + ++PCMK__OUTPUT_ARGS("override", "const char *", "const char *", "const char *") ++static int ++override_default(pcmk__output_t *out, va_list args) { ++ const char *rsc_name = va_arg(args, const char *); ++ const char *name = va_arg(args, const char *); ++ const char *value = va_arg(args, const char *); ++ ++ if (rsc_name == NULL) { ++ out->list_item(out, NULL, "Overriding the cluster configuration with '%s' = '%s'", ++ name, value); ++ } else { ++ out->list_item(out, NULL, "Overriding the cluster configuration for '%s' with '%s' = '%s'", ++ rsc_name, name, value); ++ } ++ ++ return pcmk_rc_ok; ++} ++ ++PCMK__OUTPUT_ARGS("override", "const char *", "const char *", "const char *") ++static int ++override_xml(pcmk__output_t *out, va_list args) { ++ const char *rsc_name = va_arg(args, const char *); ++ const char *name = va_arg(args, const char *); ++ const char *value = va_arg(args, const char *); ++ ++ xmlNodePtr node = pcmk__output_create_xml_node(out, "override", ++ "name", name, ++ "value", value, ++ NULL); ++ ++ if (rsc_name != NULL) { ++ crm_xml_add(node, "rsc", rsc_name); ++ } ++ ++ return pcmk_rc_ok; ++} ++ + PCMK__OUTPUT_ARGS("property-list", "pe_resource_t *", "char *") + static int + property_list_default(pcmk__output_t *out, va_list args) { +@@ -617,6 +654,8 @@ static pcmk__message_entry_t fmt_functions[] = { + { "agent-status", "xml", agent_status_xml }, + { "attribute-list", "default", attribute_list_default }, + { "attribute-list", "text", attribute_list_text }, ++ { "override", "default", override_default }, ++ { "override", "xml", override_xml }, + { "property-list", "default", property_list_default }, + { "property-list", "text", property_list_text }, + { "resource-check-list", "default", resource_check_list_default }, +-- +1.8.3.1 + + +From e5e24592c7c3231c619fb5253e7925ffbc634a99 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 4 Jun 2021 10:24:51 -0400 +Subject: [PATCH 08/10] Low: tools: Use simple XML lists for resource actions + as well. + +See: rhbz#1644628 +--- + tools/crm_resource.c | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/tools/crm_resource.c b/tools/crm_resource.c +index 37a0bb0..e957011 100644 +--- a/tools/crm_resource.c ++++ b/tools/crm_resource.c +@@ -1643,6 +1643,7 @@ main(int argc, char **argv) + * saves from having to write custom messages to build the lists around all these things + */ + switch (options.rsc_cmd) { ++ case cmd_execute_agent: + case cmd_list_resources: + case cmd_query_xml: + case cmd_query_raw_xml: +-- +1.8.3.1 + + +From 3e75174d0bc31b261adb1994214a5878b79da85b Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 4 Jun 2021 10:30:10 -0400 +Subject: [PATCH 09/10] Feature: tools: Add an output message for resource + actions. + +This wraps up the override and agent-status messages into a single +message, along with any stdout/stderr from the resource action. This +message should be called after taking the action. + +This also implements handling XML output from resource actions. Check +to see if the validate-all action returns XML. If so, output it as a +CDATA block under a "command" element. If not, treat it as plain text +and output it as stdout/stderr from a command. + +See: rhbz#1644628 +--- + tools/crm_resource_print.c | 122 +++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 122 insertions(+) + +diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c +index 119d83f..19a366d 100644 +--- a/tools/crm_resource_print.c ++++ b/tools/crm_resource_print.c +@@ -293,6 +293,126 @@ property_list_text(pcmk__output_t *out, va_list args) { + return pcmk_rc_ok; + } + ++PCMK__OUTPUT_ARGS("resource-agent-action", "int", "const char *", "const char *", ++ "const char *", "const char *", "const char *", "GHashTable *", ++ "int", "int", "char *", "char *") ++static int ++resource_agent_action_default(pcmk__output_t *out, va_list args) { ++ int verbose = va_arg(args, int); ++ ++ const char *class = va_arg(args, const char *); ++ const char *provider = va_arg(args, const char *); ++ const char *type = va_arg(args, const char *); ++ const char *rsc_name = va_arg(args, const char *); ++ const char *action = va_arg(args, const char *); ++ GHashTable *overrides = va_arg(args, GHashTable *); ++ int rc = va_arg(args, int); ++ int status = va_arg(args, int); ++ char *stdout_data = va_arg(args, char *); ++ char *stderr_data = va_arg(args, char *); ++ ++ if (overrides) { ++ GHashTableIter iter; ++ char *name = NULL; ++ char *value = NULL; ++ ++ out->begin_list(out, NULL, NULL, "overrides"); ++ ++ g_hash_table_iter_init(&iter, overrides); ++ while (g_hash_table_iter_next(&iter, (gpointer *) &name, (gpointer *) &value)) { ++ out->message(out, "override", rsc_name, name, value); ++ } ++ ++ out->end_list(out); ++ } ++ ++ out->message(out, "agent-status", status, action, rsc_name, class, provider, ++ type, rc); ++ ++ /* hide output for validate-all if not in verbose */ ++ if (verbose == 0 && pcmk__str_eq(action, "validate-all", pcmk__str_casei)) { ++ return pcmk_rc_ok; ++ } ++ ++ if (stdout_data || stderr_data) { ++ xmlNodePtr doc = string2xml(stdout_data); ++ ++ if (doc != NULL) { ++ out->output_xml(out, "command", stdout_data); ++ xmlFreeNode(doc); ++ } else { ++ out->subprocess_output(out, rc, stdout_data, stderr_data); ++ } ++ } ++ ++ return pcmk_rc_ok; ++} ++ ++PCMK__OUTPUT_ARGS("resource-agent-action", "int", "const char *", "const char *", ++ "const char *", "const char *", "const char *", "GHashTable *", ++ "int", "int", "char *", "char *") ++static int ++resource_agent_action_xml(pcmk__output_t *out, va_list args) { ++ int verbose G_GNUC_UNUSED = va_arg(args, int); ++ ++ const char *class = va_arg(args, const char *); ++ const char *provider = va_arg(args, const char *); ++ const char *type = va_arg(args, const char *); ++ const char *rsc_name = va_arg(args, const char *); ++ const char *action = va_arg(args, const char *); ++ GHashTable *overrides = va_arg(args, GHashTable *); ++ int rc = va_arg(args, int); ++ int status = va_arg(args, int); ++ char *stdout_data = va_arg(args, char *); ++ char *stderr_data = va_arg(args, char *); ++ ++ xmlNodePtr node = pcmk__output_xml_create_parent(out, "resource-agent-action", ++ "action", action, ++ "class", class, ++ "type", type, ++ NULL); ++ ++ if (rsc_name) { ++ crm_xml_add(node, "rsc", rsc_name); ++ } ++ ++ if (provider) { ++ crm_xml_add(node, "provider", provider); ++ } ++ ++ if (overrides) { ++ GHashTableIter iter; ++ char *name = NULL; ++ char *value = NULL; ++ ++ out->begin_list(out, NULL, NULL, "overrides"); ++ ++ g_hash_table_iter_init(&iter, overrides); ++ while (g_hash_table_iter_next(&iter, (gpointer *) &name, (gpointer *) &value)) { ++ out->message(out, "override", rsc_name, name, value); ++ } ++ ++ out->end_list(out); ++ } ++ ++ out->message(out, "agent-status", status, action, rsc_name, class, provider, ++ type, rc); ++ ++ if (stdout_data || stderr_data) { ++ xmlNodePtr doc = string2xml(stdout_data); ++ ++ if (doc != NULL) { ++ out->output_xml(out, "command", stdout_data); ++ xmlFreeNode(doc); ++ } else { ++ out->subprocess_output(out, rc, stdout_data, stderr_data); ++ } ++ } ++ ++ pcmk__output_xml_pop_parent(out); ++ return pcmk_rc_ok; ++} ++ + PCMK__OUTPUT_ARGS("resource-check-list", "resource_checks_t *") + static int + resource_check_list_default(pcmk__output_t *out, va_list args) { +@@ -658,6 +778,8 @@ static pcmk__message_entry_t fmt_functions[] = { + { "override", "xml", override_xml }, + { "property-list", "default", property_list_default }, + { "property-list", "text", property_list_text }, ++ { "resource-agent-action", "default", resource_agent_action_default }, ++ { "resource-agent-action", "xml", resource_agent_action_xml }, + { "resource-check-list", "default", resource_check_list_default }, + { "resource-check-list", "xml", resource_check_list_xml }, + { "resource-search-list", "default", resource_search_list_default }, +-- +1.8.3.1 + + +From b50b2418e1e997b42f5370b4672a3f105d74634f Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 4 Jun 2021 10:40:16 -0400 +Subject: [PATCH 10/10] Feature: tools: Use the new resource-agent-action + message. + +See: rhbz#1644628 +--- + tools/crm_resource_runtime.c | 21 +++------------------ + 1 file changed, 3 insertions(+), 18 deletions(-) + +diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c +index ebf48bb..755be9f 100644 +--- a/tools/crm_resource_runtime.c ++++ b/tools/crm_resource_runtime.c +@@ -1765,28 +1765,13 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, + if (services_action_sync(op)) { + exit_code = op->rc; + +- if (op->status == PCMK_LRM_OP_DONE) { +- out->info(out, "Operation %s for %s (%s:%s:%s) returned: '%s' (%d)", +- action, rsc_name, rsc_class, rsc_prov ? rsc_prov : "", rsc_type, +- services_ocf_exitcode_str(op->rc), op->rc); +- } else { +- out->err(out, "Operation %s for %s (%s:%s:%s) failed: '%s' (%d)", +- action, rsc_name, rsc_class, rsc_prov ? rsc_prov : "", rsc_type, +- services_lrm_status_str(op->status), op->status); +- } +- +- /* hide output for validate-all if not in verbose */ +- if (resource_verbose == 0 && pcmk__str_eq(action, "validate-all", pcmk__str_casei)) +- goto done; +- +- if (op->stdout_data || op->stderr_data) { +- out->subprocess_output(out, op->rc, op->stdout_data, op->stderr_data); +- } ++ out->message(out, "resource-agent-action", resource_verbose, rsc_class, ++ rsc_prov, rsc_type, rsc_name, action, override_hash, op->rc, ++ op->status, op->stdout_data, op->stderr_data); + } else { + exit_code = op->rc == 0 ? CRM_EX_ERROR : op->rc; + } + +-done: + services_action_free(op); + /* See comment above about why we free params here. */ + g_hash_table_destroy(params); +-- +1.8.3.1 + diff --git a/006-crm_simulate.patch b/006-crm_simulate.patch new file mode 100644 index 0000000..c8d4e3f --- /dev/null +++ b/006-crm_simulate.patch @@ -0,0 +1,896 @@ +From 97571e6ccc9b7fa339a7e27d9b0b9ab782ff3003 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Wed, 16 Jun 2021 13:54:10 -0400 +Subject: [PATCH 1/5] Low: schemas: Copy crm_mon.rng in preparation for + changes. + +--- + xml/api/crm_mon-2.12.rng | 243 +++++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 243 insertions(+) + create mode 100644 xml/api/crm_mon-2.12.rng + +diff --git a/xml/api/crm_mon-2.12.rng b/xml/api/crm_mon-2.12.rng +new file mode 100644 +index 0000000..ffec923 +--- /dev/null ++++ b/xml/api/crm_mon-2.12.rng +@@ -0,0 +1,243 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="element-crm-mon"/> ++ </start> ++ ++ <define name="element-crm-mon"> ++ <optional> ++ <ref name="element-summary" /> ++ </optional> ++ <optional> ++ <ref name="nodes-list" /> ++ </optional> ++ <optional> ++ <ref name="resources-list" /> ++ </optional> ++ <optional> ++ <ref name="node-attributes-list" /> ++ </optional> ++ <optional> ++ <ref name="node-history-list" /> ++ </optional> ++ <optional> ++ <ref name="failures-list" /> ++ </optional> ++ <optional> ++ <ref name="fence-event-list" /> ++ </optional> ++ <optional> ++ <ref name="tickets-list" /> ++ </optional> ++ <optional> ++ <ref name="bans-list" /> ++ </optional> ++ </define> ++ ++ <define name="element-summary"> ++ <element name="summary"> ++ <optional> ++ <element name="stack"> ++ <attribute name="type"> <text /> </attribute> ++ </element> ++ </optional> ++ <optional> ++ <element name="current_dc"> ++ <attribute name="present"> <data type="boolean" /> </attribute> ++ <optional> ++ <group> ++ <attribute name="version"> <text /> </attribute> ++ <attribute name="name"> <text /> </attribute> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="with_quorum"> <data type="boolean" /> </attribute> ++ </group> ++ </optional> ++ </element> ++ </optional> ++ <optional> ++ <element name="last_update"> ++ <attribute name="time"> <text /> </attribute> ++ </element> ++ <element name="last_change"> ++ <attribute name="time"> <text /> </attribute> ++ <attribute name="user"> <text /> </attribute> ++ <attribute name="client"> <text /> </attribute> ++ <attribute name="origin"> <text /> </attribute> ++ </element> ++ </optional> ++ <optional> ++ <element name="nodes_configured"> ++ <attribute name="number"> <data type="nonNegativeInteger" /> </attribute> ++ </element> ++ <element name="resources_configured"> ++ <attribute name="number"> <data type="nonNegativeInteger" /> </attribute> ++ <attribute name="disabled"> <data type="nonNegativeInteger" /> </attribute> ++ <attribute name="blocked"> <data type="nonNegativeInteger" /> </attribute> ++ </element> ++ </optional> ++ <optional> ++ <element name="cluster_options"> ++ <attribute name="stonith-enabled"> <data type="boolean" /> </attribute> ++ <attribute name="symmetric-cluster"> <data type="boolean" /> </attribute> ++ <attribute name="no-quorum-policy"> <text /> </attribute> ++ <attribute name="maintenance-mode"> <data type="boolean" /> </attribute> ++ <attribute name="stop-all-resources"> <data type="boolean" /> </attribute> ++ </element> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="resources-list"> ++ <element name="resources"> ++ <zeroOrMore> ++ <externalRef href="resources-2.4.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="nodes-list"> ++ <element name="nodes"> ++ <zeroOrMore> ++ <externalRef href="nodes-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="node-attributes-list"> ++ <element name="node_attributes"> ++ <zeroOrMore> ++ <externalRef href="node-attrs-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="node-history-list"> ++ <element name="node_history"> ++ <zeroOrMore> ++ <ref name="element-node-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="failures-list"> ++ <element name="failures"> ++ <zeroOrMore> ++ <externalRef href="failure-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="fence-event-list"> ++ <element name="fence_history"> ++ <optional> ++ <attribute name="status"> <data type="integer" /> </attribute> ++ </optional> ++ <zeroOrMore> ++ <externalRef href="fence-event-2.0.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="tickets-list"> ++ <element name="tickets"> ++ <zeroOrMore> ++ <ref name="element-ticket" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="bans-list"> ++ <element name="bans"> ++ <zeroOrMore> ++ <ref name="element-ban" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-node-history"> ++ <element name="node"> ++ <attribute name="name"> <text /> </attribute> ++ <zeroOrMore> ++ <ref name="element-resource-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-resource-history"> ++ <element name="resource_history"> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="orphan"> <data type="boolean" /> </attribute> ++ <optional> ++ <group> ++ <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> ++ <optional> ++ <attribute name="fail-count"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-failure"> <text /> </attribute> ++ </optional> ++ </group> ++ </optional> ++ <zeroOrMore> ++ <ref name="element-operation-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-operation-history"> ++ <element name="operation_history"> ++ <attribute name="call"> <text /> </attribute> ++ <attribute name="task"> <text /> </attribute> ++ <optional> ++ <attribute name="interval"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-rc-change"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-run"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="exec-time"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="queue-time"> <text /> </attribute> ++ </optional> ++ <attribute name="rc"> <data type="integer" /> </attribute> ++ <attribute name="rc_text"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-ticket"> ++ <element name="ticket"> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="status"> ++ <choice> ++ <value>granted</value> ++ <value>revoked</value> ++ </choice> ++ </attribute> ++ <attribute name="standby"> <data type="boolean" /> </attribute> ++ <optional> ++ <attribute name="last-granted"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-ban"> ++ <element name="ban"> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="resource"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="weight"> <data type="integer" /> </attribute> ++ <attribute name="promoted-only"> <data type="boolean" /> </attribute> ++  ++ <attribute name="master_only"> <data type="boolean" /> </attribute> ++ </element> ++ </define> ++</grammar> +-- +1.8.3.1 + + +From da394983f106f974274ddd94675a04c85086010e Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 18 Jun 2021 15:06:34 -0400 +Subject: [PATCH 2/5] Refactor: Split node history out into its own XML schema. + +This allows for sharing it between crm_mon and crm_simulate. +--- + xml/Makefile.am | 2 +- + xml/api/crm_mon-2.12.rng | 64 +-------------------------------------- + xml/api/node-history-2.12.rng | 70 +++++++++++++++++++++++++++++++++++++++++++ + 3 files changed, 72 insertions(+), 64 deletions(-) + create mode 100644 xml/api/node-history-2.12.rng + +diff --git a/xml/Makefile.am b/xml/Makefile.am +index b9448d4..8e7b6d3 100644 +--- a/xml/Makefile.am ++++ b/xml/Makefile.am +@@ -64,7 +64,7 @@ API_request_base = command-output \ + CIB_cfg_base = options nodes resources constraints fencing acls tags alerts + + # Names of all schemas (including top level and those included by others) +-API_base = $(API_request_base) fence-event failure generic-list item node-attrs nodes resources status ++API_base = $(API_request_base) fence-event failure generic-list item node-attrs node-history nodes resources status + CIB_base = cib $(CIB_cfg_base) status score rule nvset + + # Static schema files and transforms (only CIB has transforms) +diff --git a/xml/api/crm_mon-2.12.rng b/xml/api/crm_mon-2.12.rng +index ffec923..be14412 100644 +--- a/xml/api/crm_mon-2.12.rng ++++ b/xml/api/crm_mon-2.12.rng +@@ -20,7 +20,7 @@ + <ref name="node-attributes-list" /> + </optional> + <optional> +- <ref name="node-history-list" /> ++ <externalRef href="node-history-2.12.rng"/> + </optional> + <optional> + <ref name="failures-list" /> +@@ -113,14 +113,6 @@ + </element> + </define> + +- <define name="node-history-list"> +- <element name="node_history"> +- <zeroOrMore> +- <ref name="element-node-history" /> +- </zeroOrMore> +- </element> +- </define> +- + <define name="failures-list"> + <element name="failures"> + <zeroOrMore> +@@ -156,60 +148,6 @@ + </element> + </define> + +- <define name="element-node-history"> +- <element name="node"> +- <attribute name="name"> <text /> </attribute> +- <zeroOrMore> +- <ref name="element-resource-history" /> +- </zeroOrMore> +- </element> +- </define> +- +- <define name="element-resource-history"> +- <element name="resource_history"> +- <attribute name="id"> <text /> </attribute> +- <attribute name="orphan"> <data type="boolean" /> </attribute> +- <optional> +- <group> +- <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> +- <optional> +- <attribute name="fail-count"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="last-failure"> <text /> </attribute> +- </optional> +- </group> +- </optional> +- <zeroOrMore> +- <ref name="element-operation-history" /> +- </zeroOrMore> +- </element> +- </define> +- +- <define name="element-operation-history"> +- <element name="operation_history"> +- <attribute name="call"> <text /> </attribute> +- <attribute name="task"> <text /> </attribute> +- <optional> +- <attribute name="interval"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="last-rc-change"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="last-run"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="exec-time"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="queue-time"> <text /> </attribute> +- </optional> +- <attribute name="rc"> <data type="integer" /> </attribute> +- <attribute name="rc_text"> <text /> </attribute> +- </element> +- </define> +- + <define name="element-ticket"> + <element name="ticket"> + <attribute name="id"> <text /> </attribute> +diff --git a/xml/api/node-history-2.12.rng b/xml/api/node-history-2.12.rng +new file mode 100644 +index 0000000..9628000 +--- /dev/null ++++ b/xml/api/node-history-2.12.rng +@@ -0,0 +1,70 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="node-history-list" /> ++ </start> ++ ++ <define name="node-history-list"> ++ <element name="node_history"> ++ <zeroOrMore> ++ <ref name="element-node-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-node-history"> ++ <element name="node"> ++ <attribute name="name"> <text /> </attribute> ++ <zeroOrMore> ++ <ref name="element-resource-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-resource-history"> ++ <element name="resource_history"> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="orphan"> <data type="boolean" /> </attribute> ++ <optional> ++ <group> ++ <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> ++ <optional> ++ <attribute name="fail-count"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-failure"> <text /> </attribute> ++ </optional> ++ </group> ++ </optional> ++ <zeroOrMore> ++ <ref name="element-operation-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-operation-history"> ++ <element name="operation_history"> ++ <attribute name="call"> <text /> </attribute> ++ <attribute name="task"> <text /> </attribute> ++ <optional> ++ <attribute name="interval"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-rc-change"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-run"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="exec-time"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="queue-time"> <text /> </attribute> ++ </optional> ++ <attribute name="rc"> <data type="integer" /> </attribute> ++ <attribute name="rc_text"> <text /> </attribute> ++ </element> ++ </define> ++</grammar> +-- +1.8.3.1 + + +From bf72b2615630eef7876e443d60b34d5a316de847 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Wed, 16 Jun 2021 14:09:31 -0400 +Subject: [PATCH 3/5] Low: schemas: Copy crm_simulate.rng in preparation for + changes. + +--- + xml/api/crm_simulate-2.12.rng | 335 ++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 335 insertions(+) + create mode 100644 xml/api/crm_simulate-2.12.rng + +diff --git a/xml/api/crm_simulate-2.12.rng b/xml/api/crm_simulate-2.12.rng +new file mode 100644 +index 0000000..9a7612d +--- /dev/null ++++ b/xml/api/crm_simulate-2.12.rng +@@ -0,0 +1,335 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="element-crm-simulate"/> ++ </start> ++ ++ <define name="element-crm-simulate"> ++ <choice> ++ <ref name="timings-list" /> ++ <group> ++ <ref name="cluster-status" /> ++ <optional> ++ <ref name="modifications-list" /> ++ </optional> ++ <optional> ++ <ref name="allocations-utilizations-list" /> ++ </optional> ++ <optional> ++ <ref name="action-list" /> ++ </optional> ++ <optional> ++ <ref name="cluster-injected-actions-list" /> ++ <ref name="revised-cluster-status" /> ++ </optional> ++ </group> ++ </choice> ++ </define> ++ ++ <define name="allocations-utilizations-list"> ++ <choice> ++ <element name="allocations"> ++ <zeroOrMore> ++ <choice> ++ <ref name="element-allocation" /> ++ <ref name="element-promotion" /> ++ </choice> ++ </zeroOrMore> ++ </element> ++ <element name="utilizations"> ++ <zeroOrMore> ++ <choice> ++ <ref name="element-capacity" /> ++ <ref name="element-utilization" /> ++ </choice> ++ </zeroOrMore> ++ </element> ++ <element name="allocations_utilizations"> ++ <zeroOrMore> ++ <choice> ++ <ref name="element-allocation" /> ++ <ref name="element-promotion" /> ++ <ref name="element-capacity" /> ++ <ref name="element-utilization" /> ++ </choice> ++ </zeroOrMore> ++ </element> ++ </choice> ++ </define> ++ ++ <define name="cluster-status"> ++ <element name="cluster_status"> ++ <ref name="nodes-list" /> ++ <ref name="resources-list" /> ++ <optional> ++ <ref name="node-attributes-list" /> ++ </optional> ++ <optional> ++ <ref name="failures-list" /> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="modifications-list"> ++ <element name="modifications"> ++ <optional> ++ <attribute name="quorum"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="watchdog"> <text /> </attribute> ++ </optional> ++ <zeroOrMore> ++ <ref name="element-inject-modify-node" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="element-inject-modify-ticket" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="element-inject-spec" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="element-inject-attr" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="revised-cluster-status"> ++ <element name="revised_cluster_status"> ++ <ref name="nodes-list" /> ++ <ref name="resources-list" /> ++ <optional> ++ <ref name="node-attributes-list" /> ++ </optional> ++ <optional> ++ <ref name="failures-list" /> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-inject-attr"> ++ <element name="inject_attr"> ++ <attribute name="cib_node"> <text /> </attribute> ++ <attribute name="name"> <text /> </attribute> ++ <attribute name="node_path"> <text /> </attribute> ++ <attribute name="value"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-inject-modify-node"> ++ <element name="modify_node"> ++ <attribute name="action"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-inject-spec"> ++ <element name="inject_spec"> ++ <attribute name="spec"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-inject-modify-ticket"> ++ <element name="modify_ticket"> ++ <attribute name="action"> <text /> </attribute> ++ <attribute name="ticket"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="cluster-injected-actions-list"> ++ <element name="transition"> ++ <zeroOrMore> ++ <ref name="element-injected-actions" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="node-attributes-list"> ++ <element name="node_attributes"> ++ <zeroOrMore> ++ <externalRef href="node-attrs-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="failures-list"> ++ <element name="failures"> ++ <zeroOrMore> ++ <externalRef href="failure-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="nodes-list"> ++ <element name="nodes"> ++ <zeroOrMore> ++ <externalRef href="nodes-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="resources-list"> ++ <element name="resources"> ++ <zeroOrMore> ++ <externalRef href="resources-2.4.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="timings-list"> ++ <element name="timings"> ++ <zeroOrMore> ++ <ref name="element-timing" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="action-list"> ++ <element name="actions"> ++ <zeroOrMore> ++ <ref name="element-node-action" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="element-rsc-action" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-allocation"> ++ <element name="node_weight"> ++ <attribute name="function"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ <externalRef href="../score.rng" /> ++ <optional> ++ <attribute name="id"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-capacity"> ++ <element name="capacity"> ++ <attribute name="comment"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ <zeroOrMore> ++ <element> ++ <anyName /> ++ <text /> ++ </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-inject-cluster-action"> ++ <element name="cluster_action"> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="task"> <text /> </attribute> ++ <optional> ++ <attribute name="id"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-injected-actions"> ++ <choice> ++ <ref name="element-inject-cluster-action" /> ++ <ref name="element-inject-fencing-action" /> ++ <ref name="element-inject-pseudo-action" /> ++ <ref name="element-inject-rsc-action" /> ++ </choice> ++ </define> ++ ++ <define name="element-inject-fencing-action"> ++ <element name="fencing_action"> ++ <attribute name="op"> <text /> </attribute> ++ <attribute name="target"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-node-action"> ++ <element name="node_action"> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="reason"> <text /> </attribute> ++ <attribute name="task"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-promotion"> ++ <element name="promotion_score"> ++ <attribute name="id"> <text /> </attribute> ++ <externalRef href="../score.rng" /> ++ <optional> ++ <attribute name="node"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-inject-pseudo-action"> ++ <element name="pseudo_action"> ++ <attribute name="task"> <text /> </attribute> ++ <optional> ++ <attribute name="node"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-inject-rsc-action"> ++ <element name="rsc_action"> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="op"> <text /> </attribute> ++ <attribute name="resource"> <text /> </attribute> ++ <optional> ++ <attribute name="interval"> <data type="integer" /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-timing"> ++ <element name="timing"> ++ <attribute name="file"> <text /> </attribute> ++ <attribute name="duration"> <data type="double" /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-rsc-action"> ++ <element name="rsc_action"> ++ <attribute name="action"> <text /> </attribute> ++ <attribute name="resource"> <text /> </attribute> ++ <optional> ++ <attribute name="blocked"> <data type="boolean" /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="dest"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="next-role"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="node"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="reason"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="role"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="source"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-utilization"> ++ <element name="utilization"> ++ <attribute name="function"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="resource"> <text /> </attribute> ++ <zeroOrMore> ++ <element> ++ <anyName /> ++ <text /> ++ </element> ++ </zeroOrMore> ++ </element> ++ </define> ++</grammar> +-- +1.8.3.1 + + +From c46e07788788acf5669e3f89b9344190a91c7331 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 18 Jun 2021 15:10:19 -0400 +Subject: [PATCH 4/5] Feature: tools: Add the node-summary to crm_simulate + output. + +If --show-failcounts is given to crm_simulate, it should also display +the node-summary message. + +See: rhbz#1686426 +--- + tools/crm_simulate.c | 7 +++++-- + xml/api/crm_simulate-2.12.rng | 3 +++ + 2 files changed, 8 insertions(+), 2 deletions(-) + +diff --git a/tools/crm_simulate.c b/tools/crm_simulate.c +index b4aa9d1..2ea292c 100644 +--- a/tools/crm_simulate.c ++++ b/tools/crm_simulate.c +@@ -409,11 +409,14 @@ print_cluster_status(pe_working_set_t * data_set, unsigned int print_opts) + FALSE, FALSE, all, all, FALSE); + + if (options.show_attrs) { +- out->message(out, "node-attribute-list", data_set, +- 0, rc == pcmk_rc_ok, FALSE, FALSE, FALSE, all, all); ++ rc = out->message(out, "node-attribute-list", data_set, ++ 0, rc == pcmk_rc_ok, FALSE, FALSE, FALSE, all, all); + } + + if (options.show_failcounts) { ++ rc = out->message(out, "node-summary", data_set, all, all, ++ 0, print_opts, FALSE, FALSE, FALSE, FALSE, rc == pcmk_rc_ok); ++ + out->message(out, "failed-action-list", data_set, all, all, + rc == pcmk_rc_ok); + } +diff --git a/xml/api/crm_simulate-2.12.rng b/xml/api/crm_simulate-2.12.rng +index 9a7612d..f90bd36 100644 +--- a/xml/api/crm_simulate-2.12.rng ++++ b/xml/api/crm_simulate-2.12.rng +@@ -67,6 +67,9 @@ + <ref name="node-attributes-list" /> + </optional> + <optional> ++ <externalRef href="node-history-2.12.rng" /> ++ </optional> ++ <optional> + <ref name="failures-list" /> + </optional> + </element> +-- +1.8.3.1 + + +From bac50336e0264604716e5997b87ee7e65311b982 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 18 Jun 2021 15:21:52 -0400 +Subject: [PATCH 5/5] Low: libcrmcommon: Increase PCMK__API_VERSION for new + crm_resource output. + +See: rhbz#1686426 +--- + include/crm/common/output_internal.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/crm/common/output_internal.h b/include/crm/common/output_internal.h +index 0436cde..ba9c423 100644 +--- a/include/crm/common/output_internal.h ++++ b/include/crm/common/output_internal.h +@@ -27,7 +27,7 @@ extern "C" { + # include <glib.h> + # include <crm/common/results.h> + +-# define PCMK__API_VERSION "2.11" ++# define PCMK__API_VERSION "2.12" + + #if defined(PCMK__WITH_ATTRIBUTE_OUTPUT_ARGS) + # define PCMK__OUTPUT_ARGS(ARGS...) __attribute__((output_args(ARGS))) +-- +1.8.3.1 + diff --git a/007-unfencing-loop.patch b/007-unfencing-loop.patch new file mode 100644 index 0000000..d4950c8 --- /dev/null +++ b/007-unfencing-loop.patch @@ -0,0 +1,733 @@ +From 6dcd6b51d7d3993bc483588d6ed75077518ed600 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 4 Jun 2021 16:30:55 -0500 +Subject: [PATCH 01/11] Low: controller: check whether unfenced node was remote + node + +... so the controller can indicate the node is remote (if known at that point, +which is not guaranteed) when setting unfencing-related node attributes. +--- + daemons/controld/controld_fencing.c | 21 ++++++++++++++++++--- + 1 file changed, 18 insertions(+), 3 deletions(-) + +diff --git a/daemons/controld/controld_fencing.c b/daemons/controld/controld_fencing.c +index 23dff28..0fba661 100644 +--- a/daemons/controld/controld_fencing.c ++++ b/daemons/controld/controld_fencing.c +@@ -757,15 +757,30 @@ tengine_stonith_callback(stonith_t *stonith, stonith_callback_data_t *data) + if (pcmk__str_eq("on", op, pcmk__str_casei)) { + const char *value = NULL; + char *now = pcmk__ttoa(time(NULL)); ++ gboolean is_remote_node = FALSE; ++ ++ /* This check is not 100% reliable, since this node is not ++ * guaranteed to have the remote node cached. However, it ++ * doesn't have to be reliable, since the attribute manager can ++ * learn a node's "remoteness" by other means sooner or later. ++ * This allows it to learn more quickly if this node does have ++ * the information. ++ */ ++ if (g_hash_table_lookup(crm_remote_peer_cache, uuid) != NULL) { ++ is_remote_node = TRUE; ++ } + +- update_attrd(target, CRM_ATTR_UNFENCED, now, NULL, FALSE); ++ update_attrd(target, CRM_ATTR_UNFENCED, now, NULL, ++ is_remote_node); + free(now); + + value = crm_meta_value(action->params, XML_OP_ATTR_DIGESTS_ALL); +- update_attrd(target, CRM_ATTR_DIGESTS_ALL, value, NULL, FALSE); ++ update_attrd(target, CRM_ATTR_DIGESTS_ALL, value, NULL, ++ is_remote_node); + + value = crm_meta_value(action->params, XML_OP_ATTR_DIGESTS_SECURE); +- update_attrd(target, CRM_ATTR_DIGESTS_SECURE, value, NULL, FALSE); ++ update_attrd(target, CRM_ATTR_DIGESTS_SECURE, value, NULL, ++ is_remote_node); + + } else if (action->sent_update == FALSE) { + send_stonith_update(action, target, uuid); +-- +1.8.3.1 + + +From 3ef6d9403f68ab8559c45cc99f5a8da05ca6420b Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 10:50:36 -0500 +Subject: [PATCH 02/11] Refactor: pacemaker-attrd: functionize adding remote + node to cache + +... for future reuse +--- + daemons/attrd/attrd_commands.c | 34 +++++++++++++++++++++++----------- + 1 file changed, 23 insertions(+), 11 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 731c243..93a165b 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -102,6 +102,28 @@ free_attribute(gpointer data) + } + } + ++/*! ++ * \internal ++ * \brief Ensure a Pacemaker Remote node is in the correct peer cache ++ * ++ * \param[in] ++ */ ++static void ++cache_remote_node(const char *node_name) ++{ ++ /* If we previously assumed this node was an unseen cluster node, ++ * remove its entry from the cluster peer cache. ++ */ ++ crm_node_t *dup = pcmk__search_cluster_node_cache(0, node_name); ++ ++ if (dup && (dup->uuid == NULL)) { ++ reap_crm_member(0, node_name); ++ } ++ ++ // Ensure node is in the remote peer cache ++ CRM_ASSERT(crm_remote_peer_get(node_name) != NULL); ++} ++ + static xmlNode * + build_attribute_xml( + xmlNode *parent, const char *name, const char *set, const char *uuid, unsigned int timeout_ms, const char *user, +@@ -709,17 +731,7 @@ attrd_lookup_or_create_value(GHashTable *values, const char *host, xmlNode *xml) + + crm_element_value_int(xml, PCMK__XA_ATTR_IS_REMOTE, &is_remote); + if (is_remote) { +- /* If we previously assumed this node was an unseen cluster node, +- * remove its entry from the cluster peer cache. +- */ +- crm_node_t *dup = pcmk__search_cluster_node_cache(0, host); +- +- if (dup && (dup->uuid == NULL)) { +- reap_crm_member(0, host); +- } +- +- /* Ensure this host is in the remote peer cache */ +- CRM_ASSERT(crm_remote_peer_get(host) != NULL); ++ cache_remote_node(host); + } + + if (v == NULL) { +-- +1.8.3.1 + + +From 6fac2c71bc2c56870ac828d7cd7b7c799279c47e Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 10:39:34 -0500 +Subject: [PATCH 03/11] Refactor: pacemaker-attrd: don't try to remove votes + for remote nodes + +Remote nodes never vote. + +This has no effect in practice since the removal would simply do nothing, +but we might as well not waste time trying. +--- + daemons/attrd/attrd_commands.c | 11 ++++++----- + 1 file changed, 6 insertions(+), 5 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 93a165b..dbe777e 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -976,7 +976,8 @@ attrd_election_cb(gpointer user_data) + void + attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *data) + { +- bool remove_voter = FALSE; ++ bool gone = false; ++ bool is_remote = pcmk_is_set(peer->flags, crm_remote_node); + + switch (kind) { + case crm_status_uname: +@@ -984,7 +985,7 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da + + case crm_status_processes: + if (!pcmk_is_set(peer->processes, crm_get_cluster_proc())) { +- remove_voter = TRUE; ++ gone = true; + } + break; + +@@ -1000,13 +1001,13 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da + } else { + // Remove all attribute values associated with lost nodes + attrd_peer_remove(peer->uname, FALSE, "loss"); +- remove_voter = TRUE; ++ gone = true; + } + break; + } + +- // In case an election is in progress, remove any vote by the node +- if (remove_voter) { ++ // Remove votes from cluster nodes that leave, in case election in progress ++ if (gone && !is_remote) { + attrd_remove_voter(peer); + } + } +-- +1.8.3.1 + + +From 54089fc663d6aaf10ca164c6c94b3b17237788de Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 10:40:06 -0500 +Subject: [PATCH 04/11] Low: pacemaker-attrd: check for remote nodes in peer + update callback + +If a remote node was started before the local cluster node joined the cluster, +the cluster node will assume its node attributes are for a cluster node until +it learns otherwise. Check for remoteness in the peer update callback, to have +another way we can learn it. +--- + daemons/attrd/attrd_commands.c | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index dbe777e..5f6a754 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -1009,6 +1009,10 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da + // Remove votes from cluster nodes that leave, in case election in progress + if (gone && !is_remote) { + attrd_remove_voter(peer); ++ ++ // Ensure remote nodes that come up are in the remote node cache ++ } else if (!gone && is_remote) { ++ cache_remote_node(peer->uname); + } + } + +-- +1.8.3.1 + + +From 8c048df0312d0d9c857d87b570a352429a710928 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 11:29:12 -0500 +Subject: [PATCH 05/11] Log: pacemaker-attrd: log peer status changes + +--- + daemons/attrd/attrd_commands.c | 9 +++++++++ + 1 file changed, 9 insertions(+) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 5f6a754..d6d179b 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -972,6 +972,7 @@ attrd_election_cb(gpointer user_data) + return FALSE; + } + ++#define state_text(state) ((state)? (const char *)(state) : "in unknown state") + + void + attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *data) +@@ -981,15 +982,23 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da + + switch (kind) { + case crm_status_uname: ++ crm_debug("%s node %s is now %s", ++ (is_remote? "Remote" : "Cluster"), ++ peer->uname, state_text(peer->state)); + break; + + case crm_status_processes: + if (!pcmk_is_set(peer->processes, crm_get_cluster_proc())) { + gone = true; + } ++ crm_debug("Node %s is %s a peer", ++ peer->uname, (gone? "no longer" : "now")); + break; + + case crm_status_nstate: ++ crm_debug("%s node %s is now %s (was %s)", ++ (is_remote? "Remote" : "Cluster"), ++ peer->uname, state_text(peer->state), state_text(data)); + if (pcmk__str_eq(peer->state, CRM_NODE_MEMBER, pcmk__str_casei)) { + /* If we're the writer, send new peers a list of all attributes + * (unless it's a remote node, which doesn't run its own attrd) +-- +1.8.3.1 + + +From 1dcc8dee4990cf0dbdec0e14db6d9a3ad67a41d5 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 11:13:53 -0500 +Subject: [PATCH 06/11] Low: pacemaker-attrd: ensure node ID is only set for + attributes when known + +In most cases, attribute updates contained the node ID, and the node ID was +used by other code, only if known (i.e. positive). However a couple places did +not check this, so add that. + +I am unsure whether the missing check caused problems in practice, but there +appears to be the possibility that a remote node would wrongly be added to the +cluster node cache. +--- + daemons/attrd/attrd_commands.c | 6 ++++-- + 1 file changed, 4 insertions(+), 2 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index d6d179b..b3f441c 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -136,7 +136,9 @@ build_attribute_xml( + crm_xml_add(xml, PCMK__XA_ATTR_UUID, uuid); + crm_xml_add(xml, PCMK__XA_ATTR_USER, user); + crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, peer); +- crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); ++ if (peerid > 0) { ++ crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); ++ } + crm_xml_add(xml, PCMK__XA_ATTR_VALUE, value); + crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, timeout_ms/1000); + crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, is_private); +@@ -937,7 +939,7 @@ attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) + /* If this is a cluster node whose node ID we are learning, remember it */ + if ((v->nodeid == 0) && (v->is_remote == FALSE) + && (crm_element_value_int(xml, PCMK__XA_ATTR_NODE_ID, +- (int*)&v->nodeid) == 0)) { ++ (int*)&v->nodeid) == 0) && (v->nodeid > 0)) { + + crm_node_t *known_peer = crm_get_peer(v->nodeid, host); + +-- +1.8.3.1 + + +From 8d12490e88b558d01db37a38f7d35175c6d2d69a Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Thu, 10 Jun 2021 17:25:57 -0500 +Subject: [PATCH 07/11] Refactor: pacemaker-attrd: functionize processing a + sync response + +... for code isolation, and because we need to add more to it +--- + daemons/attrd/attrd_commands.c | 59 ++++++++++++++++++++++++++++-------------- + 1 file changed, 39 insertions(+), 20 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index b3f441c..d02d3e6 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -572,6 +572,43 @@ attrd_peer_clear_failure(crm_node_t *peer, xmlNode *xml) + } + + /*! ++ * \internal ++ * \brief Load attributes from a peer sync response ++ * ++ * \param[in] peer Peer that sent clear request ++ * \param[in] peer_won Whether peer is the attribute writer ++ * \param[in] xml Request XML ++ */ ++static void ++process_peer_sync_response(crm_node_t *peer, bool peer_won, xmlNode *xml) ++{ ++ crm_info("Processing " PCMK__ATTRD_CMD_SYNC_RESPONSE " from %s", ++ peer->uname); ++ ++ if (peer_won) { ++ /* Initialize the "seen" flag for all attributes to cleared, so we can ++ * detect attributes that local node has but the writer doesn't. ++ */ ++ clear_attribute_value_seen(); ++ } ++ ++ // Process each attribute update in the sync response ++ for (xmlNode *child = pcmk__xml_first_child(xml); child != NULL; ++ child = pcmk__xml_next(child)) { ++ attrd_peer_update(peer, child, ++ crm_element_value(child, PCMK__XA_ATTR_NODE_NAME), ++ TRUE); ++ } ++ ++ if (peer_won) { ++ /* If any attributes are still not marked as seen, the writer doesn't ++ * know about them, so send all peers an update with them. ++ */ ++ attrd_current_only_attribute_update(peer, xml); ++ } ++} ++ ++/*! + \internal + \brief Broadcast private attribute for local node with protocol version + */ +@@ -596,7 +633,7 @@ attrd_peer_message(crm_node_t *peer, xmlNode *xml) + const char *op = crm_element_value(xml, PCMK__XA_TASK); + const char *election_op = crm_element_value(xml, F_CRM_TASK); + const char *host = crm_element_value(xml, PCMK__XA_ATTR_NODE_NAME); +- bool peer_won = FALSE; ++ bool peer_won = false; + + if (election_op) { + attrd_handle_election_op(peer, xml); +@@ -631,25 +668,7 @@ attrd_peer_message(crm_node_t *peer, xmlNode *xml) + + } else if (pcmk__str_eq(op, PCMK__ATTRD_CMD_SYNC_RESPONSE, pcmk__str_casei) + && !pcmk__str_eq(peer->uname, attrd_cluster->uname, pcmk__str_casei)) { +- xmlNode *child = NULL; +- +- crm_info("Processing %s from %s", op, peer->uname); +- +- /* Clear the seen flag for attribute processing held only in the own node. */ +- if (peer_won) { +- clear_attribute_value_seen(); +- } +- +- for (child = pcmk__xml_first_child(xml); child != NULL; +- child = pcmk__xml_next(child)) { +- host = crm_element_value(child, PCMK__XA_ATTR_NODE_NAME); +- attrd_peer_update(peer, child, host, TRUE); +- } +- +- if (peer_won) { +- /* Synchronize if there is an attribute held only by own node that Writer does not have. */ +- attrd_current_only_attribute_update(peer, xml); +- } ++ process_peer_sync_response(peer, peer_won, xml); + + } else if (pcmk__str_eq(op, PCMK__ATTRD_CMD_FLUSH, pcmk__str_casei)) { + /* Ignore. The flush command was removed in 2.0.0 but may be +-- +1.8.3.1 + + +From a890a0e5bbbcabf907f51ed0460868035f72464d Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 11 Jun 2021 14:40:39 -0500 +Subject: [PATCH 08/11] Refactor: pacemaker-attrd: functionize broadcasting + local override + +... for code isolation +--- + daemons/attrd/attrd_commands.c | 42 +++++++++++++++++++++++++++++------------- + 1 file changed, 29 insertions(+), 13 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index d02d3e6..4783427 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -804,6 +804,34 @@ attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml) + free_xml(sync); + } + ++/*! ++ * \internal ++ * \brief Override an attribute sync with a local value ++ * ++ * Broadcast the local node's value for an attribute that's different from the ++ * value provided in a peer's attribute synchronization response. This ensures a ++ * node's values for itself take precedence and all peers are kept in sync. ++ * ++ * \param[in] a Attribute entry to override ++ * ++ * \return Local instance of attribute value ++ */ ++static attribute_value_t * ++broadcast_local_value(attribute_t *a) ++{ ++ attribute_value_t *v = g_hash_table_lookup(a->values, attrd_cluster->uname); ++ xmlNode *sync = create_xml_node(NULL, __func__); ++ ++ crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); ++ build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, ++ a->user, a->is_private, v->nodename, v->nodeid, ++ v->current, FALSE); ++ attrd_xml_add_writer(sync); ++ send_attrd_message(NULL, sync); ++ free_xml(sync); ++ return v; ++} ++ + void + attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) + { +@@ -899,21 +927,9 @@ attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) + if (filter && !pcmk__str_eq(v->current, value, pcmk__str_casei) + && pcmk__str_eq(host, attrd_cluster->uname, pcmk__str_casei)) { + +- xmlNode *sync = create_xml_node(NULL, __func__); +- + crm_notice("%s[%s]: local value '%s' takes priority over '%s' from %s", + attr, host, v->current, value, peer->uname); +- +- crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); +- v = g_hash_table_lookup(a->values, host); +- build_attribute_xml(sync, attr, a->set, a->uuid, a->timeout_ms, a->user, +- a->is_private, v->nodename, v->nodeid, v->current, FALSE); +- +- attrd_xml_add_writer(sync); +- +- /* Broadcast in case any other nodes had the inconsistent value */ +- send_attrd_message(NULL, sync); +- free_xml(sync); ++ v = broadcast_local_value(a); + + } else if (!pcmk__str_eq(v->current, value, pcmk__str_casei)) { + crm_notice("Setting %s[%s]: %s -> %s " CRM_XS " from %s", +-- +1.8.3.1 + + +From f6f65e3dab070f1bbdf6d1383f4d6173a8840bc9 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 11 Jun 2021 14:50:29 -0500 +Subject: [PATCH 09/11] Log: pacemaker-attrd: improve messages when + broadcasting local-only values + +The traces aren't necessary since build_attribute_xml() already logs the same +info at debug. Also, rename function for clarity, and make static. +--- + daemons/attrd/attrd_commands.c | 35 ++++++++++++++++------------------- + 1 file changed, 16 insertions(+), 19 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 4783427..356defb 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -51,11 +51,12 @@ GHashTable *attributes = NULL; + + void write_attribute(attribute_t *a, bool ignore_delay); + void write_or_elect_attribute(attribute_t *a); +-void attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml); + void attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter); + void attrd_peer_sync(crm_node_t *peer, xmlNode *xml); + void attrd_peer_remove(const char *host, gboolean uncache, const char *source); + ++static void broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml); ++ + static gboolean + send_attrd_message(crm_node_t * node, xmlNode * data) + { +@@ -604,7 +605,7 @@ process_peer_sync_response(crm_node_t *peer, bool peer_won, xmlNode *xml) + /* If any attributes are still not marked as seen, the writer doesn't + * know about them, so send all peers an update with them. + */ +- attrd_current_only_attribute_update(peer, xml); ++ broadcast_unseen_local_values(peer, xml); + } + } + +@@ -768,40 +769,36 @@ attrd_lookup_or_create_value(GHashTable *values, const char *host, xmlNode *xml) + return(v); + } + +-void +-attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml) ++void ++broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml) + { + GHashTableIter aIter; + GHashTableIter vIter; +- attribute_t *a; ++ attribute_t *a = NULL; + attribute_value_t *v = NULL; +- xmlNode *sync = create_xml_node(NULL, __func__); +- gboolean build = FALSE; +- +- crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); ++ xmlNode *sync = NULL; + + g_hash_table_iter_init(&aIter, attributes); + while (g_hash_table_iter_next(&aIter, NULL, (gpointer *) & a)) { + g_hash_table_iter_init(&vIter, a->values); + while (g_hash_table_iter_next(&vIter, NULL, (gpointer *) & v)) { +- if (pcmk__str_eq(v->nodename, attrd_cluster->uname, pcmk__str_casei) && v->seen == FALSE) { +- crm_trace("Syncing %s[%s] = %s to everyone.(from local only attributes)", a->id, v->nodename, v->current); +- +- build = TRUE; ++ if (!(v->seen) && pcmk__str_eq(v->nodename, attrd_cluster->uname, ++ pcmk__str_casei)) { ++ if (sync == NULL) { ++ sync = create_xml_node(NULL, __func__); ++ crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); ++ } + build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, + v->nodename, v->nodeid, v->current, (a->timeout_ms && a->timer ? TRUE : FALSE)); +- } else { +- crm_trace("Local attribute(%s[%s] = %s) was ignore.(another host) : [%s]", a->id, v->nodename, v->current, attrd_cluster->uname); +- continue; + } + } + } + +- if (build) { +- crm_debug("Syncing values to everyone.(from local only attributes)"); ++ if (sync != NULL) { ++ crm_debug("Broadcasting local-only values"); + send_attrd_message(NULL, sync); ++ free_xml(sync); + } +- free_xml(sync); + } + + /*! +-- +1.8.3.1 + + +From ab90ffb785ea018556f216b8f540f8c3429a3947 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 11 Jun 2021 15:04:20 -0500 +Subject: [PATCH 10/11] Refactor: pacemaker-attrd: simplify attribute XML + creation function + +... and rename for clarity +--- + daemons/attrd/attrd_commands.c | 48 ++++++++++++++++++++++++------------------ + 1 file changed, 27 insertions(+), 21 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 356defb..5b32a77 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -125,25 +125,35 @@ cache_remote_node(const char *node_name) + CRM_ASSERT(crm_remote_peer_get(node_name) != NULL); + } + ++/*! ++ * \internal ++ * \brief Create an XML representation of an attribute for use in peer messages ++ * ++ * \param[in] parent Create attribute XML as child element of this element ++ * \param[in] a Attribute to represent ++ * \param[in] v Attribute value to represent ++ * \param[in] force_write If true, value should be written even if unchanged ++ * ++ * \return XML representation of attribute ++ */ + static xmlNode * +-build_attribute_xml( +- xmlNode *parent, const char *name, const char *set, const char *uuid, unsigned int timeout_ms, const char *user, +- gboolean is_private, const char *peer, uint32_t peerid, const char *value, gboolean is_force_write) ++add_attribute_value_xml(xmlNode *parent, attribute_t *a, attribute_value_t *v, ++ bool force_write) + { + xmlNode *xml = create_xml_node(parent, __func__); + +- crm_xml_add(xml, PCMK__XA_ATTR_NAME, name); +- crm_xml_add(xml, PCMK__XA_ATTR_SET, set); +- crm_xml_add(xml, PCMK__XA_ATTR_UUID, uuid); +- crm_xml_add(xml, PCMK__XA_ATTR_USER, user); +- crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, peer); +- if (peerid > 0) { +- crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); ++ crm_xml_add(xml, PCMK__XA_ATTR_NAME, a->id); ++ crm_xml_add(xml, PCMK__XA_ATTR_SET, a->set); ++ crm_xml_add(xml, PCMK__XA_ATTR_UUID, a->uuid); ++ crm_xml_add(xml, PCMK__XA_ATTR_USER, a->user); ++ crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, v->nodename); ++ if (v->nodeid > 0) { ++ crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, v->nodeid); + } +- crm_xml_add(xml, PCMK__XA_ATTR_VALUE, value); +- crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, timeout_ms/1000); +- crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, is_private); +- crm_xml_add_int(xml, PCMK__XA_ATTR_FORCE, is_force_write); ++ crm_xml_add(xml, PCMK__XA_ATTR_VALUE, v->current); ++ crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, a->timeout_ms / 1000); ++ crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, a->is_private); ++ crm_xml_add_int(xml, PCMK__XA_ATTR_FORCE, force_write); + + return xml; + } +@@ -695,8 +705,7 @@ attrd_peer_sync(crm_node_t *peer, xmlNode *xml) + g_hash_table_iter_init(&vIter, a->values); + while (g_hash_table_iter_next(&vIter, NULL, (gpointer *) & v)) { + crm_debug("Syncing %s[%s] = %s to %s", a->id, v->nodename, v->current, peer?peer->uname:"everyone"); +- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, +- v->nodename, v->nodeid, v->current, FALSE); ++ add_attribute_value_xml(sync, a, v, false); + } + } + +@@ -788,8 +797,7 @@ broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml) + sync = create_xml_node(NULL, __func__); + crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); + } +- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, +- v->nodename, v->nodeid, v->current, (a->timeout_ms && a->timer ? TRUE : FALSE)); ++ add_attribute_value_xml(sync, a, v, a->timeout_ms && a->timer); + } + } + } +@@ -820,9 +828,7 @@ broadcast_local_value(attribute_t *a) + xmlNode *sync = create_xml_node(NULL, __func__); + + crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); +- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, +- a->user, a->is_private, v->nodename, v->nodeid, +- v->current, FALSE); ++ add_attribute_value_xml(sync, a, v, false); + attrd_xml_add_writer(sync); + send_attrd_message(NULL, sync); + free_xml(sync); +-- +1.8.3.1 + + +From 540d74130c5c8d9c626d6c50475e4dc4f64234e7 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 4 Jun 2021 16:34:26 -0500 +Subject: [PATCH 11/11] Fix: pacemaker-attrd: avoid repeated unfencing of + remote nodes + +The attribute manager can't record a remote node's attributes to the CIB until +it knows the node is remote. Normally, this is learned when the remote node +starts, because the controller clears the CRM_OP_PROBED attribute and indicates +that it is for a remote node. + +However, if a cluster node is down when a remote node starts, and later comes +up, it learns the remote node's existing attributes as part of the attribute +sync. Previously, this did not include whether each value is for a cluster or +remote node, so the newly joined attribute manager couldn't write out remote +nodes' attributes until it learned that via some other event -- which might not +happen before the node becomes DC, in which case its scheduler will not see any +unfencing-related node attributes and may wrongly schedule unfencing. + +The sync response handling already calls attrd_lookup_or_create_value(), which +checks PCMK__XA_ATTR_IS_REMOTE, so all we need to do is add that to the sync +response. +--- + daemons/attrd/attrd_commands.c | 6 +++++- + 1 file changed, 5 insertions(+), 1 deletion(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 5b32a77..0142383 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -43,8 +43,9 @@ + * 1 1.1.15 PCMK__ATTRD_CMD_UPDATE_BOTH, + * PCMK__ATTRD_CMD_UPDATE_DELAY + * 2 1.1.17 PCMK__ATTRD_CMD_CLEAR_FAILURE ++ * 3 2.1.1 PCMK__ATTRD_CMD_SYNC_RESPONSE indicates remote nodes + */ +-#define ATTRD_PROTOCOL_VERSION "2" ++#define ATTRD_PROTOCOL_VERSION "3" + + int last_cib_op_done = 0; + GHashTable *attributes = NULL; +@@ -150,6 +151,9 @@ add_attribute_value_xml(xmlNode *parent, attribute_t *a, attribute_value_t *v, + if (v->nodeid > 0) { + crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, v->nodeid); + } ++ if (v->is_remote != 0) { ++ crm_xml_add_int(xml, PCMK__XA_ATTR_IS_REMOTE, 1); ++ } + crm_xml_add(xml, PCMK__XA_ATTR_VALUE, v->current); + crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, a->timeout_ms / 1000); + crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, a->is_private); +-- +1.8.3.1 + diff --git a/gating.yaml b/gating.yaml index 9e15ced..e8aadb9 100644 --- a/gating.yaml +++ b/gating.yaml @@ -5,6 +5,7 @@ decision_context: bodhi_update_push_testing subject_type: koji_build rules: - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} + --- !Policy product_versions: - fedora-* @@ -13,3 +14,9 @@ subject_type: koji_build rules: - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} +--- !Policy +product_versions: + - rhel-* +decision_context: osci_compose_gate +rules: + - !PassingTestCaseRule {test_case_name: osci.brew-build.tier0.functional} diff --git a/pacemaker.spec b/pacemaker.spec index 1f9dce2..48b6a44 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -1,9 +1,9 @@ -# Globals and defines to control package behavior (configure these as desired) +# User-configurable globals and defines to control package behavior +# (these should not test {with X} values, which are declared later) ## User and group to use for nonprivileged services %global uname hacluster %global gname haclient -%global hacluster_id 189 ## Where to install Pacemaker documentation %if 0%{?rhel} @@ -17,6 +17,13 @@ ## Where bug reports should be submitted ## Leave bug_url undefined to use ClusterLabs default, others define it here +%if 0%{?rhel} +%global bug_url https://bugzilla.redhat.com/ +%else +%if 0%{?fedora} +%global bug_url https://bugz.fedoraproject.org/%{name} +%endif +%endif ## What to use as the OCF resource agent root directory %global ocf_root %{_prefix}/lib/ocf @@ -25,19 +32,21 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.0 -%global specversion 4 +%global specversion 6 + +## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build +%global commit 7c3f660707a495a1331716ad32cd3ac9d9f8ff58 -## Upstream commit (or git tag, such as "Pacemaker-" plus the -## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.1.0-rc3 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 + # Define conditionals so that "rpmbuild --with <feature>" and # "rpmbuild --without <feature>" can enable and disable specific features -## NOTE: skip --with stonithd +## Add option to enable support for stonith/external fencing agents +%bcond_with stonithd ## Add option for whether to support storing sensitive information outside CIB %if (0%{?fedora} && 0%{?fedora} <= 33) || (0%{?rhel} && 0%{?rhel} <= 8) @@ -52,8 +61,13 @@ ## Add option to create binaries with coverage analysis %bcond_with coverage -## Add option to skip/enable generating documentation +## Add option to skip (or enable, on RHEL) generating documentation +## (the build tools aren't available everywhere) +%if 0%{?rhel} +%bcond_with doc +%else %bcond_without doc +%endif ## Add option to default to start-up synchronization with SBD. ## @@ -66,16 +80,19 @@ ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) -%bcond_without pre_release +%bcond_with pre_release ## NOTE: skip --with upstart_job ## Add option to turn off hardening of libraries and daemon executables %bcond_without hardening -## Add option to enable links for legacy daemon names +## Add option to enable (or disable, on RHEL 8) links for legacy daemon names +%if 0%{?rhel} && 0%{?rhel} <= 8 +%bcond_without legacy_links +%else %bcond_with legacy_links - +%endif ## Nagios source control identifiers %global nagios_name nagios-agents-metadata @@ -94,29 +111,36 @@ ## Portion of export/dist tarball name after "pacemaker-", and release version %if 0%{tag_release} -%define archive_version %{commit} +%define archive_version %(c=%{commit}; echo ${c:10}) %define archive_github_url %{commit}#/%{name}-%{archive_version}.tar.gz -%define pcmk_release %(c=%{commit}; case $c in *-rc[[:digit:]]*%{rparen} - echo 0.%{specversion}.${c: -3} ;; - *%{rparen} echo %{specversion} ;; esac) %else %define archive_version %(c=%{commit}; echo ${c:0:%{commit_abbrev}}) %define archive_github_url %{archive_version}#/%{name}-%{archive_version}.tar.gz -%if %{with pre_release} -%define pcmk_release 0.%{specversion}.%{archive_version}.git -%else -%define pcmk_release %{specversion}.%{archive_version}.git -%endif %endif +### Always use a simple release number +%define pcmk_release %{specversion} ## Base GnuTLS cipher priorities (presumably only the initial, required keyword) ## overridable with "rpmbuild --define 'pcmk_gnutls_priorities PRIORITY-SPEC'" %define gnutls_priorities %{?pcmk_gnutls_priorities}%{!?pcmk_gnutls_priorities:@SYSTEM} +## Different distros name certain packages differently +## (note: corosync libraries also differ, but all provide corosync-devel) +%global pkgname_libtool_devel libtool-ltdl-devel +%global pkgname_libtool_devel_arch libtool-ltdl-devel%{?_isa} +%global pkgname_bzip2_devel bzip2-devel +%global pkgname_docbook_xsl docbook-style-xsl +%global pkgname_gnutls_devel gnutls-devel +%global pkgname_shadow_utils shadow-utils +%global pkgname_procps procps-ng +%global pkgname_glue_libs cluster-glue-libs +%global pkgname_pcmk_libs %{name}-libs +%global hacluster_id 189 + ## Distro-specific configuration choices ### Use 2.0-style output when other distro packages don't support current output -%if 0%{?fedora} +%if 0%{?fedora} || ( 0%{?rhel} && 0%{?rhel} <= 8 ) %global compat20 --enable-compat-2.0 %endif @@ -130,6 +154,7 @@ %global resource_stickiness --with-resource-stickiness-default=1 %endif + # Python-related definitions ## Turn off auto-compilation of Python files outside Python specific paths, @@ -145,13 +170,24 @@ sed -e 's!/usr/lib[^[:space:]]*/brp-python-bytecompile[[:space:]].*$!!g'; }) %endif -## Values that differ by Python major version +## Prefer Python 3 definitions explicitly, in case 2 is also available +%if %{defined __python3} %global python_name python3 -%global python_path %{?__python3}%{!?__python3:/usr/bin/python%{?python3_pkgversion}%{!?python3_pkgversion:3}} +%global python_path %{__python3} %define python_site %{?python3_sitelib}%{!?python3_sitelib:%( %{python_path} -c 'from distutils.sysconfig import get_python_lib as gpl; print(gpl(1))' 2>/dev/null)} -%global python_min 3.2 -# python_min still required? +%else +%if %{defined python_version} +%global python_name python%(echo %{python_version} | cut -d'.' -f1) +%define python_path %{?__python}%{!?__python:/usr/bin/%{python_name}} +%else +%global python_name python +%global python_path %{?__python}%{!?__python:/usr/bin/python%{?python_pkgversion}} +%endif +%define python_site %{?python_sitelib}%{!?python_sitelib:%( + %{python_name} -c 'from distutils.sysconfig import get_python_lib as gpl; print(gpl(1))' 2>/dev/null)} +%endif + # Keep sane profiling data if requested %if %{with profiling} @@ -165,25 +201,46 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ -Url: https://www.clusterlabs.org - -# Hint: use "spectool -s 0 pacemaker.spec" (rpmdevtools) to check the final URL +Url: https://www.clusterlabs.org/ + +# Example: https://codeload.github.com/ClusterLabs/pacemaker/tar.gz/e91769e +# will download pacemaker-e91769e.tar.gz +# +# The ending part starting with '#' is ignored by github but necessary for +# rpmbuild to know what the tar archive name is. (The downloaded file will be +# named correctly only for commit IDs, not tagged releases.) +# +# You can use "spectool -s 0 pacemaker.spec" (rpmdevtools) to show final URL. Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{archive_gith... Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... -# --- + +# upstream commits +Patch1: 001-ping-agent.patch +Patch2: 002-pacemakerd-options.patch +Patch3: 003-pacemakerd-output.patch +Patch4: 004-check-level.patch +Patch5: 005-crm_resource.patch +Patch6: 006-crm_simulate.patch +Patch7: 007-unfencing-loop.patch Requires: resource-agents -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Requires: %{name}-cluster-libs%{?_isa} = %{version}-%{release} Requires: %{name}-cli = %{version}-%{release} %{?systemd_requires} -# Pacemaker requires a minimum Python functionality -Requires: %{python_name} >= %{python_min} -BuildRequires: make -BuildRequires: %{python_name}-devel >= %{python_min} +%if %{defined centos} +ExclusiveArch: aarch64 i686 ppc64le s390x x86_64 %{arm} +%else +%if 0%{?rhel} +ExclusiveArch: aarch64 i686 ppc64le s390x x86_64 +%endif +%endif + +Requires: %{python_path} +BuildRequires: %{python_name}-devel # Pacemaker requires a minimum libqb functionality Requires: libqb >= 0.17.0 @@ -192,37 +249,41 @@ BuildRequires: libqb-devel >= 0.17.0 # Required basic build tools BuildRequires: coreutils findutils grep sed BuildRequires: autoconf automake gcc make pkgconfig -BuildRequires: libtool libtool-ltdl-devel +BuildRequires: libtool %{?pkgname_libtool_devel} # Required for core functionality BuildRequires: pkgconfig(glib-2.0) >= 2.42 BuildRequires: libxml2-devel libxslt-devel libuuid-devel -BuildRequires: bzip2-devel +BuildRequires: %{pkgname_bzip2_devel} # Enables optional functionality -BuildRequires: ncurses-devel docbook-style-xsl -BuildRequires: help2man gnutls-devel pam-devel pkgconfig(dbus-1) +BuildRequires: ncurses-devel %{pkgname_docbook_xsl} +BuildRequires: help2man %{pkgname_gnutls_devel} pam-devel pkgconfig(dbus-1) BuildRequires: pkgconfig(systemd) +# RH patches are created by git, so we need git to apply them +BuildRequires: git + Requires: corosync >= 2.0.0 BuildRequires: corosync-devel >= 2.0.0 -#XXX -#BuildRequires: pkgconfig(libcpg) -#BuildRequires: pkgconfig(libcfg) + +%if %{with stonithd} +BuildRequires: %{pkgname_glue_libs}-devel +%endif %if %{with doc} BuildRequires: asciidoc inkscape %{python_name}-sphinx %endif -# git-style patch application -#BuildRequires: git - Provides: pcmk-cluster-manager = %{version}-%{release} Provides: pcmk-cluster-manager%{?_isa} = %{version}-%{release} -# Pacemaker uses the crypto/md5 module from gnulib +# Bundled bits +## Pacemaker uses the crypto/md5-buffer module from gnulib +%if 0%{?fedora} || 0%{?rhel} Provides: bundled(gnulib) +%endif %description Pacemaker is an advanced, scalable High-Availability cluster resource @@ -236,18 +297,18 @@ when related resources fail and can be configured to periodically check resource health. Available rpmbuild rebuild options: - --with(out) : cibsecrets coverage doc hardening pre_release profiling + --with(out) : cibsecrets coverage doc hardening pre_release profiling stonithd %package cli License: GPLv2+ and LGPLv2+ Summary: Command line tools for controlling Pacemaker clusters -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Recommends: pcmk-cluster-manager = %{version}-%{release} # For crm_report Recommends: tar Recommends: bzip2 Requires: perl-TimeDate -Requires: procps-ng +Requires: %{pkgname_procps} Requires: psmisc Requires(post):coreutils @@ -259,28 +320,29 @@ The %{name}-cli package contains command line tools that can be used to query and control the cluster from machines that may, or may not, be part of the cluster. -%package libs +%package -n %{pkgname_pcmk_libs} License: GPLv2+ and LGPLv2+ Summary: Core Pacemaker libraries -Requires(pre): shadow-utils +Requires(pre): %{pkgname_shadow_utils} Requires: %{name}-schemas = %{version}-%{release} # sbd 1.4.0+ supports the libpe_status API for pe_working_set_t # sbd 1.4.2+ supports startup/shutdown handshake via pacemakerd-api # and handshake defaults to enabled for rhel builds -# sbd 1.4.3+ handshake defaults to enabled for fedora builds -Conflicts: sbd < 1.4.3 +# sbd 1.5.0+ handshake defaults to enabled with upstream sbd-release +# implicitly supports handshake defaults to enabled in this spec +Conflicts: sbd < 1.5.0 -%description libs +%description -n %{pkgname_pcmk_libs} Pacemaker is an advanced, scalable High-Availability cluster resource manager. -The %{name}-libs package contains shared libraries needed for cluster +The %{pkgname_pcmk_libs} package contains shared libraries needed for cluster nodes and those just running the CLI tools. %package cluster-libs License: GPLv2+ and LGPLv2+ Summary: Cluster Libraries used by Pacemaker -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} %description cluster-libs Pacemaker is an advanced, scalable High-Availability cluster resource @@ -292,7 +354,7 @@ libraries needed for nodes that will form part of the cluster nodes. %package remote License: GPLv2+ and LGPLv2+ Summary: Pacemaker remote executor daemon for non-cluster nodes -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Requires: %{name}-cli = %{version}-%{release} Requires: resource-agents # -remote can be fully independent of systemd @@ -308,35 +370,40 @@ The %{name}-remote package contains the Pacemaker Remote daemon which is capable of extending pacemaker functionality to remote nodes not running the full corosync/cluster stack. -%package libs-devel +%package -n %{pkgname_pcmk_libs}-devel License: GPLv2+ and LGPLv2+ Summary: Pacemaker development package -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Requires: %{name}-cluster-libs%{?_isa} = %{version}-%{release} -Requires: libtool-ltdl-devel%{?_isa} libuuid-devel%{?_isa} +Requires: %{?pkgname_libtool_devel_arch} libuuid-devel%{?_isa} Requires: libxml2-devel%{?_isa} libxslt-devel%{?_isa} -Requires: bzip2-devel%{?_isa} glib2-devel%{?_isa} +Requires: %{pkgname_bzip2_devel}%{?_isa} glib2-devel%{?_isa} Requires: libqb-devel%{?_isa} Requires: corosync-devel%{?_isa} >= 2.0.0 -%description libs-devel +%description -n %{pkgname_pcmk_libs}-devel Pacemaker is an advanced, scalable High-Availability cluster resource manager. -The %{name}-libs-devel package contains headers and shared libraries +The %{pkgname_pcmk_libs}-devel package contains headers and shared libraries for developing tools for Pacemaker. %package cts License: GPLv2+ and LGPLv2+ Summary: Test framework for cluster-related technologies like Pacemaker Requires: %{python_path} -Requires: %{python_name} >= %{python_min} -Requires: %{name}-libs = %{version}-%{release} -Requires: procps-ng +Requires: %{pkgname_pcmk_libs} = %{version}-%{release} +Requires: %{name}-cli = %{version}-%{release} +Requires: %{pkgname_procps} Requires: psmisc BuildArch: noarch +# systemd Python bindings are a separate package in some distros +%if %{defined systemd_requires} +%if %{defined fedora} || %{defined rhel} Requires: %{python_name}-systemd +%endif +%endif %description cts Test framework for cluster-related technologies like Pacemaker @@ -382,7 +449,10 @@ The metadata files required for Pacemaker to execute the nagios plugin monitor resources. %prep -%setup -q -a 1 -n %{name}-%{archive_version} +%autosetup -a 1 -n %{name}-%{archive_version} -S git_am -p 1 +# in f33 s390x complains but shouldn't hurt globally +# as configure.ac is checking for support +sed -i configure.ac -e "s/-Wall/-Wall -Wno-format-truncation/" %build @@ -420,11 +490,10 @@ export LDFLAGS_HARDENED_LIB="%{?_hardening_ldflags}" --with-initdir=%{_initrddir} \ --with-runstatedir=%{_rundir} \ --localstatedir=%{_var} \ - --with-version=%{version}-%{release} \ - --with-bug-url=https://bugz.fedoraproject.org/%{name} \ - --with-nagios \ - --with-nagios-metadata-dir=%{_datadir}/pacemaker/nagios/plugins-metadata/ \ - --with-nagios-plugin-dir=%{_libdir}/nagios/plugins/ + --with-nagios \ + --with-nagios-metadata-dir=%{_datadir}/pacemaker/nagios/plugins-metadata/ \ + --with-nagios-plugin-dir=%{_libdir}/nagios/plugins/ \ + --with-version=%{version}-%{release} make %{_smp_mflags} V=1 @@ -453,11 +522,7 @@ done mkdir -p ${RPM_BUILD_ROOT}%{_localstatedir}/lib/rpm-state/%{name} -# These are not actually scripts -find %{buildroot} -name '*.xml' -type f -print0 | xargs -0 chmod a-x - -# Don't package static libs -find %{buildroot} -name '*.a' -type f -print0 | xargs -0 rm -f +# Don't package libtool archives find %{buildroot} -name '*.la' -type f -print0 | xargs -0 rm -f # Do not package these either @@ -475,7 +540,7 @@ rm -f %{buildroot}/%{_initrddir}/pacemaker rm -f %{buildroot}/%{_initrddir}/pacemaker_remote # Byte-compile Python sources where suitable and the distro procedures known -%if %{defined py_byte_compile} && %{defined python_path} +%if %{defined py_byte_compile} %{py_byte_compile %{python_path} %{buildroot}%{_datadir}/pacemaker/tests} %if !%{defined _python_bytecompile_extra} %{py_byte_compile %{python_path} %{buildroot}%{python_site}/cts} @@ -552,15 +617,14 @@ fi %postun cli %systemd_postun_with_restart crm_mon.service -%pre libs -# XXX keep an eye on https://fedoraproject.org/wiki/Changes/SystemdSysusers -# reopened recently: -# https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.o... +%pre -n %{pkgname_pcmk_libs} +# @TODO Use sysusers.d: +# https://fedoraproject.org/wiki/Changes/Adopting_sysusers.d_format getent group %{gname} >/dev/null || groupadd -r %{gname} -g %{hacluster_id} getent passwd %{uname} >/dev/null || useradd -r -g %{gname} -u %{hacluster_id} -s /sbin/nologin -c "cluster user" %{uname} exit 0 -%ldconfig_scriptlets libs +%ldconfig_scriptlets -n %{pkgname_pcmk_libs} %ldconfig_scriptlets cluster-libs %files @@ -667,7 +731,7 @@ exit 0 %dir %attr (770, %{uname}, %{gname}) %{_var}/log/pacemaker %dir %attr (770, %{uname}, %{gname}) %{_var}/log/pacemaker/bundles -%files libs +%files -n %{pkgname_pcmk_libs} %{_libdir}/libcib.so.* %{_libdir}/liblrmd.so.* %{_libdir}/libcrmservice.so.* @@ -716,7 +780,7 @@ exit 0 %doc COPYING %doc ChangeLog -%files libs-devel +%files -n %{pkgname_pcmk_libs}-devel %{_includedir}/pacemaker %{_libdir}/*.so %if %{with coverage} @@ -742,6 +806,12 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Jul 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-6 +- synced/merged with CS9 spec-file for current 2.1.0-release build + +* Tue Jun 8 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.5.rc3 +- silence f33 s390x build complaining about possible format-trucation + * Mon Jun 07 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.4.rc3.1 - Rebuilt for Python 3.10 @@ -753,7 +823,7 @@ exit 0 * Fri Jun 04 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.3.rc2.1 - Rebuilt for Python 3.10 -* Mon Jun 1 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 +* Mon May 31 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc2, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc2 diff --git a/sources b/sources index af5cd77..2ab7f32 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.1.0-rc3.tar.gz) = eb17566e079d313394dab509b055e326b642508844d974a21cde62509a3a526e44977a57c65f80d5094f085fec8ad92eda0deed4f4dfd32ecf0c3b80722e5504 +SHA512 (pacemaker-7c3f66070.tar.gz) = e1c53d019c965395affc1bd78358927617c9bc8572c405ee884737a8213455c5e85102e6f58bb5239ab23ebe5aa794f72c9cc0746900b7a6cc14fd3cf1879064 commit 5dc83e38659be95da4423eed082e2fb0029e2848 Author: Python Maint <python-maint(a)redhat.com> Date: Mon Jun 7 19:14:33 2021 +0200 Rebuilt for Python 3.10 diff --git a/pacemaker.spec b/pacemaker.spec index bf413b5..1f9dce2 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -165,7 +165,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist} +Release: %{pcmk_release}%{?dist}.1 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -742,6 +742,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Jun 07 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.4.rc3.1 +- Rebuilt for Python 3.10 + * Mon Jun 07 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.4.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc3, for full details, see included ChangeLog file or commit e52de4390a10fcc15efd749a705386ea8b46e0b4 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Jun 7 15:55:07 2021 +0200 * Mon Jun 07 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.4.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc3, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc3 diff --git a/pacemaker.spec b/pacemaker.spec index a6800fc..bf413b5 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -25,11 +25,11 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.0 -%global specversion 3 +%global specversion 4 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.1.0-rc2 +%global commit Pacemaker-2.1.0-rc3 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -165,7 +165,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -742,6 +742,11 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Jun 07 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.4.rc3 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc3, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc3 + * Fri Jun 04 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.3.rc2.1 - Rebuilt for Python 3.10 diff --git a/sources b/sources index 76e3c9a..af5cd77 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.1.0-rc2.tar.gz) = 01396cd23b0cb49cab40b870e227b132f1e0c9b94cf6ac29d58e61bd3ff4ee4ea95fa6509c9a4a09179284b8fdbdba8319ceb46e8f94ce9cea92cf13832f9f4d +SHA512 (pacemaker-Pacemaker-2.1.0-rc3.tar.gz) = eb17566e079d313394dab509b055e326b642508844d974a21cde62509a3a526e44977a57c65f80d5094f085fec8ad92eda0deed4f4dfd32ecf0c3b80722e5504 commit 172718bb48a11ed751025770698e5452ae20a815 Author: Python Maint <python-maint(a)redhat.com> Date: Fri Jun 4 20:14:25 2021 +0200 Rebuilt for Python 3.10 diff --git a/pacemaker.spec b/pacemaker.spec index 979a0e0..a6800fc 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -165,7 +165,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist} +Release: %{pcmk_release}%{?dist}.1 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -742,6 +742,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Fri Jun 04 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.3.rc2.1 +- Rebuilt for Python 3.10 + * Mon Jun 1 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc2, for full details, see included ChangeLog file or commit 595ee6bf2a7d18022e3d17a40b07aafea1960ecf Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Tue Jun 1 13:50:20 2021 +0200 * Mon Jun 1 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc2, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc2 - merge changes in upstream specfile sind Pacemaker-2.1.0-rc1 add configurable ocf_root enable cibsecrets for > f33 require libqb >= 0.17.0 instead of 0.13.0 default to syncing with sbd conflict all sbd < 1.4.3 to enforce sbd-build has the same default diff --git a/pacemaker.spec b/pacemaker.spec index 885a70e..979a0e0 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -15,15 +15,21 @@ ## GitHub entity that distributes source (for ease of using a fork) %global github_owner ClusterLabs +## Where bug reports should be submitted +## Leave bug_url undefined to use ClusterLabs default, others define it here + +## What to use as the OCF resource agent root directory +%global ocf_root %{_prefix}/lib/ocf + ## Upstream pacemaker version, and its package version (specversion ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.0 -%global specversion 2 +%global specversion 3 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.1.0-rc1 +%global commit Pacemaker-2.1.0-rc2 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -33,8 +39,12 @@ ## NOTE: skip --with stonithd -## Add option to enable support for storing sensitive information outside CIB +## Add option for whether to support storing sensitive information outside CIB +%if (0%{?fedora} && 0%{?fedora} <= 33) || (0%{?rhel} && 0%{?rhel} <= 8) %bcond_with cibsecrets +%else +%bcond_without cibsecrets +%endif ## Add option to create binaries suitable for use with profiling tools %bcond_with profiling @@ -45,6 +55,15 @@ ## Add option to skip/enable generating documentation %bcond_without doc +## Add option to default to start-up synchronization with SBD. +## +## If enabled, SBD *MUST* be built to default similarly, otherwise data +## corruption could occur. Building both Pacemaker and SBD to default +## to synchronization improves safety, without requiring higher-level tools +## to be aware of the setting or requiring users to modify configurations +## after upgrading to versions that support synchronization. +%bcond_without sbd_sync + ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) %bcond_without pre_release @@ -167,14 +186,15 @@ BuildRequires: make BuildRequires: %{python_name}-devel >= %{python_min} # Pacemaker requires a minimum libqb functionality -Requires: libqb >= 0.13.0 -BuildRequires: libqb-devel >= 0.13.0 +Requires: libqb >= 0.17.0 +BuildRequires: libqb-devel >= 0.17.0 -# Basics required for the build (even if usually satisfied through other BRs) +# Required basic build tools BuildRequires: coreutils findutils grep sed +BuildRequires: autoconf automake gcc make pkgconfig +BuildRequires: libtool libtool-ltdl-devel # Required for core functionality -BuildRequires: automake autoconf gcc libtool pkgconfig libtool-ltdl-devel BuildRequires: pkgconfig(glib-2.0) >= 2.42 BuildRequires: libxml2-devel libxslt-devel libuuid-devel BuildRequires: bzip2-devel @@ -245,7 +265,10 @@ Summary: Core Pacemaker libraries Requires(pre): shadow-utils Requires: %{name}-schemas = %{version}-%{release} # sbd 1.4.0+ supports the libpe_status API for pe_working_set_t -Conflicts: sbd < 1.4.0 +# sbd 1.4.2+ supports startup/shutdown handshake via pacemakerd-api +# and handshake defaults to enabled for rhel builds +# sbd 1.4.3+ handshake defaults to enabled for fedora builds +Conflicts: sbd < 1.4.3 %description libs Pacemaker is an advanced, scalable High-Availability cluster resource @@ -268,7 +291,7 @@ libraries needed for nodes that will form part of the cluster nodes. %package remote License: GPLv2+ and LGPLv2+ -Summary: Pacemaker remote daemon for non-cluster nodes +Summary: Pacemaker remote executor daemon for non-cluster nodes Requires: %{name}-libs%{?_isa} = %{version}-%{release} Requires: %{name}-cli = %{version}-%{release} Requires: resource-agents @@ -386,7 +409,10 @@ export LDFLAGS_HARDENED_LIB="%{?_hardening_ldflags}" %{?with_profiling: --with-profiling} \ %{?with_coverage: --with-coverage} \ %{?with_cibsecrets: --with-cibsecrets} \ + %{?with_sbd_sync: --with-sbd-sync-default="true"} \ %{?gnutls_priorities: --with-gnutls-priorities="%{gnutls_priorities}"} \ + %{?bug_url: --with-bug-url=%{bug_url}} \ + %{?ocf_root: --with-ocfdir=%{ocf_root}} \ %{?concurrent_fencing} \ %{?resource_stickiness} \ %{?compat20} \ @@ -572,8 +598,8 @@ exit 0 %dir %attr (750, %{uname}, %{gname}) %{_var}/lib/pacemaker/cib %dir %attr (750, %{uname}, %{gname}) %{_var}/lib/pacemaker/pengine -/usr/lib/ocf/resource.d/pacemaker/controld -/usr/lib/ocf/resource.d/pacemaker/remote +%{ocf_root}/resource.d/pacemaker/controld +%{ocf_root}/resource.d/pacemaker/remote %files cli %dir %attr (750, root, %{gname}) %{_sysconfdir}/pacemaker @@ -609,13 +635,13 @@ exit 0 # XXX "dirname" is not owned by any prerequisite %{_datadir}/snmp/mibs/PCMK-MIB.txt -%exclude /usr/lib/ocf/resource.d/pacemaker/controld -%exclude /usr/lib/ocf/resource.d/pacemaker/o2cb -%exclude /usr/lib/ocf/resource.d/pacemaker/remote +%exclude %{ocf_root}/resource.d/pacemaker/controld +%exclude %{ocf_root}/resource.d/pacemaker/o2cb +%exclude %{ocf_root}/resource.d/pacemaker/remote -%dir /usr/lib/ocf -%dir /usr/lib/ocf/resource.d -/usr/lib/ocf/resource.d/pacemaker +%dir %{ocf_root} +%dir %{ocf_root}/resource.d +%{ocf_root}/resource.d/pacemaker %doc %{_mandir}/man7/* %exclude %{_mandir}/man7/pacemaker-controld.* @@ -716,6 +742,17 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Jun 1 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc2, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc2 +- merge changes in upstream specfile sind Pacemaker-2.1.0-rc1 + add configurable ocf_root + enable cibsecrets for > f33 + require libqb >= 0.17.0 instead of 0.13.0 + default to syncing with sbd + conflict all sbd < 1.4.3 to enforce sbd-build has the same default + * Wed May 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.2.rc1 - remove PCMK_TIME_EMERGENCY_CGT not present in pacemaker codebase anymore - enable Pacemaker-2.0-compatibility for a fedora versions diff --git a/sources b/sources index a976443..76e3c9a 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.1.0-rc1.tar.gz) = 64fef270ac0f0df63a2ac974c4467dfb6a646cbe2089c6b523f14311bf236653caa75cd9e2851af7882057d63651ecd3c9d40647349a76619c4522c938063acf +SHA512 (pacemaker-Pacemaker-2.1.0-rc2.tar.gz) = 01396cd23b0cb49cab40b870e227b132f1e0c9b94cf6ac29d58e61bd3ff4ee4ea95fa6509c9a4a09179284b8fdbdba8319ceb46e8f94ce9cea92cf13832f9f4d commit e7aab8014f11ec96139f581de2cfe66c85975ed0 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri May 7 11:11:12 2021 +0200 * Wed May 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.2.rc1 - remove PCMK_TIME_EMERGENCY_CGT not present in pacemaker codebase anymore - enable Pacemaker-2.0-compatibility for a fedora versions diff --git a/pacemaker.spec b/pacemaker.spec index 676075c..885a70e 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -19,7 +19,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.0 -%global specversion 1 +%global specversion 2 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -97,7 +97,7 @@ ## Distro-specific configuration choices ### Use 2.0-style output when other distro packages don't support current output -%if 0%{?fedora} && 0%{?fedora} <= 34 +%if 0%{?fedora} %global compat20 --enable-compat-2.0 %endif @@ -379,9 +379,6 @@ export LDFLAGS_HARDENED_LIB="%{?_hardening_ldflags}" ./autogen.sh -# Rawhide glibc doesn't like ftime at all -export CPPFLAGS="-UPCMK_TIME_EMERGENCY_CGT $CPPFLAGS" - %{configure} \ PYTHON=%{python_path} \ %{!?with_hardening: --disable-hardening} \ @@ -719,6 +716,10 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Wed May 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.2.rc1 +- remove PCMK_TIME_EMERGENCY_CGT not present in pacemaker codebase anymore +- enable Pacemaker-2.0-compatibility for a fedora versions + * Tue May 4 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc1, for full details, see included ChangeLog file or commit c8cc15254d66b4d69d4d3eb547808fcfd172662a Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Tue May 4 22:24:44 2021 +0200 * Tue May 4 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc1, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc1 - merge changes in upstream spec-file since Pacemaker-2.0.5 - disable legacy-links diff --git a/pacemaker.spec b/pacemaker.spec index b786f9c..676075c 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -18,12 +18,12 @@ ## Upstream pacemaker version, and its package version (specversion ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) -%global pcmkversion 2.0.5 -%global specversion 10 +%global pcmkversion 2.1.0 +%global specversion 1 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.0.5 +%global commit Pacemaker-2.1.0-rc1 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -43,24 +43,19 @@ %bcond_with coverage ## Add option to skip/enable generating documentation -## (the build tools aren't available everywhere) -%if 0%{?rhel} - %bcond_with doc -%else - %bcond_without doc -%endif +%bcond_without doc ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) -%bcond_with pre_release +%bcond_without pre_release ## NOTE: skip --with upstart_job ## Add option to turn off hardening of libraries and daemon executables %bcond_without hardening -## Add option to disable links for legacy daemon names -%bcond_without legacy_links +## Add option to enable links for legacy daemon names +%bcond_with legacy_links ## Nagios source control identifiers @@ -95,14 +90,27 @@ %endif %endif -## Heuristic used to infer bleeding-edge deployments that are -## less likely to have working versions of the documentation tools -%define bleeding %(test ! -e /etc/yum.repos.d/fedora-rawhide.repo; echo $?) - ## Base GnuTLS cipher priorities (presumably only the initial, required keyword) ## overridable with "rpmbuild --define 'pcmk_gnutls_priorities PRIORITY-SPEC'" %define gnutls_priorities %{?pcmk_gnutls_priorities}%{!?pcmk_gnutls_priorities:@SYSTEM} +## Distro-specific configuration choices + +### Use 2.0-style output when other distro packages don't support current output +%if 0%{?fedora} && 0%{?fedora} <= 34 +%global compat20 --enable-compat-2.0 +%endif + +### Default concurrent-fencing to true when distro prefers that +%if 0%{?rhel} +%global concurrent_fencing --with-concurrent-fencing-default=true +%endif + +### Default resource-stickiness to 1 when distro prefers that +%if 0%{?fedora} >= 35 || 0%{?rhel} >= 9 +%global resource_stickiness --with-resource-stickiness-default=1 +%endif + # Python-related definitions ## Turn off auto-compilation of Python files outside Python specific paths, @@ -138,7 +146,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.2 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -167,7 +175,7 @@ BuildRequires: coreutils findutils grep sed # Required for core functionality BuildRequires: automake autoconf gcc libtool pkgconfig libtool-ltdl-devel -BuildRequires: pkgconfig(glib-2.0) >= 2.16 +BuildRequires: pkgconfig(glib-2.0) >= 2.42 BuildRequires: libxml2-devel libxslt-devel libuuid-devel BuildRequires: bzip2-devel @@ -183,11 +191,8 @@ BuildRequires: corosync-devel >= 2.0.0 #BuildRequires: pkgconfig(libcpg) #BuildRequires: pkgconfig(libcfg) -## (note no avoiding effect when building through non-customized mock) -%if !%{bleeding} %if %{with doc} -BuildRequires: asciidoc inkscape publican -%endif +BuildRequires: asciidoc inkscape %{python_name}-sphinx %endif # git-style patch application @@ -380,12 +385,14 @@ export CPPFLAGS="-UPCMK_TIME_EMERGENCY_CGT $CPPFLAGS" %{configure} \ PYTHON=%{python_path} \ %{!?with_hardening: --disable-hardening} \ - %{!?with_legacy_links: --disable-legacy-links} \ + %{?with_legacy_links: --enable-legacy-links} \ %{?with_profiling: --with-profiling} \ %{?with_coverage: --with-coverage} \ %{?with_cibsecrets: --with-cibsecrets} \ - %{!?with_doc: --with-brand=} \ %{?gnutls_priorities: --with-gnutls-priorities="%{gnutls_priorities}"} \ + %{?concurrent_fencing} \ + %{?resource_stickiness} \ + %{?compat20} \ --disable-static \ --with-initdir=%{_initrddir} \ --with-runstatedir=%{_rundir} \ @@ -415,10 +422,6 @@ make install \ DESTDIR=%{buildroot} V=1 docdir=%{pcmk_docdir} \ %{?_python_bytecompile_extra:%{?py_byte_compile:am__py_compile=true}} -mkdir -p ${RPM_BUILD_ROOT}%{_sysconfdir}/sysconfig -install -m 644 daemons/pacemakerd/pacemaker.sysconfig ${RPM_BUILD_ROOT}%{_sysconfdir}/sysconfig/pacemaker -install -m 644 tools/crm_mon.sysconfig ${RPM_BUILD_ROOT}%{_sysconfdir}/sysconfig/crm_mon - mkdir -p %{buildroot}%{_datadir}/pacemaker/nagios/plugins-metadata for file in $(find %{nagios_name}-%{nagios_hash}/metadata -type f); do install -m 644 $file %{buildroot}%{_datadir}/pacemaker/nagios/plugins-metadata @@ -549,9 +552,7 @@ exit 0 %exclude %{_libexecdir}/pacemaker/cts-log-watcher %exclude %{_libexecdir}/pacemaker/cts-support %exclude %{_sbindir}/pacemaker-remoted -%if %{with legacy_links} %exclude %{_sbindir}/pacemaker_remoted -%endif %{_libexecdir}/pacemaker/* %{_sbindir}/crm_attribute @@ -671,9 +672,7 @@ exit 0 %{_unitdir}/pacemaker_remote.service %{_sbindir}/pacemaker-remoted -%if %{with legacy_links} %{_sbindir}/pacemaker_remoted -%endif %{_mandir}/man8/pacemaker-remoted.* %license licenses/GPLv2 %doc COPYING @@ -720,6 +719,13 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Tue May 4 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.1.rc1 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc1, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc1 +- merge changes in upstream spec-file since Pacemaker-2.0.5 +- disable legacy-links + * Tue Mar 02 2021 Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> - 2.0.5-10.2 - Rebuilt for updated systemd-rpm-macros See https://pagure.io/fesco/issue/2583. diff --git a/sources b/sources index b19a593..a976443 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.0.5.tar.gz) = 5fd3614f0284297babb66ea2dc567583315052fcf77f49107c52161e8e8c164ae3169d98528fdc1316d8eabaacc98ed24e9c6e6c90b3286f2f012a4ee874bbba +SHA512 (pacemaker-Pacemaker-2.1.0-rc1.tar.gz) = 64fef270ac0f0df63a2ac974c4467dfb6a646cbe2089c6b523f14311bf236653caa75cd9e2851af7882057d63651ecd3c9d40647349a76619c4522c938063acf commit 3978725c064d9bf7d504f7c8118f3c9d34bfb715 Author: Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> Date: Tue Mar 2 16:13:07 2021 +0100 Rebuilt for updated systemd-rpm-macros See https://pagure.io/fesco/issue/2583. diff --git a/pacemaker.spec b/pacemaker.spec index 8f15ea0..b786f9c 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -138,7 +138,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist}.2 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -720,6 +720,10 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Tue Mar 02 2021 Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> - 2.0.5-10.2 +- Rebuilt for updated systemd-rpm-macros + See https://pagure.io/fesco/issue/2583. + * Tue Jan 26 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 2.0.5-10.1 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild commit 5069bd8f40edfdf1691a34044350bec9164be344 Author: Fedora Release Engineering <releng(a)fedoraproject.org> Date: Tue Jan 26 22:48:40 2021 +0000 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild Signed-off-by: Fedora Release Engineering <releng(a)fedoraproject.org> diff --git a/pacemaker.spec b/pacemaker.spec index 1f2badf..8f15ea0 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -138,7 +138,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist} +Release: %{pcmk_release}%{?dist}.1 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -720,6 +720,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Tue Jan 26 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 2.0.5-10.1 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild + * Mon Dec 7 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-10 - Conflicts of doc package introduced to fix upgrade/downgrade issues needs to be independent from arch commit 190f2c862460b6c1e5db34b8a607fa22375ae019 Author: Tom Stellard <tstellar(a)redhat.com> Date: Thu Jan 7 06:50:48 2021 +0000 Add BuildRequires: make https://fedoraproject.org/wiki/Changes/Remove_make_from_BuildRoot diff --git a/pacemaker.spec b/pacemaker.spec index 54c9f68..1f2badf 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -155,6 +155,7 @@ Requires: %{name}-cli = %{version}-%{release} # Pacemaker requires a minimum Python functionality Requires: %{python_name} >= %{python_min} +BuildRequires: make BuildRequires: %{python_name}-devel >= %{python_min} # Pacemaker requires a minimum libqb functionality commit 83ce149390888dd8f2ed65b5c7e43b2451c464e0 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Dec 7 17:55:17 2020 +0100 * Mon Dec 7 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-10 - Conflicts of doc package introduced to fix upgrade/downgrade issues needs to be independent from arch diff --git a/pacemaker.spec b/pacemaker.spec index bbdd023..54c9f68 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -19,7 +19,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 9 +%global specversion 10 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -316,8 +316,8 @@ Test framework for cluster-related technologies like Pacemaker License: CC-BY-SA-4.0 Summary: Documentation for Pacemaker BuildArch: noarch -Conflicts: %{name}-libs%{?_isa} > %{version}-%{release} -Conflicts: %{name}-libs%{?_isa} < %{version}-%{release} +Conflicts: %{name}-libs > %{version}-%{release} +Conflicts: %{name}-libs < %{version}-%{release} %description doc Documentation for Pacemaker. @@ -719,6 +719,10 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Dec 7 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-10 +- Conflicts of doc package introduced to fix upgrade/downgrade + issues needs to be independent from arch + * Fri Dec 4 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-9 - Make doc-package conflict with wrong version of libs to fix upgrade/downgrade issues commit e2224005a94e0ee24cac2a955bb1741c6b40a1cb Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Dec 7 17:23:55 2020 +0100 * Fri Dec 4 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-9 - Make doc-package conflict with wrong version of libs to fix upgrade/downgrade issues diff --git a/pacemaker.spec b/pacemaker.spec index 056493c..bbdd023 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -19,7 +19,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 8 +%global specversion 9 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -316,6 +316,8 @@ Test framework for cluster-related technologies like Pacemaker License: CC-BY-SA-4.0 Summary: Documentation for Pacemaker BuildArch: noarch +Conflicts: %{name}-libs%{?_isa} > %{version}-%{release} +Conflicts: %{name}-libs%{?_isa} < %{version}-%{release} %description doc Documentation for Pacemaker. @@ -717,6 +719,10 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Fri Dec 4 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-9 +- Make doc-package conflict with wrong version of libs + to fix upgrade/downgrade issues + * Fri Dec 4 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-8 - Update for new upstream release tarball: Pacemaker-2.0.5 for full details, see included ChangeLog file or commit a8619d3eb126acef158f32277e3ee7c917446a57 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri Dec 4 17:11:33 2020 +0100 * Fri Dec 4 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-8 - Update for new upstream release tarball: Pacemaker-2.0.5 for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.0.5 diff --git a/pacemaker.spec b/pacemaker.spec index a8d6773..056493c 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -19,11 +19,11 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 7 +%global specversion 8 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.0.5-rc3 +%global commit Pacemaker-2.0.5 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -52,7 +52,7 @@ ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) -%bcond_without pre_release +%bcond_with pre_release ## NOTE: skip --with upstart_job @@ -717,6 +717,11 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Fri Dec 4 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-8 +- Update for new upstream release tarball: Pacemaker-2.0.5 + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.0.5 + * Wed Nov 18 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.7.rc3 - a little more syncing with upstream spec-file diff --git a/sources b/sources index f863b6a..b19a593 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.0.5-rc3.tar.gz) = adf558d80d93ee7944b8e9eb5d07304e374ee61a4d81159daa9c6a9108ee77294e109766c21ed6f6eef2847ebc67d98925b8c63ff49bba958058bb7ef68d0f07 +SHA512 (pacemaker-Pacemaker-2.0.5.tar.gz) = 5fd3614f0284297babb66ea2dc567583315052fcf77f49107c52161e8e8c164ae3169d98528fdc1316d8eabaacc98ed24e9c6e6c90b3286f2f012a4ee874bbba commit fecb07e0d0e09f1a5056fd1cef3962745cc18b1d Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Wed Nov 18 11:49:19 2020 +0100 * Wed Nov 18 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.7.rc3 - a little more syncing with upstream spec-file diff --git a/pacemaker.spec b/pacemaker.spec index bcab6ca..a8d6773 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -3,6 +3,7 @@ ## User and group to use for nonprivileged services %global uname hacluster %global gname haclient +%global hacluster_id 189 ## Where to install Pacemaker documentation %if 0%{?rhel} @@ -18,7 +19,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 6 +%global specversion 7 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -508,7 +509,7 @@ fi %post cli %systemd_post crm_mon.service -if [ "$1" = 2 ]; then +if [ "$1" -eq 2 ]; then # Package upgrade, not initial install: # Move any pre-2.0 logs to new location to ensure they get rotated { mv -fbS.rpmsave %{_var}/log/pacemaker.log* %{_var}/log/pacemaker \ @@ -526,8 +527,8 @@ fi # XXX keep an eye on https://fedoraproject.org/wiki/Changes/SystemdSysusers # reopened recently: # https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.o... -getent group %{gname} >/dev/null || groupadd -r %{gname} -g 189 -getent passwd %{uname} >/dev/null || useradd -r -g %{gname} -u 189 -s /sbin/nologin -c "cluster user" %{uname} +getent group %{gname} >/dev/null || groupadd -r %{gname} -g %{hacluster_id} +getent passwd %{uname} >/dev/null || useradd -r -g %{gname} -u %{hacluster_id} -s /sbin/nologin -c "cluster user" %{uname} exit 0 %ldconfig_scriptlets libs @@ -716,6 +717,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Wed Nov 18 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.7.rc3 +- a little more syncing with upstream spec-file + * Tue Nov 17 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.6.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc3 for full details, see included ChangeLog file or commit b8f03333b11afe4a833b4c91ac0d881d9a956958 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Tue Nov 17 16:15:13 2020 +0100 * Tue Nov 17 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.6.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc3 for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.0.5-rc3 - Corosync in Fedora now provides corosync-devel as well in isa-flavor diff --git a/pacemaker.spec b/pacemaker.spec index 816df62..bcab6ca 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -18,11 +18,11 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 5 +%global specversion 6 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.0.5-rc2 +%global commit Pacemaker-2.0.5-rc3 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -176,7 +176,7 @@ BuildRequires: help2man gnutls-devel pam-devel pkgconfig(dbus-1) BuildRequires: pkgconfig(systemd) Requires: corosync >= 2.0.0 -BuildRequires: corosynclib-devel >= 2.0.0 +BuildRequires: corosync-devel >= 2.0.0 #XXX #BuildRequires: pkgconfig(libcpg) #BuildRequires: pkgconfig(libcfg) @@ -287,7 +287,7 @@ Requires: libtool-ltdl-devel%{?_isa} libuuid-devel%{?_isa} Requires: libxml2-devel%{?_isa} libxslt-devel%{?_isa} Requires: bzip2-devel%{?_isa} glib2-devel%{?_isa} Requires: libqb-devel%{?_isa} -Requires: corosynclib-devel%{?_isa} >= 2.0.0 +Requires: corosync-devel%{?_isa} >= 2.0.0 %description libs-devel Pacemaker is an advanced, scalable High-Availability cluster resource @@ -716,6 +716,11 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Tue Nov 17 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.6.rc3 +- Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc3 + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.0.5-rc3 +- Corosync in Fedora now provides corosync-devel as well in isa-flavor * Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.5.rc2 - remove no more working dist.rpmdeplint from gating diff --git a/sources b/sources index 19d2b5b..f863b6a 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.0.5-rc2.tar.gz) = 67fe1ca539f4a690c8b9860c9b82679d77a77294ee9278c384b68099f788ba4db4d2c35bf34d1340daa6d3bac7aae550ef06527046da601a7bde30b78ee110a7 +SHA512 (pacemaker-Pacemaker-2.0.5-rc3.tar.gz) = adf558d80d93ee7944b8e9eb5d07304e374ee61a4d81159daa9c6a9108ee77294e109766c21ed6f6eef2847ebc67d98925b8c63ff49bba958058bb7ef68d0f07 commit be156c4421004a24b5bb62b4c638b06befc9ad72 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Sun Nov 1 23:13:39 2020 +0100 * Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.5.rc2 - remove no more working dist.rpmdeplint from gating diff --git a/pacemaker.spec b/pacemaker.spec index 5261cae..816df62 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -18,7 +18,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 6 +%global specversion 5 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -717,7 +717,7 @@ exit 0 %changelog -* Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.6.rc2 +* Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.5.rc2 - remove no more working dist.rpmdeplint from gating * Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.4.rc2 commit 6d62f98baff974d549d51c25427647a9dfa8dfc4 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Sun Nov 1 23:11:04 2020 +0100 * Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.6.rc2 - remove no more working dist.rpmdeplint from gating diff --git a/gating.yaml b/gating.yaml index b829170..9e15ced 100644 --- a/gating.yaml +++ b/gating.yaml @@ -4,7 +4,6 @@ product_versions: decision_context: bodhi_update_push_testing subject_type: koji_build rules: - - !PassingTestCaseRule {test_case_name: dist.rpmdeplint} - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} --- !Policy product_versions: @@ -12,6 +11,5 @@ product_versions: decision_context: bodhi_update_push_stable subject_type: koji_build rules: - - !PassingTestCaseRule {test_case_name: dist.rpmdeplint} - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} diff --git a/pacemaker.spec b/pacemaker.spec index fe13aed..5261cae 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -18,7 +18,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 5 +%global specversion 6 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -716,7 +716,8 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog -* Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.5.rc2 + +* Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.6.rc2 - remove no more working dist.rpmdeplint from gating * Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.4.rc2 commit 5ed78e234f212f871e38af6e50ec94ad5efa8711 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Sun Nov 1 22:52:35 2020 +0100 * Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.5.rc2 - remove no more working dist.rpmdeplint from gating diff --git a/pacemaker.spec b/pacemaker.spec index 56510b2..fe13aed 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -18,7 +18,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 4 +%global specversion 5 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -716,6 +716,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Sun Nov 1 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.5.rc2 +- remove no more working dist.rpmdeplint from gating + * Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.4.rc2 - never use spec-variables in changelog - replace dist.depcheck by dist.rpmdeplint commit 20ba4de547c39a877978f48b670bbc3fb105125e Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri Oct 30 12:26:27 2020 +0100 * Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.4.rc2 - never use spec-variables in changelog - replace dist.depcheck by dist.rpmdeplint - do gate stable as well to be effective on rawhide diff --git a/pacemaker.spec b/pacemaker.spec index 7bfd66f..56510b2 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -18,7 +18,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 3 +%global specversion 4 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package commit 1576d8e7818e16c7f86d01f0d3d89ac3d45eab31 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri Oct 30 12:24:05 2020 +0100 * Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.4.rc2 - never use spec-variables in changelog - replace dist.depcheck by dist.rpmdeplint - do gate stable as well to be effective on rawhide diff --git a/gating.yaml b/gating.yaml index 1af3453..b829170 100644 --- a/gating.yaml +++ b/gating.yaml @@ -4,6 +4,14 @@ product_versions: decision_context: bodhi_update_push_testing subject_type: koji_build rules: - - !PassingTestCaseRule {test_case_name: dist.depcheck} + - !PassingTestCaseRule {test_case_name: dist.rpmdeplint} + - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} +--- !Policy +product_versions: + - fedora-* +decision_context: bodhi_update_push_stable +subject_type: koji_build +rules: + - !PassingTestCaseRule {test_case_name: dist.rpmdeplint} - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} diff --git a/pacemaker.spec b/pacemaker.spec index 4d14ad5..7bfd66f 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -716,9 +716,14 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.4.rc2 +- never use spec-variables in changelog +- replace dist.depcheck by dist.rpmdeplint +- do gate stable as well to be effective on rawhide + * Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.3.rc2 - revert dependency corosync-devel back to corosynclib-devel as long - as corosynclib-devel-package doesn't provide corosync-devel%{?_isa} + as corosynclib-devel-package doesn't provide corosync-devel(isa) we would need for pacemaker-libs-devel to require - enable some basic gating-tests - re-add building documentation using publican to everything but ELN commit af37d53a69a8deabad0a23cf7dca1f2009c145b2 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri Oct 30 08:24:58 2020 +0100 * Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.3.rc2 - revert dependency corosync-devel back to corosynclib-devel as long as corosynclib-devel-package doesn't provide corosync-devel%{?_isa} we would need for pacemaker-libs-devel to require - enable some basic gating-tests - re-add building documentation using publican to everything but ELN - rename doc-dir for ELN diff --git a/gating.yaml b/gating.yaml new file mode 100644 index 0000000..1af3453 --- /dev/null +++ b/gating.yaml @@ -0,0 +1,9 @@ +--- !Policy +product_versions: + - fedora-* +decision_context: bodhi_update_push_testing +subject_type: koji_build +rules: + - !PassingTestCaseRule {test_case_name: dist.depcheck} + - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} + diff --git a/pacemaker.spec b/pacemaker.spec index 256e4c7..4d14ad5 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -5,7 +5,11 @@ %global gname haclient ## Where to install Pacemaker documentation +%if 0%{?rhel} +%global pcmk_docdir %{_docdir}/%{name}-doc +%else %global pcmk_docdir %{_docdir}/%{name} +%endif ## GitHub entity that distributes source (for ease of using a fork) %global github_owner ClusterLabs @@ -14,7 +18,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 2 +%global specversion 3 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -37,9 +41,13 @@ ## Add option to create binaries with coverage analysis %bcond_with coverage -## Add option to skip generating documentation +## Add option to skip/enable generating documentation ## (the build tools aren't available everywhere) -%bcond_with doc +%if 0%{?rhel} + %bcond_with doc +%else + %bcond_without doc +%endif ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) @@ -168,7 +176,7 @@ BuildRequires: help2man gnutls-devel pam-devel pkgconfig(dbus-1) BuildRequires: pkgconfig(systemd) Requires: corosync >= 2.0.0 -BuildRequires: corosync-devel >= 2.0.0 +BuildRequires: corosynclib-devel >= 2.0.0 #XXX #BuildRequires: pkgconfig(libcpg) #BuildRequires: pkgconfig(libcfg) @@ -279,7 +287,7 @@ Requires: libtool-ltdl-devel%{?_isa} libuuid-devel%{?_isa} Requires: libxml2-devel%{?_isa} libxslt-devel%{?_isa} Requires: bzip2-devel%{?_isa} glib2-devel%{?_isa} Requires: libqb-devel%{?_isa} -Requires: corosync-devel%{?_isa} >= 2.0.0 +Requires: corosynclib-devel%{?_isa} >= 2.0.0 %description libs-devel Pacemaker is an advanced, scalable High-Availability cluster resource @@ -708,6 +716,14 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Fri Oct 30 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.3.rc2 +- revert dependency corosync-devel back to corosynclib-devel as long + as corosynclib-devel-package doesn't provide corosync-devel%{?_isa} + we would need for pacemaker-libs-devel to require +- enable some basic gating-tests +- re-add building documentation using publican to everything but ELN +- rename doc-dir for ELN + * Wed Oct 28 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.2.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc2, includes fix for CVE-2020-25654 diff --git a/tests/inventory b/tests/inventory new file mode 100755 index 0000000..52687db --- /dev/null +++ b/tests/inventory @@ -0,0 +1,4 @@ +#!/bin/bash +export TEST_DOCKER_EXTRA_ARGS="--network host" +exec merge-standard-inventory "$@" + diff --git a/tests/tests.yml b/tests/tests.yml new file mode 100644 index 0000000..71d4612 --- /dev/null +++ b/tests/tests.yml @@ -0,0 +1,14 @@ +--- +- hosts: localhost + roles: + - role: standard-test-basic + tags: + - classic + - container + tests: + - cts-regression: + dir: . + run: /usr/share/pacemaker/tests/cts-regression cli scheduler + required_packages: + - pacemaker + - pacemaker-cts commit 739244b77b91a37a1c52828cfbac4d6930f95cd9 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Wed Oct 28 11:31:25 2020 +0100 * Wed Oct 28 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.2.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc2, includes fix for CVE-2020-25654 for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.0.5-rc2 diff --git a/pacemaker.spec b/pacemaker.spec index d1076e0..256e4c7 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -14,11 +14,11 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.0.5 -%global specversion 1 +%global specversion 2 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.0.5-rc1 +%global commit Pacemaker-2.0.5-rc2 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -71,7 +71,7 @@ ## Portion of export/dist tarball name after "pacemaker-", and release version %if 0%{tag_release} -%define archive_version %(c=%{commit}; echo ${c:10}) +%define archive_version %{commit} %define archive_github_url %{commit}#/%{name}-%{archive_version}.tar.gz %define pcmk_release %(c=%{commit}; case $c in *-rc[[:digit:]]*%{rparen} echo 0.%{specversion}.${c: -3} ;; @@ -342,7 +342,7 @@ The metadata files required for Pacemaker to execute the nagios plugin monitor resources. %prep -%setup -q -a 1 -n %{name}-%{commit} +%setup -q -a 1 -n %{name}-%{archive_version} %build @@ -708,6 +708,12 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Wed Oct 28 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.2.rc2 +- Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc2, + includes fix for CVE-2020-25654 + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.0.5-rc2 + * Thu Oct 22 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc1, for full details, see included ChangeLog file or diff --git a/sources b/sources index fa48479..19d2b5b 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-2.0.5-rc1.tar.gz) = 90e2994df8ee60f525dd919a5edad2c48bbe60fabd42318527c02bc47900bff24901f73eb6498d3fdf75996539e647460b540375008d263baf7890f271fae76c +SHA512 (pacemaker-Pacemaker-2.0.5-rc2.tar.gz) = 67fe1ca539f4a690c8b9860c9b82679d77a77294ee9278c384b68099f788ba4db4d2c35bf34d1340daa6d3bac7aae550ef06527046da601a7bde30b78ee110a7 commit c7391e41b80340cf9b0cbac6c88c21a7d45f3b8f Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Oct 26 14:09:03 2020 +0100 * Thu Oct 22 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc1, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.0.5-rc1 - Disable building of documentation - as not to pull in publican - Remove dependencies to nagios-plugins from metadata-package - some sync with structure of upstream spec-file - removed some legacy conditionals - added with-cibsecrets diff --git a/pacemaker.spec b/pacemaker.spec index 7b56863..d1076e0 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -13,20 +13,51 @@ ## Upstream pacemaker version, and its package version (specversion ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) -%global pcmkversion 2.0.4 +%global pcmkversion 2.0.5 %global specversion 1 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.0.4 +%global commit Pacemaker-2.0.5-rc1 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 +# Define conditionals so that "rpmbuild --with <feature>" and +# "rpmbuild --without <feature>" can enable and disable specific features + +## NOTE: skip --with stonithd + +## Add option to enable support for storing sensitive information outside CIB +%bcond_with cibsecrets + +## Add option to create binaries suitable for use with profiling tools +%bcond_with profiling + +## Add option to create binaries with coverage analysis +%bcond_with coverage + +## Add option to skip generating documentation +## (the build tools aren't available everywhere) +%bcond_with doc + +## Add option to prefix package version with "0." +## (so later "official" packages will be considered updates) +%bcond_without pre_release + +## NOTE: skip --with upstart_job + +## Add option to turn off hardening of libraries and daemon executables +%bcond_without hardening + +## Add option to disable links for legacy daemon names +%bcond_without legacy_links + + ## Nagios source control identifiers %global nagios_name nagios-agents-metadata %global nagios_hash 105ab8a7b2c16b9a29cf1c1596b80136eeef332b - +%global nagios_archive_github_url %{nagios_hash}#/%{nagios_name}-%{nagios_hash}.tar.gz # Define globals for convenient use later @@ -34,18 +65,26 @@ %global lparen ( %global rparen ) -## Short version of git commit -%define shortcommit %(c=%{commit}; case ${c} in - Pacemaker-*%{rparen} echo ${c:10};; - *%{rparen} echo ${c:0:%{commit_abbrev}};; esac) +## Whether this is a tagged release (final or release candidate) +%define tag_release %(c=%{commit}; case ${c} in Pacemaker-*%{rparen} echo 1 ;; + *%{rparen} echo 0 ;; esac) -## Whether this is a tagged release -%define tag_release %([ %{commit} != Pacemaker-%{shortcommit} ]; echo $?) - -## Whether this is a release candidate (in case of a tagged release) -%define pre_release %([ "%{tag_release}" -eq 0 ] || { - case "%{shortcommit}" in *-rc[[:digit:]]*%{rparen} false;; - esac; }; echo $?) +## Portion of export/dist tarball name after "pacemaker-", and release version +%if 0%{tag_release} +%define archive_version %(c=%{commit}; echo ${c:10}) +%define archive_github_url %{commit}#/%{name}-%{archive_version}.tar.gz +%define pcmk_release %(c=%{commit}; case $c in *-rc[[:digit:]]*%{rparen} + echo 0.%{specversion}.${c: -3} ;; + *%{rparen} echo %{specversion} ;; esac) +%else +%define archive_version %(c=%{commit}; echo ${c:0:%{commit_abbrev}}) +%define archive_github_url %{archive_version}#/%{name}-%{archive_version}.tar.gz +%if %{with pre_release} +%define pcmk_release 0.%{specversion}.%{archive_version}.git +%else +%define pcmk_release %{specversion}.%{archive_version}.git +%endif +%endif ## Heuristic used to infer bleeding-edge deployments that are ## less likely to have working versions of the documentation tools @@ -71,40 +110,12 @@ %endif ## Values that differ by Python major version -%global python_path /usr/bin/python%{?python3_pkgversion}%{!?python3_pkgversion:3} -%global python_pkg python3 +%global python_name python3 +%global python_path %{?__python3}%{!?__python3:/usr/bin/python%{?python3_pkgversion}%{!?python3_pkgversion:3}} +%define python_site %{?python3_sitelib}%{!?python3_sitelib:%( + %{python_path} -c 'from distutils.sysconfig import get_python_lib as gpl; print(gpl(1))' 2>/dev/null)} %global python_min 3.2 -%define py_site %{?python3_sitelib}%{!?python3_sitelib:%( - python3 -c 'from distutils.sysconfig import get_python_lib as gpl; print(gpl(1))' 2>/dev/null)} - - -# Define conditionals so that "rpmbuild --with <feature>" and -# "rpmbuild --without <feature>" can enable and disable specific features - -## NOTE: skip --with stonith - -## Add option to create binaries suitable for use with profiling tools -%bcond_with profiling - -## Add option to create binaries with coverage analysis -%bcond_with coverage - -## Add option to skip generating documentation -## (the build tools aren't available everywhere) -%bcond_without doc - -## Add option to prefix package version with "0." -## (so later "official" packages will be considered updates) -%bcond_with pre_release - -## NOTE: skip --with upstart_job - -## Add option to turn off hardening of libraries and daemon executables -%bcond_without hardening - -## Add option to disable links for legacy daemon names -%bcond_without legacy_links - +# python_min still required? # Keep sane profiling data if requested %if %{with profiling} @@ -115,33 +126,16 @@ %endif -# Define the release version -# (do not look at externally enforced pre-release flag for tagged releases -# as only -rc tags, captured with the second condition, implies that then) -%if (!%{tag_release} && %{with pre_release}) || 0%{pre_release} -%if 0%{pre_release} -%define pcmk_release 0.%{specversion}.%(s=%{shortcommit}; echo ${s: -3}) -%else -%define pcmk_release 0.%{specversion}.%{shortcommit}.git -%endif -%else -%if 0%{tag_release} -%define pcmk_release %{specversion} -%else -%define pcmk_release %{specversion}.%{shortcommit}.git -%endif -%endif - Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ -Url: http://www.clusterlabs.org +Url: https://www.clusterlabs.org # Hint: use "spectool -s 0 pacemaker.spec" (rpmdevtools) to check the final URL -Source0: https://github.com/%{github_owner}/%{name}/archive/%{commit}/%{name}-%{sh... -Source1: https://github.com/%{github_owner}/%{nagios_name}/archive/%{nagios_hash}/... +Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{archive_gith... +Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... # --- Requires: resource-agents @@ -151,8 +145,8 @@ Requires: %{name}-cli = %{version}-%{release} %{?systemd_requires} # Pacemaker requires a minimum Python functionality -Requires: %{python_pkg} >= %{python_min} -BuildRequires: %{python_pkg}-devel >= %{python_min} +Requires: %{python_name} >= %{python_min} +BuildRequires: %{python_name}-devel >= %{python_min} # Pacemaker requires a minimum libqb functionality Requires: libqb >= 0.13.0 @@ -174,7 +168,7 @@ BuildRequires: help2man gnutls-devel pam-devel pkgconfig(dbus-1) BuildRequires: pkgconfig(systemd) Requires: corosync >= 2.0.0 -BuildRequires: corosynclib-devel >= 2.0.0 +BuildRequires: corosync-devel >= 2.0.0 #XXX #BuildRequires: pkgconfig(libcpg) #BuildRequires: pkgconfig(libcfg) @@ -207,15 +201,16 @@ when related resources fail and can be configured to periodically check resource health. Available rpmbuild rebuild options: - --with(out) : coverage doc hardening pre_release profiling + --with(out) : cibsecrets coverage doc hardening pre_release profiling %package cli License: GPLv2+ and LGPLv2+ Summary: Command line tools for controlling Pacemaker clusters Requires: %{name}-libs%{?_isa} = %{version}-%{release} -%if 0%{?fedora} > 22 || 0%{?rhel} > 7 Recommends: pcmk-cluster-manager = %{version}-%{release} -%endif +# For crm_report +Recommends: tar +Recommends: bzip2 Requires: perl-TimeDate Requires: procps-ng Requires: psmisc @@ -284,7 +279,7 @@ Requires: libtool-ltdl-devel%{?_isa} libuuid-devel%{?_isa} Requires: libxml2-devel%{?_isa} libxslt-devel%{?_isa} Requires: bzip2-devel%{?_isa} glib2-devel%{?_isa} Requires: libqb-devel%{?_isa} -Requires: corosynclib-devel%{?_isa} >= 2.0.0 +Requires: corosync-devel%{?_isa} >= 2.0.0 %description libs-devel Pacemaker is an advanced, scalable High-Availability cluster resource @@ -296,19 +291,20 @@ for developing tools for Pacemaker. %package cts License: GPLv2+ and LGPLv2+ Summary: Test framework for cluster-related technologies like Pacemaker -Requires: %{python_pkg} >= %{python_min} +Requires: %{python_path} +Requires: %{python_name} >= %{python_min} Requires: %{name}-libs = %{version}-%{release} Requires: procps-ng Requires: psmisc BuildArch: noarch -Requires: %{python_pkg}-systemd +Requires: %{python_name}-systemd %description cts Test framework for cluster-related technologies like Pacemaker %package doc -License: CC-BY-SA +License: CC-BY-SA-4.0 Summary: Documentation for Pacemaker BuildArch: noarch @@ -334,11 +330,11 @@ License: GPLv3 Summary: Pacemaker Nagios Metadata BuildArch: noarch # NOTE below are the plugins this metadata uses. -Requires: nagios-plugins-http -Requires: nagios-plugins-ldap -Requires: nagios-plugins-mysql -Requires: nagios-plugins-pgsql -Requires: nagios-plugins-tcp +# Requires: nagios-plugins-http +# Requires: nagios-plugins-ldap +# Requires: nagios-plugins-mysql +# Requires: nagios-plugins-pgsql +# Requires: nagios-plugins-tcp Requires: pcmk-cluster-manager %description nagios-plugins-metadata @@ -347,15 +343,9 @@ monitor resources. %prep %setup -q -a 1 -n %{name}-%{commit} -#global __scm git_am -#__scm_setup_git -#autopatch -p1 %build -# Early versions of autotools (e.g. RHEL <= 5) do not support --docdir -export docdir=%{pcmk_docdir} - export systemdsystemunitdir=%{?_unitdir}%{!?_unitdir:no} %if %{with hardening} @@ -381,6 +371,7 @@ export CPPFLAGS="-UPCMK_TIME_EMERGENCY_CGT $CPPFLAGS" %{!?with_legacy_links: --disable-legacy-links} \ %{?with_profiling: --with-profiling} \ %{?with_coverage: --with-coverage} \ + %{?with_cibsecrets: --with-cibsecrets} \ %{!?with_doc: --with-brand=} \ %{?gnutls_priorities: --with-gnutls-priorities="%{gnutls_priorities}"} \ --disable-static \ @@ -396,6 +387,7 @@ export CPPFLAGS="-UPCMK_TIME_EMERGENCY_CGT $CPPFLAGS" make %{_smp_mflags} V=1 %check +make %{_smp_mflags} check { cts/cts-scheduler --run load-stopped-loop \ && cts/cts-cli \ && touch .CHECKED @@ -448,7 +440,7 @@ rm -f %{buildroot}/%{_initrddir}/pacemaker_remote %if %{defined py_byte_compile} && %{defined python_path} %{py_byte_compile %{python_path} %{buildroot}%{_datadir}/pacemaker/tests} %if !%{defined _python_bytecompile_extra} -%{py_byte_compile %{python_path} %{buildroot}%{py_site}/cts} +%{py_byte_compile %{python_path} %{buildroot}%{python_site}/cts} %endif %endif @@ -582,6 +574,9 @@ exit 0 %{_sbindir}/attrd_updater %{_sbindir}/cibadmin +%if %{with cibsecrets} +%{_sbindir}/cibsecret +%endif %{_sbindir}/crm_diff %{_sbindir}/crm_error %{_sbindir}/crm_failcount @@ -677,7 +672,7 @@ exit 0 %license licenses/CC-BY-SA-4.0 %files cts -%{py_site}/cts +%{python_site}/cts %{_datadir}/pacemaker/tests %{_libexecdir}/pacemaker/cts-log-watcher @@ -713,6 +708,16 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Thu Oct 22 2020 Klaus Wenninger <kwenning(a)redhat.com> - 2.0.5-0.1.rc1 +- Update for new upstream tarball for release candidate: Pacemaker-2.0.5-rc1, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.0.5-rc1 +- Disable building of documentation - as not to pull in publican +- Remove dependencies to nagios-plugins from metadata-package +- some sync with structure of upstream spec-file +- removed some legacy conditionals +- added with-cibsecrets + * Tue Jul 28 2020 Fedora Release Engineering <releng(a)fedoraproject.org> - 2.0.4-1.1 - Rebuilt for https://fedoraproject.org/wiki/Fedora_33_Mass_Rebuild diff --git a/sources b/sources index f0f399b..fa48479 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-2.0.4.tar.gz) = fbff3b5ab05ad52d469304d5bc7fca518df2f491a1176a24735cd1a9b46f7ff90dc5aeae65e5e29feb86e8a210e69e528261138847d6f8773933fb557e71133d +SHA512 (pacemaker-2.0.5-rc1.tar.gz) = 90e2994df8ee60f525dd919a5edad2c48bbe60fabd42318527c02bc47900bff24901f73eb6498d3fdf75996539e647460b540375008d263baf7890f271fae76c

2 years, 9 months

1
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Architecture specific change in rpms/pacemaker.git

by githook-noreply＠fedoraproject.org

The package rpms/pacemaker.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/pacemaker.git/commit/?id=15ac1a3c.... Change: +ExclusiveArch: aarch64 i686 ppc64le s390x x86_64 Thanks. Full change: ============ commit a9ddf9be665d4fda694ee27bf35dfe51e2c5b614 Merge: 28e8e45 a74f8cf Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri Aug 20 13:12:54 2021 +0200 Merge branch 'rawhide' into f34 commit a74f8cfffa01425166cf6793858b614b09280026 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri Aug 20 01:22:00 2021 +0200 * Thu Aug 19 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.5.rc3 - Fix malformed xml in fence_watchdog metadata diff --git a/0007-Fix-fence_watchdog-fix-malformed-xml-in-metadata.patch b/0007-Fix-fence_watchdog-fix-malformed-xml-in-metadata.patch new file mode 100644 index 0000000..0d2c32e --- /dev/null +++ b/0007-Fix-fence_watchdog-fix-malformed-xml-in-metadata.patch @@ -0,0 +1,25 @@ +From 46dd1118cae948649e000b2159e8e92623520ad9 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Thu, 19 Aug 2021 09:28:54 +0200 +Subject: [PATCH] Fix: fence_watchdog: fix malformed xml in metadata + +--- + daemons/fenced/fence_watchdog.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/daemons/fenced/fence_watchdog.in b/daemons/fenced/fence_watchdog.in +index 700065e..eefa739 100755 +--- a/daemons/fenced/fence_watchdog.in ++++ b/daemons/fenced/fence_watchdog.in +@@ -124,7 +124,7 @@ def metadata(avail_opt, options): + for option, dummy in sorted_options(avail_opt): + if "shortdesc" in ALL_OPT[option]: + print(' <parameter name="' + option + +- 'required="' + ALL_OPT[option]["required"] + '">') ++ '" required="' + ALL_OPT[option]["required"] + '">') + + default = "" + default_name_arg = "-" + ALL_OPT[option]["getopt"][:-1] +-- +1.8.3.1 + diff --git a/pacemaker.spec b/pacemaker.spec index 2cd4aab..92eafb3 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -32,7 +32,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.1 -%global specversion 0.4.rc3 +%global specversion 0.5.rc3 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build %global commit c6a4f6e6cdcedf08e0bfd81248b86812c2a571b2 @@ -221,6 +221,7 @@ Patch2: 0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch Patch3: 0004-Build-rpm-package-fence_watchdog-in-base-package.patch Patch4: 0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch Patch5: 0006-Build-manpages-using-help2man-check-exit-code-of-too.patch +Patch6: 0007-Fix-fence_watchdog-fix-malformed-xml-in-metadata.patch # upstream commits @@ -829,6 +830,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Thu Aug 19 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.5.rc3 +- Fix malformed xml in fence_watchdog metadata + * Tue Aug 17 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.4.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc3, for full details, see included ChangeLog file or commit b2569f82a6db1b7ddd4c28fc4e317f96fa3f5518 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Tue Aug 17 09:42:18 2021 +0200 * Tue Aug 17 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.4.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc3, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc3 - Make tools exit-codes consistent for --version - Check exit-codes of tools prior to manpage-generation diff --git a/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch b/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch deleted file mode 100644 index 3e64b25..0000000 --- a/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch +++ /dev/null @@ -1,122 +0,0 @@ -From ee7eba6a7a05bdf0a12d60ebabb334d8ee021101 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 9 Aug 2021 14:48:57 -0500 -Subject: [PATCH] Fix: controller: ensure lost node's transient attributes are - cleared without DC - -Previously, peer_update_callback() cleared a lost node's transient attributes -if either the local node is DC, or there is no DC. - -However, that left the possibility of the DC being lost at the same time as -another node -- the local node would still have fsa_our_dc set while processing -the leave notifications, so no node would clear the attributes for the non-DC -node. - -Now, the controller has its own CPG configuration change callback, which sets a -global boolean before calling the usual one, so that peer_update_callback() can -know when the DC has been lost. ---- - daemons/controld/controld_callbacks.c | 4 ++- - daemons/controld/controld_corosync.c | 57 ++++++++++++++++++++++++++++++++++- - 2 files changed, 59 insertions(+), 2 deletions(-) - -diff --git a/daemons/controld/controld_callbacks.c b/daemons/controld/controld_callbacks.c -index af24856..e564b3d 100644 ---- a/daemons/controld/controld_callbacks.c -+++ b/daemons/controld/controld_callbacks.c -@@ -99,6 +99,8 @@ node_alive(const crm_node_t *node) - - #define state_text(state) ((state)? (const char *)(state) : "in unknown state") - -+bool controld_dc_left = false; -+ - void - peer_update_callback(enum crm_status_type type, crm_node_t * node, const void *data) - { -@@ -217,7 +219,7 @@ peer_update_callback(enum crm_status_type type, crm_node_t * node, const void *d - cib_scope_local); - } - -- } else if (AM_I_DC || (fsa_our_dc == NULL)) { -+ } else if (AM_I_DC || controld_dc_left || (fsa_our_dc == NULL)) { - /* This only needs to be done once, so normally the DC should do - * it. However if there is no DC, every node must do it, since - * there is no other way to ensure some one node does it. -diff --git a/daemons/controld/controld_corosync.c b/daemons/controld/controld_corosync.c -index db99630..c5ab658 100644 ---- a/daemons/controld/controld_corosync.c -+++ b/daemons/controld/controld_corosync.c -@@ -87,6 +87,61 @@ crmd_cs_destroy(gpointer user_data) - } - } - -+extern bool controld_dc_left; -+ -+/*! -+ * \brief Handle a Corosync notification of a CPG configuration change -+ * -+ * \param[in] handle CPG connection -+ * \param[in] cpg_name CPG group name -+ * \param[in] member_list List of current CPG members -+ * \param[in] member_list_entries Number of entries in \p member_list -+ * \param[in] left_list List of CPG members that left -+ * \param[in] left_list_entries Number of entries in \p left_list -+ * \param[in] joined_list List of CPG members that joined -+ * \param[in] joined_list_entries Number of entries in \p joined_list -+ */ -+static void -+cpg_membership_callback(cpg_handle_t handle, const struct cpg_name *cpg_name, -+ const struct cpg_address *member_list, -+ size_t member_list_entries, -+ const struct cpg_address *left_list, -+ size_t left_list_entries, -+ const struct cpg_address *joined_list, -+ size_t joined_list_entries) -+{ -+ /* When nodes leave CPG, the DC clears their transient node attributes. -+ * -+ * However if there is no DC, or the DC is among the nodes that left, each -+ * remaining node needs to do the clearing, to ensure it gets done. -+ * Otherwise, the attributes would persist when the nodes rejoin, which -+ * could have serious consequences for unfencing, agents that use attributes -+ * for internal logic, etc. -+ * -+ * Here, we set a global boolean if the DC is among the nodes that left, for -+ * use by the peer callback. -+ */ -+ if (fsa_our_dc != NULL) { -+ crm_node_t *peer = pcmk__search_cluster_node_cache(0, fsa_our_dc); -+ -+ if (peer != NULL) { -+ for (int i = 0; i < left_list_entries; ++i) { -+ if (left_list[i].nodeid == peer->id) { -+ controld_dc_left = true; -+ break; -+ } -+ } -+ } -+ } -+ -+ // Process the change normally, which will call the peer callback as needed -+ pcmk_cpg_membership(handle, cpg_name, member_list, member_list_entries, -+ left_list, left_list_entries, -+ joined_list, joined_list_entries); -+ -+ controld_dc_left = false; -+} -+ - extern gboolean crm_connect_corosync(crm_cluster_t * cluster); - - gboolean -@@ -95,7 +150,7 @@ crm_connect_corosync(crm_cluster_t * cluster) - if (is_corosync_cluster()) { - crm_set_status_callback(&peer_update_callback); - cluster->cpg.cpg_deliver_fn = crmd_cs_dispatch; -- cluster->cpg.cpg_confchg_fn = pcmk_cpg_membership; -+ cluster->cpg.cpg_confchg_fn = cpg_membership_callback; - cluster->destroy = crmd_cs_destroy; - - if (crm_cluster_connect(cluster)) { --- -1.8.3.1 - diff --git a/0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch b/0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch new file mode 100644 index 0000000..f72774f --- /dev/null +++ b/0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch @@ -0,0 +1,82 @@ +From b34570ecaeb4fb0106dd0aa5a8776a5417a07f90 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Mon, 16 Aug 2021 16:41:18 +0200 +Subject: [PATCH] Fix: tools: make exit-code stdout/stderr consistent with + --version + +--- + tools/crm_attribute.c | 2 +- + tools/crm_diff.c | 2 +- + tools/crm_error.c | 2 +- + tools/crm_node.c | 2 +- + tools/crm_rule.c | 2 +- + 5 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/tools/crm_attribute.c b/tools/crm_attribute.c +index 6bd4e2a..faf4aae 100644 +--- a/tools/crm_attribute.c ++++ b/tools/crm_attribute.c +@@ -326,7 +326,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_attribute is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + if (options.promotion_score && options.attr_name == NULL) { +diff --git a/tools/crm_diff.c b/tools/crm_diff.c +index 9890c10..18f5d48 100644 +--- a/tools/crm_diff.c ++++ b/tools/crm_diff.c +@@ -322,7 +322,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_diff is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + if (options.apply && options.no_version) { +diff --git a/tools/crm_error.c b/tools/crm_error.c +index 923f393..f26efe7 100644 +--- a/tools/crm_error.c ++++ b/tools/crm_error.c +@@ -93,7 +93,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_error is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + if (options.do_list) { +diff --git a/tools/crm_node.c b/tools/crm_node.c +index 25da978..489a39a 100644 +--- a/tools/crm_node.c ++++ b/tools/crm_node.c +@@ -549,7 +549,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_node is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + if (options.command == 0) { +diff --git a/tools/crm_rule.c b/tools/crm_rule.c +index 30c5155..0880415 100644 +--- a/tools/crm_rule.c ++++ b/tools/crm_rule.c +@@ -252,7 +252,7 @@ main(int argc, char **argv) + g_strfreev(processed_args); + pcmk__free_arg_context(context); + /* FIXME: When crm_rule is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ pcmk__cli_help('v', CRM_EX_OK); + } + + /* Check command line arguments before opening a connection to +-- +1.8.3.1 + diff --git a/0006-Build-manpages-using-help2man-check-exit-code-of-too.patch b/0006-Build-manpages-using-help2man-check-exit-code-of-too.patch new file mode 100644 index 0000000..7c408b8 --- /dev/null +++ b/0006-Build-manpages-using-help2man-check-exit-code-of-too.patch @@ -0,0 +1,29 @@ +From 2e0ac6390327e387e9b94e50080d13fd95f545d6 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Mon, 16 Aug 2021 16:42:51 +0200 +Subject: [PATCH] Build: manpages: using help2man check exit-code of tools + +--- + mk/common.mk | 6 ++++++ + 1 file changed, 6 insertions(+) + +diff --git a/mk/common.mk b/mk/common.mk +index aa59feb..c3d1993 100644 +--- a/mk/common.mk ++++ b/mk/common.mk +@@ -68,6 +68,12 @@ HELP2MAN_ARGS = -N --section 8 --name "Part of the Pacemaker cluster resource ma + # and all wrappers to C code. + %.8: % $(MAN8DEPS) + $(AM_V_at)chmod a+x $(abs_builddir)/$< ++ PATH=$(abs_builddir):$$PATH $(abs_builddir)/$< --version >/dev/null ++ if [ -f $(abs_srcdir)/$@.inc ]; then \ ++ PATH=$(abs_builddir):$$PATH $(abs_builddir)/$< --help-all >/dev/null; \ ++ else \ ++ PATH=$(abs_builddir):$$PATH $(abs_builddir)/$< --help >/dev/null; \ ++ fi + $(AM_V_MAN)if [ -f $(abs_srcdir)/$@.inc ]; then \ + PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ + -h --help-all \ +-- +1.8.3.1 + diff --git a/pacemaker.spec b/pacemaker.spec index a138e31..2cd4aab 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -32,10 +32,10 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.1 -%global specversion 0.3.rc2 +%global specversion 0.4.rc3 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build -%global commit a64ad221abe9cdd968ceacd35c23832ce0fcd189 +%global commit c6a4f6e6cdcedf08e0bfd81248b86812c2a571b2 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. @@ -219,7 +219,8 @@ Patch0: 0001-feature-watchdog-fencing-allow-restriction-to-certai.patch Patch1: 0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch Patch2: 0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch Patch3: 0004-Build-rpm-package-fence_watchdog-in-base-package.patch -Patch4: 0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch +Patch4: 0005-Fix-tools-make-exit-code-stdout-stderr-consistent-wi.patch +Patch5: 0006-Build-manpages-using-help2man-check-exit-code-of-too.patch # upstream commits @@ -828,6 +829,13 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Tue Aug 17 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.4.rc3 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc3, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc3 +- Make tools exit-codes consistent for --version +- Check exit-codes of tools prior to manpage-generation + * Wed Aug 11 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.3.rc2 - package fence_watchdog in base-package instead if cli-subpackage - fix version output of fence_watchdog as needed for help2man diff --git a/sources b/sources index 2ccc4d0..edc4941 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-a64ad221a.tar.gz) = ee954bd8efd135965290f9958b65680cbf101e14e2fd22d326e53a250281a7e5b6b6ec979c7f76072514dbf4d29868e99931842dbcc99bab5e5ba5e4bbc4ef0a +SHA512 (pacemaker-c6a4f6e6c.tar.gz) = 28a313c016add4f95ec2b546c468826c8234bafdc1a7a7d26b785733ee10ec209dc0dbf3f107df57604990b5f89b2d05831684b5d3adfd45479706d9c6d5654f commit 7889c6669e78faaef3ce77ff149430c179bb6792 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Wed Aug 11 11:48:10 2021 +0200 * Wed Aug 11 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.3.rc2 - package fence_watchdog in base-package instead if cli-subpackage - fix version output of fence_watchdog as needed for help2man - ensure transient attributes of lost nodes are cleared reliably diff --git a/0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch b/0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch new file mode 100644 index 0000000..8245e4f --- /dev/null +++ b/0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch @@ -0,0 +1,24 @@ +From 88e75d5b98df197fa731e7642434951a24a67095 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Tue, 10 Aug 2021 09:10:23 +0200 +Subject: [PATCH] Fix: fence_watchdog: fix version output needed for help2man + +--- + daemons/fenced/fence_watchdog.in | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/daemons/fenced/fence_watchdog.in b/daemons/fenced/fence_watchdog.in +index c83304f..700065e 100755 +--- a/daemons/fenced/fence_watchdog.in ++++ b/daemons/fenced/fence_watchdog.in +@@ -12,6 +12,7 @@ import sys + import atexit + import getopt + ++AGENT_VERSION = "1.0.0" + SHORT_DESC = "Dummy watchdog fence agent" + LONG_DESC = """fence_watchdog just provides + meta-data - actual fencing is done by the pacemaker internal watchdog agent.""" +-- +1.8.3.1 + diff --git a/0004-Build-rpm-package-fence_watchdog-in-base-package.patch b/0004-Build-rpm-package-fence_watchdog-in-base-package.patch new file mode 100644 index 0000000..d112c40 --- /dev/null +++ b/0004-Build-rpm-package-fence_watchdog-in-base-package.patch @@ -0,0 +1,32 @@ +From 61eb9c240004d1dbd0b5973e2fecda3686bb4c53 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Tue, 10 Aug 2021 09:06:55 +0200 +Subject: [PATCH] Build: rpm: package fence_watchdog in base-package + +--- + rpm/pacemaker.spec.in | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/rpm/pacemaker.spec.in b/rpm/pacemaker.spec.in +index f58357a..0c569b9 100644 +--- a/rpm/pacemaker.spec.in ++++ b/rpm/pacemaker.spec.in +@@ -734,6 +734,7 @@ exit 0 + %{_sbindir}/crm_attribute + %{_sbindir}/crm_master + %{_sbindir}/fence_legacy ++%{_sbindir}/fence_watchdog + + %doc %{_mandir}/man7/pacemaker-controld.* + %doc %{_mandir}/man7/pacemaker-schedulerd.* +@@ -797,7 +798,6 @@ exit 0 + %{_sbindir}/crm_simulate + %{_sbindir}/crm_report + %{_sbindir}/crm_ticket +-%{_sbindir}/fence_watchdog + %{_sbindir}/stonith_admin + # "dirname" is owned by -schemas, which is a prerequisite + %{_datadir}/pacemaker/report.collector +-- +1.8.3.1 + diff --git a/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch b/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch new file mode 100644 index 0000000..3e64b25 --- /dev/null +++ b/0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch @@ -0,0 +1,122 @@ +From ee7eba6a7a05bdf0a12d60ebabb334d8ee021101 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 9 Aug 2021 14:48:57 -0500 +Subject: [PATCH] Fix: controller: ensure lost node's transient attributes are + cleared without DC + +Previously, peer_update_callback() cleared a lost node's transient attributes +if either the local node is DC, or there is no DC. + +However, that left the possibility of the DC being lost at the same time as +another node -- the local node would still have fsa_our_dc set while processing +the leave notifications, so no node would clear the attributes for the non-DC +node. + +Now, the controller has its own CPG configuration change callback, which sets a +global boolean before calling the usual one, so that peer_update_callback() can +know when the DC has been lost. +--- + daemons/controld/controld_callbacks.c | 4 ++- + daemons/controld/controld_corosync.c | 57 ++++++++++++++++++++++++++++++++++- + 2 files changed, 59 insertions(+), 2 deletions(-) + +diff --git a/daemons/controld/controld_callbacks.c b/daemons/controld/controld_callbacks.c +index af24856..e564b3d 100644 +--- a/daemons/controld/controld_callbacks.c ++++ b/daemons/controld/controld_callbacks.c +@@ -99,6 +99,8 @@ node_alive(const crm_node_t *node) + + #define state_text(state) ((state)? (const char *)(state) : "in unknown state") + ++bool controld_dc_left = false; ++ + void + peer_update_callback(enum crm_status_type type, crm_node_t * node, const void *data) + { +@@ -217,7 +219,7 @@ peer_update_callback(enum crm_status_type type, crm_node_t * node, const void *d + cib_scope_local); + } + +- } else if (AM_I_DC || (fsa_our_dc == NULL)) { ++ } else if (AM_I_DC || controld_dc_left || (fsa_our_dc == NULL)) { + /* This only needs to be done once, so normally the DC should do + * it. However if there is no DC, every node must do it, since + * there is no other way to ensure some one node does it. +diff --git a/daemons/controld/controld_corosync.c b/daemons/controld/controld_corosync.c +index db99630..c5ab658 100644 +--- a/daemons/controld/controld_corosync.c ++++ b/daemons/controld/controld_corosync.c +@@ -87,6 +87,61 @@ crmd_cs_destroy(gpointer user_data) + } + } + ++extern bool controld_dc_left; ++ ++/*! ++ * \brief Handle a Corosync notification of a CPG configuration change ++ * ++ * \param[in] handle CPG connection ++ * \param[in] cpg_name CPG group name ++ * \param[in] member_list List of current CPG members ++ * \param[in] member_list_entries Number of entries in \p member_list ++ * \param[in] left_list List of CPG members that left ++ * \param[in] left_list_entries Number of entries in \p left_list ++ * \param[in] joined_list List of CPG members that joined ++ * \param[in] joined_list_entries Number of entries in \p joined_list ++ */ ++static void ++cpg_membership_callback(cpg_handle_t handle, const struct cpg_name *cpg_name, ++ const struct cpg_address *member_list, ++ size_t member_list_entries, ++ const struct cpg_address *left_list, ++ size_t left_list_entries, ++ const struct cpg_address *joined_list, ++ size_t joined_list_entries) ++{ ++ /* When nodes leave CPG, the DC clears their transient node attributes. ++ * ++ * However if there is no DC, or the DC is among the nodes that left, each ++ * remaining node needs to do the clearing, to ensure it gets done. ++ * Otherwise, the attributes would persist when the nodes rejoin, which ++ * could have serious consequences for unfencing, agents that use attributes ++ * for internal logic, etc. ++ * ++ * Here, we set a global boolean if the DC is among the nodes that left, for ++ * use by the peer callback. ++ */ ++ if (fsa_our_dc != NULL) { ++ crm_node_t *peer = pcmk__search_cluster_node_cache(0, fsa_our_dc); ++ ++ if (peer != NULL) { ++ for (int i = 0; i < left_list_entries; ++i) { ++ if (left_list[i].nodeid == peer->id) { ++ controld_dc_left = true; ++ break; ++ } ++ } ++ } ++ } ++ ++ // Process the change normally, which will call the peer callback as needed ++ pcmk_cpg_membership(handle, cpg_name, member_list, member_list_entries, ++ left_list, left_list_entries, ++ joined_list, joined_list_entries); ++ ++ controld_dc_left = false; ++} ++ + extern gboolean crm_connect_corosync(crm_cluster_t * cluster); + + gboolean +@@ -95,7 +150,7 @@ crm_connect_corosync(crm_cluster_t * cluster) + if (is_corosync_cluster()) { + crm_set_status_callback(&peer_update_callback); + cluster->cpg.cpg_deliver_fn = crmd_cs_dispatch; +- cluster->cpg.cpg_confchg_fn = pcmk_cpg_membership; ++ cluster->cpg.cpg_confchg_fn = cpg_membership_callback; + cluster->destroy = crmd_cs_destroy; + + if (crm_cluster_connect(cluster)) { +-- +1.8.3.1 + diff --git a/pacemaker.spec b/pacemaker.spec index a8f1d51..a138e31 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -32,7 +32,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.1 -%global specversion 0.2.rc2 +%global specversion 0.3.rc2 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build %global commit a64ad221abe9cdd968ceacd35c23832ce0fcd189 @@ -217,6 +217,9 @@ Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{arch Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... Patch0: 0001-feature-watchdog-fencing-allow-restriction-to-certai.patch Patch1: 0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch +Patch2: 0003-Fix-fence_watchdog-fix-version-output-needed-for-hel.patch +Patch3: 0004-Build-rpm-package-fence_watchdog-in-base-package.patch +Patch4: 0005-Fix-controller-ensure-lost-node-s-transient-attribut.patch # upstream commits @@ -660,6 +663,7 @@ exit 0 %{_sbindir}/crm_attribute %{_sbindir}/crm_master +%{_sbindir}/fence_watchdog %doc %{_mandir}/man7/pacemaker-controld.* %doc %{_mandir}/man7/pacemaker-schedulerd.* @@ -709,7 +713,6 @@ exit 0 %{_sbindir}/crm_simulate %{_sbindir}/crm_report %{_sbindir}/crm_ticket -%{_sbindir}/fence_watchdog %{_sbindir}/stonith_admin # "dirname" is owned by -schemas, which is a prerequisite %{_datadir}/pacemaker/report.collector @@ -825,6 +828,11 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Wed Aug 11 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.3.rc2 +- package fence_watchdog in base-package instead if cli-subpackage +- fix version output of fence_watchdog as needed for help2man +- ensure transient attributes of lost nodes are cleared reliably + * Mon Aug 9 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.2.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc2, for full details, see included ChangeLog file or commit e8f53e7d76dd1680d55e0436757380baf9abdc38 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Aug 9 17:50:26 2021 +0200 * Mon Aug 9 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.2.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc2, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc2 - Added feature patch that allows to explicitly specify nodes that should do watchdog-fencing diff --git a/0001-feature-watchdog-fencing-allow-restriction-to-certai.patch b/0001-feature-watchdog-fencing-allow-restriction-to-certai.patch new file mode 100644 index 0000000..97e6071 --- /dev/null +++ b/0001-feature-watchdog-fencing-allow-restriction-to-certai.patch @@ -0,0 +1,1119 @@ +From 5dd1e4459335764e0adf5fa78d81c875ae2332e9 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Fri, 30 Jul 2021 18:15:10 +0200 +Subject: [PATCH] feature: watchdog-fencing: allow restriction to certain nodes + +Bump CRM_FEATURE_SET to 3.11.0 to encourage cluster being +fully upgraded to a version that supports the feature +before explicitly adding a watchdog-fence-device. +--- + configure.ac | 1 + + daemons/controld/controld_control.c | 2 +- + daemons/controld/controld_fencing.c | 14 ++ + daemons/controld/controld_fencing.h | 1 + + daemons/fenced/Makefile.am | 2 +- + daemons/fenced/fence_watchdog.in | 283 ++++++++++++++++++++++++++++++++++++ + daemons/fenced/fenced_commands.c | 141 ++++++++++++++---- + daemons/fenced/fenced_remote.c | 71 ++++++--- + daemons/fenced/pacemaker-fenced.c | 131 ++++++++++++----- + daemons/fenced/pacemaker-fenced.h | 5 +- + include/crm/crm.h | 2 +- + include/crm/fencing/internal.h | 8 +- + lib/fencing/st_client.c | 61 ++++++++ + lib/lrmd/lrmd_client.c | 6 +- + rpm/pacemaker.spec.in | 3 + + 16 files changed, 635 insertions(+), 97 deletions(-) + create mode 100755 daemons/fenced/fence_watchdog.in + +diff --git a/configure.ac b/configure.ac +index 436100c..013562e 100644 +--- a/configure.ac ++++ b/configure.ac +@@ -1972,6 +1972,7 @@ CONFIG_FILES_EXEC([cts/cts-cli], + [cts/support/fence_dummy], + [cts/support/pacemaker-cts-dummyd], + [daemons/fenced/fence_legacy], ++ [daemons/fenced/fence_watchdog], + [doc/abi-check], + [extra/resources/ClusterMon], + [extra/resources/HealthSMART], +diff --git a/daemons/controld/controld_control.c b/daemons/controld/controld_control.c +index 45a70bb..b5da6a4 100644 +--- a/daemons/controld/controld_control.c ++++ b/daemons/controld/controld_control.c +@@ -615,7 +615,7 @@ static pcmk__cluster_option_t crmd_opts[] = { + }, + { + "stonith-watchdog-timeout", NULL, "time", NULL, +- "0", pcmk__valid_sbd_timeout, ++ "0", controld_verify_stonith_watchdog_timeout, + "How long to wait before we can assume nodes are safely down " + "when watchdog-based self-fencing via SBD is in use", + "If nonzero, along with `have-watchdog=true` automatically set by the " +diff --git a/daemons/controld/controld_fencing.c b/daemons/controld/controld_fencing.c +index 0fba661..6c2a6c5 100644 +--- a/daemons/controld/controld_fencing.c ++++ b/daemons/controld/controld_fencing.c +@@ -11,6 +11,7 @@ + #include <crm/crm.h> + #include <crm/msg_xml.h> + #include <crm/common/xml.h> ++#include <crm/stonith-ng.h> + #include <crm/fencing/internal.h> + + #include <pacemaker-controld.h> +@@ -886,6 +887,19 @@ te_fence_node(crm_graph_t *graph, crm_action_t *action) + return TRUE; + } + ++bool ++controld_verify_stonith_watchdog_timeout(const char *value) ++{ ++ gboolean rv = TRUE; ++ ++ if (stonith_api && (stonith_api->state != stonith_disconnected) && ++ stonith__watchdog_fencing_enabled_for_node_api(stonith_api, ++ fsa_our_uname)) { ++ rv = pcmk__valid_sbd_timeout(value); ++ } ++ return rv; ++} ++ + /* end stonith API client functions */ + + +diff --git a/daemons/controld/controld_fencing.h b/daemons/controld/controld_fencing.h +index d0ecc82..ef68a0c 100644 +--- a/daemons/controld/controld_fencing.h ++++ b/daemons/controld/controld_fencing.h +@@ -24,6 +24,7 @@ void update_stonith_max_attempts(const char* value); + void controld_trigger_fencer_connect(void); + void controld_disconnect_fencer(bool destroy); + gboolean te_fence_node(crm_graph_t *graph, crm_action_t *action); ++bool controld_verify_stonith_watchdog_timeout(const char *value); + + // stonith cleanup list + void add_stonith_cleanup(const char *target); +diff --git a/daemons/fenced/Makefile.am b/daemons/fenced/Makefile.am +index 43413e1..2923d7c 100644 +--- a/daemons/fenced/Makefile.am ++++ b/daemons/fenced/Makefile.am +@@ -15,7 +15,7 @@ halibdir = $(CRM_DAEMON_DIR) + + halib_PROGRAMS = pacemaker-fenced cts-fence-helper + +-sbin_SCRIPTS = fence_legacy ++sbin_SCRIPTS = fence_legacy fence_watchdog + + noinst_HEADERS = pacemaker-fenced.h + +diff --git a/daemons/fenced/fence_watchdog.in b/daemons/fenced/fence_watchdog.in +new file mode 100755 +index 0000000..c83304f +--- /dev/null ++++ b/daemons/fenced/fence_watchdog.in +@@ -0,0 +1,283 @@ ++#!@PYTHON@ ++"""Dummy watchdog fence agent for providing meta-data for the pacemaker internal agent ++""" ++ ++__copyright__ = "Copyright 2012-2021 the Pacemaker project contributors" ++__license__ = "GNU General Public License version 2 or later (GPLv2+) WITHOUT ANY WARRANTY" ++ ++import io ++import os ++import re ++import sys ++import atexit ++import getopt ++ ++SHORT_DESC = "Dummy watchdog fence agent" ++LONG_DESC = """fence_watchdog just provides ++meta-data - actual fencing is done by the pacemaker internal watchdog agent.""" ++ ++ALL_OPT = { ++ "version" : { ++ "getopt" : "V", ++ "longopt" : "version", ++ "help" : "-V, --version Display version information and exit", ++ "required" : "0", ++ "shortdesc" : "Display version information and exit", ++ "order" : 53 ++ }, ++ "help" : { ++ "getopt" : "h", ++ "longopt" : "help", ++ "help" : "-h, --help Display this help and exit", ++ "required" : "0", ++ "shortdesc" : "Display help and exit", ++ "order" : 54 ++ }, ++ "action" : { ++ "getopt" : "o:", ++ "longopt" : "action", ++ "help" : "-o, --action=[action] Action: metadata", ++ "required" : "1", ++ "shortdesc" : "Fencing Action", ++ "default" : "metadata", ++ "order" : 1 ++ }, ++ "nodename" : { ++ "getopt" : "N:", ++ "longopt" : "nodename", ++ "help" : "-N, --nodename Node name of fence victim (ignored)", ++ "required" : "0", ++ "shortdesc" : "Ignored", ++ "order" : 2 ++ }, ++ "plug" : { ++ "getopt" : "n:", ++ "longopt" : "plug", ++ "help" : "-n, --plug=[id] Physical plug number on device (ignored)", ++ "required" : "1", ++ "shortdesc" : "Ignored", ++ "order" : 4 ++ } ++} ++ ++ ++def agent(): ++ """ Return name this file was run as. """ ++ ++ return os.path.basename(sys.argv[0]) ++ ++ ++def fail_usage(message): ++ """ Print a usage message and exit. """ ++ ++ sys.exit("%s\nPlease use '-h' for usage" % message) ++ ++ ++def show_docs(options): ++ """ Handle informational options (display info and exit). """ ++ ++ device_opt = options["device_opt"] ++ ++ if "-h" in options: ++ usage(device_opt) ++ sys.exit(0) ++ ++ if "-o" in options and options["-o"].lower() == "metadata": ++ metadata(device_opt, options) ++ sys.exit(0) ++ ++ if "-V" in options: ++ print(AGENT_VERSION) ++ sys.exit(0) ++ ++ ++def sorted_options(avail_opt): ++ """ Return a list of all options, in their internally specified order. """ ++ ++ sorted_list = [(key, ALL_OPT[key]) for key in avail_opt] ++ sorted_list.sort(key=lambda x: x[1]["order"]) ++ return sorted_list ++ ++ ++def usage(avail_opt): ++ """ Print a usage message. """ ++ print(LONG_DESC) ++ print() ++ print("Usage:") ++ print("\t" + agent() + " [options]") ++ print("Options:") ++ ++ for dummy, value in sorted_options(avail_opt): ++ if len(value["help"]) != 0: ++ print(" " + value["help"]) ++ ++ ++def metadata(avail_opt, options): ++ """ Print agent metadata. """ ++ ++ print("""<?xml version="1.0" ?> ++<resource-agent name="%s" shortdesc="%s"> ++<longdesc>%s</longdesc> ++<parameters>""" % (agent(), SHORT_DESC, LONG_DESC)) ++ ++ for option, dummy in sorted_options(avail_opt): ++ if "shortdesc" in ALL_OPT[option]: ++ print(' <parameter name="' + option + ++ 'required="' + ALL_OPT[option]["required"] + '">') ++ ++ default = "" ++ default_name_arg = "-" + ALL_OPT[option]["getopt"][:-1] ++ default_name_no_arg = "-" + ALL_OPT[option]["getopt"] ++ ++ if "default" in ALL_OPT[option]: ++ default = 'default="%s"' % str(ALL_OPT[option]["default"]) ++ elif default_name_arg in options: ++ if options[default_name_arg]: ++ try: ++ default = 'default="%s"' % options[default_name_arg] ++ except TypeError: ++ ## @todo/@note: Currently there is no clean way how to handle lists ++ ## we can create a string from it but we can't set it on command line ++ default = 'default="%s"' % str(options[default_name_arg]) ++ elif default_name_no_arg in options: ++ default = 'default="true"' ++ ++ mixed = ALL_OPT[option]["help"] ++ ## split it between option and help text ++ res = re.compile(r"^(.*--\S+)\s+", re.IGNORECASE | re.S).search(mixed) ++ if None != res: ++ mixed = res.group(1) ++ mixed = mixed.replace("<", "<").replace(">", ">") ++ print(' <getopt mixed="' + mixed + '" />') ++ ++ if ALL_OPT[option]["getopt"].count(":") > 0: ++ print(' <content type="string" ' + default + ' />') ++ else: ++ print(' <content type="boolean" ' + default + ' />') ++ ++ print(' <shortdesc lang="en">' + ALL_OPT[option]["shortdesc"] + '</shortdesc>') ++ print(' </parameter>') ++ ++ print(' </parameters>\n <actions>') ++ print(' <action name="on" />') ++ print(' <action name="off" />') ++ print(' <action name="reboot" />') ++ print(' <action name="monitor" />') ++ print(' <action name="list" />') ++ print(' <action name="metadata" />') ++ print(' </actions>') ++ print('</resource-agent>') ++ ++ ++def option_longopt(option): ++ """ Return the getopt-compatible long-option name of the given option. """ ++ ++ if ALL_OPT[option]["getopt"].endswith(":"): ++ return ALL_OPT[option]["longopt"] + "=" ++ else: ++ return ALL_OPT[option]["longopt"] ++ ++ ++def opts_from_command_line(argv, avail_opt): ++ """ Read options from command-line arguments. """ ++ ++ # Prepare list of options for getopt ++ getopt_string = "" ++ longopt_list = [] ++ for k in avail_opt: ++ if k in ALL_OPT: ++ getopt_string += ALL_OPT[k]["getopt"] ++ else: ++ fail_usage("Parse error: unknown option '" + k + "'") ++ ++ if k in ALL_OPT and "longopt" in ALL_OPT[k]: ++ longopt_list.append(option_longopt(k)) ++ ++ try: ++ opt, dummy = getopt.gnu_getopt(argv, getopt_string, longopt_list) ++ except getopt.GetoptError as error: ++ fail_usage("Parse error: " + error.msg) ++ ++ # Transform longopt to short one which are used in fencing agents ++ old_opt = opt ++ opt = {} ++ for old_option in dict(old_opt).keys(): ++ if old_option.startswith("--"): ++ for option in ALL_OPT.keys(): ++ if "longopt" in ALL_OPT[option] and "--" + ALL_OPT[option]["longopt"] == old_option: ++ opt["-" + ALL_OPT[option]["getopt"].rstrip(":")] = dict(old_opt)[old_option] ++ else: ++ opt[old_option] = dict(old_opt)[old_option] ++ ++ return opt ++ ++ ++def opts_from_stdin(avail_opt): ++ """ Read options from standard input. """ ++ ++ opt = {} ++ name = "" ++ for line in sys.stdin.readlines(): ++ line = line.strip() ++ if line.startswith("#") or (len(line) == 0): ++ continue ++ ++ (name, value) = (line + "=").split("=", 1) ++ value = value[:-1] ++ ++ if name not in avail_opt: ++ print("Parse error: Ignoring unknown option '%s'" % line, ++ file=sys.stderr) ++ continue ++ ++ if ALL_OPT[name]["getopt"].endswith(":"): ++ opt["-"+ALL_OPT[name]["getopt"].rstrip(":")] = value ++ elif value.lower() in ["1", "yes", "on", "true"]: ++ opt["-"+ALL_OPT[name]["getopt"]] = "1" ++ ++ return opt ++ ++ ++def process_input(avail_opt): ++ """ Set standard environment variables, and parse all options. """ ++ ++ # Set standard environment ++ os.putenv("LANG", "C") ++ os.putenv("LC_ALL", "C") ++ ++ # Read options from command line or standard input ++ if len(sys.argv) > 1: ++ return opts_from_command_line(sys.argv[1:], avail_opt) ++ else: ++ return opts_from_stdin(avail_opt) ++ ++ ++def atexit_handler(): ++ """ Close stdout on exit. """ ++ ++ try: ++ sys.stdout.close() ++ os.close(1) ++ except IOError: ++ sys.exit("%s failed to close standard output" % agent()) ++ ++ ++def main(): ++ """ Make it so! """ ++ ++ device_opt = ALL_OPT.keys() ++ ++ ## Defaults for fence agent ++ atexit.register(atexit_handler) ++ options = process_input(device_opt) ++ options["device_opt"] = device_opt ++ show_docs(options) ++ ++ print("Watchdog fencing may be initiated only by the cluster, not this agent.", ++ file=sys.stderr) ++ ++ sys.exit(1) ++ ++ ++if __name__ == "__main__": ++ main() +diff --git a/daemons/fenced/fenced_commands.c b/daemons/fenced/fenced_commands.c +index cd9968f..9470ea2 100644 +--- a/daemons/fenced/fenced_commands.c ++++ b/daemons/fenced/fenced_commands.c +@@ -397,15 +397,13 @@ stonith_device_execute(stonith_device_t * device) + return TRUE; + } + +- if(pcmk__str_eq(device->agent, STONITH_WATCHDOG_AGENT, pcmk__str_casei)) { +- if(pcmk__str_eq(cmd->action, "reboot", pcmk__str_casei)) { +- pcmk__panic(__func__); +- goto done; +- +- } else if(pcmk__str_eq(cmd->action, "off", pcmk__str_casei)) { +- pcmk__panic(__func__); +- goto done; +- ++ if (pcmk__str_any_of(device->agent, STONITH_WATCHDOG_AGENT, ++ STONITH_WATCHDOG_AGENT_INTERNAL, NULL)) { ++ if (pcmk__strcase_any_of(cmd->action, "reboot", "off", NULL)) { ++ if (node_does_watchdog_fencing(stonith_our_uname)) { ++ pcmk__panic(__func__); ++ goto done; ++ } + } else { + crm_info("Faking success for %s watchdog operation", cmd->action); + cmd->done_cb(0, 0, NULL, cmd); +@@ -716,7 +714,7 @@ get_agent_metadata(const char *agent, xmlNode ** metadata) + return EINVAL; + } + *metadata = NULL; +- if (pcmk__str_eq(agent, STONITH_WATCHDOG_AGENT, pcmk__str_none)) { ++ if (pcmk__str_eq(agent, STONITH_WATCHDOG_AGENT_INTERNAL, pcmk__str_none)) { + return pcmk_rc_ok; + } + init_metadata_cache(); +@@ -1050,24 +1048,6 @@ schedule_internal_command(const char *origin, + schedule_stonith_command(cmd, device); + } + +-gboolean +-string_in_list(GList *list, const char *item) +-{ +- int lpc = 0; +- int max = g_list_length(list); +- +- for (lpc = 0; lpc < max; lpc++) { +- const char *value = g_list_nth_data(list, lpc); +- +- if (pcmk__str_eq(item, value, pcmk__str_casei)) { +- return TRUE; +- } else { +- crm_trace("%d: '%s' != '%s'", lpc, item, value); +- } +- } +- return FALSE; +-} +- + static void + status_search_cb(GPid pid, int rc, const char *output, gpointer user_data) + { +@@ -1144,7 +1124,7 @@ dynamic_list_search_cb(GPid pid, int rc, const char *output, gpointer user_data) + if (!alias) { + alias = search->host; + } +- if (string_in_list(dev->targets, alias)) { ++ if (pcmk__str_in_list(dev->targets, alias, pcmk__str_casei)) { + can_fence = TRUE; + } + } +@@ -1215,9 +1195,62 @@ stonith_device_register(xmlNode * msg, const char **desc, gboolean from_cib) + stonith_device_t *dup = NULL; + stonith_device_t *device = build_device_from_xml(msg); + guint ndevices = 0; ++ int rv = pcmk_ok; + + CRM_CHECK(device != NULL, return -ENOMEM); + ++ /* do we have a watchdog-device? */ ++ if (pcmk__str_eq(device->id, STONITH_WATCHDOG_ID, pcmk__str_none) || ++ pcmk__str_any_of(device->agent, STONITH_WATCHDOG_AGENT, ++ STONITH_WATCHDOG_AGENT_INTERNAL, NULL)) do { ++ if (stonith_watchdog_timeout_ms <= 0) { ++ crm_err("Ignoring watchdog fence device without " ++ "stonith-watchdog-timeout set."); ++ rv = -ENODEV; ++ /* fall through to cleanup & return */ ++ } else if (!pcmk__str_any_of(device->agent, STONITH_WATCHDOG_AGENT, ++ STONITH_WATCHDOG_AGENT_INTERNAL, NULL)) { ++ crm_err("Ignoring watchdog fence device with unknown " ++ "agent '%s' unequal '" STONITH_WATCHDOG_AGENT "'.", ++ device->agent?device->agent:""); ++ rv = -ENODEV; ++ /* fall through to cleanup & return */ ++ } else if (!pcmk__str_eq(device->id, STONITH_WATCHDOG_ID, ++ pcmk__str_none)) { ++ crm_err("Ignoring watchdog fence device " ++ "named %s !='"STONITH_WATCHDOG_ID"'.", ++ device->id?device->id:""); ++ rv = -ENODEV; ++ /* fall through to cleanup & return */ ++ } else { ++ if (pcmk__str_eq(device->agent, STONITH_WATCHDOG_AGENT, ++ pcmk__str_none)) { ++ /* this either has an empty list or the targets ++ configured for watchdog-fencing ++ */ ++ g_list_free_full(stonith_watchdog_targets, free); ++ stonith_watchdog_targets = device->targets; ++ device->targets = NULL; ++ } ++ if (node_does_watchdog_fencing(stonith_our_uname)) { ++ g_list_free_full(device->targets, free); ++ device->targets = stonith__parse_targets(stonith_our_uname); ++ g_hash_table_replace(device->params, ++ strdup(PCMK_STONITH_HOST_LIST), ++ strdup(stonith_our_uname)); ++ /* proceed as with any other stonith-device */ ++ break; ++ } ++ ++ crm_debug("Skip registration of watchdog fence device on node not in host-list."); ++ /* cleanup and fall through to more cleanup and return */ ++ device->targets = NULL; ++ stonith_device_remove(device->id, from_cib); ++ } ++ free_device(device); ++ return rv; ++ } while (0); ++ + dup = device_has_duplicate(device); + if (dup) { + ndevices = g_hash_table_size(device_list); +@@ -1598,6 +1631,39 @@ stonith_level_remove(xmlNode *msg, char **desc) + * (CIB registration is not sufficient), because monitor should not be + * possible unless the device is "started" (API registered). + */ ++ ++static char * ++list_to_string(GList *list, const char *delim, gboolean terminate_with_delim) ++{ ++ int max = g_list_length(list); ++ size_t delim_len = delim?strlen(delim):0; ++ size_t alloc_size = 1 + (max?((max-1+(terminate_with_delim?1:0))*delim_len):0); ++ char *rv; ++ GList *gIter; ++ ++ for (gIter = list; gIter != NULL; gIter = gIter->next) { ++ const char *value = (const char *) gIter->data; ++ ++ alloc_size += strlen(value); ++ } ++ rv = calloc(alloc_size, sizeof(char)); ++ if (rv) { ++ char *pos = rv; ++ const char *lead_delim = ""; ++ ++ for (gIter = list; gIter != NULL; gIter = gIter->next) { ++ const char *value = (const char *) gIter->data; ++ ++ pos = &pos[sprintf(pos, "%s%s", lead_delim, value)]; ++ lead_delim = delim; ++ } ++ if (max && terminate_with_delim) { ++ sprintf(pos, "%s", delim); ++ } ++ } ++ return rv; ++} ++ + static int + stonith_device_action(xmlNode * msg, char **output) + { +@@ -1615,6 +1681,19 @@ stonith_device_action(xmlNode * msg, char **output) + return -EPROTO; + } + ++ if (pcmk__str_eq(id, STONITH_WATCHDOG_ID, pcmk__str_none)) { ++ if (stonith_watchdog_timeout_ms <= 0) { ++ return -ENODEV; ++ } else { ++ if (pcmk__str_eq(action, "list", pcmk__str_casei)) { ++ *output = list_to_string(stonith_watchdog_targets, "\n", TRUE); ++ return pcmk_ok; ++ } else if (pcmk__str_eq(action, "monitor", pcmk__str_casei)) { ++ return pcmk_ok; ++ } ++ } ++ } ++ + device = g_hash_table_lookup(device_list, id); + if ((device == NULL) + || (!device->api_registered && !strcmp(action, "monitor"))) { +@@ -1742,7 +1821,7 @@ can_fence_host_with_device(stonith_device_t * dev, struct device_search_s *searc + * Only use if all hosts on which the device can be active can always fence all listed hosts + */ + +- if (string_in_list(dev->targets, host)) { ++ if (pcmk__str_in_list(dev->targets, host, pcmk__str_casei)) { + can = TRUE; + } else if (g_hash_table_lookup(dev->params, PCMK_STONITH_HOST_MAP) + && g_hash_table_lookup(dev->aliases, host)) { +@@ -1763,7 +1842,7 @@ can_fence_host_with_device(stonith_device_t * dev, struct device_search_s *searc + return; + } + +- if (string_in_list(dev->targets, alias)) { ++ if (pcmk__str_in_list(dev->targets, alias, pcmk__str_casei)) { + can = TRUE; + } + +diff --git a/daemons/fenced/fenced_remote.c b/daemons/fenced/fenced_remote.c +index cf91aca..224f2ba 100644 +--- a/daemons/fenced/fenced_remote.c ++++ b/daemons/fenced/fenced_remote.c +@@ -1522,6 +1522,25 @@ advance_topology_device_in_level(remote_fencing_op_t *op, const char *device, + } + } + ++static gboolean ++check_watchdog_fencing_and_wait(remote_fencing_op_t * op) ++{ ++ if (node_does_watchdog_fencing(op->target)) { ++ ++ crm_notice("Waiting %lds for %s to self-fence (%s) for " ++ "client %s " CRM_XS " id=%.8s", ++ (stonith_watchdog_timeout_ms / 1000), ++ op->target, op->action, op->client_name, op->id); ++ op->op_timer_one = g_timeout_add(stonith_watchdog_timeout_ms, ++ remote_op_watchdog_done, op); ++ return TRUE; ++ } else { ++ crm_debug("Skipping fallback to watchdog-fencing as %s is " ++ "not in host-list", op->target); ++ } ++ return FALSE; ++} ++ + void + call_remote_stonith(remote_fencing_op_t * op, st_query_result_t * peer, int rc) + { +@@ -1592,26 +1611,33 @@ call_remote_stonith(remote_fencing_op_t * op, st_query_result_t * peer, int rc) + g_source_remove(op->op_timer_one); + } + +- if(stonith_watchdog_timeout_ms > 0 && device && pcmk__str_eq(device, "watchdog", pcmk__str_casei)) { +- crm_notice("Waiting %lds for %s to self-fence (%s) for client %s " +- CRM_XS " id=%.8s", (stonith_watchdog_timeout_ms / 1000), +- op->target, op->action, op->client_name, op->id); +- op->op_timer_one = g_timeout_add(stonith_watchdog_timeout_ms, remote_op_watchdog_done, op); +- +- /* TODO check devices to verify watchdog will be in use */ +- } else if(stonith_watchdog_timeout_ms > 0 +- && pcmk__str_eq(peer->host, op->target, pcmk__str_casei) +- && !pcmk__str_eq(op->action, "on", pcmk__str_casei)) { +- crm_notice("Waiting %lds for %s to self-fence (%s) for client %s " +- CRM_XS " id=%.8s", (stonith_watchdog_timeout_ms / 1000), +- op->target, op->action, op->client_name, op->id); +- op->op_timer_one = g_timeout_add(stonith_watchdog_timeout_ms, remote_op_watchdog_done, op); +- +- } else { ++ if (!(stonith_watchdog_timeout_ms > 0 && ( ++ (pcmk__str_eq(device, STONITH_WATCHDOG_ID, ++ pcmk__str_none)) || ++ (pcmk__str_eq(peer->host, op->target, pcmk__str_casei) ++ && !pcmk__str_eq(op->action, "on", pcmk__str_casei))) && ++ check_watchdog_fencing_and_wait(op))) { ++ ++ /* Some thoughts about self-fencing cases reaching this point: ++ - Actually check in check_watchdog_fencing_and_wait ++ shouldn't fail if STONITH_WATCHDOG_ID is ++ chosen as fencing-device and it being present implies ++ watchdog-fencing is enabled anyway ++ - If watchdog-fencing is disabled either in general or for ++ a specific target - detected in check_watchdog_fencing_and_wait - ++ for some other kind of self-fencing we can't expect ++ a success answer but timeout is fine if the node doesn't ++ come back in between ++ - Delicate might be the case where we have watchdog-fencing ++ enabled for a node but the watchdog-fencing-device isn't ++ explicitly chosen for suicide. Local pe-execution in sbd ++ may detect the node as unclean and lead to timely suicide. ++ Otherwise the selection of stonith-watchdog-timeout at ++ least is questionable. ++ */ + op->op_timer_one = g_timeout_add((1000 * timeout_one), remote_op_timeout_one, op); + } + +- + send_cluster_message(crm_get_peer(0, peer->host), crm_msg_stonith_ng, remote_op, FALSE); + peer->tried = TRUE; + free_xml(remote_op); +@@ -1645,12 +1671,11 @@ call_remote_stonith(remote_fencing_op_t * op, st_query_result_t * peer, int rc) + * but we have all the expected replies, then no devices + * are available to execute the fencing operation. */ + +- if(stonith_watchdog_timeout_ms && pcmk__str_eq(device, "watchdog", pcmk__str_null_matches | pcmk__str_casei)) { +- crm_notice("Waiting %lds for %s to self-fence (%s) for client %s " +- CRM_XS " id=%.8s", (stonith_watchdog_timeout_ms / 1000), +- op->target, op->action, op->client_name, op->id); +- op->op_timer_one = g_timeout_add(stonith_watchdog_timeout_ms, remote_op_watchdog_done, op); +- return; ++ if(stonith_watchdog_timeout_ms > 0 && pcmk__str_eq(device, ++ STONITH_WATCHDOG_ID, pcmk__str_null_matches)) { ++ if (check_watchdog_fencing_and_wait(op)) { ++ return; ++ } + } + + if (op->state == st_query) { +diff --git a/daemons/fenced/pacemaker-fenced.c b/daemons/fenced/pacemaker-fenced.c +index 39738d8..7f8b427 100644 +--- a/daemons/fenced/pacemaker-fenced.c ++++ b/daemons/fenced/pacemaker-fenced.c +@@ -42,6 +42,7 @@ + + char *stonith_our_uname = NULL; + long stonith_watchdog_timeout_ms = 0; ++GList *stonith_watchdog_targets = NULL; + + static GMainLoop *mainloop = NULL; + +@@ -578,7 +579,44 @@ our_node_allowed_for(pe_resource_t *rsc) + } + + static void +-watchdog_device_update(xmlNode *cib) ++watchdog_device_update(void) ++{ ++ if (stonith_watchdog_timeout_ms > 0) { ++ if (!g_hash_table_lookup(device_list, STONITH_WATCHDOG_ID) && ++ !stonith_watchdog_targets) { ++ /* getting here watchdog-fencing enabled, no device there yet ++ and reason isn't stonith_watchdog_targets preventing that ++ */ ++ int rc; ++ xmlNode *xml; ++ ++ xml = create_device_registration_xml( ++ STONITH_WATCHDOG_ID, ++ st_namespace_internal, ++ STONITH_WATCHDOG_AGENT, ++ NULL, /* stonith_device_register will add our ++ own name as PCMK_STONITH_HOST_LIST param ++ so we can skip that here ++ */ ++ NULL); ++ rc = stonith_device_register(xml, NULL, TRUE); ++ free_xml(xml); ++ if (rc != pcmk_ok) { ++ crm_crit("Cannot register watchdog pseudo fence agent"); ++ crm_exit(CRM_EX_FATAL); ++ } ++ } ++ ++ } else { ++ /* be silent if no device - todo parameter to stonith_device_remove */ ++ if (g_hash_table_lookup(device_list, STONITH_WATCHDOG_ID)) { ++ stonith_device_remove(STONITH_WATCHDOG_ID, TRUE); ++ } ++ } ++} ++ ++static void ++update_stonith_watchdog_timeout_ms(xmlNode *cib) + { + xmlNode *stonith_enabled_xml = NULL; + const char *stonith_enabled_s = NULL; +@@ -608,33 +646,7 @@ watchdog_device_update(xmlNode *cib) + } + } + +- if (timeout_ms != stonith_watchdog_timeout_ms) { +- crm_notice("New watchdog timeout %lds (was %lds)", timeout_ms/1000, stonith_watchdog_timeout_ms/1000); +- stonith_watchdog_timeout_ms = timeout_ms; +- +- if (stonith_watchdog_timeout_ms > 0) { +- int rc; +- xmlNode *xml; +- stonith_key_value_t *params = NULL; +- +- params = stonith_key_value_add(params, PCMK_STONITH_HOST_LIST, +- stonith_our_uname); +- +- xml = create_device_registration_xml("watchdog", st_namespace_internal, +- STONITH_WATCHDOG_AGENT, params, +- NULL); +- stonith_key_value_freeall(params, 1, 1); +- rc = stonith_device_register(xml, NULL, FALSE); +- free_xml(xml); +- if (rc != pcmk_ok) { +- crm_crit("Cannot register watchdog pseudo fence agent"); +- crm_exit(CRM_EX_FATAL); +- } +- +- } else { +- stonith_device_remove("watchdog", FALSE); +- } +- } ++ stonith_watchdog_timeout_ms = timeout_ms; + } + + /*! +@@ -677,6 +689,16 @@ static void cib_device_update(pe_resource_t *rsc, pe_working_set_t *data_set) + return; + } + ++ /* if watchdog-fencing is disabled handle any watchdog-fence ++ resource as if it was disabled ++ */ ++ if ((stonith_watchdog_timeout_ms <= 0) && ++ pcmk__str_eq(rsc->id, STONITH_WATCHDOG_ID, pcmk__str_none)) { ++ crm_info("Watchdog-fencing disabled thus handling " ++ "device %s as disabled", rsc->id); ++ return; ++ } ++ + /* Check whether our node is allowed for this resource (and its parent if in a group) */ + node = our_node_allowed_for(rsc); + if (rsc->parent && (rsc->parent->variant == pe_group)) { +@@ -772,6 +794,12 @@ cib_devices_update(void) + } + } + ++ /* have list repopulated if cib has a watchdog-fencing-resource ++ TODO: keep a cached list for queries happening while we are refreshing ++ */ ++ g_list_free_full(stonith_watchdog_targets, free); ++ stonith_watchdog_targets = NULL; ++ + for (gIter = fenced_data_set->resources; gIter != NULL; gIter = gIter->next) { + cib_device_update(gIter->data, fenced_data_set); + } +@@ -825,6 +853,8 @@ update_cib_stonith_devices_v2(const char *event, xmlNode * msg) + if (search != NULL) { + *search = 0; + stonith_device_remove(rsc_id, TRUE); ++ /* watchdog_device_update called afterwards ++ to fall back to implicit definition if needed */ + } else { + crm_warn("Ignoring malformed CIB update (resource deletion)"); + } +@@ -968,6 +998,24 @@ node_has_attr(const char *node, const char *name, const char *value) + return (match != NULL); + } + ++/*! ++ * \internal ++ * \brief Check whether a node does watchdog-fencing ++ * ++ * \param[in] node Name of node to check ++ * ++ * \return TRUE if node found in stonith_watchdog_targets ++ * or stonith_watchdog_targets is empty indicating ++ * all nodes are doing watchdog-fencing ++ */ ++gboolean ++node_does_watchdog_fencing(const char *node) ++{ ++ return ((stonith_watchdog_targets == NULL) || ++ pcmk__str_in_list(stonith_watchdog_targets, node, pcmk__str_casei)); ++} ++ ++ + static void + update_fencing_topology(const char *event, xmlNode * msg) + { +@@ -1073,6 +1121,8 @@ update_cib_cache_cb(const char *event, xmlNode * msg) + xmlNode *stonith_enabled_xml = NULL; + const char *stonith_enabled_s = NULL; + static gboolean stonith_enabled_saved = TRUE; ++ long timeout_ms_saved = stonith_watchdog_timeout_ms; ++ gboolean need_full_refresh = FALSE; + + if(!have_cib_devices) { + crm_trace("Skipping updates until we get a full dump"); +@@ -1127,6 +1177,7 @@ update_cib_cache_cb(const char *event, xmlNode * msg) + } + + pcmk__refresh_node_caches_from_cib(local_cib); ++ update_stonith_watchdog_timeout_ms(local_cib); + + stonith_enabled_xml = get_xpath_object("//nvpair[@name='stonith-enabled']", + local_cib, LOG_NEVER); +@@ -1134,23 +1185,30 @@ update_cib_cache_cb(const char *event, xmlNode * msg) + stonith_enabled_s = crm_element_value(stonith_enabled_xml, XML_NVPAIR_ATTR_VALUE); + } + +- watchdog_device_update(local_cib); +- + if (stonith_enabled_s && crm_is_true(stonith_enabled_s) == FALSE) { + crm_trace("Ignoring CIB updates while fencing is disabled"); + stonith_enabled_saved = FALSE; +- return; + + } else if (stonith_enabled_saved == FALSE) { + crm_info("Updating fencing device and topology lists " + "now that fencing is enabled"); + stonith_enabled_saved = TRUE; +- fencing_topology_init(); +- cib_devices_update(); ++ need_full_refresh = TRUE; + + } else { +- update_fencing_topology(event, msg); +- update_cib_stonith_devices(event, msg); ++ if (timeout_ms_saved != stonith_watchdog_timeout_ms) { ++ need_full_refresh = TRUE; ++ } else { ++ update_fencing_topology(event, msg); ++ update_cib_stonith_devices(event, msg); ++ watchdog_device_update(); ++ } ++ } ++ ++ if (need_full_refresh) { ++ fencing_topology_init(); ++ cib_devices_update(); ++ watchdog_device_update(); + } + } + +@@ -1162,10 +1220,11 @@ init_cib_cache_cb(xmlNode * msg, int call_id, int rc, xmlNode * output, void *us + local_cib = copy_xml(output); + + pcmk__refresh_node_caches_from_cib(local_cib); ++ update_stonith_watchdog_timeout_ms(local_cib); + + fencing_topology_init(); +- watchdog_device_update(local_cib); + cib_devices_update(); ++ watchdog_device_update(); + } + + static void +diff --git a/daemons/fenced/pacemaker-fenced.h b/daemons/fenced/pacemaker-fenced.h +index d330fda..14e085e 100644 +--- a/daemons/fenced/pacemaker-fenced.h ++++ b/daemons/fenced/pacemaker-fenced.h +@@ -260,14 +260,15 @@ bool fencing_peer_active(crm_node_t *peer); + + int stonith_manual_ack(xmlNode * msg, remote_fencing_op_t * op); + +-gboolean string_in_list(GList *list, const char *item); +- + gboolean node_has_attr(const char *node, const char *name, const char *value); + ++gboolean node_does_watchdog_fencing(const char *node); ++ + extern char *stonith_our_uname; + extern gboolean stand_alone; + extern GHashTable *device_list; + extern GHashTable *topology; + extern long stonith_watchdog_timeout_ms; ++extern GList *stonith_watchdog_targets; + + extern GHashTable *stonith_remote_op_list; +diff --git a/include/crm/crm.h b/include/crm/crm.h +index ee52c36..7861c16 100644 +--- a/include/crm/crm.h ++++ b/include/crm/crm.h +@@ -66,7 +66,7 @@ extern "C" { + * >=3.0.13: Fail counts include operation name and interval + * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED + */ +-# define CRM_FEATURE_SET "3.10.2" ++# define CRM_FEATURE_SET "3.11.0" + + /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and + * recipient of a CPG message. This imposes an arbitrary limit on cluster node +diff --git a/include/crm/fencing/internal.h b/include/crm/fencing/internal.h +index 8bcb544..f222edb 100644 +--- a/include/crm/fencing/internal.h ++++ b/include/crm/fencing/internal.h +@@ -164,7 +164,10 @@ void stonith__device_parameter_flags(uint32_t *device_flags, + # define STONITH_OP_LEVEL_ADD "st_level_add" + # define STONITH_OP_LEVEL_DEL "st_level_remove" + +-# define STONITH_WATCHDOG_AGENT "#watchdog" ++# define STONITH_WATCHDOG_AGENT "fence_watchdog" ++/* Don't change 2 below as it would break rolling upgrade */ ++# define STONITH_WATCHDOG_AGENT_INTERNAL "#watchdog" ++# define STONITH_WATCHDOG_ID "watchdog" + + # ifdef HAVE_STONITH_STONITH_H + // utilities from st_lha.c +@@ -211,4 +214,7 @@ stonith__op_state_pending(enum op_state state) + return state != st_failed && state != st_done; + } + ++gboolean stonith__watchdog_fencing_enabled_for_node(const char *node); ++gboolean stonith__watchdog_fencing_enabled_for_node_api(stonith_t *st, const char *node); ++ + #endif +diff --git a/lib/fencing/st_client.c b/lib/fencing/st_client.c +index e285f51..0ff9815 100644 +--- a/lib/fencing/st_client.c ++++ b/lib/fencing/st_client.c +@@ -195,6 +195,67 @@ stonith_get_namespace(const char *agent, const char *namespace_s) + return st_namespace_invalid; + } + ++gboolean ++stonith__watchdog_fencing_enabled_for_node_api(stonith_t *st, const char *node) ++{ ++ gboolean rv = FALSE; ++ stonith_t *stonith_api = st?st:stonith_api_new(); ++ char *list = NULL; ++ ++ if(stonith_api) { ++ if (stonith_api->state == stonith_disconnected) { ++ int rc = stonith_api->cmds->connect(stonith_api, "stonith-api", NULL); ++ ++ if (rc != pcmk_ok) { ++ crm_err("Failed connecting to Stonith-API for watchdog-fencing-query."); ++ } ++ } ++ ++ if (stonith_api->state != stonith_disconnected) { ++ /* caveat!!! ++ * this might fail when when stonithd is just updating the device-list ++ * probably something we should fix as well for other api-calls */ ++ int rc = stonith_api->cmds->list(stonith_api, st_opt_sync_call, STONITH_WATCHDOG_ID, &list, 0); ++ if ((rc != pcmk_ok) || (list == NULL)) { ++ /* due to the race described above it can happen that ++ * we drop in here - so as not to make remote nodes ++ * panic on that answer ++ */ ++ crm_warn("watchdog-fencing-query failed"); ++ } else if (list[0] == '\0') { ++ crm_warn("watchdog-fencing-query returned an empty list - any node"); ++ rv = TRUE; ++ } else { ++ GList *targets = stonith__parse_targets(list); ++ rv = pcmk__str_in_list(targets, node, pcmk__str_casei); ++ g_list_free_full(targets, free); ++ } ++ free(list); ++ if (!st) { ++ /* if we're provided the api we still might have done the ++ * connection - but let's assume the caller won't bother ++ */ ++ stonith_api->cmds->disconnect(stonith_api); ++ } ++ } ++ ++ if (!st) { ++ stonith_api_delete(stonith_api); ++ } ++ } else { ++ crm_err("Stonith-API for watchdog-fencing-query couldn't be created."); ++ } ++ crm_trace("Pacemaker assumes node %s %sto do watchdog-fencing.", ++ node, rv?"":"not "); ++ return rv; ++} ++ ++gboolean ++stonith__watchdog_fencing_enabled_for_node(const char *node) ++{ ++ return stonith__watchdog_fencing_enabled_for_node_api(NULL, node); ++} ++ + static void + log_action(stonith_action_t *action, pid_t pid) + { +diff --git a/lib/lrmd/lrmd_client.c b/lib/lrmd/lrmd_client.c +index 87d050e..bf4bceb 100644 +--- a/lib/lrmd/lrmd_client.c ++++ b/lib/lrmd/lrmd_client.c +@@ -34,6 +34,7 @@ + #include <crm/msg_xml.h> + + #include <crm/stonith-ng.h> ++#include <crm/fencing/internal.h> + + #ifdef HAVE_GNUTLS_GNUTLS_H + # undef KEYFILE +@@ -934,7 +935,10 @@ lrmd__validate_remote_settings(lrmd_t *lrmd, GHashTable *hash) + crm_xml_add(data, F_LRMD_ORIGIN, __func__); + + value = g_hash_table_lookup(hash, "stonith-watchdog-timeout"); +- crm_xml_add(data, F_LRMD_WATCHDOG, value); ++ if ((value) && ++ (stonith__watchdog_fencing_enabled_for_node(native->remote_nodename))) { ++ crm_xml_add(data, F_LRMD_WATCHDOG, value); ++ } + + rc = lrmd_send_command(lrmd, LRMD_OP_CHECK, data, NULL, 0, 0, + (native->type == pcmk__client_ipc)); +diff --git a/rpm/pacemaker.spec.in b/rpm/pacemaker.spec.in +index 79e78ed..f58357a 100644 +--- a/rpm/pacemaker.spec.in ++++ b/rpm/pacemaker.spec.in +@@ -744,6 +744,7 @@ exit 0 + %doc %{_mandir}/man8/crm_attribute.* + %doc %{_mandir}/man8/crm_master.* + %doc %{_mandir}/man8/fence_legacy.* ++%doc %{_mandir}/man8/fence_watchdog.* + %doc %{_mandir}/man8/pacemakerd.* + + %doc %{_datadir}/pacemaker/alerts +@@ -796,6 +797,7 @@ exit 0 + %{_sbindir}/crm_simulate + %{_sbindir}/crm_report + %{_sbindir}/crm_ticket ++%{_sbindir}/fence_watchdog + %{_sbindir}/stonith_admin + # "dirname" is owned by -schemas, which is a prerequisite + %{_datadir}/pacemaker/report.collector +@@ -822,6 +824,7 @@ exit 0 + %exclude %{_mandir}/man8/crm_attribute.* + %exclude %{_mandir}/man8/crm_master.* + %exclude %{_mandir}/man8/fence_legacy.* ++%exclude %{_mandir}/man8/fence_watchdog.* + %exclude %{_mandir}/man8/pacemakerd.* + %exclude %{_mandir}/man8/pacemaker-remoted.* + +-- +1.8.3.1 + diff --git a/0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch b/0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch new file mode 100644 index 0000000..ccfbccc --- /dev/null +++ b/0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch @@ -0,0 +1,25 @@ +From 53dd360f096e5f005e3221e8d44d82d3654b5172 Mon Sep 17 00:00:00 2001 +From: Klaus Wenninger <klaus.wenninger(a)aon.at> +Date: Wed, 4 Aug 2021 15:57:23 +0200 +Subject: [PATCH] Fix: watchdog-fencing: Silence warning without node + restriction + +--- + lib/fencing/st_client.c | 1 - + 1 file changed, 1 deletion(-) + +diff --git a/lib/fencing/st_client.c b/lib/fencing/st_client.c +index 0ff9815..14fa7b2 100644 +--- a/lib/fencing/st_client.c ++++ b/lib/fencing/st_client.c +@@ -223,7 +223,6 @@ stonith__watchdog_fencing_enabled_for_node_api(stonith_t *st, const char *node) + */ + crm_warn("watchdog-fencing-query failed"); + } else if (list[0] == '\0') { +- crm_warn("watchdog-fencing-query returned an empty list - any node"); + rv = TRUE; + } else { + GList *targets = stonith__parse_targets(list); +-- +1.8.3.1 + diff --git a/pacemaker.spec b/pacemaker.spec index b3f962b..a8f1d51 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -32,10 +32,10 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.1 -%global specversion 0.1.rc1 +%global specversion 0.2.rc2 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build -%global commit 9e3a841a33c3125034922ec061f6516d307f20d1 +%global commit a64ad221abe9cdd968ceacd35c23832ce0fcd189 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. @@ -215,6 +215,8 @@ Url: https://www.clusterlabs.org/ # You can use "spectool -s 0 pacemaker.spec" (rpmdevtools) to show final URL. Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{archive_gith... Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... +Patch0: 0001-feature-watchdog-fencing-allow-restriction-to-certai.patch +Patch1: 0002-Fix-watchdog-fencing-Silence-warning-without-node-re.patch # upstream commits @@ -240,9 +242,19 @@ Requires: libqb >= 0.17.0 BuildRequires: libqb-devel >= 0.17.0 # Required basic build tools -BuildRequires: coreutils findutils grep sed -BuildRequires: autoconf automake gcc make pkgconfig -BuildRequires: libtool %{?pkgname_libtool_devel} +BuildRequires: autoconf +BuildRequires: automake +BuildRequires: coreutils +BuildRequires: findutils +BuildRequires: gcc +BuildRequires: grep +BuildRequires: libtool +BuildRequires: make +%if %{defined pkgname_libtool_devel} +BuildRequires: %{?pkgname_libtool_devel} +%endif +BuildRequires: pkgconfig +BuildRequires: sed # Required for core functionality BuildRequires: pkgconfig(glib-2.0) >= 2.42 @@ -250,8 +262,12 @@ BuildRequires: libxml2-devel libxslt-devel libuuid-devel BuildRequires: %{pkgname_bzip2_devel} # Enables optional functionality -BuildRequires: ncurses-devel %{pkgname_docbook_xsl} -BuildRequires: help2man %{pkgname_gnutls_devel} pam-devel pkgconfig(dbus-1) +BuildRequires: pkgconfig(dbus-1) +BuildRequires: %{pkgname_docbook_xsl} +BuildRequires: %{pkgname_gnutls_devel} +BuildRequires: help2man +BuildRequires: ncurses-devel +BuildRequires: pam-devel BuildRequires: pkgconfig(systemd) @@ -266,7 +282,9 @@ BuildRequires: %{pkgname_glue_libs}-devel %endif %if %{with doc} -BuildRequires: asciidoc inkscape %{python_name}-sphinx +BuildRequires: asciidoc +BuildRequires: inkscape +BuildRequires: %{python_name}-sphinx %endif Provides: pcmk-cluster-manager = %{version}-%{release} @@ -368,11 +386,16 @@ License: GPLv2+ and LGPLv2+ Summary: Pacemaker development package Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Requires: %{name}-cluster-libs%{?_isa} = %{version}-%{release} -Requires: %{?pkgname_libtool_devel_arch} libuuid-devel%{?_isa} -Requires: libxml2-devel%{?_isa} libxslt-devel%{?_isa} -Requires: %{pkgname_bzip2_devel}%{?_isa} glib2-devel%{?_isa} +Requires: %{pkgname_bzip2_devel}%{?_isa} +Requires: corosync-devel >= 2.0.0 +Requires: glib2-devel%{?_isa} Requires: libqb-devel%{?_isa} -Requires: corosync-devel%{?_isa} >= 2.0.0 +%if %{defined pkgname_libtool_devel_arch} +Requires: %{?pkgname_libtool_devel_arch} +%endif +Requires: libuuid-devel%{?_isa} +Requires: libxml2-devel%{?_isa} +Requires: libxslt-devel%{?_isa} %description -n %{pkgname_pcmk_libs}-devel Pacemaker is an advanced, scalable High-Availability cluster resource @@ -645,6 +668,7 @@ exit 0 %doc %{_mandir}/man7/ocf_pacemaker_remote.* %doc %{_mandir}/man8/crm_attribute.* %doc %{_mandir}/man8/crm_master.* +%doc %{_mandir}/man8/fence_watchdog.* %doc %{_mandir}/man8/pacemakerd.* %doc %{_datadir}/pacemaker/alerts @@ -685,6 +709,7 @@ exit 0 %{_sbindir}/crm_simulate %{_sbindir}/crm_report %{_sbindir}/crm_ticket +%{_sbindir}/fence_watchdog %{_sbindir}/stonith_admin # "dirname" is owned by -schemas, which is a prerequisite %{_datadir}/pacemaker/report.collector @@ -711,6 +736,7 @@ exit 0 %exclude %{_mandir}/man8/crm_attribute.* %exclude %{_mandir}/man8/crm_master.* %exclude %{_mandir}/man8/fence_legacy.* +%exclude %{_mandir}/man8/fence_watchdog.* %exclude %{_mandir}/man8/pacemakerd.* %exclude %{_mandir}/man8/pacemaker-remoted.* @@ -799,6 +825,13 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Aug 9 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.2.rc2 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc2, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc2 +- Added feature patch that allows to explicitly specify nodes that + should do watchdog-fencing + * Wed Jul 28 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc1, for full details, see included ChangeLog file or diff --git a/sources b/sources index b933127..2ccc4d0 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-9e3a841a3.tar.gz) = 26745ba0d9f6730de13ad106fe57beaff9d49c7df1ec528f0689c2faa872608408fb04401a4d49d73deec5422bd7665496a964b1fcbe69866a5983ac2306b6be +SHA512 (pacemaker-a64ad221a.tar.gz) = ee954bd8efd135965290f9958b65680cbf101e14e2fd22d326e53a250281a7e5b6b6ec979c7f76072514dbf4d29868e99931842dbcc99bab5e5ba5e4bbc4ef0a commit 6fcc0b8f5b6f278f33126c445552ad30336e5380 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Wed Jul 28 14:28:47 2021 +0200 * Wed Jul 28 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc1, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc1 diff --git a/001-ping-agent.patch b/001-ping-agent.patch deleted file mode 100644 index 89fe41a..0000000 --- a/001-ping-agent.patch +++ /dev/null @@ -1,225 +0,0 @@ -From c6ee0973522268ed7b3241cf0ec2e06398444114 Mon Sep 17 00:00:00 2001 -From: Grace Chin <gchin(a)redhat.com> -Date: Tue, 4 May 2021 12:02:17 -0400 -Subject: [PATCH 1/4] Remove deprecated attrd_options - ---- - extra/resources/ping | 11 +++-------- - 1 file changed, 3 insertions(+), 8 deletions(-) - -diff --git a/extra/resources/ping b/extra/resources/ping -index 3cf8dfe..2e93f22 100755 ---- a/extra/resources/ping -+++ b/extra/resources/ping -@@ -178,7 +178,7 @@ ping_stop() { - - rm -f "${OCF_RESKEY_pidfile}" - -- attrd_updater -D -n "$OCF_RESKEY_name" -d "$OCF_RESKEY_dampen" $attrd_options -+ attrd_updater -D -n "$OCF_RESKEY_name" -d "$OCF_RESKEY_dampen" - - return $OCF_SUCCESS - } -@@ -302,9 +302,9 @@ ping_update() { - - score=$(expr $active \* $OCF_RESKEY_multiplier) - if [ "$__OCF_ACTION" = "start" ] ; then -- attrd_updater -n "$OCF_RESKEY_name" -B "$score" -d "$OCF_RESKEY_dampen" $attrd_options -+ attrd_updater -n "$OCF_RESKEY_name" -B "$score" -d "$OCF_RESKEY_dampen" - else -- attrd_updater -n "$OCF_RESKEY_name" -v "$score" -d "$OCF_RESKEY_dampen" $attrd_options -+ attrd_updater -n "$OCF_RESKEY_name" -v "$score" -d "$OCF_RESKEY_dampen" - fi - rc=$? - case $rc in -@@ -396,11 +396,6 @@ case "${OCF_RESKEY_debug}" in - ;; - esac - --attrd_options='-q' --if [ "${OCF_RESKEY_debug}" = "true" ]; then -- attrd_options='' --fi -- - case "$__OCF_ACTION" in - meta-data) meta_data - exit $OCF_SUCCESS --- -1.8.3.1 - - -From 6d6c4691cf0970059689856c354daf9e098b4451 Mon Sep 17 00:00:00 2001 -From: Grace Chin <gchin(a)redhat.com> -Date: Tue, 4 May 2021 14:50:37 -0400 -Subject: [PATCH 2/4] Replace debug values, true and false, with 0 and 1 - ---- - extra/resources/ping | 8 ++++---- - 1 file changed, 4 insertions(+), 4 deletions(-) - -diff --git a/extra/resources/ping b/extra/resources/ping -index 2e93f22..fee019b 100755 ---- a/extra/resources/ping -+++ b/extra/resources/ping -@@ -24,7 +24,7 @@ - : ${OCF_RESKEY_dampen:="5s"} - : ${OCF_RESKEY_attempts:="3"} - : ${OCF_RESKEY_multiplier:="1"} --: ${OCF_RESKEY_debug:="false"} -+: ${OCF_RESKEY_debug:="0"} - : ${OCF_RESKEY_failure_score:="0"} - : ${OCF_RESKEY_use_fping:="1"} - : ${OCF_RESKEY_host_list:=""} -@@ -152,7 +152,7 @@ END - - ping_conditional_log() { - level="$1"; shift -- if [ "${OCF_RESKEY_debug}" = "true" ]; then -+ if [ $OCF_RESKEY_debug -gt 0 ]; then - ocf_log "$level" "$*" - fi - } -@@ -388,8 +388,8 @@ fi - - # Check the debug option - case "${OCF_RESKEY_debug}" in -- true|True|TRUE|1) OCF_RESKEY_debug=true;; -- false|False|FALSE|0) OCF_RESKEY_debug=false;; -+ true|True|TRUE|1) OCF_RESKEY_debug=0;; -+ false|False|FALSE|0) OCF_RESKEY_debug=1;; - *) - ocf_log warn "Value for 'debug' is incorrect. Please specify 'true' or 'false' not: ${OCF_RESKEY_debug}" - OCF_RESKEY_debug=false --- -1.8.3.1 - - -From a886a31056b6aca764c6911f5432af2c5ebf51df Mon Sep 17 00:00:00 2001 -From: Grace Chin <gchin(a)redhat.com> -Date: Tue, 11 May 2021 11:04:50 -0400 -Subject: [PATCH 3/4] Add verbose debug mode which logs ping and fping output - when set - ---- - extra/resources/ping | 19 ++++++++++++++----- - 1 file changed, 14 insertions(+), 5 deletions(-) - -diff --git a/extra/resources/ping b/extra/resources/ping -index fee019b..cc796af 100755 ---- a/extra/resources/ping -+++ b/extra/resources/ping -@@ -249,10 +249,13 @@ fping_check() { - - case $rc in - 0) -+ if [ $OCF_RESKEY_debug -gt 1 ]; then -+ ping_conditional_log info "$output" -+ fi - ;; - 1) - for h in $(echo "$output" | grep "is unreachable" | awk '{print $1}'); do -- ping_conditional_log warn "$h is inactive" -+ ping_conditional_log warn "$h is inactive: $output" - done - ;; - *) -@@ -282,7 +285,12 @@ ping_check() { - p_out=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? - - case $rc in -- 0) active=$(expr $active + 1);; -+ 0) -+ active=$(expr $active + 1) -+ if [ $OCF_RESKEY_debug -gt 1 ]; then -+ ping_conditional_log info "$p_out" -+ fi -+ ;; - 1) ping_conditional_log warn "$host is inactive: $p_out";; - *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $p_out";; - esac -@@ -388,10 +396,11 @@ fi - - # Check the debug option - case "${OCF_RESKEY_debug}" in -- true|True|TRUE|1) OCF_RESKEY_debug=0;; -- false|False|FALSE|0) OCF_RESKEY_debug=1;; -+ true|True|TRUE|1) OCF_RESKEY_debug=1;; -+ false|False|FALSE|0) OCF_RESKEY_debug=0;; -+ verbose|Verbose|VERBOSE|2) OCF_RESKEY_debug=2;; - *) -- ocf_log warn "Value for 'debug' is incorrect. Please specify 'true' or 'false' not: ${OCF_RESKEY_debug}" -+ ocf_log warn "Value for 'debug' is incorrect. Please specify 'true', 'false', or 'verbose', not: ${OCF_RESKEY_debug}" - OCF_RESKEY_debug=false - ;; - esac --- -1.8.3.1 - - -From 460043f133ced80e923b1290af70502a72deb7f8 Mon Sep 17 00:00:00 2001 -From: Grace Chin <gchin(a)redhat.com> -Date: Tue, 11 May 2021 11:07:05 -0400 -Subject: [PATCH 4/4] Improve variable names - ---- - extra/resources/ping | 20 ++++++++++---------- - 1 file changed, 10 insertions(+), 10 deletions(-) - -diff --git a/extra/resources/ping b/extra/resources/ping -index cc796af..9763b60 100755 ---- a/extra/resources/ping -+++ b/extra/resources/ping -@@ -244,22 +244,22 @@ fping_check() { - timeout=$(expr $OCF_RESKEY_timeout \* 1000 / $OCF_RESKEY_attempts) - - cmd="$p_exe -r $OCF_RESKEY_attempts -t $timeout -B 1.0 $OCF_RESKEY_options $OCF_RESKEY_host_list" -- output=$($cmd 2>&1); rc=$? -- active=$(echo "$output" | grep "is alive" | wc -l) -+ fping_output=$($cmd 2>&1); rc=$? -+ active=$(echo "$fping_output" | grep "is alive" | wc -l) - - case $rc in - 0) - if [ $OCF_RESKEY_debug -gt 1 ]; then -- ping_conditional_log info "$output" -+ ping_conditional_log info "$fping_output" - fi - ;; - 1) -- for h in $(echo "$output" | grep "is unreachable" | awk '{print $1}'); do -- ping_conditional_log warn "$h is inactive: $output" -+ for h in $(echo "$fping_output" | grep "is unreachable" | awk '{print $1}'); do -+ ping_conditional_log warn "$h is inactive: $fping_output" - done - ;; - *) -- ocf_log err "Unexpected result for '$cmd' $rc: $(echo "$output" | tr '\n' ';')" -+ ocf_log err "Unexpected result for '$cmd' $rc: $(echo "$fping_output" | tr '\n' ';')" - ;; - esac - -@@ -282,17 +282,17 @@ ping_check() { - *:*) p_exe=ping6 - esac - -- p_out=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? -+ ping_output=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? - - case $rc in - 0) - active=$(expr $active + 1) - if [ $OCF_RESKEY_debug -gt 1 ]; then -- ping_conditional_log info "$p_out" -+ ping_conditional_log info "$ping_output" - fi - ;; -- 1) ping_conditional_log warn "$host is inactive: $p_out";; -- *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $p_out";; -+ 1) ping_conditional_log warn "$host is inactive: $ping_output";; -+ *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $ping_output";; - esac - done - return $active --- -1.8.3.1 - diff --git a/002-pacemakerd-options.patch b/002-pacemakerd-options.patch deleted file mode 100644 index 56941ec..0000000 --- a/002-pacemakerd-options.patch +++ /dev/null @@ -1,451 +0,0 @@ -From 0d40ebf10b1794ece2c5c9768ea7222d3834d3b3 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 13 May 2021 11:42:18 -0400 -Subject: [PATCH 1/4] Build: Use a different variable to find man page - includes. - -With other programs outside of the tools directory being converted to -use glib for command line handling, their includes are not going to be -in tools/. So we need to use a different autoconf variable to find -them. ---- - mk/common.mk | 6 +++--- - 1 file changed, 3 insertions(+), 3 deletions(-) - -diff --git a/mk/common.mk b/mk/common.mk -index b247670..aa59feb 100644 ---- a/mk/common.mk -+++ b/mk/common.mk -@@ -1,5 +1,5 @@ - # --# Copyright 2014-2020 the Pacemaker project contributors -+# Copyright 2014-2021 the Pacemaker project contributors - # - # The version control history for this file may have further details. - # -@@ -68,11 +68,11 @@ HELP2MAN_ARGS = -N --section 8 --name "Part of the Pacemaker cluster resource ma - # and all wrappers to C code. - %.8: % $(MAN8DEPS) - $(AM_V_at)chmod a+x $(abs_builddir)/$< -- $(AM_V_MAN)if [ -f $(top_srcdir)/tools/$@.inc ]; then \ -+ $(AM_V_MAN)if [ -f $(abs_srcdir)/$@.inc ]; then \ - PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ - -h --help-all \ - --no-discard-stderr \ -- -i $(top_srcdir)/tools/$@.inc $(abs_builddir)/$< \ -+ -i $(abs_srcdir)/$@.inc $(abs_builddir)/$< \ - | sed -f $(top_srcdir)/tools/fix-manpages > $@ ; \ - else \ - PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ --- -1.8.3.1 - - -From c7ab1d901bcbbf0137277e783e072777ca2f82d9 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 13 May 2021 11:44:16 -0400 -Subject: [PATCH 2/4] Refactor: daemons: Remove the pid_file variable from - pacemakerd. - -It's never used anywhere. ---- - daemons/pacemakerd/pacemakerd.c | 3 --- - 1 file changed, 3 deletions(-) - -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index 8ec9708..03d688e 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -27,8 +27,7 @@ - - static crm_trigger_t *shutdown_trigger = NULL; - static crm_trigger_t *startup_trigger = NULL; --static const char *pid_file = PCMK_RUN_DIR "/pacemaker.pid"; - - /* state we report when asked via pacemakerd-api status-ping */ - static const char *pacemakerd_state = XML_PING_ATTR_PACEMAKERDSTATE_INIT; - static gboolean running_with_sbd = FALSE; /* local copy */ -@@ -224,7 +222,6 @@ main(int argc, char **argv) - /* Legacy */ - break; - case 'p': -- pid_file = optarg; - break; - case 's': - pcmk__set_env_option("node_start_state", "standby"); --- -1.8.3.1 - - -From 98990eed9f6a5dbde7c8a5aa0783e93d5479295b Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 13 May 2021 13:14:38 -0400 -Subject: [PATCH 3/4] Refactor: daemons: Use glib for command line handling in - pacemakerd. - ---- - daemons/pacemakerd/Makefile.am | 2 + - daemons/pacemakerd/pacemakerd.8.inc | 5 + - daemons/pacemakerd/pacemakerd.c | 195 ++++++++++++++++++------------------ - 3 files changed, 102 insertions(+), 100 deletions(-) - create mode 100644 daemons/pacemakerd/pacemakerd.8.inc - -diff --git a/daemons/pacemakerd/Makefile.am b/daemons/pacemakerd/Makefile.am -index cc657f5..84517a3 100644 ---- a/daemons/pacemakerd/Makefile.am -+++ b/daemons/pacemakerd/Makefile.am -@@ -15,6 +15,8 @@ if BUILD_SYSTEMD - systemdsystemunit_DATA = pacemaker.service - endif - -+EXTRA_DIST = pacemakerd.8.inc -+ - ## SOURCES - - noinst_HEADERS = pacemakerd.h -diff --git a/daemons/pacemakerd/pacemakerd.8.inc b/daemons/pacemakerd/pacemakerd.8.inc -new file mode 100644 -index 0000000..902af4e ---- /dev/null -+++ b/daemons/pacemakerd/pacemakerd.8.inc -@@ -0,0 +1,5 @@ -+[synopsis] -+pacemakerd [options] -+ -+/subsidiary Pacemaker daemons/ -+.SH OPTIONS -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index 03d688e..ce194bf 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -23,12 +23,54 @@ - #include <crm/msg_xml.h> - #include <crm/common/ipc_internal.h> - #include <crm/common/mainloop.h> -+#include <crm/common/cmdline_internal.h> - #include <crm/cluster/internal.h> - #include <crm/cluster.h> - - #include <dirent.h> - #include <ctype.h> - -+#define SUMMARY "pacemakerd - primary Pacemaker daemon that launches and monitors all subsidiary Pacemaker daemons" -+ -+struct { -+ gboolean features; -+ gboolean foreground; -+ gboolean shutdown; -+ gboolean standby; -+} options; -+ -+static gboolean -+pid_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { -+ return TRUE; -+} -+ -+static gboolean -+standby_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { -+ options.standby = TRUE; -+ pcmk__set_env_option("node_start_state", "standby"); -+ return TRUE; -+} -+ -+static GOptionEntry entries[] = { -+ { "features", 'F', 0, G_OPTION_ARG_NONE, &options.features, -+ "Display full version and list of features Pacemaker was built with", -+ NULL }, -+ { "foreground", 'f', 0, G_OPTION_ARG_NONE, &options.foreground, -+ "(Ignored) Pacemaker always runs in the foreground", -+ NULL }, -+ { "pid-file", 'p', 0, G_OPTION_ARG_CALLBACK, pid_cb, -+ "(Ignored) Daemon pid file location", -+ "FILE" }, -+ { "shutdown", 'S', 0, G_OPTION_ARG_NONE, &options.shutdown, -+ "Instruct Pacemaker to shutdown on this machine", -+ NULL }, -+ { "standby", 's', G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, standby_cb, -+ "Start node in standby state", -+ NULL }, -+ -+ { NULL } -+}; -+ - static gboolean fatal_error = FALSE; - static GMainLoop *mainloop = NULL; - static bool global_keep_tracking = false; -@@ -642,49 +685,6 @@ pcmk_sigquit(int nsig) - .connection_destroyed = pcmk_ipc_destroy - }; - --static pcmk__cli_option_t long_options[] = { -- // long option, argument type, storage, short option, description, flags -- { -- "help", no_argument, NULL, '?', -- "\tThis text", pcmk__option_default -- }, -- { -- "version", no_argument, NULL, '$', -- "\tVersion information", pcmk__option_default -- }, -- { -- "verbose", no_argument, NULL, 'V', -- "\tIncrease debug output", pcmk__option_default -- }, -- { -- "shutdown", no_argument, NULL, 'S', -- "\tInstruct Pacemaker to shutdown on this machine", pcmk__option_default -- }, -- { -- "features", no_argument, NULL, 'F', -- "\tDisplay full version and list of features Pacemaker was built with", -- pcmk__option_default -- }, -- { -- "-spacer-", no_argument, NULL, '-', -- "\nAdditional Options:", pcmk__option_default -- }, -- { -- "foreground", no_argument, NULL, 'f', -- "\t(Ignored) Pacemaker always runs in the foreground", -- pcmk__option_default -- }, -- { -- "pid-file", required_argument, NULL, 'p', -- "\t(Ignored) Daemon pid file location", pcmk__option_default -- }, -- { -- "standby", no_argument, NULL, 's', -- "\tStart node in standby state", pcmk__option_default -- }, -- { 0, 0, 0, 0 } --}; -- - static void - mcp_chown(const char *path, uid_t uid, gid_t gid) - { -@@ -1168,83 +1211,66 @@ request_shutdown(crm_ipc_t *ipc) - return status; - } - -+static GOptionContext * -+build_arg_context(pcmk__common_args_t *args) { -+ GOptionContext *context = NULL; -+ -+ context = pcmk__build_arg_context(args, NULL, NULL, NULL); -+ pcmk__add_main_args(context, entries); -+ return context; -+} -+ - int - main(int argc, char **argv) - { -- int flag; -- int argerr = 0; -+ crm_exit_t exit_code = CRM_EX_OK; -+ -+ GError *error = NULL; -+ -+ pcmk__common_args_t *args = pcmk__new_common_args(SUMMARY); -+ gchar **processed_args = pcmk__cmdline_preproc(argv, "p"); -+ GOptionContext *context = build_arg_context(args); - -- int option_index = 0; - bool old_instance_connected = false; -- gboolean shutdown = FALSE; - - crm_ipc_t *old_instance = NULL; - qb_ipcs_service_t *ipcs = NULL; - - crm_log_preinit(NULL, argc, argv); -- pcmk__set_cli_options(NULL, "[options]", long_options, -- "primary Pacemaker daemon that launches and " -- "monitors all subsidiary Pacemaker daemons"); - mainloop_add_signal(SIGHUP, pcmk_ignore); - mainloop_add_signal(SIGQUIT, pcmk_sigquit); - -- while (1) { -- flag = pcmk__next_cli_option(argc, argv, &option_index, NULL); -- if (flag == -1) -- break; -- -- switch (flag) { -- case 'V': -- crm_bump_log_level(argc, argv); -- break; -- case 'f': -- /* Legacy */ -- break; -- case 'p': -- break; -- case 's': -- pcmk__set_env_option("node_start_state", "standby"); -- break; -- case '$': -- case '?': -- pcmk__cli_help(flag, CRM_EX_OK); -- break; -- case 'S': -- shutdown = TRUE; -- break; -- case 'F': -- printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, -- CRM_FEATURE_SET, CRM_FEATURES); -- crm_exit(CRM_EX_OK); -- default: -- printf("Argument code 0%o (%c) is not (?yet?) supported\n", flag, flag); -- ++argerr; -- break; -- } -+ if (!g_option_context_parse_strv(context, &processed_args, &error)) { -+ exit_code = CRM_EX_USAGE; -+ goto done; - } - -- if (optind < argc) { -- printf("non-option ARGV-elements: "); -- while (optind < argc) -- printf("%s ", argv[optind++]); -- printf("\n"); -- } -- if (argerr) { -- pcmk__cli_help('?', CRM_EX_USAGE); -+ if (options.features) { -+ printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, -+ CRM_FEATURE_SET, CRM_FEATURES); -+ exit_code = CRM_EX_OK; -+ goto done; - } - -+ if (args->version) { -+ g_strfreev(processed_args); -+ pcmk__free_arg_context(context); -+ /* FIXME: When pacemakerd is converted to use formatted output, this can go. */ -+ pcmk__cli_help('v', CRM_EX_USAGE); -+ } - - setenv("LC_ALL", "C", 1); - - pcmk__set_env_option("mcp", "true"); - -+ pcmk__cli_init_logging("pacemakerd", args->verbosity); - crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); - - crm_debug("Checking for existing Pacemaker instance"); - old_instance = crm_ipc_new(CRM_SYSTEM_MCP, 0); - old_instance_connected = crm_ipc_connect(old_instance); - -- if (shutdown) { -+ if (options.shutdown) { - if (old_instance_connected) { - crm_exit(request_shutdown(old_instance)); - } else { -@@ -1253,22 +1279,25 @@ main(int argc, char **argv) - "Pacemaker instance: %s", strerror(errno)); - crm_ipc_close(old_instance); - crm_ipc_destroy(old_instance); -- crm_exit(CRM_EX_DISCONNECT); -+ exit_code = CRM_EX_DISCONNECT; -+ goto done; - } - - } else if (old_instance_connected) { - crm_ipc_close(old_instance); - crm_ipc_destroy(old_instance); - crm_err("Aborting start-up because active Pacemaker instance found"); -- crm_exit(CRM_EX_FATAL); -+ exit_code = CRM_EX_FATAL; -+ goto done; - } - - crm_ipc_close(old_instance); - crm_ipc_destroy(old_instance); - - #ifdef SUPPORT_COROSYNC - if (mcp_read_config() == FALSE) { -- crm_exit(CRM_EX_UNAVAILABLE); -+ exit_code = CRM_EX_UNAVAILABLE; -+ goto done; - } - #endif - -@@ -1292,7 +1321,8 @@ main(int argc, char **argv) - #ifdef SUPPORT_COROSYNC - /* Allows us to block shutdown */ - if (!cluster_connect_cfg()) { -- crm_exit(CRM_EX_PROTOCOL); -+ exit_code = CRM_EX_PROTOCOL; -+ goto done; - } - #endif - -@@ -1307,9 +1337,11 @@ main(int argc, char **argv) - case pcmk_rc_ok: - break; - case pcmk_rc_ipc_unauthorized: -- crm_exit(CRM_EX_CANTCREAT); -+ exit_code = CRM_EX_CANTCREAT; -+ goto done; - default: -- crm_exit(CRM_EX_FATAL); -+ exit_code = CRM_EX_FATAL; -+ goto done; - }; - - mainloop_add_signal(SIGTERM, pcmk_shutdown); -@@ -1342,5 +1374,11 @@ main(int argc, char **argv) - #ifdef SUPPORT_COROSYNC - cluster_disconnect_cfg(); - #endif -- crm_exit(CRM_EX_OK); -+ -+done: -+ g_strfreev(processed_args); -+ pcmk__free_arg_context(context); -+ -+ pcmk__output_and_clear_error(error, NULL); -+ crm_exit(exit_code); - } --- -1.8.3.1 - - -From 8f7924fbb2a012bedcad59335b7bebc5020b26e3 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 13 May 2021 13:27:13 -0400 -Subject: [PATCH 4/4] Low: pacemaker.service: Don't start pacemakerd with -f. - -This option is completely ignored by pacemakerd. ---- - daemons/pacemakerd/pacemaker.service.in | 2 +- - doc/sphinx/Clusters_from_Scratch/verification.rst | 2 +- - 2 files changed, 2 insertions(+), 2 deletions(-) - -diff --git a/daemons/pacemakerd/pacemaker.service.in b/daemons/pacemakerd/pacemaker.service.in -index b128ddc..0363a22 100644 ---- a/daemons/pacemakerd/pacemaker.service.in -+++ b/daemons/pacemakerd/pacemaker.service.in -@@ -44,7 +44,7 @@ EnvironmentFile=-@CONFIGDIR@/pacemaker - EnvironmentFile=-@CONFIGDIR@/sbd - SuccessExitStatus=100 - --ExecStart=@sbindir@/pacemakerd -f -+ExecStart=@sbindir@/pacemakerd - - # Systemd v227 and above can limit the number of processes spawned by a - # service. That is a bad idea for an HA cluster resource manager, so disable it -diff --git a/doc/sphinx/Clusters_from_Scratch/verification.rst b/doc/sphinx/Clusters_from_Scratch/verification.rst -index 9d647f8..b7fa20e 100644 ---- a/doc/sphinx/Clusters_from_Scratch/verification.rst -+++ b/doc/sphinx/Clusters_from_Scratch/verification.rst -@@ -103,7 +103,7 @@ the necessary processes are running: - 2 ? S 0:00 [kthreadd] - ...lots of processes... - 17121 ? SLsl 0:01 /usr/sbin/corosync -f -- 17133 ? Ss 0:00 /usr/sbin/pacemakerd -f -+ 17133 ? Ss 0:00 /usr/sbin/pacemakerd - 17134 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-based - 17135 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-fenced - 17136 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-execd --- -1.8.3.1 - diff --git a/003-pacemakerd-output.patch b/003-pacemakerd-output.patch deleted file mode 100644 index 167e22b..0000000 --- a/003-pacemakerd-output.patch +++ /dev/null @@ -1,343 +0,0 @@ -From 7c35387a9896cb968cf4087b5cbed94af44e1ea5 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 14 May 2021 12:03:46 -0400 -Subject: [PATCH 1/5] Feature: daemons: Convert pacemakerd to formatted output. - -The main purpose of this is to finish getting pacemakerd moved off the -existing command line handling code (pcmk__cli_help in particular) so -that code can eventually be deprecated or removed. pacemakerd itself -does fairly little printing. ---- - daemons/pacemakerd/pacemakerd.c | 58 ++++++++++++++++++++++++++++++----------- - 1 file changed, 43 insertions(+), 15 deletions(-) - -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index ce194bf..bd59729 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -25,6 +25,7 @@ - #include <crm/common/ipc_internal.h> - #include <crm/common/mainloop.h> - #include <crm/common/cmdline_internal.h> -+#include <crm/common/output_internal.h> - #include <crm/cluster/internal.h> - #include <crm/cluster.h> - -@@ -37,6 +38,14 @@ struct { - gboolean standby; - } options; - -+static pcmk__output_t *out = NULL; -+ -+static pcmk__supported_format_t formats[] = { -+ PCMK__SUPPORTED_FORMAT_NONE, -+ PCMK__SUPPORTED_FORMAT_TEXT, -+ { NULL, NULL, NULL } -+}; -+ - static gboolean - pid_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { - return TRUE; -@@ -1167,10 +1176,10 @@ pacemakerd_event_cb(pcmk_ipc_api_t *pacemakerd_api, - } - - static GOptionContext * --build_arg_context(pcmk__common_args_t *args) { -+build_arg_context(pcmk__common_args_t *args, GOptionGroup **group) { - GOptionContext *context = NULL; - -- context = pcmk__build_arg_context(args, NULL, NULL, NULL); -+ context = pcmk__build_arg_context(args, "text", group, NULL); - pcmk__add_main_args(context, entries); - return context; - } -@@ -1182,9 +1191,11 @@ main(int argc, char **argv) - - GError *error = NULL; - -+ int rc = pcmk_rc_ok; -+ GOptionGroup *output_group = NULL; - pcmk__common_args_t *args = pcmk__new_common_args(SUMMARY); - gchar **processed_args = pcmk__cmdline_preproc(argv, "p"); -- GOptionContext *context = build_arg_context(args); -+ GOptionContext *context = build_arg_context(args, &output_group); - - bool old_instance_connected = false; - -@@ -1195,23 +1205,30 @@ main(int argc, char **argv) - mainloop_add_signal(SIGHUP, pcmk_ignore); - mainloop_add_signal(SIGQUIT, pcmk_sigquit); - -+ pcmk__register_formats(output_group, formats); - if (!g_option_context_parse_strv(context, &processed_args, &error)) { - exit_code = CRM_EX_USAGE; - goto done; - } - -+ rc = pcmk__output_new(&out, args->output_ty, args->output_dest, argv); -+ if (rc != pcmk_rc_ok) { -+ exit_code = CRM_EX_ERROR; -+ g_set_error(&error, PCMK__EXITC_ERROR, exit_code, "Error creating output format %s: %s", -+ args->output_ty, pcmk_rc_str(rc)); -+ goto done; -+ } -+ - if (options.features) { -- printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, -- CRM_FEATURE_SET, CRM_FEATURES); -+ out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, -+ BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); - exit_code = CRM_EX_OK; - goto done; - } - - if (args->version) { -- g_strfreev(processed_args); -- pcmk__free_arg_context(context); -- /* FIXME: When pacemakerd is converted to use formatted output, this can go. */ -- pcmk__cli_help('v', CRM_EX_USAGE); -+ out->version(out, false); -+ goto done; - } - - setenv("LC_ALL", "C", 1); -@@ -1248,6 +1265,13 @@ main(int argc, char **argv) - crm_ipc_close(old_instance); - crm_ipc_destroy(old_instance); - -+ /* Don't allow any accidental output after this point. */ -+ if (out != NULL) { -+ out->finish(out, exit_code, true, NULL); -+ pcmk__output_free(out); -+ out = NULL; -+ } -+ - #ifdef SUPPORT_COROSYNC - if (mcp_read_config() == FALSE) { - exit_code = CRM_EX_UNAVAILABLE; -@@ -1333,6 +1357,11 @@ done: - g_strfreev(processed_args); - pcmk__free_arg_context(context); - -- pcmk__output_and_clear_error(error, NULL); -+ pcmk__output_and_clear_error(error, out); -+ -+ if (out != NULL) { -+ out->finish(out, exit_code, true, NULL); -+ pcmk__output_free(out); -+ } - crm_exit(exit_code); - } --- -1.8.3.1 - - -From 35e6da64381fcb092d81ce16835cc28670b077cb Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 17 May 2021 10:04:04 -0400 -Subject: [PATCH 2/5] Features: daemons: Output the pacemakerd feature list in - XML. - ---- - daemons/pacemakerd/pacemakerd.c | 45 ++++++++++++++++++++++++++++++++++++++--- - 1 file changed, 42 insertions(+), 3 deletions(-) - -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index bd59729..93cf743 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -43,6 +43,42 @@ static pcmk__output_t *out = NULL; - static pcmk__supported_format_t formats[] = { - PCMK__SUPPORTED_FORMAT_NONE, - PCMK__SUPPORTED_FORMAT_TEXT, -+ PCMK__SUPPORTED_FORMAT_XML, -+ { NULL, NULL, NULL } -+}; -+ -+static int -+pacemakerd_features(pcmk__output_t *out, va_list args) { -+ out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, -+ BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); -+ return pcmk_rc_ok; -+} -+ -+static int -+pacemakerd_features_xml(pcmk__output_t *out, va_list args) { -+ gchar **feature_list = g_strsplit(CRM_FEATURES, " ", 0); -+ -+ pcmk__output_xml_create_parent(out, "pacemakerd", -+ "version", PACEMAKER_VERSION, -+ "build", BUILD_VERSION, -+ "feature_set", CRM_FEATURE_SET, -+ NULL); -+ out->begin_list(out, NULL, NULL, "features"); -+ -+ for (char **s = feature_list; *s != NULL; s++) { -+ pcmk__output_create_xml_text_node(out, "feature", *s); -+ } -+ -+ out->end_list(out); -+ -+ g_strfreev(feature_list); -+ return pcmk_rc_ok; -+} -+ -+static pcmk__message_entry_t fmt_functions[] = { -+ { "features", "default", pacemakerd_features }, -+ { "features", "xml", pacemakerd_features_xml }, -+ - { NULL, NULL, NULL } - }; - -@@ -200,7 +236,7 @@ static GOptionContext * - build_arg_context(pcmk__common_args_t *args, GOptionGroup **group) { - GOptionContext *context = NULL; - -- context = pcmk__build_arg_context(args, "text", group, NULL); -+ context = pcmk__build_arg_context(args, "text (default), xml", group, NULL); - pcmk__add_main_args(context, entries); - return context; - } -@@ -241,9 +277,12 @@ main(int argc, char **argv) - goto done; - } - -+ pcmk__force_args(context, &error, "%s --xml-simple-list", g_get_prgname()); -+ -+ pcmk__register_messages(out, fmt_functions); -+ - if (options.features) { -- out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, -- BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); -+ out->message(out, "features"); - exit_code = CRM_EX_OK; - goto done; - } --- -1.8.3.1 - - -From 5b7f5eb35b025b59805cf3c7c3dcb6a3cf4b71b3 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 17 May 2021 11:09:53 -0400 -Subject: [PATCH 3/5] Low: daemons: Conditionally enable logging in pacemakerd. - -If we're doing an interactive command-line call, use -pcmk__cli_init_logging. At the moment, all command line calls except -for --shutdown do their work before logging would even come up, so we -really only need to do this for --shutdown. - -If we're doing a daemon call, use crm_log_init. ---- - daemons/pacemakerd/pacemakerd.c | 7 +++++-- - 1 file changed, 5 insertions(+), 2 deletions(-) - -diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c -index 93cf743..c20bde7 100644 ---- a/daemons/pacemakerd/pacemakerd.c -+++ b/daemons/pacemakerd/pacemakerd.c -@@ -296,8 +296,11 @@ main(int argc, char **argv) - - pcmk__set_env_option("mcp", "true"); - -- pcmk__cli_init_logging("pacemakerd", args->verbosity); -- crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); -+ if (options.shutdown) { -+ pcmk__cli_init_logging("pacemakerd", args->verbosity); -+ } else { -+ crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); -+ } - - crm_debug("Checking for existing Pacemaker instance"); - old_instance = crm_ipc_new(CRM_SYSTEM_MCP, 0); --- -1.8.3.1 - - -From 2393362bb7489e86d937ed46a1c5cfb93d9bf3ab Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 17 May 2021 11:58:06 -0400 -Subject: [PATCH 4/5] Fix: include: Bump CRM_FEATURE_SET for new pacemakerd - args. - ---- - include/crm/crm.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/include/crm/crm.h b/include/crm/crm.h -index fdfc825..92a98fa 100644 ---- a/include/crm/crm.h -+++ b/include/crm/crm.h -@@ -66,7 +66,7 @@ extern "C" { - * >=3.0.13: Fail counts include operation name and interval - * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED - */ --# define CRM_FEATURE_SET "3.10.0" -+# define CRM_FEATURE_SET "3.10.1" - - /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and - * recipient of a CPG message. This imposes an arbitrary limit on cluster node --- -1.8.3.1 - - -From 3ad8edbd91631b87ef5f53fa2d68f0c8bbb9ee2b Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 17 May 2021 11:57:09 -0400 -Subject: [PATCH 5/5] Feature: xml: Add schema for pacemakerd. - ---- - xml/Makefile.am | 1 + - xml/api/pacemakerd-2.10.rng | 28 ++++++++++++++++++++++++++++ - 2 files changed, 29 insertions(+) - create mode 100644 xml/api/pacemakerd-2.10.rng - -diff --git a/xml/Makefile.am b/xml/Makefile.am -index 12a51c5..b9448d4 100644 ---- a/xml/Makefile.am -+++ b/xml/Makefile.am -@@ -56,6 +56,7 @@ API_request_base = command-output \ - crm_simulate \ - crmadmin \ - digests \ -+ pacemakerd \ - stonith_admin \ - version - -diff --git a/xml/api/pacemakerd-2.10.rng b/xml/api/pacemakerd-2.10.rng -new file mode 100644 -index 0000000..41a11e7 ---- /dev/null -+++ b/xml/api/pacemakerd-2.10.rng -@@ -0,0 +1,28 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="element-pacemakerd"/> -+ </start> -+ -+ <define name="element-pacemakerd"> -+ <element name="pacemakerd"> -+ <attribute name="version"> <text /> </attribute> -+ <attribute name="build"> <text /> </attribute> -+ <attribute name="feature_set"> <text /> </attribute> -+ -+ <optional> -+ <ref name="feature-list" /> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="feature-list"> -+ <element name="features"> -+ <oneOrMore> -+ <element name="feature"> <text/> </element> -+ </oneOrMore> -+ </element> -+ </define> -+</grammar> --- -1.8.3.1 - diff --git a/004-check-level.patch b/004-check-level.patch deleted file mode 100644 index f2abb5f..0000000 --- a/004-check-level.patch +++ /dev/null @@ -1,199 +0,0 @@ -From 3905e7eac11298fc20efd567a773666f948edf61 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 3 May 2021 11:19:04 -0400 -Subject: [PATCH 1/2] Feature: tools: Add OCF_CHECK_LEVEL to crm_resource - environment. - -If --validate= or --force-check= are given with a level, pass that along -as OCF_CHECK_LEVEL. This argument is optional, and if no value is given -then the environment variable will not be set and whatever's the default -on the resource agent will be used. - -See: rhbz#1955792. ---- - tools/crm_resource.c | 29 +++++++++++++++++++++-------- - tools/crm_resource.h | 4 ++-- - tools/crm_resource_runtime.c | 13 ++++++++++--- - 3 files changed, 33 insertions(+), 13 deletions(-) - -diff --git a/tools/crm_resource.c b/tools/crm_resource.c -index 45db2b2..6ca96f8 100644 ---- a/tools/crm_resource.c -+++ b/tools/crm_resource.c -@@ -100,6 +100,7 @@ struct { - int timeout_ms; // Parsed from --timeout value - char *agent_spec; // Standard and/or provider and/or agent - gchar *xml_file; // Value of (deprecated) --xml-file -+ int check_level; // Optional value of --validate or --force-check - - // Resource configuration specified via command-line arguments - gboolean cmdline_config; // Resource configuration was via arguments -@@ -113,6 +114,7 @@ struct { - GHashTable *override_params; // Resource parameter values that override config - } options = { - .attr_set_type = XML_TAG_ATTR_SETS, -+ .check_level = -1, - .cib_options = cib_sync_call, - .require_cib = TRUE, - .require_dataset = TRUE, -@@ -402,14 +404,15 @@ static GOptionEntry query_entries[] = { - }; - - static GOptionEntry command_entries[] = { -- { "validate", 0, G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, -+ { "validate", 0, G_OPTION_FLAG_OPTIONAL_ARG, G_OPTION_ARG_CALLBACK, - validate_or_force_cb, - "Validate resource configuration by calling agent's validate-all\n" - INDENT "action. The configuration may be specified either by giving an\n" - INDENT "existing resource name with -r, or by specifying --class,\n" - INDENT "--agent, and --provider arguments, along with any number of\n" -- INDENT "--option arguments.", -- NULL }, -+ INDENT "--option arguments. An optional LEVEL argument can be given\n" -+ INDENT "to control the level of checking performed.", -+ "LEVEL" }, - { "cleanup", 'C', G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, cleanup_refresh_cb, - "If resource has any past failures, clear its history and fail\n" - INDENT "count. Optionally filtered by --resource, --node, --operation\n" -@@ -546,11 +549,12 @@ static GOptionEntry advanced_entries[] = { - INDENT "the cluster believes the resource is a clone instance already\n" - INDENT "running on the local node.", - NULL }, -- { "force-check", 0, G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, -+ { "force-check", 0, G_OPTION_FLAG_OPTIONAL_ARG, G_OPTION_ARG_CALLBACK, - validate_or_force_cb, - "(Advanced) Bypass the cluster and check the state of a resource on\n" -- INDENT "the local node", -- NULL }, -+ INDENT "the local node. An optional LEVEL argument can be given\n" -+ INDENT "to control the level of checking performed.", -+ "LEVEL" }, - - { NULL } - }; -@@ -910,6 +914,15 @@ validate_or_force_cb(const gchar *option_name, const gchar *optarg, - if (options.override_params == NULL) { - options.override_params = pcmk__strkey_table(free, free); - } -+ -+ if (optarg != NULL) { -+ if (pcmk__scan_min_int(optarg, &options.check_level, 0) != pcmk_rc_ok) { -+ g_set_error(error, G_OPTION_ERROR, CRM_EX_INVALID_PARAM, -+ "Invalid check level setting: %s", optarg); -+ return FALSE; -+ } -+ } -+ - return TRUE; - } - -@@ -1826,12 +1839,12 @@ main(int argc, char **argv) - options.v_class, options.v_provider, options.v_agent, - "validate-all", options.cmdline_params, - options.override_params, options.timeout_ms, -- args->verbosity, options.force); -+ args->verbosity, options.force, options.check_level); - } else { - exit_code = cli_resource_execute(rsc, options.rsc_id, - options.operation, options.override_params, - options.timeout_ms, cib_conn, data_set, -- args->verbosity, options.force); -+ args->verbosity, options.force, options.check_level); - } - goto done; - -diff --git a/tools/crm_resource.h b/tools/crm_resource.h -index 3560377..5ab10d6 100644 ---- a/tools/crm_resource.h -+++ b/tools/crm_resource.h -@@ -88,11 +88,11 @@ crm_exit_t cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc - const char *rsc_type, const char *rsc_action, - GHashTable *params, GHashTable *override_hash, - int timeout_ms, int resource_verbose, -- gboolean force); -+ gboolean force, int check_level); - crm_exit_t cli_resource_execute(pe_resource_t *rsc, const char *requested_name, - const char *rsc_action, GHashTable *override_hash, - int timeout_ms, cib_t *cib, pe_working_set_t *data_set, -- int resource_verbose, gboolean force); -+ int resource_verbose, gboolean force, int check_level); - - int cli_resource_update_attribute(pe_resource_t *rsc, const char *requested_name, - const char *attr_set, const char *attr_set_type, -diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c -index fe0ec98..bde83b6 100644 ---- a/tools/crm_resource_runtime.c -+++ b/tools/crm_resource_runtime.c -@@ -1679,7 +1679,8 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, - const char *rsc_class, const char *rsc_prov, - const char *rsc_type, const char *action, - GHashTable *params, GHashTable *override_hash, -- int timeout_ms, int resource_verbose, gboolean force) -+ int timeout_ms, int resource_verbose, gboolean force, -+ int check_level) - { - GHashTable *params_copy = NULL; - crm_exit_t exit_code = CRM_EX_OK; -@@ -1703,6 +1704,12 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, - /* add crm_feature_set env needed by some resource agents */ - g_hash_table_insert(params, strdup(XML_ATTR_CRM_VERSION), strdup(CRM_FEATURE_SET)); - -+ if (check_level >= 0) { -+ char *level = crm_strdup_printf("%d", check_level); -+ setenv("OCF_CHECK_LEVEL", level, 1); -+ free(level); -+ } -+ - /* resources_action_create frees the params hash table it's passed, but we - * may need to reuse it in a second call to resources_action_create. Thus - * we'll make a copy here so that gets freed and the original remains for -@@ -1790,7 +1797,7 @@ crm_exit_t - cli_resource_execute(pe_resource_t *rsc, const char *requested_name, - const char *rsc_action, GHashTable *override_hash, - int timeout_ms, cib_t * cib, pe_working_set_t *data_set, -- int resource_verbose, gboolean force) -+ int resource_verbose, gboolean force, int check_level) - { - pcmk__output_t *out = data_set->priv; - crm_exit_t exit_code = CRM_EX_OK; -@@ -1856,7 +1863,7 @@ cli_resource_execute(pe_resource_t *rsc, const char *requested_name, - - exit_code = cli_resource_execute_from_params(out, rid, rclass, rprov, rtype, action, - params, override_hash, timeout_ms, -- resource_verbose, force); -+ resource_verbose, force, check_level); - return exit_code; - } - --- -1.8.3.1 - - -From d13ba4bd6defe0dd81fdf8ab39ae5b889513c0c0 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 20 May 2021 10:59:23 -0400 -Subject: [PATCH 2/2] Fix: include: Bump feature set to 3.10.2. - -This is for the OCF_CHECK_LEVEL environment variable. - -See: rhbz#1955792. ---- - include/crm/crm.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/include/crm/crm.h b/include/crm/crm.h -index 92a98fa..ee52c36 100644 ---- a/include/crm/crm.h -+++ b/include/crm/crm.h -@@ -66,7 +66,7 @@ extern "C" { - * >=3.0.13: Fail counts include operation name and interval - * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED - */ --# define CRM_FEATURE_SET "3.10.1" -+# define CRM_FEATURE_SET "3.10.2" - - /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and - * recipient of a CPG message. This imposes an arbitrary limit on cluster node --- -1.8.3.1 - diff --git a/005-crm_resource.patch b/005-crm_resource.patch deleted file mode 100644 index 1683026..0000000 --- a/005-crm_resource.patch +++ /dev/null @@ -1,866 +0,0 @@ -From a5a507d4e1abf242903472719a19977811e6f164 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 20 May 2021 11:59:36 -0400 -Subject: [PATCH 01/10] Feature: libcrmcommon: Add OCF_OUTPUT_FORMAT to - crm_resource environment. - -See: rhbz#1644628 ---- - lib/common/output.c | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git a/lib/common/output.c b/lib/common/output.c -index 6cb49b5..58872e0 100644 ---- a/lib/common/output.c -+++ b/lib/common/output.c -@@ -71,6 +71,8 @@ pcmk__output_new(pcmk__output_t **out, const char *fmt_name, const char *filenam - return ENOMEM; - } - -+ setenv("OCF_OUTPUT_FORMAT", (*out)->fmt_name, 1); -+ - return pcmk_rc_ok; - } - --- -1.8.3.1 - - -From acc6ecdbfb797d69794e68f75a734d6252434e01 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 21 May 2021 14:20:30 -0400 -Subject: [PATCH 02/10] Feature: schemas: Copy crm_resource schema in - preparation for changes. - -See: rhbz#1644628 ---- - xml/api/crm_resource-2.11.rng | 238 ++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 238 insertions(+) - create mode 100644 xml/api/crm_resource-2.11.rng - -diff --git a/xml/api/crm_resource-2.11.rng b/xml/api/crm_resource-2.11.rng -new file mode 100644 -index 0000000..8e386db ---- /dev/null -+++ b/xml/api/crm_resource-2.11.rng -@@ -0,0 +1,238 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="element-crm-resource"/> -+ </start> -+ -+ <define name="element-crm-resource"> -+ <choice> -+ <ref name="agents-list" /> -+ <ref name="alternatives-list" /> -+ <ref name="constraints-list" /> -+ <externalRef href="generic-list-2.4.rng"/> -+ <element name="metadata"> <text/> </element> -+ <ref name="locate-list" /> -+ <ref name="operations-list" /> -+ <ref name="providers-list" /> -+ <ref name="reasons-list" /> -+ <ref name="resource-check" /> -+ <ref name="resource-config" /> -+ <ref name="resources-list" /> -+ </choice> -+ </define> -+ -+ <define name="agents-list"> -+ <element name="agents"> -+ <attribute name="standard"> <text/> </attribute> -+ <optional> -+ <attribute name="provider"> <text/> </attribute> -+ </optional> -+ <zeroOrMore> -+ <element name="agent"> <text/> </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="alternatives-list"> -+ <element name="providers"> -+ <attribute name="for"> <text/> </attribute> -+ <zeroOrMore> -+ <element name="provider"> <text/> </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="constraints-list"> -+ <element name="constraints"> -+ <interleave> -+ <zeroOrMore> -+ <ref name="rsc-location" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="rsc-colocation" /> -+ </zeroOrMore> -+ </interleave> -+ </element> -+ </define> -+ -+ <define name="locate-list"> -+ <element name="nodes"> -+ <attribute name="resource"> <text/> </attribute> -+ <zeroOrMore> -+ <element name="node"> -+ <optional> -+ <attribute name="state"><value>promoted</value></attribute> -+ </optional> -+ <text/> -+ </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="rsc-location"> -+ <element name="rsc_location"> -+ <attribute name="node"> <text/> </attribute> -+ <attribute name="rsc"> <text/> </attribute> -+ <attribute name="id"> <text/> </attribute> -+ <externalRef href="../score.rng"/> -+ </element> -+ </define> -+ -+ <define name="operations-list"> -+ <element name="operations"> -+ <oneOrMore> -+ <ref name="element-operation-list" /> -+ </oneOrMore> -+ </element> -+ </define> -+ -+ <define name="providers-list"> -+ <element name="providers"> -+ <attribute name="standard"> <value>ocf</value> </attribute> -+ <optional> -+ <attribute name="agent"> <text/> </attribute> -+ </optional> -+ <zeroOrMore> -+ <element name="provider"> <text/> </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="reasons-list"> -+ <choice> -+ <ref name="no-resource-or-uname"/> -+ <ref name="resource-and-uname"/> -+ <ref name="no-resource-but-uname"/> -+ <ref name="resource-but-no-uname"/> -+ </choice> -+ </define> -+ -+ <define name="no-resource-or-uname"> -+ <element name="reason"> -+ <element name="resources"> -+ <zeroOrMore> -+ <element name="resource"> -+ <attribute name="id"> <text/> </attribute> -+ <attribute name="running"> <data type="boolean"/> </attribute> -+ <ref name="resource-check"/> -+ </element> -+ </zeroOrMore> -+ </element> -+ </element> -+ </define> -+ -+ <define name="resource-and-uname"> -+ <element name="reason"> -+ <attribute name="running_on"> <text/> </attribute> -+ <ref name="resource-check"/> -+ </element> -+ </define> -+ -+ <define name="no-resource-but-uname"> -+ <element name="reason"> -+ <element name="resources"> -+ <zeroOrMore> -+ <element name="resource"> -+ <attribute name="id"> <text/> </attribute> -+ <attribute name="running"> <data type="boolean"/> </attribute> -+ <attribute name="host"> <text/> </attribute> -+ <ref name="resource-check"/> -+ </element> -+ </zeroOrMore> -+ </element> -+ </element> -+ </define> -+ -+ <define name="resource-but-no-uname"> -+ <element name="reason"> -+ <attribute name="running"> <data type="boolean"/> </attribute> -+ <ref name="resource-check"/> -+ </element> -+ </define> -+ -+ <define name="resource-config"> -+ <element name="resource_config"> -+ <externalRef href="resources-2.4.rng" /> -+ <element name="xml"> <text/> </element> -+ </element> -+ </define> -+ -+ <define name="resource-check"> -+ <element name="check"> -+ <attribute name="id"> <text/> </attribute> -+ <optional> -+ <choice> -+ <attribute name="remain_stopped"><value>true</value></attribute> -+ <attribute name="promotable"><value>false</value></attribute> -+ </choice> -+ </optional> -+ <optional> -+ <attribute name="unmanaged"><value>true</value></attribute> -+ </optional> -+ <optional> -+ <attribute name="locked-to"> <text/> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="resources-list"> -+ <element name="resources"> -+ <zeroOrMore> -+ <externalRef href="resources-2.4.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="rsc-colocation"> -+ <element name="rsc_colocation"> -+ <attribute name="id"> <text/> </attribute> -+ <attribute name="rsc"> <text/> </attribute> -+ <attribute name="with-rsc"> <text/> </attribute> -+ <externalRef href="../score.rng"/> -+ <optional> -+ <attribute name="node-attribute"> <text/> </attribute> -+ </optional> -+ <optional> -+ <attribute name="rsc-role"> -+ <ref name="attribute-roles"/> -+ </attribute> -+ </optional> -+ <optional> -+ <attribute name="with-rsc-role"> -+ <ref name="attribute-roles"/> -+ </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-operation-list"> -+ <element name="operation"> -+ <optional> -+ <group> -+ <attribute name="rsc"> <text/> </attribute> -+ <attribute name="agent"> <text/> </attribute> -+ </group> -+ </optional> -+ <attribute name="op"> <text/> </attribute> -+ <attribute name="node"> <text/> </attribute> -+ <attribute name="call"> <data type="integer" /> </attribute> -+ <attribute name="rc"> <data type="nonNegativeInteger" /> </attribute> -+ <optional> -+ <attribute name="last-rc-change"> <text/> </attribute> -+ <attribute name="exec-time"> <data type="nonNegativeInteger" /> </attribute> -+ </optional> -+ <attribute name="status"> <text/> </attribute> -+ </element> -+ </define> -+ -+ <define name="attribute-roles"> -+ <choice> -+ <value>Stopped</value> -+ <value>Started</value> -+ <value>Master</value> -+ <value>Slave</value> -+ </choice> -+ </define> -+</grammar> --- -1.8.3.1 - - -From 1bbdf2149a111e9e19c388834f82001e0d31c427 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 24 May 2021 12:23:55 -0400 -Subject: [PATCH 03/10] Feature: xml: Update the crm_resource schema for XML - output. - -See: rhbz#1644628 ---- - xml/api/crm_resource-2.11.rng | 50 +++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 50 insertions(+) - -diff --git a/xml/api/crm_resource-2.11.rng b/xml/api/crm_resource-2.11.rng -index 8e386db..aaa54d6 100644 ---- a/xml/api/crm_resource-2.11.rng -+++ b/xml/api/crm_resource-2.11.rng -@@ -20,6 +20,7 @@ - <ref name="resource-check" /> - <ref name="resource-config" /> - <ref name="resources-list" /> -+ <ref name="resource-agent-action" /> - </choice> - </define> - -@@ -227,6 +228,55 @@ - </element> - </define> - -+ <define name="resource-agent-action"> -+ <element name="resource-agent-action"> -+ <attribute name="action"> <text/> </attribute> -+ <optional> -+ <attribute name="rsc"> <text/> </attribute> -+ </optional> -+ <attribute name="class"> <text/> </attribute> -+ <attribute name="type"> <text/> </attribute> -+ <optional> -+ <attribute name="provider"> <text/> </attribute> -+ </optional> -+ <optional> -+ <ref name="overrides-list"/> -+ </optional> -+ <ref name="agent-status"/> -+ <optional> -+ <choice> -+ <element name="command"> -+ <text /> -+ </element> -+ <externalRef href="command-output-1.0.rng"/> -+ </choice> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="overrides-list"> -+ <element name="overrides"> -+ <zeroOrMore> -+ <element name="override"> -+ <optional> -+ <attribute name="rsc"> <text/> </attribute> -+ </optional> -+ <attribute name="name"> <text/> </attribute> -+ <attribute name="value"> <text/> </attribute> -+ </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="agent-status"> -+ <element name="agent-status"> -+ <attribute name="code"> <data type="integer" /> </attribute> -+ <optional> -+ <attribute name="message"> <text/> </attribute> -+ </optional> -+ </element> -+ </define> -+ - <define name="attribute-roles"> - <choice> - <value>Stopped</value> --- -1.8.3.1 - - -From d89f5bc7fec856fdcd32fa14edbd0019507d5d15 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Tue, 1 Jun 2021 15:26:58 -0400 -Subject: [PATCH 04/10] Low: libcrmcommon: Increase PCMK__API_VERSION for new - crm_resource output. - -See: rhbz#1644628 ---- - include/crm/common/output_internal.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/include/crm/common/output_internal.h b/include/crm/common/output_internal.h -index 10b315b..0436cde 100644 ---- a/include/crm/common/output_internal.h -+++ b/include/crm/common/output_internal.h -@@ -27,7 +27,7 @@ extern "C" { - # include <glib.h> - # include <crm/common/results.h> - --# define PCMK__API_VERSION "2.9" -+# define PCMK__API_VERSION "2.11" - - #if defined(PCMK__WITH_ATTRIBUTE_OUTPUT_ARGS) - # define PCMK__OUTPUT_ARGS(ARGS...) __attribute__((output_args(ARGS))) --- -1.8.3.1 - - -From 30bd2ddf43ee2a911681e51f40ed9ba20ec250b0 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Thu, 27 May 2021 13:57:12 -0400 -Subject: [PATCH 05/10] Low: tools: Pass NULL to - cli_resource_execute_from_params... - -if no resource name is given. This happens if we are validating based -on the --class/--agent/--provider command line options instead. ---- - tools/crm_resource.c | 2 +- - tools/crm_resource_runtime.c | 8 ++++---- - 2 files changed, 5 insertions(+), 5 deletions(-) - -diff --git a/tools/crm_resource.c b/tools/crm_resource.c -index 24f1121..37a0bb0 100644 ---- a/tools/crm_resource.c -+++ b/tools/crm_resource.c -@@ -1840,7 +1840,7 @@ main(int argc, char **argv) - - case cmd_execute_agent: - if (options.cmdline_config) { -- exit_code = cli_resource_execute_from_params(out, "test", -+ exit_code = cli_resource_execute_from_params(out, NULL, - options.v_class, options.v_provider, options.v_agent, - "validate-all", options.cmdline_params, - options.override_params, options.timeout_ms, -diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c -index 48a4b40..ebf48bb 100644 ---- a/tools/crm_resource_runtime.c -+++ b/tools/crm_resource_runtime.c -@@ -1717,14 +1717,14 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, - */ - params_copy = pcmk__str_table_dup(params); - -- op = resources_action_create(rsc_name, rsc_class, rsc_prov, rsc_type, action, 0, -- timeout_ms, params_copy, 0); -+ op = resources_action_create(rsc_name ? rsc_name : "test", rsc_class, rsc_prov, -+ rsc_type, action, 0, timeout_ms, params_copy, 0); - if (op == NULL) { - /* Re-run with stderr enabled so we can display a sane error message */ - crm_enable_stderr(TRUE); - params_copy = pcmk__str_table_dup(params); -- op = resources_action_create(rsc_name, rsc_class, rsc_prov, rsc_type, action, 0, -- timeout_ms, params_copy, 0); -+ op = resources_action_create(rsc_name ? rsc_name : "test", rsc_class, rsc_prov, -+ rsc_type, action, 0, timeout_ms, params_copy, 0); - - /* Callers of cli_resource_execute expect that the params hash table will - * be freed. That function uses this one, so for that reason and for --- -1.8.3.1 - - -From ee56efd53d14cfc4f902769540b72b3bb6096a73 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Mon, 24 May 2021 12:08:52 -0400 -Subject: [PATCH 06/10] Feature: tools: Add an agent-status message for - crm_resource. - -This moves what was previously only done in an out->info call to its own -output message, which means it will appear in XML output as well. Also, -note that if --class/--agent/--provider are given, the resource name -will be set to "test". In that case, do not display the resource name -in the output. - -This message will be used for --validate and the --force-* command line -options to crm_resource. - -See: rhbz#1644628 ---- - tools/crm_resource_print.c | 53 ++++++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 53 insertions(+) - -diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c -index 9d82cf8..88d5878 100644 ---- a/tools/crm_resource_print.c -+++ b/tools/crm_resource_print.c -@@ -152,6 +152,57 @@ attribute_list_default(pcmk__output_t *out, va_list args) { - return pcmk_rc_ok; - } - -+PCMK__OUTPUT_ARGS("agent-status", "int", "const char *", "const char *", "const char *", -+ "const char *", "const char *", "int") -+static int -+agent_status_default(pcmk__output_t *out, va_list args) { -+ int status = va_arg(args, int); -+ const char *action = va_arg(args, const char *); -+ const char *name = va_arg(args, const char *); -+ const char *class = va_arg(args, const char *); -+ const char *provider = va_arg(args, const char *); -+ const char *type = va_arg(args, const char *); -+ int rc = va_arg(args, int); -+ -+ if (status == PCMK_LRM_OP_DONE) { -+ out->info(out, "Operation %s%s%s (%s%s%s:%s) returned: '%s' (%d)", -+ action, name ? " for " : "", name ? name : "", -+ class, provider ? ":" : "", provider ? provider : "", type, -+ services_ocf_exitcode_str(rc), rc); -+ } else { -+ out->err(out, "Operation %s%s%s (%s%s%s:%s) failed: '%s' (%d)", -+ action, name ? " for " : "", name ? name : "", -+ class, provider ? ":" : "", provider ? provider : "", type, -+ services_lrm_status_str(status), status); -+ } -+ -+ return pcmk_rc_ok; -+} -+ -+PCMK__OUTPUT_ARGS("agent-status", "int", "const char *", "const char *", "const char *", -+ "const char *", "const char *", "int") -+static int -+agent_status_xml(pcmk__output_t *out, va_list args) { -+ int status G_GNUC_UNUSED = va_arg(args, int); -+ const char *action G_GNUC_UNUSED = va_arg(args, const char *); -+ const char *name G_GNUC_UNUSED = va_arg(args, const char *); -+ const char *class G_GNUC_UNUSED = va_arg(args, const char *); -+ const char *provider G_GNUC_UNUSED = va_arg(args, const char *); -+ const char *type G_GNUC_UNUSED = va_arg(args, const char *); -+ int rc = va_arg(args, int); -+ -+ char *status_str = pcmk__itoa(rc); -+ -+ pcmk__output_create_xml_node(out, "agent-status", -+ "code", status_str, -+ "message", services_ocf_exitcode_str(rc), -+ NULL); -+ -+ free(status_str); -+ -+ return pcmk_rc_ok; -+} -+ - PCMK__OUTPUT_ARGS("attribute-list", "pe_resource_t *", "char *", "GHashTable *") - static int - attribute_list_text(pcmk__output_t *out, va_list args) { -@@ -562,6 +613,8 @@ resource_names(pcmk__output_t *out, va_list args) { - } - - static pcmk__message_entry_t fmt_functions[] = { -+ { "agent-status", "default", agent_status_default }, -+ { "agent-status", "xml", agent_status_xml }, - { "attribute-list", "default", attribute_list_default }, - { "attribute-list", "text", attribute_list_text }, - { "property-list", "default", property_list_default }, --- -1.8.3.1 - - -From 85cb6b6bff96b18c5174d11e4de4d49cbfb20bb7 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Tue, 1 Jun 2021 14:47:30 -0400 -Subject: [PATCH 07/10] Feature: tools: Add an overridden params output - message. - -This also replaces what was previously being done in an out->info call -with an output message. This means it shows up in XML output as well. -Also, note that if --class/--agent/--provider are given, the resource -name will be set to "test". In that case, do not display the resource -name in the output. - -See: rhbz#1644628 ---- - tools/crm_resource_print.c | 39 +++++++++++++++++++++++++++++++++++++++ - 1 file changed, 39 insertions(+) - -diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c -index 88d5878..119d83f 100644 ---- a/tools/crm_resource_print.c -+++ b/tools/crm_resource_print.c -@@ -224,6 +224,43 @@ attribute_list_text(pcmk__output_t *out, va_list args) { - return pcmk_rc_ok; - } - -+PCMK__OUTPUT_ARGS("override", "const char *", "const char *", "const char *") -+static int -+override_default(pcmk__output_t *out, va_list args) { -+ const char *rsc_name = va_arg(args, const char *); -+ const char *name = va_arg(args, const char *); -+ const char *value = va_arg(args, const char *); -+ -+ if (rsc_name == NULL) { -+ out->list_item(out, NULL, "Overriding the cluster configuration with '%s' = '%s'", -+ name, value); -+ } else { -+ out->list_item(out, NULL, "Overriding the cluster configuration for '%s' with '%s' = '%s'", -+ rsc_name, name, value); -+ } -+ -+ return pcmk_rc_ok; -+} -+ -+PCMK__OUTPUT_ARGS("override", "const char *", "const char *", "const char *") -+static int -+override_xml(pcmk__output_t *out, va_list args) { -+ const char *rsc_name = va_arg(args, const char *); -+ const char *name = va_arg(args, const char *); -+ const char *value = va_arg(args, const char *); -+ -+ xmlNodePtr node = pcmk__output_create_xml_node(out, "override", -+ "name", name, -+ "value", value, -+ NULL); -+ -+ if (rsc_name != NULL) { -+ crm_xml_add(node, "rsc", rsc_name); -+ } -+ -+ return pcmk_rc_ok; -+} -+ - PCMK__OUTPUT_ARGS("property-list", "pe_resource_t *", "char *") - static int - property_list_default(pcmk__output_t *out, va_list args) { -@@ -617,6 +654,8 @@ static pcmk__message_entry_t fmt_functions[] = { - { "agent-status", "xml", agent_status_xml }, - { "attribute-list", "default", attribute_list_default }, - { "attribute-list", "text", attribute_list_text }, -+ { "override", "default", override_default }, -+ { "override", "xml", override_xml }, - { "property-list", "default", property_list_default }, - { "property-list", "text", property_list_text }, - { "resource-check-list", "default", resource_check_list_default }, --- -1.8.3.1 - - -From e5e24592c7c3231c619fb5253e7925ffbc634a99 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 4 Jun 2021 10:24:51 -0400 -Subject: [PATCH 08/10] Low: tools: Use simple XML lists for resource actions - as well. - -See: rhbz#1644628 ---- - tools/crm_resource.c | 1 + - 1 file changed, 1 insertion(+) - -diff --git a/tools/crm_resource.c b/tools/crm_resource.c -index 37a0bb0..e957011 100644 ---- a/tools/crm_resource.c -+++ b/tools/crm_resource.c -@@ -1643,6 +1643,7 @@ main(int argc, char **argv) - * saves from having to write custom messages to build the lists around all these things - */ - switch (options.rsc_cmd) { -+ case cmd_execute_agent: - case cmd_list_resources: - case cmd_query_xml: - case cmd_query_raw_xml: --- -1.8.3.1 - - -From 3e75174d0bc31b261adb1994214a5878b79da85b Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 4 Jun 2021 10:30:10 -0400 -Subject: [PATCH 09/10] Feature: tools: Add an output message for resource - actions. - -This wraps up the override and agent-status messages into a single -message, along with any stdout/stderr from the resource action. This -message should be called after taking the action. - -This also implements handling XML output from resource actions. Check -to see if the validate-all action returns XML. If so, output it as a -CDATA block under a "command" element. If not, treat it as plain text -and output it as stdout/stderr from a command. - -See: rhbz#1644628 ---- - tools/crm_resource_print.c | 122 +++++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 122 insertions(+) - -diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c -index 119d83f..19a366d 100644 ---- a/tools/crm_resource_print.c -+++ b/tools/crm_resource_print.c -@@ -293,6 +293,126 @@ property_list_text(pcmk__output_t *out, va_list args) { - return pcmk_rc_ok; - } - -+PCMK__OUTPUT_ARGS("resource-agent-action", "int", "const char *", "const char *", -+ "const char *", "const char *", "const char *", "GHashTable *", -+ "int", "int", "char *", "char *") -+static int -+resource_agent_action_default(pcmk__output_t *out, va_list args) { -+ int verbose = va_arg(args, int); -+ -+ const char *class = va_arg(args, const char *); -+ const char *provider = va_arg(args, const char *); -+ const char *type = va_arg(args, const char *); -+ const char *rsc_name = va_arg(args, const char *); -+ const char *action = va_arg(args, const char *); -+ GHashTable *overrides = va_arg(args, GHashTable *); -+ int rc = va_arg(args, int); -+ int status = va_arg(args, int); -+ char *stdout_data = va_arg(args, char *); -+ char *stderr_data = va_arg(args, char *); -+ -+ if (overrides) { -+ GHashTableIter iter; -+ char *name = NULL; -+ char *value = NULL; -+ -+ out->begin_list(out, NULL, NULL, "overrides"); -+ -+ g_hash_table_iter_init(&iter, overrides); -+ while (g_hash_table_iter_next(&iter, (gpointer *) &name, (gpointer *) &value)) { -+ out->message(out, "override", rsc_name, name, value); -+ } -+ -+ out->end_list(out); -+ } -+ -+ out->message(out, "agent-status", status, action, rsc_name, class, provider, -+ type, rc); -+ -+ /* hide output for validate-all if not in verbose */ -+ if (verbose == 0 && pcmk__str_eq(action, "validate-all", pcmk__str_casei)) { -+ return pcmk_rc_ok; -+ } -+ -+ if (stdout_data || stderr_data) { -+ xmlNodePtr doc = string2xml(stdout_data); -+ -+ if (doc != NULL) { -+ out->output_xml(out, "command", stdout_data); -+ xmlFreeNode(doc); -+ } else { -+ out->subprocess_output(out, rc, stdout_data, stderr_data); -+ } -+ } -+ -+ return pcmk_rc_ok; -+} -+ -+PCMK__OUTPUT_ARGS("resource-agent-action", "int", "const char *", "const char *", -+ "const char *", "const char *", "const char *", "GHashTable *", -+ "int", "int", "char *", "char *") -+static int -+resource_agent_action_xml(pcmk__output_t *out, va_list args) { -+ int verbose G_GNUC_UNUSED = va_arg(args, int); -+ -+ const char *class = va_arg(args, const char *); -+ const char *provider = va_arg(args, const char *); -+ const char *type = va_arg(args, const char *); -+ const char *rsc_name = va_arg(args, const char *); -+ const char *action = va_arg(args, const char *); -+ GHashTable *overrides = va_arg(args, GHashTable *); -+ int rc = va_arg(args, int); -+ int status = va_arg(args, int); -+ char *stdout_data = va_arg(args, char *); -+ char *stderr_data = va_arg(args, char *); -+ -+ xmlNodePtr node = pcmk__output_xml_create_parent(out, "resource-agent-action", -+ "action", action, -+ "class", class, -+ "type", type, -+ NULL); -+ -+ if (rsc_name) { -+ crm_xml_add(node, "rsc", rsc_name); -+ } -+ -+ if (provider) { -+ crm_xml_add(node, "provider", provider); -+ } -+ -+ if (overrides) { -+ GHashTableIter iter; -+ char *name = NULL; -+ char *value = NULL; -+ -+ out->begin_list(out, NULL, NULL, "overrides"); -+ -+ g_hash_table_iter_init(&iter, overrides); -+ while (g_hash_table_iter_next(&iter, (gpointer *) &name, (gpointer *) &value)) { -+ out->message(out, "override", rsc_name, name, value); -+ } -+ -+ out->end_list(out); -+ } -+ -+ out->message(out, "agent-status", status, action, rsc_name, class, provider, -+ type, rc); -+ -+ if (stdout_data || stderr_data) { -+ xmlNodePtr doc = string2xml(stdout_data); -+ -+ if (doc != NULL) { -+ out->output_xml(out, "command", stdout_data); -+ xmlFreeNode(doc); -+ } else { -+ out->subprocess_output(out, rc, stdout_data, stderr_data); -+ } -+ } -+ -+ pcmk__output_xml_pop_parent(out); -+ return pcmk_rc_ok; -+} -+ - PCMK__OUTPUT_ARGS("resource-check-list", "resource_checks_t *") - static int - resource_check_list_default(pcmk__output_t *out, va_list args) { -@@ -658,6 +778,8 @@ static pcmk__message_entry_t fmt_functions[] = { - { "override", "xml", override_xml }, - { "property-list", "default", property_list_default }, - { "property-list", "text", property_list_text }, -+ { "resource-agent-action", "default", resource_agent_action_default }, -+ { "resource-agent-action", "xml", resource_agent_action_xml }, - { "resource-check-list", "default", resource_check_list_default }, - { "resource-check-list", "xml", resource_check_list_xml }, - { "resource-search-list", "default", resource_search_list_default }, --- -1.8.3.1 - - -From b50b2418e1e997b42f5370b4672a3f105d74634f Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 4 Jun 2021 10:40:16 -0400 -Subject: [PATCH 10/10] Feature: tools: Use the new resource-agent-action - message. - -See: rhbz#1644628 ---- - tools/crm_resource_runtime.c | 21 +++------------------ - 1 file changed, 3 insertions(+), 18 deletions(-) - -diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c -index ebf48bb..755be9f 100644 ---- a/tools/crm_resource_runtime.c -+++ b/tools/crm_resource_runtime.c -@@ -1765,28 +1765,13 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, - if (services_action_sync(op)) { - exit_code = op->rc; - -- if (op->status == PCMK_LRM_OP_DONE) { -- out->info(out, "Operation %s for %s (%s:%s:%s) returned: '%s' (%d)", -- action, rsc_name, rsc_class, rsc_prov ? rsc_prov : "", rsc_type, -- services_ocf_exitcode_str(op->rc), op->rc); -- } else { -- out->err(out, "Operation %s for %s (%s:%s:%s) failed: '%s' (%d)", -- action, rsc_name, rsc_class, rsc_prov ? rsc_prov : "", rsc_type, -- services_lrm_status_str(op->status), op->status); -- } -- -- /* hide output for validate-all if not in verbose */ -- if (resource_verbose == 0 && pcmk__str_eq(action, "validate-all", pcmk__str_casei)) -- goto done; -- -- if (op->stdout_data || op->stderr_data) { -- out->subprocess_output(out, op->rc, op->stdout_data, op->stderr_data); -- } -+ out->message(out, "resource-agent-action", resource_verbose, rsc_class, -+ rsc_prov, rsc_type, rsc_name, action, override_hash, op->rc, -+ op->status, op->stdout_data, op->stderr_data); - } else { - exit_code = op->rc == 0 ? CRM_EX_ERROR : op->rc; - } - --done: - services_action_free(op); - /* See comment above about why we free params here. */ - g_hash_table_destroy(params); --- -1.8.3.1 - diff --git a/006-crm_simulate.patch b/006-crm_simulate.patch deleted file mode 100644 index c8d4e3f..0000000 --- a/006-crm_simulate.patch +++ /dev/null @@ -1,896 +0,0 @@ -From 97571e6ccc9b7fa339a7e27d9b0b9ab782ff3003 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Wed, 16 Jun 2021 13:54:10 -0400 -Subject: [PATCH 1/5] Low: schemas: Copy crm_mon.rng in preparation for - changes. - ---- - xml/api/crm_mon-2.12.rng | 243 +++++++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 243 insertions(+) - create mode 100644 xml/api/crm_mon-2.12.rng - -diff --git a/xml/api/crm_mon-2.12.rng b/xml/api/crm_mon-2.12.rng -new file mode 100644 -index 0000000..ffec923 ---- /dev/null -+++ b/xml/api/crm_mon-2.12.rng -@@ -0,0 +1,243 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="element-crm-mon"/> -+ </start> -+ -+ <define name="element-crm-mon"> -+ <optional> -+ <ref name="element-summary" /> -+ </optional> -+ <optional> -+ <ref name="nodes-list" /> -+ </optional> -+ <optional> -+ <ref name="resources-list" /> -+ </optional> -+ <optional> -+ <ref name="node-attributes-list" /> -+ </optional> -+ <optional> -+ <ref name="node-history-list" /> -+ </optional> -+ <optional> -+ <ref name="failures-list" /> -+ </optional> -+ <optional> -+ <ref name="fence-event-list" /> -+ </optional> -+ <optional> -+ <ref name="tickets-list" /> -+ </optional> -+ <optional> -+ <ref name="bans-list" /> -+ </optional> -+ </define> -+ -+ <define name="element-summary"> -+ <element name="summary"> -+ <optional> -+ <element name="stack"> -+ <attribute name="type"> <text /> </attribute> -+ </element> -+ </optional> -+ <optional> -+ <element name="current_dc"> -+ <attribute name="present"> <data type="boolean" /> </attribute> -+ <optional> -+ <group> -+ <attribute name="version"> <text /> </attribute> -+ <attribute name="name"> <text /> </attribute> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="with_quorum"> <data type="boolean" /> </attribute> -+ </group> -+ </optional> -+ </element> -+ </optional> -+ <optional> -+ <element name="last_update"> -+ <attribute name="time"> <text /> </attribute> -+ </element> -+ <element name="last_change"> -+ <attribute name="time"> <text /> </attribute> -+ <attribute name="user"> <text /> </attribute> -+ <attribute name="client"> <text /> </attribute> -+ <attribute name="origin"> <text /> </attribute> -+ </element> -+ </optional> -+ <optional> -+ <element name="nodes_configured"> -+ <attribute name="number"> <data type="nonNegativeInteger" /> </attribute> -+ </element> -+ <element name="resources_configured"> -+ <attribute name="number"> <data type="nonNegativeInteger" /> </attribute> -+ <attribute name="disabled"> <data type="nonNegativeInteger" /> </attribute> -+ <attribute name="blocked"> <data type="nonNegativeInteger" /> </attribute> -+ </element> -+ </optional> -+ <optional> -+ <element name="cluster_options"> -+ <attribute name="stonith-enabled"> <data type="boolean" /> </attribute> -+ <attribute name="symmetric-cluster"> <data type="boolean" /> </attribute> -+ <attribute name="no-quorum-policy"> <text /> </attribute> -+ <attribute name="maintenance-mode"> <data type="boolean" /> </attribute> -+ <attribute name="stop-all-resources"> <data type="boolean" /> </attribute> -+ </element> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="resources-list"> -+ <element name="resources"> -+ <zeroOrMore> -+ <externalRef href="resources-2.4.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="nodes-list"> -+ <element name="nodes"> -+ <zeroOrMore> -+ <externalRef href="nodes-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="node-attributes-list"> -+ <element name="node_attributes"> -+ <zeroOrMore> -+ <externalRef href="node-attrs-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="node-history-list"> -+ <element name="node_history"> -+ <zeroOrMore> -+ <ref name="element-node-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="failures-list"> -+ <element name="failures"> -+ <zeroOrMore> -+ <externalRef href="failure-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="fence-event-list"> -+ <element name="fence_history"> -+ <optional> -+ <attribute name="status"> <data type="integer" /> </attribute> -+ </optional> -+ <zeroOrMore> -+ <externalRef href="fence-event-2.0.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="tickets-list"> -+ <element name="tickets"> -+ <zeroOrMore> -+ <ref name="element-ticket" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="bans-list"> -+ <element name="bans"> -+ <zeroOrMore> -+ <ref name="element-ban" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-node-history"> -+ <element name="node"> -+ <attribute name="name"> <text /> </attribute> -+ <zeroOrMore> -+ <ref name="element-resource-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-resource-history"> -+ <element name="resource_history"> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="orphan"> <data type="boolean" /> </attribute> -+ <optional> -+ <group> -+ <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> -+ <optional> -+ <attribute name="fail-count"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-failure"> <text /> </attribute> -+ </optional> -+ </group> -+ </optional> -+ <zeroOrMore> -+ <ref name="element-operation-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-operation-history"> -+ <element name="operation_history"> -+ <attribute name="call"> <text /> </attribute> -+ <attribute name="task"> <text /> </attribute> -+ <optional> -+ <attribute name="interval"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-rc-change"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-run"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="exec-time"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="queue-time"> <text /> </attribute> -+ </optional> -+ <attribute name="rc"> <data type="integer" /> </attribute> -+ <attribute name="rc_text"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-ticket"> -+ <element name="ticket"> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="status"> -+ <choice> -+ <value>granted</value> -+ <value>revoked</value> -+ </choice> -+ </attribute> -+ <attribute name="standby"> <data type="boolean" /> </attribute> -+ <optional> -+ <attribute name="last-granted"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-ban"> -+ <element name="ban"> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="resource"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="weight"> <data type="integer" /> </attribute> -+ <attribute name="promoted-only"> <data type="boolean" /> </attribute> -+  -+ <attribute name="master_only"> <data type="boolean" /> </attribute> -+ </element> -+ </define> -+</grammar> --- -1.8.3.1 - - -From da394983f106f974274ddd94675a04c85086010e Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 18 Jun 2021 15:06:34 -0400 -Subject: [PATCH 2/5] Refactor: Split node history out into its own XML schema. - -This allows for sharing it between crm_mon and crm_simulate. ---- - xml/Makefile.am | 2 +- - xml/api/crm_mon-2.12.rng | 64 +-------------------------------------- - xml/api/node-history-2.12.rng | 70 +++++++++++++++++++++++++++++++++++++++++++ - 3 files changed, 72 insertions(+), 64 deletions(-) - create mode 100644 xml/api/node-history-2.12.rng - -diff --git a/xml/Makefile.am b/xml/Makefile.am -index b9448d4..8e7b6d3 100644 ---- a/xml/Makefile.am -+++ b/xml/Makefile.am -@@ -64,7 +64,7 @@ API_request_base = command-output \ - CIB_cfg_base = options nodes resources constraints fencing acls tags alerts - - # Names of all schemas (including top level and those included by others) --API_base = $(API_request_base) fence-event failure generic-list item node-attrs nodes resources status -+API_base = $(API_request_base) fence-event failure generic-list item node-attrs node-history nodes resources status - CIB_base = cib $(CIB_cfg_base) status score rule nvset - - # Static schema files and transforms (only CIB has transforms) -diff --git a/xml/api/crm_mon-2.12.rng b/xml/api/crm_mon-2.12.rng -index ffec923..be14412 100644 ---- a/xml/api/crm_mon-2.12.rng -+++ b/xml/api/crm_mon-2.12.rng -@@ -20,7 +20,7 @@ - <ref name="node-attributes-list" /> - </optional> - <optional> -- <ref name="node-history-list" /> -+ <externalRef href="node-history-2.12.rng"/> - </optional> - <optional> - <ref name="failures-list" /> -@@ -113,14 +113,6 @@ - </element> - </define> - -- <define name="node-history-list"> -- <element name="node_history"> -- <zeroOrMore> -- <ref name="element-node-history" /> -- </zeroOrMore> -- </element> -- </define> -- - <define name="failures-list"> - <element name="failures"> - <zeroOrMore> -@@ -156,60 +148,6 @@ - </element> - </define> - -- <define name="element-node-history"> -- <element name="node"> -- <attribute name="name"> <text /> </attribute> -- <zeroOrMore> -- <ref name="element-resource-history" /> -- </zeroOrMore> -- </element> -- </define> -- -- <define name="element-resource-history"> -- <element name="resource_history"> -- <attribute name="id"> <text /> </attribute> -- <attribute name="orphan"> <data type="boolean" /> </attribute> -- <optional> -- <group> -- <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> -- <optional> -- <attribute name="fail-count"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="last-failure"> <text /> </attribute> -- </optional> -- </group> -- </optional> -- <zeroOrMore> -- <ref name="element-operation-history" /> -- </zeroOrMore> -- </element> -- </define> -- -- <define name="element-operation-history"> -- <element name="operation_history"> -- <attribute name="call"> <text /> </attribute> -- <attribute name="task"> <text /> </attribute> -- <optional> -- <attribute name="interval"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="last-rc-change"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="last-run"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="exec-time"> <text /> </attribute> -- </optional> -- <optional> -- <attribute name="queue-time"> <text /> </attribute> -- </optional> -- <attribute name="rc"> <data type="integer" /> </attribute> -- <attribute name="rc_text"> <text /> </attribute> -- </element> -- </define> -- - <define name="element-ticket"> - <element name="ticket"> - <attribute name="id"> <text /> </attribute> -diff --git a/xml/api/node-history-2.12.rng b/xml/api/node-history-2.12.rng -new file mode 100644 -index 0000000..9628000 ---- /dev/null -+++ b/xml/api/node-history-2.12.rng -@@ -0,0 +1,70 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="node-history-list" /> -+ </start> -+ -+ <define name="node-history-list"> -+ <element name="node_history"> -+ <zeroOrMore> -+ <ref name="element-node-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-node-history"> -+ <element name="node"> -+ <attribute name="name"> <text /> </attribute> -+ <zeroOrMore> -+ <ref name="element-resource-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-resource-history"> -+ <element name="resource_history"> -+ <attribute name="id"> <text /> </attribute> -+ <attribute name="orphan"> <data type="boolean" /> </attribute> -+ <optional> -+ <group> -+ <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> -+ <optional> -+ <attribute name="fail-count"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-failure"> <text /> </attribute> -+ </optional> -+ </group> -+ </optional> -+ <zeroOrMore> -+ <ref name="element-operation-history" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-operation-history"> -+ <element name="operation_history"> -+ <attribute name="call"> <text /> </attribute> -+ <attribute name="task"> <text /> </attribute> -+ <optional> -+ <attribute name="interval"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-rc-change"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="last-run"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="exec-time"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="queue-time"> <text /> </attribute> -+ </optional> -+ <attribute name="rc"> <data type="integer" /> </attribute> -+ <attribute name="rc_text"> <text /> </attribute> -+ </element> -+ </define> -+</grammar> --- -1.8.3.1 - - -From bf72b2615630eef7876e443d60b34d5a316de847 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Wed, 16 Jun 2021 14:09:31 -0400 -Subject: [PATCH 3/5] Low: schemas: Copy crm_simulate.rng in preparation for - changes. - ---- - xml/api/crm_simulate-2.12.rng | 335 ++++++++++++++++++++++++++++++++++++++++++ - 1 file changed, 335 insertions(+) - create mode 100644 xml/api/crm_simulate-2.12.rng - -diff --git a/xml/api/crm_simulate-2.12.rng b/xml/api/crm_simulate-2.12.rng -new file mode 100644 -index 0000000..9a7612d ---- /dev/null -+++ b/xml/api/crm_simulate-2.12.rng -@@ -0,0 +1,335 @@ -+<?xml version="1.0" encoding="UTF-8"?> -+<grammar xmlns="http://relaxng.org/ns/structure/1.0" -+ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> -+ -+ <start> -+ <ref name="element-crm-simulate"/> -+ </start> -+ -+ <define name="element-crm-simulate"> -+ <choice> -+ <ref name="timings-list" /> -+ <group> -+ <ref name="cluster-status" /> -+ <optional> -+ <ref name="modifications-list" /> -+ </optional> -+ <optional> -+ <ref name="allocations-utilizations-list" /> -+ </optional> -+ <optional> -+ <ref name="action-list" /> -+ </optional> -+ <optional> -+ <ref name="cluster-injected-actions-list" /> -+ <ref name="revised-cluster-status" /> -+ </optional> -+ </group> -+ </choice> -+ </define> -+ -+ <define name="allocations-utilizations-list"> -+ <choice> -+ <element name="allocations"> -+ <zeroOrMore> -+ <choice> -+ <ref name="element-allocation" /> -+ <ref name="element-promotion" /> -+ </choice> -+ </zeroOrMore> -+ </element> -+ <element name="utilizations"> -+ <zeroOrMore> -+ <choice> -+ <ref name="element-capacity" /> -+ <ref name="element-utilization" /> -+ </choice> -+ </zeroOrMore> -+ </element> -+ <element name="allocations_utilizations"> -+ <zeroOrMore> -+ <choice> -+ <ref name="element-allocation" /> -+ <ref name="element-promotion" /> -+ <ref name="element-capacity" /> -+ <ref name="element-utilization" /> -+ </choice> -+ </zeroOrMore> -+ </element> -+ </choice> -+ </define> -+ -+ <define name="cluster-status"> -+ <element name="cluster_status"> -+ <ref name="nodes-list" /> -+ <ref name="resources-list" /> -+ <optional> -+ <ref name="node-attributes-list" /> -+ </optional> -+ <optional> -+ <ref name="failures-list" /> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="modifications-list"> -+ <element name="modifications"> -+ <optional> -+ <attribute name="quorum"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="watchdog"> <text /> </attribute> -+ </optional> -+ <zeroOrMore> -+ <ref name="element-inject-modify-node" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="element-inject-modify-ticket" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="element-inject-spec" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="element-inject-attr" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="revised-cluster-status"> -+ <element name="revised_cluster_status"> -+ <ref name="nodes-list" /> -+ <ref name="resources-list" /> -+ <optional> -+ <ref name="node-attributes-list" /> -+ </optional> -+ <optional> -+ <ref name="failures-list" /> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-inject-attr"> -+ <element name="inject_attr"> -+ <attribute name="cib_node"> <text /> </attribute> -+ <attribute name="name"> <text /> </attribute> -+ <attribute name="node_path"> <text /> </attribute> -+ <attribute name="value"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-inject-modify-node"> -+ <element name="modify_node"> -+ <attribute name="action"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-inject-spec"> -+ <element name="inject_spec"> -+ <attribute name="spec"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-inject-modify-ticket"> -+ <element name="modify_ticket"> -+ <attribute name="action"> <text /> </attribute> -+ <attribute name="ticket"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="cluster-injected-actions-list"> -+ <element name="transition"> -+ <zeroOrMore> -+ <ref name="element-injected-actions" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="node-attributes-list"> -+ <element name="node_attributes"> -+ <zeroOrMore> -+ <externalRef href="node-attrs-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="failures-list"> -+ <element name="failures"> -+ <zeroOrMore> -+ <externalRef href="failure-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="nodes-list"> -+ <element name="nodes"> -+ <zeroOrMore> -+ <externalRef href="nodes-2.8.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="resources-list"> -+ <element name="resources"> -+ <zeroOrMore> -+ <externalRef href="resources-2.4.rng" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="timings-list"> -+ <element name="timings"> -+ <zeroOrMore> -+ <ref name="element-timing" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="action-list"> -+ <element name="actions"> -+ <zeroOrMore> -+ <ref name="element-node-action" /> -+ </zeroOrMore> -+ <zeroOrMore> -+ <ref name="element-rsc-action" /> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-allocation"> -+ <element name="node_weight"> -+ <attribute name="function"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ <externalRef href="../score.rng" /> -+ <optional> -+ <attribute name="id"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-capacity"> -+ <element name="capacity"> -+ <attribute name="comment"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ <zeroOrMore> -+ <element> -+ <anyName /> -+ <text /> -+ </element> -+ </zeroOrMore> -+ </element> -+ </define> -+ -+ <define name="element-inject-cluster-action"> -+ <element name="cluster_action"> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="task"> <text /> </attribute> -+ <optional> -+ <attribute name="id"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-injected-actions"> -+ <choice> -+ <ref name="element-inject-cluster-action" /> -+ <ref name="element-inject-fencing-action" /> -+ <ref name="element-inject-pseudo-action" /> -+ <ref name="element-inject-rsc-action" /> -+ </choice> -+ </define> -+ -+ <define name="element-inject-fencing-action"> -+ <element name="fencing_action"> -+ <attribute name="op"> <text /> </attribute> -+ <attribute name="target"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-node-action"> -+ <element name="node_action"> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="reason"> <text /> </attribute> -+ <attribute name="task"> <text /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-promotion"> -+ <element name="promotion_score"> -+ <attribute name="id"> <text /> </attribute> -+ <externalRef href="../score.rng" /> -+ <optional> -+ <attribute name="node"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-inject-pseudo-action"> -+ <element name="pseudo_action"> -+ <attribute name="task"> <text /> </attribute> -+ <optional> -+ <attribute name="node"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-inject-rsc-action"> -+ <element name="rsc_action"> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="op"> <text /> </attribute> -+ <attribute name="resource"> <text /> </attribute> -+ <optional> -+ <attribute name="interval"> <data type="integer" /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-timing"> -+ <element name="timing"> -+ <attribute name="file"> <text /> </attribute> -+ <attribute name="duration"> <data type="double" /> </attribute> -+ </element> -+ </define> -+ -+ <define name="element-rsc-action"> -+ <element name="rsc_action"> -+ <attribute name="action"> <text /> </attribute> -+ <attribute name="resource"> <text /> </attribute> -+ <optional> -+ <attribute name="blocked"> <data type="boolean" /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="dest"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="next-role"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="node"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="reason"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="role"> <text /> </attribute> -+ </optional> -+ <optional> -+ <attribute name="source"> <text /> </attribute> -+ </optional> -+ </element> -+ </define> -+ -+ <define name="element-utilization"> -+ <element name="utilization"> -+ <attribute name="function"> <text /> </attribute> -+ <attribute name="node"> <text /> </attribute> -+ <attribute name="resource"> <text /> </attribute> -+ <zeroOrMore> -+ <element> -+ <anyName /> -+ <text /> -+ </element> -+ </zeroOrMore> -+ </element> -+ </define> -+</grammar> --- -1.8.3.1 - - -From c46e07788788acf5669e3f89b9344190a91c7331 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 18 Jun 2021 15:10:19 -0400 -Subject: [PATCH 4/5] Feature: tools: Add the node-summary to crm_simulate - output. - -If --show-failcounts is given to crm_simulate, it should also display -the node-summary message. - -See: rhbz#1686426 ---- - tools/crm_simulate.c | 7 +++++-- - xml/api/crm_simulate-2.12.rng | 3 +++ - 2 files changed, 8 insertions(+), 2 deletions(-) - -diff --git a/tools/crm_simulate.c b/tools/crm_simulate.c -index b4aa9d1..2ea292c 100644 ---- a/tools/crm_simulate.c -+++ b/tools/crm_simulate.c -@@ -409,11 +409,14 @@ print_cluster_status(pe_working_set_t * data_set, unsigned int print_opts) - FALSE, FALSE, all, all, FALSE); - - if (options.show_attrs) { -- out->message(out, "node-attribute-list", data_set, -- 0, rc == pcmk_rc_ok, FALSE, FALSE, FALSE, all, all); -+ rc = out->message(out, "node-attribute-list", data_set, -+ 0, rc == pcmk_rc_ok, FALSE, FALSE, FALSE, all, all); - } - - if (options.show_failcounts) { -+ rc = out->message(out, "node-summary", data_set, all, all, -+ 0, print_opts, FALSE, FALSE, FALSE, FALSE, rc == pcmk_rc_ok); -+ - out->message(out, "failed-action-list", data_set, all, all, - rc == pcmk_rc_ok); - } -diff --git a/xml/api/crm_simulate-2.12.rng b/xml/api/crm_simulate-2.12.rng -index 9a7612d..f90bd36 100644 ---- a/xml/api/crm_simulate-2.12.rng -+++ b/xml/api/crm_simulate-2.12.rng -@@ -67,6 +67,9 @@ - <ref name="node-attributes-list" /> - </optional> - <optional> -+ <externalRef href="node-history-2.12.rng" /> -+ </optional> -+ <optional> - <ref name="failures-list" /> - </optional> - </element> --- -1.8.3.1 - - -From bac50336e0264604716e5997b87ee7e65311b982 Mon Sep 17 00:00:00 2001 -From: Chris Lumens <clumens(a)redhat.com> -Date: Fri, 18 Jun 2021 15:21:52 -0400 -Subject: [PATCH 5/5] Low: libcrmcommon: Increase PCMK__API_VERSION for new - crm_resource output. - -See: rhbz#1686426 ---- - include/crm/common/output_internal.h | 2 +- - 1 file changed, 1 insertion(+), 1 deletion(-) - -diff --git a/include/crm/common/output_internal.h b/include/crm/common/output_internal.h -index 0436cde..ba9c423 100644 ---- a/include/crm/common/output_internal.h -+++ b/include/crm/common/output_internal.h -@@ -27,7 +27,7 @@ extern "C" { - # include <glib.h> - # include <crm/common/results.h> - --# define PCMK__API_VERSION "2.11" -+# define PCMK__API_VERSION "2.12" - - #if defined(PCMK__WITH_ATTRIBUTE_OUTPUT_ARGS) - # define PCMK__OUTPUT_ARGS(ARGS...) __attribute__((output_args(ARGS))) --- -1.8.3.1 - diff --git a/007-unfencing-loop.patch b/007-unfencing-loop.patch deleted file mode 100644 index d4950c8..0000000 --- a/007-unfencing-loop.patch +++ /dev/null @@ -1,733 +0,0 @@ -From 6dcd6b51d7d3993bc483588d6ed75077518ed600 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 4 Jun 2021 16:30:55 -0500 -Subject: [PATCH 01/11] Low: controller: check whether unfenced node was remote - node - -... so the controller can indicate the node is remote (if known at that point, -which is not guaranteed) when setting unfencing-related node attributes. ---- - daemons/controld/controld_fencing.c | 21 ++++++++++++++++++--- - 1 file changed, 18 insertions(+), 3 deletions(-) - -diff --git a/daemons/controld/controld_fencing.c b/daemons/controld/controld_fencing.c -index 23dff28..0fba661 100644 ---- a/daemons/controld/controld_fencing.c -+++ b/daemons/controld/controld_fencing.c -@@ -757,15 +757,30 @@ tengine_stonith_callback(stonith_t *stonith, stonith_callback_data_t *data) - if (pcmk__str_eq("on", op, pcmk__str_casei)) { - const char *value = NULL; - char *now = pcmk__ttoa(time(NULL)); -+ gboolean is_remote_node = FALSE; -+ -+ /* This check is not 100% reliable, since this node is not -+ * guaranteed to have the remote node cached. However, it -+ * doesn't have to be reliable, since the attribute manager can -+ * learn a node's "remoteness" by other means sooner or later. -+ * This allows it to learn more quickly if this node does have -+ * the information. -+ */ -+ if (g_hash_table_lookup(crm_remote_peer_cache, uuid) != NULL) { -+ is_remote_node = TRUE; -+ } - -- update_attrd(target, CRM_ATTR_UNFENCED, now, NULL, FALSE); -+ update_attrd(target, CRM_ATTR_UNFENCED, now, NULL, -+ is_remote_node); - free(now); - - value = crm_meta_value(action->params, XML_OP_ATTR_DIGESTS_ALL); -- update_attrd(target, CRM_ATTR_DIGESTS_ALL, value, NULL, FALSE); -+ update_attrd(target, CRM_ATTR_DIGESTS_ALL, value, NULL, -+ is_remote_node); - - value = crm_meta_value(action->params, XML_OP_ATTR_DIGESTS_SECURE); -- update_attrd(target, CRM_ATTR_DIGESTS_SECURE, value, NULL, FALSE); -+ update_attrd(target, CRM_ATTR_DIGESTS_SECURE, value, NULL, -+ is_remote_node); - - } else if (action->sent_update == FALSE) { - send_stonith_update(action, target, uuid); --- -1.8.3.1 - - -From 3ef6d9403f68ab8559c45cc99f5a8da05ca6420b Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 10:50:36 -0500 -Subject: [PATCH 02/11] Refactor: pacemaker-attrd: functionize adding remote - node to cache - -... for future reuse ---- - daemons/attrd/attrd_commands.c | 34 +++++++++++++++++++++++----------- - 1 file changed, 23 insertions(+), 11 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 731c243..93a165b 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -102,6 +102,28 @@ free_attribute(gpointer data) - } - } - -+/*! -+ * \internal -+ * \brief Ensure a Pacemaker Remote node is in the correct peer cache -+ * -+ * \param[in] -+ */ -+static void -+cache_remote_node(const char *node_name) -+{ -+ /* If we previously assumed this node was an unseen cluster node, -+ * remove its entry from the cluster peer cache. -+ */ -+ crm_node_t *dup = pcmk__search_cluster_node_cache(0, node_name); -+ -+ if (dup && (dup->uuid == NULL)) { -+ reap_crm_member(0, node_name); -+ } -+ -+ // Ensure node is in the remote peer cache -+ CRM_ASSERT(crm_remote_peer_get(node_name) != NULL); -+} -+ - static xmlNode * - build_attribute_xml( - xmlNode *parent, const char *name, const char *set, const char *uuid, unsigned int timeout_ms, const char *user, -@@ -709,17 +731,7 @@ attrd_lookup_or_create_value(GHashTable *values, const char *host, xmlNode *xml) - - crm_element_value_int(xml, PCMK__XA_ATTR_IS_REMOTE, &is_remote); - if (is_remote) { -- /* If we previously assumed this node was an unseen cluster node, -- * remove its entry from the cluster peer cache. -- */ -- crm_node_t *dup = pcmk__search_cluster_node_cache(0, host); -- -- if (dup && (dup->uuid == NULL)) { -- reap_crm_member(0, host); -- } -- -- /* Ensure this host is in the remote peer cache */ -- CRM_ASSERT(crm_remote_peer_get(host) != NULL); -+ cache_remote_node(host); - } - - if (v == NULL) { --- -1.8.3.1 - - -From 6fac2c71bc2c56870ac828d7cd7b7c799279c47e Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 10:39:34 -0500 -Subject: [PATCH 03/11] Refactor: pacemaker-attrd: don't try to remove votes - for remote nodes - -Remote nodes never vote. - -This has no effect in practice since the removal would simply do nothing, -but we might as well not waste time trying. ---- - daemons/attrd/attrd_commands.c | 11 ++++++----- - 1 file changed, 6 insertions(+), 5 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 93a165b..dbe777e 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -976,7 +976,8 @@ attrd_election_cb(gpointer user_data) - void - attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *data) - { -- bool remove_voter = FALSE; -+ bool gone = false; -+ bool is_remote = pcmk_is_set(peer->flags, crm_remote_node); - - switch (kind) { - case crm_status_uname: -@@ -984,7 +985,7 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da - - case crm_status_processes: - if (!pcmk_is_set(peer->processes, crm_get_cluster_proc())) { -- remove_voter = TRUE; -+ gone = true; - } - break; - -@@ -1000,13 +1001,13 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da - } else { - // Remove all attribute values associated with lost nodes - attrd_peer_remove(peer->uname, FALSE, "loss"); -- remove_voter = TRUE; -+ gone = true; - } - break; - } - -- // In case an election is in progress, remove any vote by the node -- if (remove_voter) { -+ // Remove votes from cluster nodes that leave, in case election in progress -+ if (gone && !is_remote) { - attrd_remove_voter(peer); - } - } --- -1.8.3.1 - - -From 54089fc663d6aaf10ca164c6c94b3b17237788de Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 10:40:06 -0500 -Subject: [PATCH 04/11] Low: pacemaker-attrd: check for remote nodes in peer - update callback - -If a remote node was started before the local cluster node joined the cluster, -the cluster node will assume its node attributes are for a cluster node until -it learns otherwise. Check for remoteness in the peer update callback, to have -another way we can learn it. ---- - daemons/attrd/attrd_commands.c | 4 ++++ - 1 file changed, 4 insertions(+) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index dbe777e..5f6a754 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -1009,6 +1009,10 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da - // Remove votes from cluster nodes that leave, in case election in progress - if (gone && !is_remote) { - attrd_remove_voter(peer); -+ -+ // Ensure remote nodes that come up are in the remote node cache -+ } else if (!gone && is_remote) { -+ cache_remote_node(peer->uname); - } - } - --- -1.8.3.1 - - -From 8c048df0312d0d9c857d87b570a352429a710928 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 11:29:12 -0500 -Subject: [PATCH 05/11] Log: pacemaker-attrd: log peer status changes - ---- - daemons/attrd/attrd_commands.c | 9 +++++++++ - 1 file changed, 9 insertions(+) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 5f6a754..d6d179b 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -972,6 +972,7 @@ attrd_election_cb(gpointer user_data) - return FALSE; - } - -+#define state_text(state) ((state)? (const char *)(state) : "in unknown state") - - void - attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *data) -@@ -981,15 +982,23 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da - - switch (kind) { - case crm_status_uname: -+ crm_debug("%s node %s is now %s", -+ (is_remote? "Remote" : "Cluster"), -+ peer->uname, state_text(peer->state)); - break; - - case crm_status_processes: - if (!pcmk_is_set(peer->processes, crm_get_cluster_proc())) { - gone = true; - } -+ crm_debug("Node %s is %s a peer", -+ peer->uname, (gone? "no longer" : "now")); - break; - - case crm_status_nstate: -+ crm_debug("%s node %s is now %s (was %s)", -+ (is_remote? "Remote" : "Cluster"), -+ peer->uname, state_text(peer->state), state_text(data)); - if (pcmk__str_eq(peer->state, CRM_NODE_MEMBER, pcmk__str_casei)) { - /* If we're the writer, send new peers a list of all attributes - * (unless it's a remote node, which doesn't run its own attrd) --- -1.8.3.1 - - -From 1dcc8dee4990cf0dbdec0e14db6d9a3ad67a41d5 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Mon, 7 Jun 2021 11:13:53 -0500 -Subject: [PATCH 06/11] Low: pacemaker-attrd: ensure node ID is only set for - attributes when known - -In most cases, attribute updates contained the node ID, and the node ID was -used by other code, only if known (i.e. positive). However a couple places did -not check this, so add that. - -I am unsure whether the missing check caused problems in practice, but there -appears to be the possibility that a remote node would wrongly be added to the -cluster node cache. ---- - daemons/attrd/attrd_commands.c | 6 ++++-- - 1 file changed, 4 insertions(+), 2 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index d6d179b..b3f441c 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -136,7 +136,9 @@ build_attribute_xml( - crm_xml_add(xml, PCMK__XA_ATTR_UUID, uuid); - crm_xml_add(xml, PCMK__XA_ATTR_USER, user); - crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, peer); -- crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); -+ if (peerid > 0) { -+ crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); -+ } - crm_xml_add(xml, PCMK__XA_ATTR_VALUE, value); - crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, timeout_ms/1000); - crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, is_private); -@@ -937,7 +939,7 @@ attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) - /* If this is a cluster node whose node ID we are learning, remember it */ - if ((v->nodeid == 0) && (v->is_remote == FALSE) - && (crm_element_value_int(xml, PCMK__XA_ATTR_NODE_ID, -- (int*)&v->nodeid) == 0)) { -+ (int*)&v->nodeid) == 0) && (v->nodeid > 0)) { - - crm_node_t *known_peer = crm_get_peer(v->nodeid, host); - --- -1.8.3.1 - - -From 8d12490e88b558d01db37a38f7d35175c6d2d69a Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Thu, 10 Jun 2021 17:25:57 -0500 -Subject: [PATCH 07/11] Refactor: pacemaker-attrd: functionize processing a - sync response - -... for code isolation, and because we need to add more to it ---- - daemons/attrd/attrd_commands.c | 59 ++++++++++++++++++++++++++++-------------- - 1 file changed, 39 insertions(+), 20 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index b3f441c..d02d3e6 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -572,6 +572,43 @@ attrd_peer_clear_failure(crm_node_t *peer, xmlNode *xml) - } - - /*! -+ * \internal -+ * \brief Load attributes from a peer sync response -+ * -+ * \param[in] peer Peer that sent clear request -+ * \param[in] peer_won Whether peer is the attribute writer -+ * \param[in] xml Request XML -+ */ -+static void -+process_peer_sync_response(crm_node_t *peer, bool peer_won, xmlNode *xml) -+{ -+ crm_info("Processing " PCMK__ATTRD_CMD_SYNC_RESPONSE " from %s", -+ peer->uname); -+ -+ if (peer_won) { -+ /* Initialize the "seen" flag for all attributes to cleared, so we can -+ * detect attributes that local node has but the writer doesn't. -+ */ -+ clear_attribute_value_seen(); -+ } -+ -+ // Process each attribute update in the sync response -+ for (xmlNode *child = pcmk__xml_first_child(xml); child != NULL; -+ child = pcmk__xml_next(child)) { -+ attrd_peer_update(peer, child, -+ crm_element_value(child, PCMK__XA_ATTR_NODE_NAME), -+ TRUE); -+ } -+ -+ if (peer_won) { -+ /* If any attributes are still not marked as seen, the writer doesn't -+ * know about them, so send all peers an update with them. -+ */ -+ attrd_current_only_attribute_update(peer, xml); -+ } -+} -+ -+/*! - \internal - \brief Broadcast private attribute for local node with protocol version - */ -@@ -596,7 +633,7 @@ attrd_peer_message(crm_node_t *peer, xmlNode *xml) - const char *op = crm_element_value(xml, PCMK__XA_TASK); - const char *election_op = crm_element_value(xml, F_CRM_TASK); - const char *host = crm_element_value(xml, PCMK__XA_ATTR_NODE_NAME); -- bool peer_won = FALSE; -+ bool peer_won = false; - - if (election_op) { - attrd_handle_election_op(peer, xml); -@@ -631,25 +668,7 @@ attrd_peer_message(crm_node_t *peer, xmlNode *xml) - - } else if (pcmk__str_eq(op, PCMK__ATTRD_CMD_SYNC_RESPONSE, pcmk__str_casei) - && !pcmk__str_eq(peer->uname, attrd_cluster->uname, pcmk__str_casei)) { -- xmlNode *child = NULL; -- -- crm_info("Processing %s from %s", op, peer->uname); -- -- /* Clear the seen flag for attribute processing held only in the own node. */ -- if (peer_won) { -- clear_attribute_value_seen(); -- } -- -- for (child = pcmk__xml_first_child(xml); child != NULL; -- child = pcmk__xml_next(child)) { -- host = crm_element_value(child, PCMK__XA_ATTR_NODE_NAME); -- attrd_peer_update(peer, child, host, TRUE); -- } -- -- if (peer_won) { -- /* Synchronize if there is an attribute held only by own node that Writer does not have. */ -- attrd_current_only_attribute_update(peer, xml); -- } -+ process_peer_sync_response(peer, peer_won, xml); - - } else if (pcmk__str_eq(op, PCMK__ATTRD_CMD_FLUSH, pcmk__str_casei)) { - /* Ignore. The flush command was removed in 2.0.0 but may be --- -1.8.3.1 - - -From a890a0e5bbbcabf907f51ed0460868035f72464d Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 11 Jun 2021 14:40:39 -0500 -Subject: [PATCH 08/11] Refactor: pacemaker-attrd: functionize broadcasting - local override - -... for code isolation ---- - daemons/attrd/attrd_commands.c | 42 +++++++++++++++++++++++++++++------------- - 1 file changed, 29 insertions(+), 13 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index d02d3e6..4783427 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -804,6 +804,34 @@ attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml) - free_xml(sync); - } - -+/*! -+ * \internal -+ * \brief Override an attribute sync with a local value -+ * -+ * Broadcast the local node's value for an attribute that's different from the -+ * value provided in a peer's attribute synchronization response. This ensures a -+ * node's values for itself take precedence and all peers are kept in sync. -+ * -+ * \param[in] a Attribute entry to override -+ * -+ * \return Local instance of attribute value -+ */ -+static attribute_value_t * -+broadcast_local_value(attribute_t *a) -+{ -+ attribute_value_t *v = g_hash_table_lookup(a->values, attrd_cluster->uname); -+ xmlNode *sync = create_xml_node(NULL, __func__); -+ -+ crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -+ build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, -+ a->user, a->is_private, v->nodename, v->nodeid, -+ v->current, FALSE); -+ attrd_xml_add_writer(sync); -+ send_attrd_message(NULL, sync); -+ free_xml(sync); -+ return v; -+} -+ - void - attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) - { -@@ -899,21 +927,9 @@ attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) - if (filter && !pcmk__str_eq(v->current, value, pcmk__str_casei) - && pcmk__str_eq(host, attrd_cluster->uname, pcmk__str_casei)) { - -- xmlNode *sync = create_xml_node(NULL, __func__); -- - crm_notice("%s[%s]: local value '%s' takes priority over '%s' from %s", - attr, host, v->current, value, peer->uname); -- -- crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -- v = g_hash_table_lookup(a->values, host); -- build_attribute_xml(sync, attr, a->set, a->uuid, a->timeout_ms, a->user, -- a->is_private, v->nodename, v->nodeid, v->current, FALSE); -- -- attrd_xml_add_writer(sync); -- -- /* Broadcast in case any other nodes had the inconsistent value */ -- send_attrd_message(NULL, sync); -- free_xml(sync); -+ v = broadcast_local_value(a); - - } else if (!pcmk__str_eq(v->current, value, pcmk__str_casei)) { - crm_notice("Setting %s[%s]: %s -> %s " CRM_XS " from %s", --- -1.8.3.1 - - -From f6f65e3dab070f1bbdf6d1383f4d6173a8840bc9 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 11 Jun 2021 14:50:29 -0500 -Subject: [PATCH 09/11] Log: pacemaker-attrd: improve messages when - broadcasting local-only values - -The traces aren't necessary since build_attribute_xml() already logs the same -info at debug. Also, rename function for clarity, and make static. ---- - daemons/attrd/attrd_commands.c | 35 ++++++++++++++++------------------- - 1 file changed, 16 insertions(+), 19 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 4783427..356defb 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -51,11 +51,12 @@ GHashTable *attributes = NULL; - - void write_attribute(attribute_t *a, bool ignore_delay); - void write_or_elect_attribute(attribute_t *a); --void attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml); - void attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter); - void attrd_peer_sync(crm_node_t *peer, xmlNode *xml); - void attrd_peer_remove(const char *host, gboolean uncache, const char *source); - -+static void broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml); -+ - static gboolean - send_attrd_message(crm_node_t * node, xmlNode * data) - { -@@ -604,7 +605,7 @@ process_peer_sync_response(crm_node_t *peer, bool peer_won, xmlNode *xml) - /* If any attributes are still not marked as seen, the writer doesn't - * know about them, so send all peers an update with them. - */ -- attrd_current_only_attribute_update(peer, xml); -+ broadcast_unseen_local_values(peer, xml); - } - } - -@@ -768,40 +769,36 @@ attrd_lookup_or_create_value(GHashTable *values, const char *host, xmlNode *xml) - return(v); - } - --void --attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml) -+void -+broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml) - { - GHashTableIter aIter; - GHashTableIter vIter; -- attribute_t *a; -+ attribute_t *a = NULL; - attribute_value_t *v = NULL; -- xmlNode *sync = create_xml_node(NULL, __func__); -- gboolean build = FALSE; -- -- crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -+ xmlNode *sync = NULL; - - g_hash_table_iter_init(&aIter, attributes); - while (g_hash_table_iter_next(&aIter, NULL, (gpointer *) & a)) { - g_hash_table_iter_init(&vIter, a->values); - while (g_hash_table_iter_next(&vIter, NULL, (gpointer *) & v)) { -- if (pcmk__str_eq(v->nodename, attrd_cluster->uname, pcmk__str_casei) && v->seen == FALSE) { -- crm_trace("Syncing %s[%s] = %s to everyone.(from local only attributes)", a->id, v->nodename, v->current); -- -- build = TRUE; -+ if (!(v->seen) && pcmk__str_eq(v->nodename, attrd_cluster->uname, -+ pcmk__str_casei)) { -+ if (sync == NULL) { -+ sync = create_xml_node(NULL, __func__); -+ crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -+ } - build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, - v->nodename, v->nodeid, v->current, (a->timeout_ms && a->timer ? TRUE : FALSE)); -- } else { -- crm_trace("Local attribute(%s[%s] = %s) was ignore.(another host) : [%s]", a->id, v->nodename, v->current, attrd_cluster->uname); -- continue; - } - } - } - -- if (build) { -- crm_debug("Syncing values to everyone.(from local only attributes)"); -+ if (sync != NULL) { -+ crm_debug("Broadcasting local-only values"); - send_attrd_message(NULL, sync); -+ free_xml(sync); - } -- free_xml(sync); - } - - /*! --- -1.8.3.1 - - -From ab90ffb785ea018556f216b8f540f8c3429a3947 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 11 Jun 2021 15:04:20 -0500 -Subject: [PATCH 10/11] Refactor: pacemaker-attrd: simplify attribute XML - creation function - -... and rename for clarity ---- - daemons/attrd/attrd_commands.c | 48 ++++++++++++++++++++++++------------------ - 1 file changed, 27 insertions(+), 21 deletions(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 356defb..5b32a77 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -125,25 +125,35 @@ cache_remote_node(const char *node_name) - CRM_ASSERT(crm_remote_peer_get(node_name) != NULL); - } - -+/*! -+ * \internal -+ * \brief Create an XML representation of an attribute for use in peer messages -+ * -+ * \param[in] parent Create attribute XML as child element of this element -+ * \param[in] a Attribute to represent -+ * \param[in] v Attribute value to represent -+ * \param[in] force_write If true, value should be written even if unchanged -+ * -+ * \return XML representation of attribute -+ */ - static xmlNode * --build_attribute_xml( -- xmlNode *parent, const char *name, const char *set, const char *uuid, unsigned int timeout_ms, const char *user, -- gboolean is_private, const char *peer, uint32_t peerid, const char *value, gboolean is_force_write) -+add_attribute_value_xml(xmlNode *parent, attribute_t *a, attribute_value_t *v, -+ bool force_write) - { - xmlNode *xml = create_xml_node(parent, __func__); - -- crm_xml_add(xml, PCMK__XA_ATTR_NAME, name); -- crm_xml_add(xml, PCMK__XA_ATTR_SET, set); -- crm_xml_add(xml, PCMK__XA_ATTR_UUID, uuid); -- crm_xml_add(xml, PCMK__XA_ATTR_USER, user); -- crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, peer); -- if (peerid > 0) { -- crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); -+ crm_xml_add(xml, PCMK__XA_ATTR_NAME, a->id); -+ crm_xml_add(xml, PCMK__XA_ATTR_SET, a->set); -+ crm_xml_add(xml, PCMK__XA_ATTR_UUID, a->uuid); -+ crm_xml_add(xml, PCMK__XA_ATTR_USER, a->user); -+ crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, v->nodename); -+ if (v->nodeid > 0) { -+ crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, v->nodeid); - } -- crm_xml_add(xml, PCMK__XA_ATTR_VALUE, value); -- crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, timeout_ms/1000); -- crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, is_private); -- crm_xml_add_int(xml, PCMK__XA_ATTR_FORCE, is_force_write); -+ crm_xml_add(xml, PCMK__XA_ATTR_VALUE, v->current); -+ crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, a->timeout_ms / 1000); -+ crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, a->is_private); -+ crm_xml_add_int(xml, PCMK__XA_ATTR_FORCE, force_write); - - return xml; - } -@@ -695,8 +705,7 @@ attrd_peer_sync(crm_node_t *peer, xmlNode *xml) - g_hash_table_iter_init(&vIter, a->values); - while (g_hash_table_iter_next(&vIter, NULL, (gpointer *) & v)) { - crm_debug("Syncing %s[%s] = %s to %s", a->id, v->nodename, v->current, peer?peer->uname:"everyone"); -- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, -- v->nodename, v->nodeid, v->current, FALSE); -+ add_attribute_value_xml(sync, a, v, false); - } - } - -@@ -788,8 +797,7 @@ broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml) - sync = create_xml_node(NULL, __func__); - crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); - } -- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, -- v->nodename, v->nodeid, v->current, (a->timeout_ms && a->timer ? TRUE : FALSE)); -+ add_attribute_value_xml(sync, a, v, a->timeout_ms && a->timer); - } - } - } -@@ -820,9 +828,7 @@ broadcast_local_value(attribute_t *a) - xmlNode *sync = create_xml_node(NULL, __func__); - - crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); -- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, -- a->user, a->is_private, v->nodename, v->nodeid, -- v->current, FALSE); -+ add_attribute_value_xml(sync, a, v, false); - attrd_xml_add_writer(sync); - send_attrd_message(NULL, sync); - free_xml(sync); --- -1.8.3.1 - - -From 540d74130c5c8d9c626d6c50475e4dc4f64234e7 Mon Sep 17 00:00:00 2001 -From: Ken Gaillot <kgaillot(a)redhat.com> -Date: Fri, 4 Jun 2021 16:34:26 -0500 -Subject: [PATCH 11/11] Fix: pacemaker-attrd: avoid repeated unfencing of - remote nodes - -The attribute manager can't record a remote node's attributes to the CIB until -it knows the node is remote. Normally, this is learned when the remote node -starts, because the controller clears the CRM_OP_PROBED attribute and indicates -that it is for a remote node. - -However, if a cluster node is down when a remote node starts, and later comes -up, it learns the remote node's existing attributes as part of the attribute -sync. Previously, this did not include whether each value is for a cluster or -remote node, so the newly joined attribute manager couldn't write out remote -nodes' attributes until it learned that via some other event -- which might not -happen before the node becomes DC, in which case its scheduler will not see any -unfencing-related node attributes and may wrongly schedule unfencing. - -The sync response handling already calls attrd_lookup_or_create_value(), which -checks PCMK__XA_ATTR_IS_REMOTE, so all we need to do is add that to the sync -response. ---- - daemons/attrd/attrd_commands.c | 6 +++++- - 1 file changed, 5 insertions(+), 1 deletion(-) - -diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c -index 5b32a77..0142383 100644 ---- a/daemons/attrd/attrd_commands.c -+++ b/daemons/attrd/attrd_commands.c -@@ -43,8 +43,9 @@ - * 1 1.1.15 PCMK__ATTRD_CMD_UPDATE_BOTH, - * PCMK__ATTRD_CMD_UPDATE_DELAY - * 2 1.1.17 PCMK__ATTRD_CMD_CLEAR_FAILURE -+ * 3 2.1.1 PCMK__ATTRD_CMD_SYNC_RESPONSE indicates remote nodes - */ --#define ATTRD_PROTOCOL_VERSION "2" -+#define ATTRD_PROTOCOL_VERSION "3" - - int last_cib_op_done = 0; - GHashTable *attributes = NULL; -@@ -150,6 +151,9 @@ add_attribute_value_xml(xmlNode *parent, attribute_t *a, attribute_value_t *v, - if (v->nodeid > 0) { - crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, v->nodeid); - } -+ if (v->is_remote != 0) { -+ crm_xml_add_int(xml, PCMK__XA_ATTR_IS_REMOTE, 1); -+ } - crm_xml_add(xml, PCMK__XA_ATTR_VALUE, v->current); - crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, a->timeout_ms / 1000); - crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, a->is_private); --- -1.8.3.1 - diff --git a/pacemaker.spec b/pacemaker.spec index a2a1dfb..b3f962b 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -31,11 +31,11 @@ ## Upstream pacemaker version, and its package version (specversion ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) -%global pcmkversion 2.1.0 -%global specversion 6 +%global pcmkversion 2.1.1 +%global specversion 0.1.rc1 ## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build -%global commit 7c3f660707a495a1331716ad32cd3ac9d9f8ff58 +%global commit 9e3a841a33c3125034922ec061f6516d307f20d1 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. @@ -80,7 +80,7 @@ ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) -%bcond_with pre_release +%bcond_without pre_release ## NOTE: skip --with upstart_job @@ -201,7 +201,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org/ @@ -217,13 +217,6 @@ Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{arch Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... # upstream commits -Patch1: 001-ping-agent.patch -Patch2: 002-pacemakerd-options.patch -Patch3: 003-pacemakerd-output.patch -Patch4: 004-check-level.patch -Patch5: 005-crm_resource.patch -Patch6: 006-crm_simulate.patch -Patch7: 007-unfencing-loop.patch Requires: resource-agents Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} @@ -806,6 +799,11 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Wed Jul 28 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.1-0.1.rc1 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.1-rc1, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.1-rc1 + * Thu Jul 22 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 2.1.0-6.1 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild diff --git a/sources b/sources index 2ab7f32..b933127 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-7c3f66070.tar.gz) = e1c53d019c965395affc1bd78358927617c9bc8572c405ee884737a8213455c5e85102e6f58bb5239ab23ebe5aa794f72c9cc0746900b7a6cc14fd3cf1879064 +SHA512 (pacemaker-9e3a841a3.tar.gz) = 26745ba0d9f6730de13ad106fe57beaff9d49c7df1ec528f0689c2faa872608408fb04401a4d49d73deec5422bd7665496a964b1fcbe69866a5983ac2306b6be commit 084488a3ae7b0d9112cb80ef1f9b0f7064fbcd72 Author: Fedora Release Engineering <releng(a)fedoraproject.org> Date: Thu Jul 22 17:33:56 2021 +0000 - Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild Signed-off-by: Fedora Release Engineering <releng(a)fedoraproject.org> diff --git a/pacemaker.spec b/pacemaker.spec index 48b6a44..a2a1dfb 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -201,7 +201,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist} +Release: %{pcmk_release}%{?dist}.1 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org/ @@ -806,6 +806,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Thu Jul 22 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 2.1.0-6.1 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Mon Jul 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-6 - synced/merged with CS9 spec-file for current 2.1.0-release build commit 15ac1a3c342218687bbddb1cdb2fc0edc968d5ac Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Jul 5 18:38:43 2021 +0200 * Mon Jul 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-6 - synced/merged with CS9 spec-file for current 2.1.0-release build * Tue Jun 8 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.5.rc3 - silence f33 s390x build complaining about possible format-trucation diff --git a/001-ping-agent.patch b/001-ping-agent.patch new file mode 100644 index 0000000..89fe41a --- /dev/null +++ b/001-ping-agent.patch @@ -0,0 +1,225 @@ +From c6ee0973522268ed7b3241cf0ec2e06398444114 Mon Sep 17 00:00:00 2001 +From: Grace Chin <gchin(a)redhat.com> +Date: Tue, 4 May 2021 12:02:17 -0400 +Subject: [PATCH 1/4] Remove deprecated attrd_options + +--- + extra/resources/ping | 11 +++-------- + 1 file changed, 3 insertions(+), 8 deletions(-) + +diff --git a/extra/resources/ping b/extra/resources/ping +index 3cf8dfe..2e93f22 100755 +--- a/extra/resources/ping ++++ b/extra/resources/ping +@@ -178,7 +178,7 @@ ping_stop() { + + rm -f "${OCF_RESKEY_pidfile}" + +- attrd_updater -D -n "$OCF_RESKEY_name" -d "$OCF_RESKEY_dampen" $attrd_options ++ attrd_updater -D -n "$OCF_RESKEY_name" -d "$OCF_RESKEY_dampen" + + return $OCF_SUCCESS + } +@@ -302,9 +302,9 @@ ping_update() { + + score=$(expr $active \* $OCF_RESKEY_multiplier) + if [ "$__OCF_ACTION" = "start" ] ; then +- attrd_updater -n "$OCF_RESKEY_name" -B "$score" -d "$OCF_RESKEY_dampen" $attrd_options ++ attrd_updater -n "$OCF_RESKEY_name" -B "$score" -d "$OCF_RESKEY_dampen" + else +- attrd_updater -n "$OCF_RESKEY_name" -v "$score" -d "$OCF_RESKEY_dampen" $attrd_options ++ attrd_updater -n "$OCF_RESKEY_name" -v "$score" -d "$OCF_RESKEY_dampen" + fi + rc=$? + case $rc in +@@ -396,11 +396,6 @@ case "${OCF_RESKEY_debug}" in + ;; + esac + +-attrd_options='-q' +-if [ "${OCF_RESKEY_debug}" = "true" ]; then +- attrd_options='' +-fi +- + case "$__OCF_ACTION" in + meta-data) meta_data + exit $OCF_SUCCESS +-- +1.8.3.1 + + +From 6d6c4691cf0970059689856c354daf9e098b4451 Mon Sep 17 00:00:00 2001 +From: Grace Chin <gchin(a)redhat.com> +Date: Tue, 4 May 2021 14:50:37 -0400 +Subject: [PATCH 2/4] Replace debug values, true and false, with 0 and 1 + +--- + extra/resources/ping | 8 ++++---- + 1 file changed, 4 insertions(+), 4 deletions(-) + +diff --git a/extra/resources/ping b/extra/resources/ping +index 2e93f22..fee019b 100755 +--- a/extra/resources/ping ++++ b/extra/resources/ping +@@ -24,7 +24,7 @@ + : ${OCF_RESKEY_dampen:="5s"} + : ${OCF_RESKEY_attempts:="3"} + : ${OCF_RESKEY_multiplier:="1"} +-: ${OCF_RESKEY_debug:="false"} ++: ${OCF_RESKEY_debug:="0"} + : ${OCF_RESKEY_failure_score:="0"} + : ${OCF_RESKEY_use_fping:="1"} + : ${OCF_RESKEY_host_list:=""} +@@ -152,7 +152,7 @@ END + + ping_conditional_log() { + level="$1"; shift +- if [ "${OCF_RESKEY_debug}" = "true" ]; then ++ if [ $OCF_RESKEY_debug -gt 0 ]; then + ocf_log "$level" "$*" + fi + } +@@ -388,8 +388,8 @@ fi + + # Check the debug option + case "${OCF_RESKEY_debug}" in +- true|True|TRUE|1) OCF_RESKEY_debug=true;; +- false|False|FALSE|0) OCF_RESKEY_debug=false;; ++ true|True|TRUE|1) OCF_RESKEY_debug=0;; ++ false|False|FALSE|0) OCF_RESKEY_debug=1;; + *) + ocf_log warn "Value for 'debug' is incorrect. Please specify 'true' or 'false' not: ${OCF_RESKEY_debug}" + OCF_RESKEY_debug=false +-- +1.8.3.1 + + +From a886a31056b6aca764c6911f5432af2c5ebf51df Mon Sep 17 00:00:00 2001 +From: Grace Chin <gchin(a)redhat.com> +Date: Tue, 11 May 2021 11:04:50 -0400 +Subject: [PATCH 3/4] Add verbose debug mode which logs ping and fping output + when set + +--- + extra/resources/ping | 19 ++++++++++++++----- + 1 file changed, 14 insertions(+), 5 deletions(-) + +diff --git a/extra/resources/ping b/extra/resources/ping +index fee019b..cc796af 100755 +--- a/extra/resources/ping ++++ b/extra/resources/ping +@@ -249,10 +249,13 @@ fping_check() { + + case $rc in + 0) ++ if [ $OCF_RESKEY_debug -gt 1 ]; then ++ ping_conditional_log info "$output" ++ fi + ;; + 1) + for h in $(echo "$output" | grep "is unreachable" | awk '{print $1}'); do +- ping_conditional_log warn "$h is inactive" ++ ping_conditional_log warn "$h is inactive: $output" + done + ;; + *) +@@ -282,7 +285,12 @@ ping_check() { + p_out=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? + + case $rc in +- 0) active=$(expr $active + 1);; ++ 0) ++ active=$(expr $active + 1) ++ if [ $OCF_RESKEY_debug -gt 1 ]; then ++ ping_conditional_log info "$p_out" ++ fi ++ ;; + 1) ping_conditional_log warn "$host is inactive: $p_out";; + *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $p_out";; + esac +@@ -388,10 +396,11 @@ fi + + # Check the debug option + case "${OCF_RESKEY_debug}" in +- true|True|TRUE|1) OCF_RESKEY_debug=0;; +- false|False|FALSE|0) OCF_RESKEY_debug=1;; ++ true|True|TRUE|1) OCF_RESKEY_debug=1;; ++ false|False|FALSE|0) OCF_RESKEY_debug=0;; ++ verbose|Verbose|VERBOSE|2) OCF_RESKEY_debug=2;; + *) +- ocf_log warn "Value for 'debug' is incorrect. Please specify 'true' or 'false' not: ${OCF_RESKEY_debug}" ++ ocf_log warn "Value for 'debug' is incorrect. Please specify 'true', 'false', or 'verbose', not: ${OCF_RESKEY_debug}" + OCF_RESKEY_debug=false + ;; + esac +-- +1.8.3.1 + + +From 460043f133ced80e923b1290af70502a72deb7f8 Mon Sep 17 00:00:00 2001 +From: Grace Chin <gchin(a)redhat.com> +Date: Tue, 11 May 2021 11:07:05 -0400 +Subject: [PATCH 4/4] Improve variable names + +--- + extra/resources/ping | 20 ++++++++++---------- + 1 file changed, 10 insertions(+), 10 deletions(-) + +diff --git a/extra/resources/ping b/extra/resources/ping +index cc796af..9763b60 100755 +--- a/extra/resources/ping ++++ b/extra/resources/ping +@@ -244,22 +244,22 @@ fping_check() { + timeout=$(expr $OCF_RESKEY_timeout \* 1000 / $OCF_RESKEY_attempts) + + cmd="$p_exe -r $OCF_RESKEY_attempts -t $timeout -B 1.0 $OCF_RESKEY_options $OCF_RESKEY_host_list" +- output=$($cmd 2>&1); rc=$? +- active=$(echo "$output" | grep "is alive" | wc -l) ++ fping_output=$($cmd 2>&1); rc=$? ++ active=$(echo "$fping_output" | grep "is alive" | wc -l) + + case $rc in + 0) + if [ $OCF_RESKEY_debug -gt 1 ]; then +- ping_conditional_log info "$output" ++ ping_conditional_log info "$fping_output" + fi + ;; + 1) +- for h in $(echo "$output" | grep "is unreachable" | awk '{print $1}'); do +- ping_conditional_log warn "$h is inactive: $output" ++ for h in $(echo "$fping_output" | grep "is unreachable" | awk '{print $1}'); do ++ ping_conditional_log warn "$h is inactive: $fping_output" + done + ;; + *) +- ocf_log err "Unexpected result for '$cmd' $rc: $(echo "$output" | tr '\n' ';')" ++ ocf_log err "Unexpected result for '$cmd' $rc: $(echo "$fping_output" | tr '\n' ';')" + ;; + esac + +@@ -282,17 +282,17 @@ ping_check() { + *:*) p_exe=ping6 + esac + +- p_out=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? ++ ping_output=$($p_exe $p_args $OCF_RESKEY_options $host 2>&1); rc=$? + + case $rc in + 0) + active=$(expr $active + 1) + if [ $OCF_RESKEY_debug -gt 1 ]; then +- ping_conditional_log info "$p_out" ++ ping_conditional_log info "$ping_output" + fi + ;; +- 1) ping_conditional_log warn "$host is inactive: $p_out";; +- *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $p_out";; ++ 1) ping_conditional_log warn "$host is inactive: $ping_output";; ++ *) ocf_log err "Unexpected result for '$p_exe $p_args $OCF_RESKEY_options $host' $rc: $ping_output";; + esac + done + return $active +-- +1.8.3.1 + diff --git a/002-pacemakerd-options.patch b/002-pacemakerd-options.patch new file mode 100644 index 0000000..56941ec --- /dev/null +++ b/002-pacemakerd-options.patch @@ -0,0 +1,451 @@ +From 0d40ebf10b1794ece2c5c9768ea7222d3834d3b3 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 13 May 2021 11:42:18 -0400 +Subject: [PATCH 1/4] Build: Use a different variable to find man page + includes. + +With other programs outside of the tools directory being converted to +use glib for command line handling, their includes are not going to be +in tools/. So we need to use a different autoconf variable to find +them. +--- + mk/common.mk | 6 +++--- + 1 file changed, 3 insertions(+), 3 deletions(-) + +diff --git a/mk/common.mk b/mk/common.mk +index b247670..aa59feb 100644 +--- a/mk/common.mk ++++ b/mk/common.mk +@@ -1,5 +1,5 @@ + # +-# Copyright 2014-2020 the Pacemaker project contributors ++# Copyright 2014-2021 the Pacemaker project contributors + # + # The version control history for this file may have further details. + # +@@ -68,11 +68,11 @@ HELP2MAN_ARGS = -N --section 8 --name "Part of the Pacemaker cluster resource ma + # and all wrappers to C code. + %.8: % $(MAN8DEPS) + $(AM_V_at)chmod a+x $(abs_builddir)/$< +- $(AM_V_MAN)if [ -f $(top_srcdir)/tools/$@.inc ]; then \ ++ $(AM_V_MAN)if [ -f $(abs_srcdir)/$@.inc ]; then \ + PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ + -h --help-all \ + --no-discard-stderr \ +- -i $(top_srcdir)/tools/$@.inc $(abs_builddir)/$< \ ++ -i $(abs_srcdir)/$@.inc $(abs_builddir)/$< \ + | sed -f $(top_srcdir)/tools/fix-manpages > $@ ; \ + else \ + PATH=$(abs_builddir):$$PATH $(HELP2MAN) $(HELP2MAN_ARGS) \ +-- +1.8.3.1 + + +From c7ab1d901bcbbf0137277e783e072777ca2f82d9 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 13 May 2021 11:44:16 -0400 +Subject: [PATCH 2/4] Refactor: daemons: Remove the pid_file variable from + pacemakerd. + +It's never used anywhere. +--- + daemons/pacemakerd/pacemakerd.c | 3 --- + 1 file changed, 3 deletions(-) + +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index 8ec9708..03d688e 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -27,8 +27,7 @@ + + static crm_trigger_t *shutdown_trigger = NULL; + static crm_trigger_t *startup_trigger = NULL; +-static const char *pid_file = PCMK_RUN_DIR "/pacemaker.pid"; + + /* state we report when asked via pacemakerd-api status-ping */ + static const char *pacemakerd_state = XML_PING_ATTR_PACEMAKERDSTATE_INIT; + static gboolean running_with_sbd = FALSE; /* local copy */ +@@ -224,7 +222,6 @@ main(int argc, char **argv) + /* Legacy */ + break; + case 'p': +- pid_file = optarg; + break; + case 's': + pcmk__set_env_option("node_start_state", "standby"); +-- +1.8.3.1 + + +From 98990eed9f6a5dbde7c8a5aa0783e93d5479295b Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 13 May 2021 13:14:38 -0400 +Subject: [PATCH 3/4] Refactor: daemons: Use glib for command line handling in + pacemakerd. + +--- + daemons/pacemakerd/Makefile.am | 2 + + daemons/pacemakerd/pacemakerd.8.inc | 5 + + daemons/pacemakerd/pacemakerd.c | 195 ++++++++++++++++++------------------ + 3 files changed, 102 insertions(+), 100 deletions(-) + create mode 100644 daemons/pacemakerd/pacemakerd.8.inc + +diff --git a/daemons/pacemakerd/Makefile.am b/daemons/pacemakerd/Makefile.am +index cc657f5..84517a3 100644 +--- a/daemons/pacemakerd/Makefile.am ++++ b/daemons/pacemakerd/Makefile.am +@@ -15,6 +15,8 @@ if BUILD_SYSTEMD + systemdsystemunit_DATA = pacemaker.service + endif + ++EXTRA_DIST = pacemakerd.8.inc ++ + ## SOURCES + + noinst_HEADERS = pacemakerd.h +diff --git a/daemons/pacemakerd/pacemakerd.8.inc b/daemons/pacemakerd/pacemakerd.8.inc +new file mode 100644 +index 0000000..902af4e +--- /dev/null ++++ b/daemons/pacemakerd/pacemakerd.8.inc +@@ -0,0 +1,5 @@ ++[synopsis] ++pacemakerd [options] ++ ++/subsidiary Pacemaker daemons/ ++.SH OPTIONS +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index 03d688e..ce194bf 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -23,12 +23,54 @@ + #include <crm/msg_xml.h> + #include <crm/common/ipc_internal.h> + #include <crm/common/mainloop.h> ++#include <crm/common/cmdline_internal.h> + #include <crm/cluster/internal.h> + #include <crm/cluster.h> + + #include <dirent.h> + #include <ctype.h> + ++#define SUMMARY "pacemakerd - primary Pacemaker daemon that launches and monitors all subsidiary Pacemaker daemons" ++ ++struct { ++ gboolean features; ++ gboolean foreground; ++ gboolean shutdown; ++ gboolean standby; ++} options; ++ ++static gboolean ++pid_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { ++ return TRUE; ++} ++ ++static gboolean ++standby_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { ++ options.standby = TRUE; ++ pcmk__set_env_option("node_start_state", "standby"); ++ return TRUE; ++} ++ ++static GOptionEntry entries[] = { ++ { "features", 'F', 0, G_OPTION_ARG_NONE, &options.features, ++ "Display full version and list of features Pacemaker was built with", ++ NULL }, ++ { "foreground", 'f', 0, G_OPTION_ARG_NONE, &options.foreground, ++ "(Ignored) Pacemaker always runs in the foreground", ++ NULL }, ++ { "pid-file", 'p', 0, G_OPTION_ARG_CALLBACK, pid_cb, ++ "(Ignored) Daemon pid file location", ++ "FILE" }, ++ { "shutdown", 'S', 0, G_OPTION_ARG_NONE, &options.shutdown, ++ "Instruct Pacemaker to shutdown on this machine", ++ NULL }, ++ { "standby", 's', G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, standby_cb, ++ "Start node in standby state", ++ NULL }, ++ ++ { NULL } ++}; ++ + static gboolean fatal_error = FALSE; + static GMainLoop *mainloop = NULL; + static bool global_keep_tracking = false; +@@ -642,49 +685,6 @@ pcmk_sigquit(int nsig) + .connection_destroyed = pcmk_ipc_destroy + }; + +-static pcmk__cli_option_t long_options[] = { +- // long option, argument type, storage, short option, description, flags +- { +- "help", no_argument, NULL, '?', +- "\tThis text", pcmk__option_default +- }, +- { +- "version", no_argument, NULL, '$', +- "\tVersion information", pcmk__option_default +- }, +- { +- "verbose", no_argument, NULL, 'V', +- "\tIncrease debug output", pcmk__option_default +- }, +- { +- "shutdown", no_argument, NULL, 'S', +- "\tInstruct Pacemaker to shutdown on this machine", pcmk__option_default +- }, +- { +- "features", no_argument, NULL, 'F', +- "\tDisplay full version and list of features Pacemaker was built with", +- pcmk__option_default +- }, +- { +- "-spacer-", no_argument, NULL, '-', +- "\nAdditional Options:", pcmk__option_default +- }, +- { +- "foreground", no_argument, NULL, 'f', +- "\t(Ignored) Pacemaker always runs in the foreground", +- pcmk__option_default +- }, +- { +- "pid-file", required_argument, NULL, 'p', +- "\t(Ignored) Daemon pid file location", pcmk__option_default +- }, +- { +- "standby", no_argument, NULL, 's', +- "\tStart node in standby state", pcmk__option_default +- }, +- { 0, 0, 0, 0 } +-}; +- + static void + mcp_chown(const char *path, uid_t uid, gid_t gid) + { +@@ -1168,83 +1211,66 @@ request_shutdown(crm_ipc_t *ipc) + return status; + } + ++static GOptionContext * ++build_arg_context(pcmk__common_args_t *args) { ++ GOptionContext *context = NULL; ++ ++ context = pcmk__build_arg_context(args, NULL, NULL, NULL); ++ pcmk__add_main_args(context, entries); ++ return context; ++} ++ + int + main(int argc, char **argv) + { +- int flag; +- int argerr = 0; ++ crm_exit_t exit_code = CRM_EX_OK; ++ ++ GError *error = NULL; ++ ++ pcmk__common_args_t *args = pcmk__new_common_args(SUMMARY); ++ gchar **processed_args = pcmk__cmdline_preproc(argv, "p"); ++ GOptionContext *context = build_arg_context(args); + +- int option_index = 0; + bool old_instance_connected = false; +- gboolean shutdown = FALSE; + + crm_ipc_t *old_instance = NULL; + qb_ipcs_service_t *ipcs = NULL; + + crm_log_preinit(NULL, argc, argv); +- pcmk__set_cli_options(NULL, "[options]", long_options, +- "primary Pacemaker daemon that launches and " +- "monitors all subsidiary Pacemaker daemons"); + mainloop_add_signal(SIGHUP, pcmk_ignore); + mainloop_add_signal(SIGQUIT, pcmk_sigquit); + +- while (1) { +- flag = pcmk__next_cli_option(argc, argv, &option_index, NULL); +- if (flag == -1) +- break; +- +- switch (flag) { +- case 'V': +- crm_bump_log_level(argc, argv); +- break; +- case 'f': +- /* Legacy */ +- break; +- case 'p': +- break; +- case 's': +- pcmk__set_env_option("node_start_state", "standby"); +- break; +- case '$': +- case '?': +- pcmk__cli_help(flag, CRM_EX_OK); +- break; +- case 'S': +- shutdown = TRUE; +- break; +- case 'F': +- printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, +- CRM_FEATURE_SET, CRM_FEATURES); +- crm_exit(CRM_EX_OK); +- default: +- printf("Argument code 0%o (%c) is not (?yet?) supported\n", flag, flag); +- ++argerr; +- break; +- } ++ if (!g_option_context_parse_strv(context, &processed_args, &error)) { ++ exit_code = CRM_EX_USAGE; ++ goto done; + } + +- if (optind < argc) { +- printf("non-option ARGV-elements: "); +- while (optind < argc) +- printf("%s ", argv[optind++]); +- printf("\n"); +- } +- if (argerr) { +- pcmk__cli_help('?', CRM_EX_USAGE); ++ if (options.features) { ++ printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, ++ CRM_FEATURE_SET, CRM_FEATURES); ++ exit_code = CRM_EX_OK; ++ goto done; + } + ++ if (args->version) { ++ g_strfreev(processed_args); ++ pcmk__free_arg_context(context); ++ /* FIXME: When pacemakerd is converted to use formatted output, this can go. */ ++ pcmk__cli_help('v', CRM_EX_USAGE); ++ } + + setenv("LC_ALL", "C", 1); + + pcmk__set_env_option("mcp", "true"); + ++ pcmk__cli_init_logging("pacemakerd", args->verbosity); + crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); + + crm_debug("Checking for existing Pacemaker instance"); + old_instance = crm_ipc_new(CRM_SYSTEM_MCP, 0); + old_instance_connected = crm_ipc_connect(old_instance); + +- if (shutdown) { ++ if (options.shutdown) { + if (old_instance_connected) { + crm_exit(request_shutdown(old_instance)); + } else { +@@ -1253,22 +1279,25 @@ main(int argc, char **argv) + "Pacemaker instance: %s", strerror(errno)); + crm_ipc_close(old_instance); + crm_ipc_destroy(old_instance); +- crm_exit(CRM_EX_DISCONNECT); ++ exit_code = CRM_EX_DISCONNECT; ++ goto done; + } + + } else if (old_instance_connected) { + crm_ipc_close(old_instance); + crm_ipc_destroy(old_instance); + crm_err("Aborting start-up because active Pacemaker instance found"); +- crm_exit(CRM_EX_FATAL); ++ exit_code = CRM_EX_FATAL; ++ goto done; + } + + crm_ipc_close(old_instance); + crm_ipc_destroy(old_instance); + + #ifdef SUPPORT_COROSYNC + if (mcp_read_config() == FALSE) { +- crm_exit(CRM_EX_UNAVAILABLE); ++ exit_code = CRM_EX_UNAVAILABLE; ++ goto done; + } + #endif + +@@ -1292,7 +1321,8 @@ main(int argc, char **argv) + #ifdef SUPPORT_COROSYNC + /* Allows us to block shutdown */ + if (!cluster_connect_cfg()) { +- crm_exit(CRM_EX_PROTOCOL); ++ exit_code = CRM_EX_PROTOCOL; ++ goto done; + } + #endif + +@@ -1307,9 +1337,11 @@ main(int argc, char **argv) + case pcmk_rc_ok: + break; + case pcmk_rc_ipc_unauthorized: +- crm_exit(CRM_EX_CANTCREAT); ++ exit_code = CRM_EX_CANTCREAT; ++ goto done; + default: +- crm_exit(CRM_EX_FATAL); ++ exit_code = CRM_EX_FATAL; ++ goto done; + }; + + mainloop_add_signal(SIGTERM, pcmk_shutdown); +@@ -1342,5 +1374,11 @@ main(int argc, char **argv) + #ifdef SUPPORT_COROSYNC + cluster_disconnect_cfg(); + #endif +- crm_exit(CRM_EX_OK); ++ ++done: ++ g_strfreev(processed_args); ++ pcmk__free_arg_context(context); ++ ++ pcmk__output_and_clear_error(error, NULL); ++ crm_exit(exit_code); + } +-- +1.8.3.1 + + +From 8f7924fbb2a012bedcad59335b7bebc5020b26e3 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 13 May 2021 13:27:13 -0400 +Subject: [PATCH 4/4] Low: pacemaker.service: Don't start pacemakerd with -f. + +This option is completely ignored by pacemakerd. +--- + daemons/pacemakerd/pacemaker.service.in | 2 +- + doc/sphinx/Clusters_from_Scratch/verification.rst | 2 +- + 2 files changed, 2 insertions(+), 2 deletions(-) + +diff --git a/daemons/pacemakerd/pacemaker.service.in b/daemons/pacemakerd/pacemaker.service.in +index b128ddc..0363a22 100644 +--- a/daemons/pacemakerd/pacemaker.service.in ++++ b/daemons/pacemakerd/pacemaker.service.in +@@ -44,7 +44,7 @@ EnvironmentFile=-@CONFIGDIR@/pacemaker + EnvironmentFile=-@CONFIGDIR@/sbd + SuccessExitStatus=100 + +-ExecStart=@sbindir@/pacemakerd -f ++ExecStart=@sbindir@/pacemakerd + + # Systemd v227 and above can limit the number of processes spawned by a + # service. That is a bad idea for an HA cluster resource manager, so disable it +diff --git a/doc/sphinx/Clusters_from_Scratch/verification.rst b/doc/sphinx/Clusters_from_Scratch/verification.rst +index 9d647f8..b7fa20e 100644 +--- a/doc/sphinx/Clusters_from_Scratch/verification.rst ++++ b/doc/sphinx/Clusters_from_Scratch/verification.rst +@@ -103,7 +103,7 @@ the necessary processes are running: + 2 ? S 0:00 [kthreadd] + ...lots of processes... + 17121 ? SLsl 0:01 /usr/sbin/corosync -f +- 17133 ? Ss 0:00 /usr/sbin/pacemakerd -f ++ 17133 ? Ss 0:00 /usr/sbin/pacemakerd + 17134 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-based + 17135 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-fenced + 17136 ? Ss 0:00 \_ /usr/libexec/pacemaker/pacemaker-execd +-- +1.8.3.1 + diff --git a/003-pacemakerd-output.patch b/003-pacemakerd-output.patch new file mode 100644 index 0000000..167e22b --- /dev/null +++ b/003-pacemakerd-output.patch @@ -0,0 +1,343 @@ +From 7c35387a9896cb968cf4087b5cbed94af44e1ea5 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 14 May 2021 12:03:46 -0400 +Subject: [PATCH 1/5] Feature: daemons: Convert pacemakerd to formatted output. + +The main purpose of this is to finish getting pacemakerd moved off the +existing command line handling code (pcmk__cli_help in particular) so +that code can eventually be deprecated or removed. pacemakerd itself +does fairly little printing. +--- + daemons/pacemakerd/pacemakerd.c | 58 ++++++++++++++++++++++++++++++----------- + 1 file changed, 43 insertions(+), 15 deletions(-) + +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index ce194bf..bd59729 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -25,6 +25,7 @@ + #include <crm/common/ipc_internal.h> + #include <crm/common/mainloop.h> + #include <crm/common/cmdline_internal.h> ++#include <crm/common/output_internal.h> + #include <crm/cluster/internal.h> + #include <crm/cluster.h> + +@@ -37,6 +38,14 @@ struct { + gboolean standby; + } options; + ++static pcmk__output_t *out = NULL; ++ ++static pcmk__supported_format_t formats[] = { ++ PCMK__SUPPORTED_FORMAT_NONE, ++ PCMK__SUPPORTED_FORMAT_TEXT, ++ { NULL, NULL, NULL } ++}; ++ + static gboolean + pid_cb(const gchar *option_name, const gchar *optarg, gpointer data, GError **err) { + return TRUE; +@@ -1167,10 +1176,10 @@ pacemakerd_event_cb(pcmk_ipc_api_t *pacemakerd_api, + } + + static GOptionContext * +-build_arg_context(pcmk__common_args_t *args) { ++build_arg_context(pcmk__common_args_t *args, GOptionGroup **group) { + GOptionContext *context = NULL; + +- context = pcmk__build_arg_context(args, NULL, NULL, NULL); ++ context = pcmk__build_arg_context(args, "text", group, NULL); + pcmk__add_main_args(context, entries); + return context; + } +@@ -1182,9 +1191,11 @@ main(int argc, char **argv) + + GError *error = NULL; + ++ int rc = pcmk_rc_ok; ++ GOptionGroup *output_group = NULL; + pcmk__common_args_t *args = pcmk__new_common_args(SUMMARY); + gchar **processed_args = pcmk__cmdline_preproc(argv, "p"); +- GOptionContext *context = build_arg_context(args); ++ GOptionContext *context = build_arg_context(args, &output_group); + + bool old_instance_connected = false; + +@@ -1195,23 +1205,30 @@ main(int argc, char **argv) + mainloop_add_signal(SIGHUP, pcmk_ignore); + mainloop_add_signal(SIGQUIT, pcmk_sigquit); + ++ pcmk__register_formats(output_group, formats); + if (!g_option_context_parse_strv(context, &processed_args, &error)) { + exit_code = CRM_EX_USAGE; + goto done; + } + ++ rc = pcmk__output_new(&out, args->output_ty, args->output_dest, argv); ++ if (rc != pcmk_rc_ok) { ++ exit_code = CRM_EX_ERROR; ++ g_set_error(&error, PCMK__EXITC_ERROR, exit_code, "Error creating output format %s: %s", ++ args->output_ty, pcmk_rc_str(rc)); ++ goto done; ++ } ++ + if (options.features) { +- printf("Pacemaker %s (Build: %s)\n Supporting v%s: %s\n", PACEMAKER_VERSION, BUILD_VERSION, +- CRM_FEATURE_SET, CRM_FEATURES); ++ out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, ++ BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); + exit_code = CRM_EX_OK; + goto done; + } + + if (args->version) { +- g_strfreev(processed_args); +- pcmk__free_arg_context(context); +- /* FIXME: When pacemakerd is converted to use formatted output, this can go. */ +- pcmk__cli_help('v', CRM_EX_USAGE); ++ out->version(out, false); ++ goto done; + } + + setenv("LC_ALL", "C", 1); +@@ -1248,6 +1265,13 @@ main(int argc, char **argv) + crm_ipc_close(old_instance); + crm_ipc_destroy(old_instance); + ++ /* Don't allow any accidental output after this point. */ ++ if (out != NULL) { ++ out->finish(out, exit_code, true, NULL); ++ pcmk__output_free(out); ++ out = NULL; ++ } ++ + #ifdef SUPPORT_COROSYNC + if (mcp_read_config() == FALSE) { + exit_code = CRM_EX_UNAVAILABLE; +@@ -1333,6 +1357,11 @@ done: + g_strfreev(processed_args); + pcmk__free_arg_context(context); + +- pcmk__output_and_clear_error(error, NULL); ++ pcmk__output_and_clear_error(error, out); ++ ++ if (out != NULL) { ++ out->finish(out, exit_code, true, NULL); ++ pcmk__output_free(out); ++ } + crm_exit(exit_code); + } +-- +1.8.3.1 + + +From 35e6da64381fcb092d81ce16835cc28670b077cb Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 17 May 2021 10:04:04 -0400 +Subject: [PATCH 2/5] Features: daemons: Output the pacemakerd feature list in + XML. + +--- + daemons/pacemakerd/pacemakerd.c | 45 ++++++++++++++++++++++++++++++++++++++--- + 1 file changed, 42 insertions(+), 3 deletions(-) + +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index bd59729..93cf743 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -43,6 +43,42 @@ static pcmk__output_t *out = NULL; + static pcmk__supported_format_t formats[] = { + PCMK__SUPPORTED_FORMAT_NONE, + PCMK__SUPPORTED_FORMAT_TEXT, ++ PCMK__SUPPORTED_FORMAT_XML, ++ { NULL, NULL, NULL } ++}; ++ ++static int ++pacemakerd_features(pcmk__output_t *out, va_list args) { ++ out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, ++ BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); ++ return pcmk_rc_ok; ++} ++ ++static int ++pacemakerd_features_xml(pcmk__output_t *out, va_list args) { ++ gchar **feature_list = g_strsplit(CRM_FEATURES, " ", 0); ++ ++ pcmk__output_xml_create_parent(out, "pacemakerd", ++ "version", PACEMAKER_VERSION, ++ "build", BUILD_VERSION, ++ "feature_set", CRM_FEATURE_SET, ++ NULL); ++ out->begin_list(out, NULL, NULL, "features"); ++ ++ for (char **s = feature_list; *s != NULL; s++) { ++ pcmk__output_create_xml_text_node(out, "feature", *s); ++ } ++ ++ out->end_list(out); ++ ++ g_strfreev(feature_list); ++ return pcmk_rc_ok; ++} ++ ++static pcmk__message_entry_t fmt_functions[] = { ++ { "features", "default", pacemakerd_features }, ++ { "features", "xml", pacemakerd_features_xml }, ++ + { NULL, NULL, NULL } + }; + +@@ -200,7 +236,7 @@ static GOptionContext * + build_arg_context(pcmk__common_args_t *args, GOptionGroup **group) { + GOptionContext *context = NULL; + +- context = pcmk__build_arg_context(args, "text", group, NULL); ++ context = pcmk__build_arg_context(args, "text (default), xml", group, NULL); + pcmk__add_main_args(context, entries); + return context; + } +@@ -241,9 +277,12 @@ main(int argc, char **argv) + goto done; + } + ++ pcmk__force_args(context, &error, "%s --xml-simple-list", g_get_prgname()); ++ ++ pcmk__register_messages(out, fmt_functions); ++ + if (options.features) { +- out->info(out, "Pacemaker %s (Build: %s)\n Supporting v%s: %s", PACEMAKER_VERSION, +- BUILD_VERSION, CRM_FEATURE_SET, CRM_FEATURES); ++ out->message(out, "features"); + exit_code = CRM_EX_OK; + goto done; + } +-- +1.8.3.1 + + +From 5b7f5eb35b025b59805cf3c7c3dcb6a3cf4b71b3 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 17 May 2021 11:09:53 -0400 +Subject: [PATCH 3/5] Low: daemons: Conditionally enable logging in pacemakerd. + +If we're doing an interactive command-line call, use +pcmk__cli_init_logging. At the moment, all command line calls except +for --shutdown do their work before logging would even come up, so we +really only need to do this for --shutdown. + +If we're doing a daemon call, use crm_log_init. +--- + daemons/pacemakerd/pacemakerd.c | 7 +++++-- + 1 file changed, 5 insertions(+), 2 deletions(-) + +diff --git a/daemons/pacemakerd/pacemakerd.c b/daemons/pacemakerd/pacemakerd.c +index 93cf743..c20bde7 100644 +--- a/daemons/pacemakerd/pacemakerd.c ++++ b/daemons/pacemakerd/pacemakerd.c +@@ -296,8 +296,11 @@ main(int argc, char **argv) + + pcmk__set_env_option("mcp", "true"); + +- pcmk__cli_init_logging("pacemakerd", args->verbosity); +- crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); ++ if (options.shutdown) { ++ pcmk__cli_init_logging("pacemakerd", args->verbosity); ++ } else { ++ crm_log_init(NULL, LOG_INFO, TRUE, FALSE, argc, argv, FALSE); ++ } + + crm_debug("Checking for existing Pacemaker instance"); + old_instance = crm_ipc_new(CRM_SYSTEM_MCP, 0); +-- +1.8.3.1 + + +From 2393362bb7489e86d937ed46a1c5cfb93d9bf3ab Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 17 May 2021 11:58:06 -0400 +Subject: [PATCH 4/5] Fix: include: Bump CRM_FEATURE_SET for new pacemakerd + args. + +--- + include/crm/crm.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/crm/crm.h b/include/crm/crm.h +index fdfc825..92a98fa 100644 +--- a/include/crm/crm.h ++++ b/include/crm/crm.h +@@ -66,7 +66,7 @@ extern "C" { + * >=3.0.13: Fail counts include operation name and interval + * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED + */ +-# define CRM_FEATURE_SET "3.10.0" ++# define CRM_FEATURE_SET "3.10.1" + + /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and + * recipient of a CPG message. This imposes an arbitrary limit on cluster node +-- +1.8.3.1 + + +From 3ad8edbd91631b87ef5f53fa2d68f0c8bbb9ee2b Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 17 May 2021 11:57:09 -0400 +Subject: [PATCH 5/5] Feature: xml: Add schema for pacemakerd. + +--- + xml/Makefile.am | 1 + + xml/api/pacemakerd-2.10.rng | 28 ++++++++++++++++++++++++++++ + 2 files changed, 29 insertions(+) + create mode 100644 xml/api/pacemakerd-2.10.rng + +diff --git a/xml/Makefile.am b/xml/Makefile.am +index 12a51c5..b9448d4 100644 +--- a/xml/Makefile.am ++++ b/xml/Makefile.am +@@ -56,6 +56,7 @@ API_request_base = command-output \ + crm_simulate \ + crmadmin \ + digests \ ++ pacemakerd \ + stonith_admin \ + version + +diff --git a/xml/api/pacemakerd-2.10.rng b/xml/api/pacemakerd-2.10.rng +new file mode 100644 +index 0000000..41a11e7 +--- /dev/null ++++ b/xml/api/pacemakerd-2.10.rng +@@ -0,0 +1,28 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="element-pacemakerd"/> ++ </start> ++ ++ <define name="element-pacemakerd"> ++ <element name="pacemakerd"> ++ <attribute name="version"> <text /> </attribute> ++ <attribute name="build"> <text /> </attribute> ++ <attribute name="feature_set"> <text /> </attribute> ++ ++ <optional> ++ <ref name="feature-list" /> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="feature-list"> ++ <element name="features"> ++ <oneOrMore> ++ <element name="feature"> <text/> </element> ++ </oneOrMore> ++ </element> ++ </define> ++</grammar> +-- +1.8.3.1 + diff --git a/004-check-level.patch b/004-check-level.patch new file mode 100644 index 0000000..f2abb5f --- /dev/null +++ b/004-check-level.patch @@ -0,0 +1,199 @@ +From 3905e7eac11298fc20efd567a773666f948edf61 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 3 May 2021 11:19:04 -0400 +Subject: [PATCH 1/2] Feature: tools: Add OCF_CHECK_LEVEL to crm_resource + environment. + +If --validate= or --force-check= are given with a level, pass that along +as OCF_CHECK_LEVEL. This argument is optional, and if no value is given +then the environment variable will not be set and whatever's the default +on the resource agent will be used. + +See: rhbz#1955792. +--- + tools/crm_resource.c | 29 +++++++++++++++++++++-------- + tools/crm_resource.h | 4 ++-- + tools/crm_resource_runtime.c | 13 ++++++++++--- + 3 files changed, 33 insertions(+), 13 deletions(-) + +diff --git a/tools/crm_resource.c b/tools/crm_resource.c +index 45db2b2..6ca96f8 100644 +--- a/tools/crm_resource.c ++++ b/tools/crm_resource.c +@@ -100,6 +100,7 @@ struct { + int timeout_ms; // Parsed from --timeout value + char *agent_spec; // Standard and/or provider and/or agent + gchar *xml_file; // Value of (deprecated) --xml-file ++ int check_level; // Optional value of --validate or --force-check + + // Resource configuration specified via command-line arguments + gboolean cmdline_config; // Resource configuration was via arguments +@@ -113,6 +114,7 @@ struct { + GHashTable *override_params; // Resource parameter values that override config + } options = { + .attr_set_type = XML_TAG_ATTR_SETS, ++ .check_level = -1, + .cib_options = cib_sync_call, + .require_cib = TRUE, + .require_dataset = TRUE, +@@ -402,14 +404,15 @@ static GOptionEntry query_entries[] = { + }; + + static GOptionEntry command_entries[] = { +- { "validate", 0, G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, ++ { "validate", 0, G_OPTION_FLAG_OPTIONAL_ARG, G_OPTION_ARG_CALLBACK, + validate_or_force_cb, + "Validate resource configuration by calling agent's validate-all\n" + INDENT "action. The configuration may be specified either by giving an\n" + INDENT "existing resource name with -r, or by specifying --class,\n" + INDENT "--agent, and --provider arguments, along with any number of\n" +- INDENT "--option arguments.", +- NULL }, ++ INDENT "--option arguments. An optional LEVEL argument can be given\n" ++ INDENT "to control the level of checking performed.", ++ "LEVEL" }, + { "cleanup", 'C', G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, cleanup_refresh_cb, + "If resource has any past failures, clear its history and fail\n" + INDENT "count. Optionally filtered by --resource, --node, --operation\n" +@@ -546,11 +549,12 @@ static GOptionEntry advanced_entries[] = { + INDENT "the cluster believes the resource is a clone instance already\n" + INDENT "running on the local node.", + NULL }, +- { "force-check", 0, G_OPTION_FLAG_NO_ARG, G_OPTION_ARG_CALLBACK, ++ { "force-check", 0, G_OPTION_FLAG_OPTIONAL_ARG, G_OPTION_ARG_CALLBACK, + validate_or_force_cb, + "(Advanced) Bypass the cluster and check the state of a resource on\n" +- INDENT "the local node", +- NULL }, ++ INDENT "the local node. An optional LEVEL argument can be given\n" ++ INDENT "to control the level of checking performed.", ++ "LEVEL" }, + + { NULL } + }; +@@ -910,6 +914,15 @@ validate_or_force_cb(const gchar *option_name, const gchar *optarg, + if (options.override_params == NULL) { + options.override_params = pcmk__strkey_table(free, free); + } ++ ++ if (optarg != NULL) { ++ if (pcmk__scan_min_int(optarg, &options.check_level, 0) != pcmk_rc_ok) { ++ g_set_error(error, G_OPTION_ERROR, CRM_EX_INVALID_PARAM, ++ "Invalid check level setting: %s", optarg); ++ return FALSE; ++ } ++ } ++ + return TRUE; + } + +@@ -1826,12 +1839,12 @@ main(int argc, char **argv) + options.v_class, options.v_provider, options.v_agent, + "validate-all", options.cmdline_params, + options.override_params, options.timeout_ms, +- args->verbosity, options.force); ++ args->verbosity, options.force, options.check_level); + } else { + exit_code = cli_resource_execute(rsc, options.rsc_id, + options.operation, options.override_params, + options.timeout_ms, cib_conn, data_set, +- args->verbosity, options.force); ++ args->verbosity, options.force, options.check_level); + } + goto done; + +diff --git a/tools/crm_resource.h b/tools/crm_resource.h +index 3560377..5ab10d6 100644 +--- a/tools/crm_resource.h ++++ b/tools/crm_resource.h +@@ -88,11 +88,11 @@ crm_exit_t cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc + const char *rsc_type, const char *rsc_action, + GHashTable *params, GHashTable *override_hash, + int timeout_ms, int resource_verbose, +- gboolean force); ++ gboolean force, int check_level); + crm_exit_t cli_resource_execute(pe_resource_t *rsc, const char *requested_name, + const char *rsc_action, GHashTable *override_hash, + int timeout_ms, cib_t *cib, pe_working_set_t *data_set, +- int resource_verbose, gboolean force); ++ int resource_verbose, gboolean force, int check_level); + + int cli_resource_update_attribute(pe_resource_t *rsc, const char *requested_name, + const char *attr_set, const char *attr_set_type, +diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c +index fe0ec98..bde83b6 100644 +--- a/tools/crm_resource_runtime.c ++++ b/tools/crm_resource_runtime.c +@@ -1679,7 +1679,8 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, + const char *rsc_class, const char *rsc_prov, + const char *rsc_type, const char *action, + GHashTable *params, GHashTable *override_hash, +- int timeout_ms, int resource_verbose, gboolean force) ++ int timeout_ms, int resource_verbose, gboolean force, ++ int check_level) + { + GHashTable *params_copy = NULL; + crm_exit_t exit_code = CRM_EX_OK; +@@ -1703,6 +1704,12 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, + /* add crm_feature_set env needed by some resource agents */ + g_hash_table_insert(params, strdup(XML_ATTR_CRM_VERSION), strdup(CRM_FEATURE_SET)); + ++ if (check_level >= 0) { ++ char *level = crm_strdup_printf("%d", check_level); ++ setenv("OCF_CHECK_LEVEL", level, 1); ++ free(level); ++ } ++ + /* resources_action_create frees the params hash table it's passed, but we + * may need to reuse it in a second call to resources_action_create. Thus + * we'll make a copy here so that gets freed and the original remains for +@@ -1790,7 +1797,7 @@ crm_exit_t + cli_resource_execute(pe_resource_t *rsc, const char *requested_name, + const char *rsc_action, GHashTable *override_hash, + int timeout_ms, cib_t * cib, pe_working_set_t *data_set, +- int resource_verbose, gboolean force) ++ int resource_verbose, gboolean force, int check_level) + { + pcmk__output_t *out = data_set->priv; + crm_exit_t exit_code = CRM_EX_OK; +@@ -1856,7 +1863,7 @@ cli_resource_execute(pe_resource_t *rsc, const char *requested_name, + + exit_code = cli_resource_execute_from_params(out, rid, rclass, rprov, rtype, action, + params, override_hash, timeout_ms, +- resource_verbose, force); ++ resource_verbose, force, check_level); + return exit_code; + } + +-- +1.8.3.1 + + +From d13ba4bd6defe0dd81fdf8ab39ae5b889513c0c0 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 20 May 2021 10:59:23 -0400 +Subject: [PATCH 2/2] Fix: include: Bump feature set to 3.10.2. + +This is for the OCF_CHECK_LEVEL environment variable. + +See: rhbz#1955792. +--- + include/crm/crm.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/crm/crm.h b/include/crm/crm.h +index 92a98fa..ee52c36 100644 +--- a/include/crm/crm.h ++++ b/include/crm/crm.h +@@ -66,7 +66,7 @@ extern "C" { + * >=3.0.13: Fail counts include operation name and interval + * >=3.2.0: DC supports PCMK_LRM_OP_INVALID and PCMK_LRM_OP_NOT_CONNECTED + */ +-# define CRM_FEATURE_SET "3.10.1" ++# define CRM_FEATURE_SET "3.10.2" + + /* Pacemaker's CPG protocols use fixed-width binary fields for the sender and + * recipient of a CPG message. This imposes an arbitrary limit on cluster node +-- +1.8.3.1 + diff --git a/005-crm_resource.patch b/005-crm_resource.patch new file mode 100644 index 0000000..1683026 --- /dev/null +++ b/005-crm_resource.patch @@ -0,0 +1,866 @@ +From a5a507d4e1abf242903472719a19977811e6f164 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 20 May 2021 11:59:36 -0400 +Subject: [PATCH 01/10] Feature: libcrmcommon: Add OCF_OUTPUT_FORMAT to + crm_resource environment. + +See: rhbz#1644628 +--- + lib/common/output.c | 2 ++ + 1 file changed, 2 insertions(+) + +diff --git a/lib/common/output.c b/lib/common/output.c +index 6cb49b5..58872e0 100644 +--- a/lib/common/output.c ++++ b/lib/common/output.c +@@ -71,6 +71,8 @@ pcmk__output_new(pcmk__output_t **out, const char *fmt_name, const char *filenam + return ENOMEM; + } + ++ setenv("OCF_OUTPUT_FORMAT", (*out)->fmt_name, 1); ++ + return pcmk_rc_ok; + } + +-- +1.8.3.1 + + +From acc6ecdbfb797d69794e68f75a734d6252434e01 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 21 May 2021 14:20:30 -0400 +Subject: [PATCH 02/10] Feature: schemas: Copy crm_resource schema in + preparation for changes. + +See: rhbz#1644628 +--- + xml/api/crm_resource-2.11.rng | 238 ++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 238 insertions(+) + create mode 100644 xml/api/crm_resource-2.11.rng + +diff --git a/xml/api/crm_resource-2.11.rng b/xml/api/crm_resource-2.11.rng +new file mode 100644 +index 0000000..8e386db +--- /dev/null ++++ b/xml/api/crm_resource-2.11.rng +@@ -0,0 +1,238 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="element-crm-resource"/> ++ </start> ++ ++ <define name="element-crm-resource"> ++ <choice> ++ <ref name="agents-list" /> ++ <ref name="alternatives-list" /> ++ <ref name="constraints-list" /> ++ <externalRef href="generic-list-2.4.rng"/> ++ <element name="metadata"> <text/> </element> ++ <ref name="locate-list" /> ++ <ref name="operations-list" /> ++ <ref name="providers-list" /> ++ <ref name="reasons-list" /> ++ <ref name="resource-check" /> ++ <ref name="resource-config" /> ++ <ref name="resources-list" /> ++ </choice> ++ </define> ++ ++ <define name="agents-list"> ++ <element name="agents"> ++ <attribute name="standard"> <text/> </attribute> ++ <optional> ++ <attribute name="provider"> <text/> </attribute> ++ </optional> ++ <zeroOrMore> ++ <element name="agent"> <text/> </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="alternatives-list"> ++ <element name="providers"> ++ <attribute name="for"> <text/> </attribute> ++ <zeroOrMore> ++ <element name="provider"> <text/> </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="constraints-list"> ++ <element name="constraints"> ++ <interleave> ++ <zeroOrMore> ++ <ref name="rsc-location" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="rsc-colocation" /> ++ </zeroOrMore> ++ </interleave> ++ </element> ++ </define> ++ ++ <define name="locate-list"> ++ <element name="nodes"> ++ <attribute name="resource"> <text/> </attribute> ++ <zeroOrMore> ++ <element name="node"> ++ <optional> ++ <attribute name="state"><value>promoted</value></attribute> ++ </optional> ++ <text/> ++ </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="rsc-location"> ++ <element name="rsc_location"> ++ <attribute name="node"> <text/> </attribute> ++ <attribute name="rsc"> <text/> </attribute> ++ <attribute name="id"> <text/> </attribute> ++ <externalRef href="../score.rng"/> ++ </element> ++ </define> ++ ++ <define name="operations-list"> ++ <element name="operations"> ++ <oneOrMore> ++ <ref name="element-operation-list" /> ++ </oneOrMore> ++ </element> ++ </define> ++ ++ <define name="providers-list"> ++ <element name="providers"> ++ <attribute name="standard"> <value>ocf</value> </attribute> ++ <optional> ++ <attribute name="agent"> <text/> </attribute> ++ </optional> ++ <zeroOrMore> ++ <element name="provider"> <text/> </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="reasons-list"> ++ <choice> ++ <ref name="no-resource-or-uname"/> ++ <ref name="resource-and-uname"/> ++ <ref name="no-resource-but-uname"/> ++ <ref name="resource-but-no-uname"/> ++ </choice> ++ </define> ++ ++ <define name="no-resource-or-uname"> ++ <element name="reason"> ++ <element name="resources"> ++ <zeroOrMore> ++ <element name="resource"> ++ <attribute name="id"> <text/> </attribute> ++ <attribute name="running"> <data type="boolean"/> </attribute> ++ <ref name="resource-check"/> ++ </element> ++ </zeroOrMore> ++ </element> ++ </element> ++ </define> ++ ++ <define name="resource-and-uname"> ++ <element name="reason"> ++ <attribute name="running_on"> <text/> </attribute> ++ <ref name="resource-check"/> ++ </element> ++ </define> ++ ++ <define name="no-resource-but-uname"> ++ <element name="reason"> ++ <element name="resources"> ++ <zeroOrMore> ++ <element name="resource"> ++ <attribute name="id"> <text/> </attribute> ++ <attribute name="running"> <data type="boolean"/> </attribute> ++ <attribute name="host"> <text/> </attribute> ++ <ref name="resource-check"/> ++ </element> ++ </zeroOrMore> ++ </element> ++ </element> ++ </define> ++ ++ <define name="resource-but-no-uname"> ++ <element name="reason"> ++ <attribute name="running"> <data type="boolean"/> </attribute> ++ <ref name="resource-check"/> ++ </element> ++ </define> ++ ++ <define name="resource-config"> ++ <element name="resource_config"> ++ <externalRef href="resources-2.4.rng" /> ++ <element name="xml"> <text/> </element> ++ </element> ++ </define> ++ ++ <define name="resource-check"> ++ <element name="check"> ++ <attribute name="id"> <text/> </attribute> ++ <optional> ++ <choice> ++ <attribute name="remain_stopped"><value>true</value></attribute> ++ <attribute name="promotable"><value>false</value></attribute> ++ </choice> ++ </optional> ++ <optional> ++ <attribute name="unmanaged"><value>true</value></attribute> ++ </optional> ++ <optional> ++ <attribute name="locked-to"> <text/> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="resources-list"> ++ <element name="resources"> ++ <zeroOrMore> ++ <externalRef href="resources-2.4.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="rsc-colocation"> ++ <element name="rsc_colocation"> ++ <attribute name="id"> <text/> </attribute> ++ <attribute name="rsc"> <text/> </attribute> ++ <attribute name="with-rsc"> <text/> </attribute> ++ <externalRef href="../score.rng"/> ++ <optional> ++ <attribute name="node-attribute"> <text/> </attribute> ++ </optional> ++ <optional> ++ <attribute name="rsc-role"> ++ <ref name="attribute-roles"/> ++ </attribute> ++ </optional> ++ <optional> ++ <attribute name="with-rsc-role"> ++ <ref name="attribute-roles"/> ++ </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-operation-list"> ++ <element name="operation"> ++ <optional> ++ <group> ++ <attribute name="rsc"> <text/> </attribute> ++ <attribute name="agent"> <text/> </attribute> ++ </group> ++ </optional> ++ <attribute name="op"> <text/> </attribute> ++ <attribute name="node"> <text/> </attribute> ++ <attribute name="call"> <data type="integer" /> </attribute> ++ <attribute name="rc"> <data type="nonNegativeInteger" /> </attribute> ++ <optional> ++ <attribute name="last-rc-change"> <text/> </attribute> ++ <attribute name="exec-time"> <data type="nonNegativeInteger" /> </attribute> ++ </optional> ++ <attribute name="status"> <text/> </attribute> ++ </element> ++ </define> ++ ++ <define name="attribute-roles"> ++ <choice> ++ <value>Stopped</value> ++ <value>Started</value> ++ <value>Master</value> ++ <value>Slave</value> ++ </choice> ++ </define> ++</grammar> +-- +1.8.3.1 + + +From 1bbdf2149a111e9e19c388834f82001e0d31c427 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 24 May 2021 12:23:55 -0400 +Subject: [PATCH 03/10] Feature: xml: Update the crm_resource schema for XML + output. + +See: rhbz#1644628 +--- + xml/api/crm_resource-2.11.rng | 50 +++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 50 insertions(+) + +diff --git a/xml/api/crm_resource-2.11.rng b/xml/api/crm_resource-2.11.rng +index 8e386db..aaa54d6 100644 +--- a/xml/api/crm_resource-2.11.rng ++++ b/xml/api/crm_resource-2.11.rng +@@ -20,6 +20,7 @@ + <ref name="resource-check" /> + <ref name="resource-config" /> + <ref name="resources-list" /> ++ <ref name="resource-agent-action" /> + </choice> + </define> + +@@ -227,6 +228,55 @@ + </element> + </define> + ++ <define name="resource-agent-action"> ++ <element name="resource-agent-action"> ++ <attribute name="action"> <text/> </attribute> ++ <optional> ++ <attribute name="rsc"> <text/> </attribute> ++ </optional> ++ <attribute name="class"> <text/> </attribute> ++ <attribute name="type"> <text/> </attribute> ++ <optional> ++ <attribute name="provider"> <text/> </attribute> ++ </optional> ++ <optional> ++ <ref name="overrides-list"/> ++ </optional> ++ <ref name="agent-status"/> ++ <optional> ++ <choice> ++ <element name="command"> ++ <text /> ++ </element> ++ <externalRef href="command-output-1.0.rng"/> ++ </choice> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="overrides-list"> ++ <element name="overrides"> ++ <zeroOrMore> ++ <element name="override"> ++ <optional> ++ <attribute name="rsc"> <text/> </attribute> ++ </optional> ++ <attribute name="name"> <text/> </attribute> ++ <attribute name="value"> <text/> </attribute> ++ </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="agent-status"> ++ <element name="agent-status"> ++ <attribute name="code"> <data type="integer" /> </attribute> ++ <optional> ++ <attribute name="message"> <text/> </attribute> ++ </optional> ++ </element> ++ </define> ++ + <define name="attribute-roles"> + <choice> + <value>Stopped</value> +-- +1.8.3.1 + + +From d89f5bc7fec856fdcd32fa14edbd0019507d5d15 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Tue, 1 Jun 2021 15:26:58 -0400 +Subject: [PATCH 04/10] Low: libcrmcommon: Increase PCMK__API_VERSION for new + crm_resource output. + +See: rhbz#1644628 +--- + include/crm/common/output_internal.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/crm/common/output_internal.h b/include/crm/common/output_internal.h +index 10b315b..0436cde 100644 +--- a/include/crm/common/output_internal.h ++++ b/include/crm/common/output_internal.h +@@ -27,7 +27,7 @@ extern "C" { + # include <glib.h> + # include <crm/common/results.h> + +-# define PCMK__API_VERSION "2.9" ++# define PCMK__API_VERSION "2.11" + + #if defined(PCMK__WITH_ATTRIBUTE_OUTPUT_ARGS) + # define PCMK__OUTPUT_ARGS(ARGS...) __attribute__((output_args(ARGS))) +-- +1.8.3.1 + + +From 30bd2ddf43ee2a911681e51f40ed9ba20ec250b0 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Thu, 27 May 2021 13:57:12 -0400 +Subject: [PATCH 05/10] Low: tools: Pass NULL to + cli_resource_execute_from_params... + +if no resource name is given. This happens if we are validating based +on the --class/--agent/--provider command line options instead. +--- + tools/crm_resource.c | 2 +- + tools/crm_resource_runtime.c | 8 ++++---- + 2 files changed, 5 insertions(+), 5 deletions(-) + +diff --git a/tools/crm_resource.c b/tools/crm_resource.c +index 24f1121..37a0bb0 100644 +--- a/tools/crm_resource.c ++++ b/tools/crm_resource.c +@@ -1840,7 +1840,7 @@ main(int argc, char **argv) + + case cmd_execute_agent: + if (options.cmdline_config) { +- exit_code = cli_resource_execute_from_params(out, "test", ++ exit_code = cli_resource_execute_from_params(out, NULL, + options.v_class, options.v_provider, options.v_agent, + "validate-all", options.cmdline_params, + options.override_params, options.timeout_ms, +diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c +index 48a4b40..ebf48bb 100644 +--- a/tools/crm_resource_runtime.c ++++ b/tools/crm_resource_runtime.c +@@ -1717,14 +1717,14 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, + */ + params_copy = pcmk__str_table_dup(params); + +- op = resources_action_create(rsc_name, rsc_class, rsc_prov, rsc_type, action, 0, +- timeout_ms, params_copy, 0); ++ op = resources_action_create(rsc_name ? rsc_name : "test", rsc_class, rsc_prov, ++ rsc_type, action, 0, timeout_ms, params_copy, 0); + if (op == NULL) { + /* Re-run with stderr enabled so we can display a sane error message */ + crm_enable_stderr(TRUE); + params_copy = pcmk__str_table_dup(params); +- op = resources_action_create(rsc_name, rsc_class, rsc_prov, rsc_type, action, 0, +- timeout_ms, params_copy, 0); ++ op = resources_action_create(rsc_name ? rsc_name : "test", rsc_class, rsc_prov, ++ rsc_type, action, 0, timeout_ms, params_copy, 0); + + /* Callers of cli_resource_execute expect that the params hash table will + * be freed. That function uses this one, so for that reason and for +-- +1.8.3.1 + + +From ee56efd53d14cfc4f902769540b72b3bb6096a73 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Mon, 24 May 2021 12:08:52 -0400 +Subject: [PATCH 06/10] Feature: tools: Add an agent-status message for + crm_resource. + +This moves what was previously only done in an out->info call to its own +output message, which means it will appear in XML output as well. Also, +note that if --class/--agent/--provider are given, the resource name +will be set to "test". In that case, do not display the resource name +in the output. + +This message will be used for --validate and the --force-* command line +options to crm_resource. + +See: rhbz#1644628 +--- + tools/crm_resource_print.c | 53 ++++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 53 insertions(+) + +diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c +index 9d82cf8..88d5878 100644 +--- a/tools/crm_resource_print.c ++++ b/tools/crm_resource_print.c +@@ -152,6 +152,57 @@ attribute_list_default(pcmk__output_t *out, va_list args) { + return pcmk_rc_ok; + } + ++PCMK__OUTPUT_ARGS("agent-status", "int", "const char *", "const char *", "const char *", ++ "const char *", "const char *", "int") ++static int ++agent_status_default(pcmk__output_t *out, va_list args) { ++ int status = va_arg(args, int); ++ const char *action = va_arg(args, const char *); ++ const char *name = va_arg(args, const char *); ++ const char *class = va_arg(args, const char *); ++ const char *provider = va_arg(args, const char *); ++ const char *type = va_arg(args, const char *); ++ int rc = va_arg(args, int); ++ ++ if (status == PCMK_LRM_OP_DONE) { ++ out->info(out, "Operation %s%s%s (%s%s%s:%s) returned: '%s' (%d)", ++ action, name ? " for " : "", name ? name : "", ++ class, provider ? ":" : "", provider ? provider : "", type, ++ services_ocf_exitcode_str(rc), rc); ++ } else { ++ out->err(out, "Operation %s%s%s (%s%s%s:%s) failed: '%s' (%d)", ++ action, name ? " for " : "", name ? name : "", ++ class, provider ? ":" : "", provider ? provider : "", type, ++ services_lrm_status_str(status), status); ++ } ++ ++ return pcmk_rc_ok; ++} ++ ++PCMK__OUTPUT_ARGS("agent-status", "int", "const char *", "const char *", "const char *", ++ "const char *", "const char *", "int") ++static int ++agent_status_xml(pcmk__output_t *out, va_list args) { ++ int status G_GNUC_UNUSED = va_arg(args, int); ++ const char *action G_GNUC_UNUSED = va_arg(args, const char *); ++ const char *name G_GNUC_UNUSED = va_arg(args, const char *); ++ const char *class G_GNUC_UNUSED = va_arg(args, const char *); ++ const char *provider G_GNUC_UNUSED = va_arg(args, const char *); ++ const char *type G_GNUC_UNUSED = va_arg(args, const char *); ++ int rc = va_arg(args, int); ++ ++ char *status_str = pcmk__itoa(rc); ++ ++ pcmk__output_create_xml_node(out, "agent-status", ++ "code", status_str, ++ "message", services_ocf_exitcode_str(rc), ++ NULL); ++ ++ free(status_str); ++ ++ return pcmk_rc_ok; ++} ++ + PCMK__OUTPUT_ARGS("attribute-list", "pe_resource_t *", "char *", "GHashTable *") + static int + attribute_list_text(pcmk__output_t *out, va_list args) { +@@ -562,6 +613,8 @@ resource_names(pcmk__output_t *out, va_list args) { + } + + static pcmk__message_entry_t fmt_functions[] = { ++ { "agent-status", "default", agent_status_default }, ++ { "agent-status", "xml", agent_status_xml }, + { "attribute-list", "default", attribute_list_default }, + { "attribute-list", "text", attribute_list_text }, + { "property-list", "default", property_list_default }, +-- +1.8.3.1 + + +From 85cb6b6bff96b18c5174d11e4de4d49cbfb20bb7 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Tue, 1 Jun 2021 14:47:30 -0400 +Subject: [PATCH 07/10] Feature: tools: Add an overridden params output + message. + +This also replaces what was previously being done in an out->info call +with an output message. This means it shows up in XML output as well. +Also, note that if --class/--agent/--provider are given, the resource +name will be set to "test". In that case, do not display the resource +name in the output. + +See: rhbz#1644628 +--- + tools/crm_resource_print.c | 39 +++++++++++++++++++++++++++++++++++++++ + 1 file changed, 39 insertions(+) + +diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c +index 88d5878..119d83f 100644 +--- a/tools/crm_resource_print.c ++++ b/tools/crm_resource_print.c +@@ -224,6 +224,43 @@ attribute_list_text(pcmk__output_t *out, va_list args) { + return pcmk_rc_ok; + } + ++PCMK__OUTPUT_ARGS("override", "const char *", "const char *", "const char *") ++static int ++override_default(pcmk__output_t *out, va_list args) { ++ const char *rsc_name = va_arg(args, const char *); ++ const char *name = va_arg(args, const char *); ++ const char *value = va_arg(args, const char *); ++ ++ if (rsc_name == NULL) { ++ out->list_item(out, NULL, "Overriding the cluster configuration with '%s' = '%s'", ++ name, value); ++ } else { ++ out->list_item(out, NULL, "Overriding the cluster configuration for '%s' with '%s' = '%s'", ++ rsc_name, name, value); ++ } ++ ++ return pcmk_rc_ok; ++} ++ ++PCMK__OUTPUT_ARGS("override", "const char *", "const char *", "const char *") ++static int ++override_xml(pcmk__output_t *out, va_list args) { ++ const char *rsc_name = va_arg(args, const char *); ++ const char *name = va_arg(args, const char *); ++ const char *value = va_arg(args, const char *); ++ ++ xmlNodePtr node = pcmk__output_create_xml_node(out, "override", ++ "name", name, ++ "value", value, ++ NULL); ++ ++ if (rsc_name != NULL) { ++ crm_xml_add(node, "rsc", rsc_name); ++ } ++ ++ return pcmk_rc_ok; ++} ++ + PCMK__OUTPUT_ARGS("property-list", "pe_resource_t *", "char *") + static int + property_list_default(pcmk__output_t *out, va_list args) { +@@ -617,6 +654,8 @@ static pcmk__message_entry_t fmt_functions[] = { + { "agent-status", "xml", agent_status_xml }, + { "attribute-list", "default", attribute_list_default }, + { "attribute-list", "text", attribute_list_text }, ++ { "override", "default", override_default }, ++ { "override", "xml", override_xml }, + { "property-list", "default", property_list_default }, + { "property-list", "text", property_list_text }, + { "resource-check-list", "default", resource_check_list_default }, +-- +1.8.3.1 + + +From e5e24592c7c3231c619fb5253e7925ffbc634a99 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 4 Jun 2021 10:24:51 -0400 +Subject: [PATCH 08/10] Low: tools: Use simple XML lists for resource actions + as well. + +See: rhbz#1644628 +--- + tools/crm_resource.c | 1 + + 1 file changed, 1 insertion(+) + +diff --git a/tools/crm_resource.c b/tools/crm_resource.c +index 37a0bb0..e957011 100644 +--- a/tools/crm_resource.c ++++ b/tools/crm_resource.c +@@ -1643,6 +1643,7 @@ main(int argc, char **argv) + * saves from having to write custom messages to build the lists around all these things + */ + switch (options.rsc_cmd) { ++ case cmd_execute_agent: + case cmd_list_resources: + case cmd_query_xml: + case cmd_query_raw_xml: +-- +1.8.3.1 + + +From 3e75174d0bc31b261adb1994214a5878b79da85b Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 4 Jun 2021 10:30:10 -0400 +Subject: [PATCH 09/10] Feature: tools: Add an output message for resource + actions. + +This wraps up the override and agent-status messages into a single +message, along with any stdout/stderr from the resource action. This +message should be called after taking the action. + +This also implements handling XML output from resource actions. Check +to see if the validate-all action returns XML. If so, output it as a +CDATA block under a "command" element. If not, treat it as plain text +and output it as stdout/stderr from a command. + +See: rhbz#1644628 +--- + tools/crm_resource_print.c | 122 +++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 122 insertions(+) + +diff --git a/tools/crm_resource_print.c b/tools/crm_resource_print.c +index 119d83f..19a366d 100644 +--- a/tools/crm_resource_print.c ++++ b/tools/crm_resource_print.c +@@ -293,6 +293,126 @@ property_list_text(pcmk__output_t *out, va_list args) { + return pcmk_rc_ok; + } + ++PCMK__OUTPUT_ARGS("resource-agent-action", "int", "const char *", "const char *", ++ "const char *", "const char *", "const char *", "GHashTable *", ++ "int", "int", "char *", "char *") ++static int ++resource_agent_action_default(pcmk__output_t *out, va_list args) { ++ int verbose = va_arg(args, int); ++ ++ const char *class = va_arg(args, const char *); ++ const char *provider = va_arg(args, const char *); ++ const char *type = va_arg(args, const char *); ++ const char *rsc_name = va_arg(args, const char *); ++ const char *action = va_arg(args, const char *); ++ GHashTable *overrides = va_arg(args, GHashTable *); ++ int rc = va_arg(args, int); ++ int status = va_arg(args, int); ++ char *stdout_data = va_arg(args, char *); ++ char *stderr_data = va_arg(args, char *); ++ ++ if (overrides) { ++ GHashTableIter iter; ++ char *name = NULL; ++ char *value = NULL; ++ ++ out->begin_list(out, NULL, NULL, "overrides"); ++ ++ g_hash_table_iter_init(&iter, overrides); ++ while (g_hash_table_iter_next(&iter, (gpointer *) &name, (gpointer *) &value)) { ++ out->message(out, "override", rsc_name, name, value); ++ } ++ ++ out->end_list(out); ++ } ++ ++ out->message(out, "agent-status", status, action, rsc_name, class, provider, ++ type, rc); ++ ++ /* hide output for validate-all if not in verbose */ ++ if (verbose == 0 && pcmk__str_eq(action, "validate-all", pcmk__str_casei)) { ++ return pcmk_rc_ok; ++ } ++ ++ if (stdout_data || stderr_data) { ++ xmlNodePtr doc = string2xml(stdout_data); ++ ++ if (doc != NULL) { ++ out->output_xml(out, "command", stdout_data); ++ xmlFreeNode(doc); ++ } else { ++ out->subprocess_output(out, rc, stdout_data, stderr_data); ++ } ++ } ++ ++ return pcmk_rc_ok; ++} ++ ++PCMK__OUTPUT_ARGS("resource-agent-action", "int", "const char *", "const char *", ++ "const char *", "const char *", "const char *", "GHashTable *", ++ "int", "int", "char *", "char *") ++static int ++resource_agent_action_xml(pcmk__output_t *out, va_list args) { ++ int verbose G_GNUC_UNUSED = va_arg(args, int); ++ ++ const char *class = va_arg(args, const char *); ++ const char *provider = va_arg(args, const char *); ++ const char *type = va_arg(args, const char *); ++ const char *rsc_name = va_arg(args, const char *); ++ const char *action = va_arg(args, const char *); ++ GHashTable *overrides = va_arg(args, GHashTable *); ++ int rc = va_arg(args, int); ++ int status = va_arg(args, int); ++ char *stdout_data = va_arg(args, char *); ++ char *stderr_data = va_arg(args, char *); ++ ++ xmlNodePtr node = pcmk__output_xml_create_parent(out, "resource-agent-action", ++ "action", action, ++ "class", class, ++ "type", type, ++ NULL); ++ ++ if (rsc_name) { ++ crm_xml_add(node, "rsc", rsc_name); ++ } ++ ++ if (provider) { ++ crm_xml_add(node, "provider", provider); ++ } ++ ++ if (overrides) { ++ GHashTableIter iter; ++ char *name = NULL; ++ char *value = NULL; ++ ++ out->begin_list(out, NULL, NULL, "overrides"); ++ ++ g_hash_table_iter_init(&iter, overrides); ++ while (g_hash_table_iter_next(&iter, (gpointer *) &name, (gpointer *) &value)) { ++ out->message(out, "override", rsc_name, name, value); ++ } ++ ++ out->end_list(out); ++ } ++ ++ out->message(out, "agent-status", status, action, rsc_name, class, provider, ++ type, rc); ++ ++ if (stdout_data || stderr_data) { ++ xmlNodePtr doc = string2xml(stdout_data); ++ ++ if (doc != NULL) { ++ out->output_xml(out, "command", stdout_data); ++ xmlFreeNode(doc); ++ } else { ++ out->subprocess_output(out, rc, stdout_data, stderr_data); ++ } ++ } ++ ++ pcmk__output_xml_pop_parent(out); ++ return pcmk_rc_ok; ++} ++ + PCMK__OUTPUT_ARGS("resource-check-list", "resource_checks_t *") + static int + resource_check_list_default(pcmk__output_t *out, va_list args) { +@@ -658,6 +778,8 @@ static pcmk__message_entry_t fmt_functions[] = { + { "override", "xml", override_xml }, + { "property-list", "default", property_list_default }, + { "property-list", "text", property_list_text }, ++ { "resource-agent-action", "default", resource_agent_action_default }, ++ { "resource-agent-action", "xml", resource_agent_action_xml }, + { "resource-check-list", "default", resource_check_list_default }, + { "resource-check-list", "xml", resource_check_list_xml }, + { "resource-search-list", "default", resource_search_list_default }, +-- +1.8.3.1 + + +From b50b2418e1e997b42f5370b4672a3f105d74634f Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 4 Jun 2021 10:40:16 -0400 +Subject: [PATCH 10/10] Feature: tools: Use the new resource-agent-action + message. + +See: rhbz#1644628 +--- + tools/crm_resource_runtime.c | 21 +++------------------ + 1 file changed, 3 insertions(+), 18 deletions(-) + +diff --git a/tools/crm_resource_runtime.c b/tools/crm_resource_runtime.c +index ebf48bb..755be9f 100644 +--- a/tools/crm_resource_runtime.c ++++ b/tools/crm_resource_runtime.c +@@ -1765,28 +1765,13 @@ cli_resource_execute_from_params(pcmk__output_t *out, const char *rsc_name, + if (services_action_sync(op)) { + exit_code = op->rc; + +- if (op->status == PCMK_LRM_OP_DONE) { +- out->info(out, "Operation %s for %s (%s:%s:%s) returned: '%s' (%d)", +- action, rsc_name, rsc_class, rsc_prov ? rsc_prov : "", rsc_type, +- services_ocf_exitcode_str(op->rc), op->rc); +- } else { +- out->err(out, "Operation %s for %s (%s:%s:%s) failed: '%s' (%d)", +- action, rsc_name, rsc_class, rsc_prov ? rsc_prov : "", rsc_type, +- services_lrm_status_str(op->status), op->status); +- } +- +- /* hide output for validate-all if not in verbose */ +- if (resource_verbose == 0 && pcmk__str_eq(action, "validate-all", pcmk__str_casei)) +- goto done; +- +- if (op->stdout_data || op->stderr_data) { +- out->subprocess_output(out, op->rc, op->stdout_data, op->stderr_data); +- } ++ out->message(out, "resource-agent-action", resource_verbose, rsc_class, ++ rsc_prov, rsc_type, rsc_name, action, override_hash, op->rc, ++ op->status, op->stdout_data, op->stderr_data); + } else { + exit_code = op->rc == 0 ? CRM_EX_ERROR : op->rc; + } + +-done: + services_action_free(op); + /* See comment above about why we free params here. */ + g_hash_table_destroy(params); +-- +1.8.3.1 + diff --git a/006-crm_simulate.patch b/006-crm_simulate.patch new file mode 100644 index 0000000..c8d4e3f --- /dev/null +++ b/006-crm_simulate.patch @@ -0,0 +1,896 @@ +From 97571e6ccc9b7fa339a7e27d9b0b9ab782ff3003 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Wed, 16 Jun 2021 13:54:10 -0400 +Subject: [PATCH 1/5] Low: schemas: Copy crm_mon.rng in preparation for + changes. + +--- + xml/api/crm_mon-2.12.rng | 243 +++++++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 243 insertions(+) + create mode 100644 xml/api/crm_mon-2.12.rng + +diff --git a/xml/api/crm_mon-2.12.rng b/xml/api/crm_mon-2.12.rng +new file mode 100644 +index 0000000..ffec923 +--- /dev/null ++++ b/xml/api/crm_mon-2.12.rng +@@ -0,0 +1,243 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="element-crm-mon"/> ++ </start> ++ ++ <define name="element-crm-mon"> ++ <optional> ++ <ref name="element-summary" /> ++ </optional> ++ <optional> ++ <ref name="nodes-list" /> ++ </optional> ++ <optional> ++ <ref name="resources-list" /> ++ </optional> ++ <optional> ++ <ref name="node-attributes-list" /> ++ </optional> ++ <optional> ++ <ref name="node-history-list" /> ++ </optional> ++ <optional> ++ <ref name="failures-list" /> ++ </optional> ++ <optional> ++ <ref name="fence-event-list" /> ++ </optional> ++ <optional> ++ <ref name="tickets-list" /> ++ </optional> ++ <optional> ++ <ref name="bans-list" /> ++ </optional> ++ </define> ++ ++ <define name="element-summary"> ++ <element name="summary"> ++ <optional> ++ <element name="stack"> ++ <attribute name="type"> <text /> </attribute> ++ </element> ++ </optional> ++ <optional> ++ <element name="current_dc"> ++ <attribute name="present"> <data type="boolean" /> </attribute> ++ <optional> ++ <group> ++ <attribute name="version"> <text /> </attribute> ++ <attribute name="name"> <text /> </attribute> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="with_quorum"> <data type="boolean" /> </attribute> ++ </group> ++ </optional> ++ </element> ++ </optional> ++ <optional> ++ <element name="last_update"> ++ <attribute name="time"> <text /> </attribute> ++ </element> ++ <element name="last_change"> ++ <attribute name="time"> <text /> </attribute> ++ <attribute name="user"> <text /> </attribute> ++ <attribute name="client"> <text /> </attribute> ++ <attribute name="origin"> <text /> </attribute> ++ </element> ++ </optional> ++ <optional> ++ <element name="nodes_configured"> ++ <attribute name="number"> <data type="nonNegativeInteger" /> </attribute> ++ </element> ++ <element name="resources_configured"> ++ <attribute name="number"> <data type="nonNegativeInteger" /> </attribute> ++ <attribute name="disabled"> <data type="nonNegativeInteger" /> </attribute> ++ <attribute name="blocked"> <data type="nonNegativeInteger" /> </attribute> ++ </element> ++ </optional> ++ <optional> ++ <element name="cluster_options"> ++ <attribute name="stonith-enabled"> <data type="boolean" /> </attribute> ++ <attribute name="symmetric-cluster"> <data type="boolean" /> </attribute> ++ <attribute name="no-quorum-policy"> <text /> </attribute> ++ <attribute name="maintenance-mode"> <data type="boolean" /> </attribute> ++ <attribute name="stop-all-resources"> <data type="boolean" /> </attribute> ++ </element> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="resources-list"> ++ <element name="resources"> ++ <zeroOrMore> ++ <externalRef href="resources-2.4.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="nodes-list"> ++ <element name="nodes"> ++ <zeroOrMore> ++ <externalRef href="nodes-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="node-attributes-list"> ++ <element name="node_attributes"> ++ <zeroOrMore> ++ <externalRef href="node-attrs-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="node-history-list"> ++ <element name="node_history"> ++ <zeroOrMore> ++ <ref name="element-node-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="failures-list"> ++ <element name="failures"> ++ <zeroOrMore> ++ <externalRef href="failure-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="fence-event-list"> ++ <element name="fence_history"> ++ <optional> ++ <attribute name="status"> <data type="integer" /> </attribute> ++ </optional> ++ <zeroOrMore> ++ <externalRef href="fence-event-2.0.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="tickets-list"> ++ <element name="tickets"> ++ <zeroOrMore> ++ <ref name="element-ticket" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="bans-list"> ++ <element name="bans"> ++ <zeroOrMore> ++ <ref name="element-ban" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-node-history"> ++ <element name="node"> ++ <attribute name="name"> <text /> </attribute> ++ <zeroOrMore> ++ <ref name="element-resource-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-resource-history"> ++ <element name="resource_history"> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="orphan"> <data type="boolean" /> </attribute> ++ <optional> ++ <group> ++ <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> ++ <optional> ++ <attribute name="fail-count"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-failure"> <text /> </attribute> ++ </optional> ++ </group> ++ </optional> ++ <zeroOrMore> ++ <ref name="element-operation-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-operation-history"> ++ <element name="operation_history"> ++ <attribute name="call"> <text /> </attribute> ++ <attribute name="task"> <text /> </attribute> ++ <optional> ++ <attribute name="interval"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-rc-change"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-run"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="exec-time"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="queue-time"> <text /> </attribute> ++ </optional> ++ <attribute name="rc"> <data type="integer" /> </attribute> ++ <attribute name="rc_text"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-ticket"> ++ <element name="ticket"> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="status"> ++ <choice> ++ <value>granted</value> ++ <value>revoked</value> ++ </choice> ++ </attribute> ++ <attribute name="standby"> <data type="boolean" /> </attribute> ++ <optional> ++ <attribute name="last-granted"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-ban"> ++ <element name="ban"> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="resource"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="weight"> <data type="integer" /> </attribute> ++ <attribute name="promoted-only"> <data type="boolean" /> </attribute> ++  ++ <attribute name="master_only"> <data type="boolean" /> </attribute> ++ </element> ++ </define> ++</grammar> +-- +1.8.3.1 + + +From da394983f106f974274ddd94675a04c85086010e Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 18 Jun 2021 15:06:34 -0400 +Subject: [PATCH 2/5] Refactor: Split node history out into its own XML schema. + +This allows for sharing it between crm_mon and crm_simulate. +--- + xml/Makefile.am | 2 +- + xml/api/crm_mon-2.12.rng | 64 +-------------------------------------- + xml/api/node-history-2.12.rng | 70 +++++++++++++++++++++++++++++++++++++++++++ + 3 files changed, 72 insertions(+), 64 deletions(-) + create mode 100644 xml/api/node-history-2.12.rng + +diff --git a/xml/Makefile.am b/xml/Makefile.am +index b9448d4..8e7b6d3 100644 +--- a/xml/Makefile.am ++++ b/xml/Makefile.am +@@ -64,7 +64,7 @@ API_request_base = command-output \ + CIB_cfg_base = options nodes resources constraints fencing acls tags alerts + + # Names of all schemas (including top level and those included by others) +-API_base = $(API_request_base) fence-event failure generic-list item node-attrs nodes resources status ++API_base = $(API_request_base) fence-event failure generic-list item node-attrs node-history nodes resources status + CIB_base = cib $(CIB_cfg_base) status score rule nvset + + # Static schema files and transforms (only CIB has transforms) +diff --git a/xml/api/crm_mon-2.12.rng b/xml/api/crm_mon-2.12.rng +index ffec923..be14412 100644 +--- a/xml/api/crm_mon-2.12.rng ++++ b/xml/api/crm_mon-2.12.rng +@@ -20,7 +20,7 @@ + <ref name="node-attributes-list" /> + </optional> + <optional> +- <ref name="node-history-list" /> ++ <externalRef href="node-history-2.12.rng"/> + </optional> + <optional> + <ref name="failures-list" /> +@@ -113,14 +113,6 @@ + </element> + </define> + +- <define name="node-history-list"> +- <element name="node_history"> +- <zeroOrMore> +- <ref name="element-node-history" /> +- </zeroOrMore> +- </element> +- </define> +- + <define name="failures-list"> + <element name="failures"> + <zeroOrMore> +@@ -156,60 +148,6 @@ + </element> + </define> + +- <define name="element-node-history"> +- <element name="node"> +- <attribute name="name"> <text /> </attribute> +- <zeroOrMore> +- <ref name="element-resource-history" /> +- </zeroOrMore> +- </element> +- </define> +- +- <define name="element-resource-history"> +- <element name="resource_history"> +- <attribute name="id"> <text /> </attribute> +- <attribute name="orphan"> <data type="boolean" /> </attribute> +- <optional> +- <group> +- <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> +- <optional> +- <attribute name="fail-count"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="last-failure"> <text /> </attribute> +- </optional> +- </group> +- </optional> +- <zeroOrMore> +- <ref name="element-operation-history" /> +- </zeroOrMore> +- </element> +- </define> +- +- <define name="element-operation-history"> +- <element name="operation_history"> +- <attribute name="call"> <text /> </attribute> +- <attribute name="task"> <text /> </attribute> +- <optional> +- <attribute name="interval"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="last-rc-change"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="last-run"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="exec-time"> <text /> </attribute> +- </optional> +- <optional> +- <attribute name="queue-time"> <text /> </attribute> +- </optional> +- <attribute name="rc"> <data type="integer" /> </attribute> +- <attribute name="rc_text"> <text /> </attribute> +- </element> +- </define> +- + <define name="element-ticket"> + <element name="ticket"> + <attribute name="id"> <text /> </attribute> +diff --git a/xml/api/node-history-2.12.rng b/xml/api/node-history-2.12.rng +new file mode 100644 +index 0000000..9628000 +--- /dev/null ++++ b/xml/api/node-history-2.12.rng +@@ -0,0 +1,70 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="node-history-list" /> ++ </start> ++ ++ <define name="node-history-list"> ++ <element name="node_history"> ++ <zeroOrMore> ++ <ref name="element-node-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-node-history"> ++ <element name="node"> ++ <attribute name="name"> <text /> </attribute> ++ <zeroOrMore> ++ <ref name="element-resource-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-resource-history"> ++ <element name="resource_history"> ++ <attribute name="id"> <text /> </attribute> ++ <attribute name="orphan"> <data type="boolean" /> </attribute> ++ <optional> ++ <group> ++ <attribute name="migration-threshold"> <data type="nonNegativeInteger" /> </attribute> ++ <optional> ++ <attribute name="fail-count"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-failure"> <text /> </attribute> ++ </optional> ++ </group> ++ </optional> ++ <zeroOrMore> ++ <ref name="element-operation-history" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-operation-history"> ++ <element name="operation_history"> ++ <attribute name="call"> <text /> </attribute> ++ <attribute name="task"> <text /> </attribute> ++ <optional> ++ <attribute name="interval"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-rc-change"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="last-run"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="exec-time"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="queue-time"> <text /> </attribute> ++ </optional> ++ <attribute name="rc"> <data type="integer" /> </attribute> ++ <attribute name="rc_text"> <text /> </attribute> ++ </element> ++ </define> ++</grammar> +-- +1.8.3.1 + + +From bf72b2615630eef7876e443d60b34d5a316de847 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Wed, 16 Jun 2021 14:09:31 -0400 +Subject: [PATCH 3/5] Low: schemas: Copy crm_simulate.rng in preparation for + changes. + +--- + xml/api/crm_simulate-2.12.rng | 335 ++++++++++++++++++++++++++++++++++++++++++ + 1 file changed, 335 insertions(+) + create mode 100644 xml/api/crm_simulate-2.12.rng + +diff --git a/xml/api/crm_simulate-2.12.rng b/xml/api/crm_simulate-2.12.rng +new file mode 100644 +index 0000000..9a7612d +--- /dev/null ++++ b/xml/api/crm_simulate-2.12.rng +@@ -0,0 +1,335 @@ ++<?xml version="1.0" encoding="UTF-8"?> ++<grammar xmlns="http://relaxng.org/ns/structure/1.0" ++ datatypeLibrary="http://www.w3.org/2001/XMLSchema-datatypes"> ++ ++ <start> ++ <ref name="element-crm-simulate"/> ++ </start> ++ ++ <define name="element-crm-simulate"> ++ <choice> ++ <ref name="timings-list" /> ++ <group> ++ <ref name="cluster-status" /> ++ <optional> ++ <ref name="modifications-list" /> ++ </optional> ++ <optional> ++ <ref name="allocations-utilizations-list" /> ++ </optional> ++ <optional> ++ <ref name="action-list" /> ++ </optional> ++ <optional> ++ <ref name="cluster-injected-actions-list" /> ++ <ref name="revised-cluster-status" /> ++ </optional> ++ </group> ++ </choice> ++ </define> ++ ++ <define name="allocations-utilizations-list"> ++ <choice> ++ <element name="allocations"> ++ <zeroOrMore> ++ <choice> ++ <ref name="element-allocation" /> ++ <ref name="element-promotion" /> ++ </choice> ++ </zeroOrMore> ++ </element> ++ <element name="utilizations"> ++ <zeroOrMore> ++ <choice> ++ <ref name="element-capacity" /> ++ <ref name="element-utilization" /> ++ </choice> ++ </zeroOrMore> ++ </element> ++ <element name="allocations_utilizations"> ++ <zeroOrMore> ++ <choice> ++ <ref name="element-allocation" /> ++ <ref name="element-promotion" /> ++ <ref name="element-capacity" /> ++ <ref name="element-utilization" /> ++ </choice> ++ </zeroOrMore> ++ </element> ++ </choice> ++ </define> ++ ++ <define name="cluster-status"> ++ <element name="cluster_status"> ++ <ref name="nodes-list" /> ++ <ref name="resources-list" /> ++ <optional> ++ <ref name="node-attributes-list" /> ++ </optional> ++ <optional> ++ <ref name="failures-list" /> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="modifications-list"> ++ <element name="modifications"> ++ <optional> ++ <attribute name="quorum"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="watchdog"> <text /> </attribute> ++ </optional> ++ <zeroOrMore> ++ <ref name="element-inject-modify-node" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="element-inject-modify-ticket" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="element-inject-spec" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="element-inject-attr" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="revised-cluster-status"> ++ <element name="revised_cluster_status"> ++ <ref name="nodes-list" /> ++ <ref name="resources-list" /> ++ <optional> ++ <ref name="node-attributes-list" /> ++ </optional> ++ <optional> ++ <ref name="failures-list" /> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-inject-attr"> ++ <element name="inject_attr"> ++ <attribute name="cib_node"> <text /> </attribute> ++ <attribute name="name"> <text /> </attribute> ++ <attribute name="node_path"> <text /> </attribute> ++ <attribute name="value"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-inject-modify-node"> ++ <element name="modify_node"> ++ <attribute name="action"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-inject-spec"> ++ <element name="inject_spec"> ++ <attribute name="spec"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-inject-modify-ticket"> ++ <element name="modify_ticket"> ++ <attribute name="action"> <text /> </attribute> ++ <attribute name="ticket"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="cluster-injected-actions-list"> ++ <element name="transition"> ++ <zeroOrMore> ++ <ref name="element-injected-actions" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="node-attributes-list"> ++ <element name="node_attributes"> ++ <zeroOrMore> ++ <externalRef href="node-attrs-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="failures-list"> ++ <element name="failures"> ++ <zeroOrMore> ++ <externalRef href="failure-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="nodes-list"> ++ <element name="nodes"> ++ <zeroOrMore> ++ <externalRef href="nodes-2.8.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="resources-list"> ++ <element name="resources"> ++ <zeroOrMore> ++ <externalRef href="resources-2.4.rng" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="timings-list"> ++ <element name="timings"> ++ <zeroOrMore> ++ <ref name="element-timing" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="action-list"> ++ <element name="actions"> ++ <zeroOrMore> ++ <ref name="element-node-action" /> ++ </zeroOrMore> ++ <zeroOrMore> ++ <ref name="element-rsc-action" /> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-allocation"> ++ <element name="node_weight"> ++ <attribute name="function"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ <externalRef href="../score.rng" /> ++ <optional> ++ <attribute name="id"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-capacity"> ++ <element name="capacity"> ++ <attribute name="comment"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ <zeroOrMore> ++ <element> ++ <anyName /> ++ <text /> ++ </element> ++ </zeroOrMore> ++ </element> ++ </define> ++ ++ <define name="element-inject-cluster-action"> ++ <element name="cluster_action"> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="task"> <text /> </attribute> ++ <optional> ++ <attribute name="id"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-injected-actions"> ++ <choice> ++ <ref name="element-inject-cluster-action" /> ++ <ref name="element-inject-fencing-action" /> ++ <ref name="element-inject-pseudo-action" /> ++ <ref name="element-inject-rsc-action" /> ++ </choice> ++ </define> ++ ++ <define name="element-inject-fencing-action"> ++ <element name="fencing_action"> ++ <attribute name="op"> <text /> </attribute> ++ <attribute name="target"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-node-action"> ++ <element name="node_action"> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="reason"> <text /> </attribute> ++ <attribute name="task"> <text /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-promotion"> ++ <element name="promotion_score"> ++ <attribute name="id"> <text /> </attribute> ++ <externalRef href="../score.rng" /> ++ <optional> ++ <attribute name="node"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-inject-pseudo-action"> ++ <element name="pseudo_action"> ++ <attribute name="task"> <text /> </attribute> ++ <optional> ++ <attribute name="node"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-inject-rsc-action"> ++ <element name="rsc_action"> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="op"> <text /> </attribute> ++ <attribute name="resource"> <text /> </attribute> ++ <optional> ++ <attribute name="interval"> <data type="integer" /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-timing"> ++ <element name="timing"> ++ <attribute name="file"> <text /> </attribute> ++ <attribute name="duration"> <data type="double" /> </attribute> ++ </element> ++ </define> ++ ++ <define name="element-rsc-action"> ++ <element name="rsc_action"> ++ <attribute name="action"> <text /> </attribute> ++ <attribute name="resource"> <text /> </attribute> ++ <optional> ++ <attribute name="blocked"> <data type="boolean" /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="dest"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="next-role"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="node"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="reason"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="role"> <text /> </attribute> ++ </optional> ++ <optional> ++ <attribute name="source"> <text /> </attribute> ++ </optional> ++ </element> ++ </define> ++ ++ <define name="element-utilization"> ++ <element name="utilization"> ++ <attribute name="function"> <text /> </attribute> ++ <attribute name="node"> <text /> </attribute> ++ <attribute name="resource"> <text /> </attribute> ++ <zeroOrMore> ++ <element> ++ <anyName /> ++ <text /> ++ </element> ++ </zeroOrMore> ++ </element> ++ </define> ++</grammar> +-- +1.8.3.1 + + +From c46e07788788acf5669e3f89b9344190a91c7331 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 18 Jun 2021 15:10:19 -0400 +Subject: [PATCH 4/5] Feature: tools: Add the node-summary to crm_simulate + output. + +If --show-failcounts is given to crm_simulate, it should also display +the node-summary message. + +See: rhbz#1686426 +--- + tools/crm_simulate.c | 7 +++++-- + xml/api/crm_simulate-2.12.rng | 3 +++ + 2 files changed, 8 insertions(+), 2 deletions(-) + +diff --git a/tools/crm_simulate.c b/tools/crm_simulate.c +index b4aa9d1..2ea292c 100644 +--- a/tools/crm_simulate.c ++++ b/tools/crm_simulate.c +@@ -409,11 +409,14 @@ print_cluster_status(pe_working_set_t * data_set, unsigned int print_opts) + FALSE, FALSE, all, all, FALSE); + + if (options.show_attrs) { +- out->message(out, "node-attribute-list", data_set, +- 0, rc == pcmk_rc_ok, FALSE, FALSE, FALSE, all, all); ++ rc = out->message(out, "node-attribute-list", data_set, ++ 0, rc == pcmk_rc_ok, FALSE, FALSE, FALSE, all, all); + } + + if (options.show_failcounts) { ++ rc = out->message(out, "node-summary", data_set, all, all, ++ 0, print_opts, FALSE, FALSE, FALSE, FALSE, rc == pcmk_rc_ok); ++ + out->message(out, "failed-action-list", data_set, all, all, + rc == pcmk_rc_ok); + } +diff --git a/xml/api/crm_simulate-2.12.rng b/xml/api/crm_simulate-2.12.rng +index 9a7612d..f90bd36 100644 +--- a/xml/api/crm_simulate-2.12.rng ++++ b/xml/api/crm_simulate-2.12.rng +@@ -67,6 +67,9 @@ + <ref name="node-attributes-list" /> + </optional> + <optional> ++ <externalRef href="node-history-2.12.rng" /> ++ </optional> ++ <optional> + <ref name="failures-list" /> + </optional> + </element> +-- +1.8.3.1 + + +From bac50336e0264604716e5997b87ee7e65311b982 Mon Sep 17 00:00:00 2001 +From: Chris Lumens <clumens(a)redhat.com> +Date: Fri, 18 Jun 2021 15:21:52 -0400 +Subject: [PATCH 5/5] Low: libcrmcommon: Increase PCMK__API_VERSION for new + crm_resource output. + +See: rhbz#1686426 +--- + include/crm/common/output_internal.h | 2 +- + 1 file changed, 1 insertion(+), 1 deletion(-) + +diff --git a/include/crm/common/output_internal.h b/include/crm/common/output_internal.h +index 0436cde..ba9c423 100644 +--- a/include/crm/common/output_internal.h ++++ b/include/crm/common/output_internal.h +@@ -27,7 +27,7 @@ extern "C" { + # include <glib.h> + # include <crm/common/results.h> + +-# define PCMK__API_VERSION "2.11" ++# define PCMK__API_VERSION "2.12" + + #if defined(PCMK__WITH_ATTRIBUTE_OUTPUT_ARGS) + # define PCMK__OUTPUT_ARGS(ARGS...) __attribute__((output_args(ARGS))) +-- +1.8.3.1 + diff --git a/007-unfencing-loop.patch b/007-unfencing-loop.patch new file mode 100644 index 0000000..d4950c8 --- /dev/null +++ b/007-unfencing-loop.patch @@ -0,0 +1,733 @@ +From 6dcd6b51d7d3993bc483588d6ed75077518ed600 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 4 Jun 2021 16:30:55 -0500 +Subject: [PATCH 01/11] Low: controller: check whether unfenced node was remote + node + +... so the controller can indicate the node is remote (if known at that point, +which is not guaranteed) when setting unfencing-related node attributes. +--- + daemons/controld/controld_fencing.c | 21 ++++++++++++++++++--- + 1 file changed, 18 insertions(+), 3 deletions(-) + +diff --git a/daemons/controld/controld_fencing.c b/daemons/controld/controld_fencing.c +index 23dff28..0fba661 100644 +--- a/daemons/controld/controld_fencing.c ++++ b/daemons/controld/controld_fencing.c +@@ -757,15 +757,30 @@ tengine_stonith_callback(stonith_t *stonith, stonith_callback_data_t *data) + if (pcmk__str_eq("on", op, pcmk__str_casei)) { + const char *value = NULL; + char *now = pcmk__ttoa(time(NULL)); ++ gboolean is_remote_node = FALSE; ++ ++ /* This check is not 100% reliable, since this node is not ++ * guaranteed to have the remote node cached. However, it ++ * doesn't have to be reliable, since the attribute manager can ++ * learn a node's "remoteness" by other means sooner or later. ++ * This allows it to learn more quickly if this node does have ++ * the information. ++ */ ++ if (g_hash_table_lookup(crm_remote_peer_cache, uuid) != NULL) { ++ is_remote_node = TRUE; ++ } + +- update_attrd(target, CRM_ATTR_UNFENCED, now, NULL, FALSE); ++ update_attrd(target, CRM_ATTR_UNFENCED, now, NULL, ++ is_remote_node); + free(now); + + value = crm_meta_value(action->params, XML_OP_ATTR_DIGESTS_ALL); +- update_attrd(target, CRM_ATTR_DIGESTS_ALL, value, NULL, FALSE); ++ update_attrd(target, CRM_ATTR_DIGESTS_ALL, value, NULL, ++ is_remote_node); + + value = crm_meta_value(action->params, XML_OP_ATTR_DIGESTS_SECURE); +- update_attrd(target, CRM_ATTR_DIGESTS_SECURE, value, NULL, FALSE); ++ update_attrd(target, CRM_ATTR_DIGESTS_SECURE, value, NULL, ++ is_remote_node); + + } else if (action->sent_update == FALSE) { + send_stonith_update(action, target, uuid); +-- +1.8.3.1 + + +From 3ef6d9403f68ab8559c45cc99f5a8da05ca6420b Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 10:50:36 -0500 +Subject: [PATCH 02/11] Refactor: pacemaker-attrd: functionize adding remote + node to cache + +... for future reuse +--- + daemons/attrd/attrd_commands.c | 34 +++++++++++++++++++++++----------- + 1 file changed, 23 insertions(+), 11 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 731c243..93a165b 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -102,6 +102,28 @@ free_attribute(gpointer data) + } + } + ++/*! ++ * \internal ++ * \brief Ensure a Pacemaker Remote node is in the correct peer cache ++ * ++ * \param[in] ++ */ ++static void ++cache_remote_node(const char *node_name) ++{ ++ /* If we previously assumed this node was an unseen cluster node, ++ * remove its entry from the cluster peer cache. ++ */ ++ crm_node_t *dup = pcmk__search_cluster_node_cache(0, node_name); ++ ++ if (dup && (dup->uuid == NULL)) { ++ reap_crm_member(0, node_name); ++ } ++ ++ // Ensure node is in the remote peer cache ++ CRM_ASSERT(crm_remote_peer_get(node_name) != NULL); ++} ++ + static xmlNode * + build_attribute_xml( + xmlNode *parent, const char *name, const char *set, const char *uuid, unsigned int timeout_ms, const char *user, +@@ -709,17 +731,7 @@ attrd_lookup_or_create_value(GHashTable *values, const char *host, xmlNode *xml) + + crm_element_value_int(xml, PCMK__XA_ATTR_IS_REMOTE, &is_remote); + if (is_remote) { +- /* If we previously assumed this node was an unseen cluster node, +- * remove its entry from the cluster peer cache. +- */ +- crm_node_t *dup = pcmk__search_cluster_node_cache(0, host); +- +- if (dup && (dup->uuid == NULL)) { +- reap_crm_member(0, host); +- } +- +- /* Ensure this host is in the remote peer cache */ +- CRM_ASSERT(crm_remote_peer_get(host) != NULL); ++ cache_remote_node(host); + } + + if (v == NULL) { +-- +1.8.3.1 + + +From 6fac2c71bc2c56870ac828d7cd7b7c799279c47e Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 10:39:34 -0500 +Subject: [PATCH 03/11] Refactor: pacemaker-attrd: don't try to remove votes + for remote nodes + +Remote nodes never vote. + +This has no effect in practice since the removal would simply do nothing, +but we might as well not waste time trying. +--- + daemons/attrd/attrd_commands.c | 11 ++++++----- + 1 file changed, 6 insertions(+), 5 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 93a165b..dbe777e 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -976,7 +976,8 @@ attrd_election_cb(gpointer user_data) + void + attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *data) + { +- bool remove_voter = FALSE; ++ bool gone = false; ++ bool is_remote = pcmk_is_set(peer->flags, crm_remote_node); + + switch (kind) { + case crm_status_uname: +@@ -984,7 +985,7 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da + + case crm_status_processes: + if (!pcmk_is_set(peer->processes, crm_get_cluster_proc())) { +- remove_voter = TRUE; ++ gone = true; + } + break; + +@@ -1000,13 +1001,13 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da + } else { + // Remove all attribute values associated with lost nodes + attrd_peer_remove(peer->uname, FALSE, "loss"); +- remove_voter = TRUE; ++ gone = true; + } + break; + } + +- // In case an election is in progress, remove any vote by the node +- if (remove_voter) { ++ // Remove votes from cluster nodes that leave, in case election in progress ++ if (gone && !is_remote) { + attrd_remove_voter(peer); + } + } +-- +1.8.3.1 + + +From 54089fc663d6aaf10ca164c6c94b3b17237788de Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 10:40:06 -0500 +Subject: [PATCH 04/11] Low: pacemaker-attrd: check for remote nodes in peer + update callback + +If a remote node was started before the local cluster node joined the cluster, +the cluster node will assume its node attributes are for a cluster node until +it learns otherwise. Check for remoteness in the peer update callback, to have +another way we can learn it. +--- + daemons/attrd/attrd_commands.c | 4 ++++ + 1 file changed, 4 insertions(+) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index dbe777e..5f6a754 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -1009,6 +1009,10 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da + // Remove votes from cluster nodes that leave, in case election in progress + if (gone && !is_remote) { + attrd_remove_voter(peer); ++ ++ // Ensure remote nodes that come up are in the remote node cache ++ } else if (!gone && is_remote) { ++ cache_remote_node(peer->uname); + } + } + +-- +1.8.3.1 + + +From 8c048df0312d0d9c857d87b570a352429a710928 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 11:29:12 -0500 +Subject: [PATCH 05/11] Log: pacemaker-attrd: log peer status changes + +--- + daemons/attrd/attrd_commands.c | 9 +++++++++ + 1 file changed, 9 insertions(+) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 5f6a754..d6d179b 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -972,6 +972,7 @@ attrd_election_cb(gpointer user_data) + return FALSE; + } + ++#define state_text(state) ((state)? (const char *)(state) : "in unknown state") + + void + attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *data) +@@ -981,15 +982,23 @@ attrd_peer_change_cb(enum crm_status_type kind, crm_node_t *peer, const void *da + + switch (kind) { + case crm_status_uname: ++ crm_debug("%s node %s is now %s", ++ (is_remote? "Remote" : "Cluster"), ++ peer->uname, state_text(peer->state)); + break; + + case crm_status_processes: + if (!pcmk_is_set(peer->processes, crm_get_cluster_proc())) { + gone = true; + } ++ crm_debug("Node %s is %s a peer", ++ peer->uname, (gone? "no longer" : "now")); + break; + + case crm_status_nstate: ++ crm_debug("%s node %s is now %s (was %s)", ++ (is_remote? "Remote" : "Cluster"), ++ peer->uname, state_text(peer->state), state_text(data)); + if (pcmk__str_eq(peer->state, CRM_NODE_MEMBER, pcmk__str_casei)) { + /* If we're the writer, send new peers a list of all attributes + * (unless it's a remote node, which doesn't run its own attrd) +-- +1.8.3.1 + + +From 1dcc8dee4990cf0dbdec0e14db6d9a3ad67a41d5 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Mon, 7 Jun 2021 11:13:53 -0500 +Subject: [PATCH 06/11] Low: pacemaker-attrd: ensure node ID is only set for + attributes when known + +In most cases, attribute updates contained the node ID, and the node ID was +used by other code, only if known (i.e. positive). However a couple places did +not check this, so add that. + +I am unsure whether the missing check caused problems in practice, but there +appears to be the possibility that a remote node would wrongly be added to the +cluster node cache. +--- + daemons/attrd/attrd_commands.c | 6 ++++-- + 1 file changed, 4 insertions(+), 2 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index d6d179b..b3f441c 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -136,7 +136,9 @@ build_attribute_xml( + crm_xml_add(xml, PCMK__XA_ATTR_UUID, uuid); + crm_xml_add(xml, PCMK__XA_ATTR_USER, user); + crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, peer); +- crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); ++ if (peerid > 0) { ++ crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); ++ } + crm_xml_add(xml, PCMK__XA_ATTR_VALUE, value); + crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, timeout_ms/1000); + crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, is_private); +@@ -937,7 +939,7 @@ attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) + /* If this is a cluster node whose node ID we are learning, remember it */ + if ((v->nodeid == 0) && (v->is_remote == FALSE) + && (crm_element_value_int(xml, PCMK__XA_ATTR_NODE_ID, +- (int*)&v->nodeid) == 0)) { ++ (int*)&v->nodeid) == 0) && (v->nodeid > 0)) { + + crm_node_t *known_peer = crm_get_peer(v->nodeid, host); + +-- +1.8.3.1 + + +From 8d12490e88b558d01db37a38f7d35175c6d2d69a Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Thu, 10 Jun 2021 17:25:57 -0500 +Subject: [PATCH 07/11] Refactor: pacemaker-attrd: functionize processing a + sync response + +... for code isolation, and because we need to add more to it +--- + daemons/attrd/attrd_commands.c | 59 ++++++++++++++++++++++++++++-------------- + 1 file changed, 39 insertions(+), 20 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index b3f441c..d02d3e6 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -572,6 +572,43 @@ attrd_peer_clear_failure(crm_node_t *peer, xmlNode *xml) + } + + /*! ++ * \internal ++ * \brief Load attributes from a peer sync response ++ * ++ * \param[in] peer Peer that sent clear request ++ * \param[in] peer_won Whether peer is the attribute writer ++ * \param[in] xml Request XML ++ */ ++static void ++process_peer_sync_response(crm_node_t *peer, bool peer_won, xmlNode *xml) ++{ ++ crm_info("Processing " PCMK__ATTRD_CMD_SYNC_RESPONSE " from %s", ++ peer->uname); ++ ++ if (peer_won) { ++ /* Initialize the "seen" flag for all attributes to cleared, so we can ++ * detect attributes that local node has but the writer doesn't. ++ */ ++ clear_attribute_value_seen(); ++ } ++ ++ // Process each attribute update in the sync response ++ for (xmlNode *child = pcmk__xml_first_child(xml); child != NULL; ++ child = pcmk__xml_next(child)) { ++ attrd_peer_update(peer, child, ++ crm_element_value(child, PCMK__XA_ATTR_NODE_NAME), ++ TRUE); ++ } ++ ++ if (peer_won) { ++ /* If any attributes are still not marked as seen, the writer doesn't ++ * know about them, so send all peers an update with them. ++ */ ++ attrd_current_only_attribute_update(peer, xml); ++ } ++} ++ ++/*! + \internal + \brief Broadcast private attribute for local node with protocol version + */ +@@ -596,7 +633,7 @@ attrd_peer_message(crm_node_t *peer, xmlNode *xml) + const char *op = crm_element_value(xml, PCMK__XA_TASK); + const char *election_op = crm_element_value(xml, F_CRM_TASK); + const char *host = crm_element_value(xml, PCMK__XA_ATTR_NODE_NAME); +- bool peer_won = FALSE; ++ bool peer_won = false; + + if (election_op) { + attrd_handle_election_op(peer, xml); +@@ -631,25 +668,7 @@ attrd_peer_message(crm_node_t *peer, xmlNode *xml) + + } else if (pcmk__str_eq(op, PCMK__ATTRD_CMD_SYNC_RESPONSE, pcmk__str_casei) + && !pcmk__str_eq(peer->uname, attrd_cluster->uname, pcmk__str_casei)) { +- xmlNode *child = NULL; +- +- crm_info("Processing %s from %s", op, peer->uname); +- +- /* Clear the seen flag for attribute processing held only in the own node. */ +- if (peer_won) { +- clear_attribute_value_seen(); +- } +- +- for (child = pcmk__xml_first_child(xml); child != NULL; +- child = pcmk__xml_next(child)) { +- host = crm_element_value(child, PCMK__XA_ATTR_NODE_NAME); +- attrd_peer_update(peer, child, host, TRUE); +- } +- +- if (peer_won) { +- /* Synchronize if there is an attribute held only by own node that Writer does not have. */ +- attrd_current_only_attribute_update(peer, xml); +- } ++ process_peer_sync_response(peer, peer_won, xml); + + } else if (pcmk__str_eq(op, PCMK__ATTRD_CMD_FLUSH, pcmk__str_casei)) { + /* Ignore. The flush command was removed in 2.0.0 but may be +-- +1.8.3.1 + + +From a890a0e5bbbcabf907f51ed0460868035f72464d Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 11 Jun 2021 14:40:39 -0500 +Subject: [PATCH 08/11] Refactor: pacemaker-attrd: functionize broadcasting + local override + +... for code isolation +--- + daemons/attrd/attrd_commands.c | 42 +++++++++++++++++++++++++++++------------- + 1 file changed, 29 insertions(+), 13 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index d02d3e6..4783427 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -804,6 +804,34 @@ attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml) + free_xml(sync); + } + ++/*! ++ * \internal ++ * \brief Override an attribute sync with a local value ++ * ++ * Broadcast the local node's value for an attribute that's different from the ++ * value provided in a peer's attribute synchronization response. This ensures a ++ * node's values for itself take precedence and all peers are kept in sync. ++ * ++ * \param[in] a Attribute entry to override ++ * ++ * \return Local instance of attribute value ++ */ ++static attribute_value_t * ++broadcast_local_value(attribute_t *a) ++{ ++ attribute_value_t *v = g_hash_table_lookup(a->values, attrd_cluster->uname); ++ xmlNode *sync = create_xml_node(NULL, __func__); ++ ++ crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); ++ build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, ++ a->user, a->is_private, v->nodename, v->nodeid, ++ v->current, FALSE); ++ attrd_xml_add_writer(sync); ++ send_attrd_message(NULL, sync); ++ free_xml(sync); ++ return v; ++} ++ + void + attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) + { +@@ -899,21 +927,9 @@ attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter) + if (filter && !pcmk__str_eq(v->current, value, pcmk__str_casei) + && pcmk__str_eq(host, attrd_cluster->uname, pcmk__str_casei)) { + +- xmlNode *sync = create_xml_node(NULL, __func__); +- + crm_notice("%s[%s]: local value '%s' takes priority over '%s' from %s", + attr, host, v->current, value, peer->uname); +- +- crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); +- v = g_hash_table_lookup(a->values, host); +- build_attribute_xml(sync, attr, a->set, a->uuid, a->timeout_ms, a->user, +- a->is_private, v->nodename, v->nodeid, v->current, FALSE); +- +- attrd_xml_add_writer(sync); +- +- /* Broadcast in case any other nodes had the inconsistent value */ +- send_attrd_message(NULL, sync); +- free_xml(sync); ++ v = broadcast_local_value(a); + + } else if (!pcmk__str_eq(v->current, value, pcmk__str_casei)) { + crm_notice("Setting %s[%s]: %s -> %s " CRM_XS " from %s", +-- +1.8.3.1 + + +From f6f65e3dab070f1bbdf6d1383f4d6173a8840bc9 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 11 Jun 2021 14:50:29 -0500 +Subject: [PATCH 09/11] Log: pacemaker-attrd: improve messages when + broadcasting local-only values + +The traces aren't necessary since build_attribute_xml() already logs the same +info at debug. Also, rename function for clarity, and make static. +--- + daemons/attrd/attrd_commands.c | 35 ++++++++++++++++------------------- + 1 file changed, 16 insertions(+), 19 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 4783427..356defb 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -51,11 +51,12 @@ GHashTable *attributes = NULL; + + void write_attribute(attribute_t *a, bool ignore_delay); + void write_or_elect_attribute(attribute_t *a); +-void attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml); + void attrd_peer_update(crm_node_t *peer, xmlNode *xml, const char *host, bool filter); + void attrd_peer_sync(crm_node_t *peer, xmlNode *xml); + void attrd_peer_remove(const char *host, gboolean uncache, const char *source); + ++static void broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml); ++ + static gboolean + send_attrd_message(crm_node_t * node, xmlNode * data) + { +@@ -604,7 +605,7 @@ process_peer_sync_response(crm_node_t *peer, bool peer_won, xmlNode *xml) + /* If any attributes are still not marked as seen, the writer doesn't + * know about them, so send all peers an update with them. + */ +- attrd_current_only_attribute_update(peer, xml); ++ broadcast_unseen_local_values(peer, xml); + } + } + +@@ -768,40 +769,36 @@ attrd_lookup_or_create_value(GHashTable *values, const char *host, xmlNode *xml) + return(v); + } + +-void +-attrd_current_only_attribute_update(crm_node_t *peer, xmlNode *xml) ++void ++broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml) + { + GHashTableIter aIter; + GHashTableIter vIter; +- attribute_t *a; ++ attribute_t *a = NULL; + attribute_value_t *v = NULL; +- xmlNode *sync = create_xml_node(NULL, __func__); +- gboolean build = FALSE; +- +- crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); ++ xmlNode *sync = NULL; + + g_hash_table_iter_init(&aIter, attributes); + while (g_hash_table_iter_next(&aIter, NULL, (gpointer *) & a)) { + g_hash_table_iter_init(&vIter, a->values); + while (g_hash_table_iter_next(&vIter, NULL, (gpointer *) & v)) { +- if (pcmk__str_eq(v->nodename, attrd_cluster->uname, pcmk__str_casei) && v->seen == FALSE) { +- crm_trace("Syncing %s[%s] = %s to everyone.(from local only attributes)", a->id, v->nodename, v->current); +- +- build = TRUE; ++ if (!(v->seen) && pcmk__str_eq(v->nodename, attrd_cluster->uname, ++ pcmk__str_casei)) { ++ if (sync == NULL) { ++ sync = create_xml_node(NULL, __func__); ++ crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); ++ } + build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, + v->nodename, v->nodeid, v->current, (a->timeout_ms && a->timer ? TRUE : FALSE)); +- } else { +- crm_trace("Local attribute(%s[%s] = %s) was ignore.(another host) : [%s]", a->id, v->nodename, v->current, attrd_cluster->uname); +- continue; + } + } + } + +- if (build) { +- crm_debug("Syncing values to everyone.(from local only attributes)"); ++ if (sync != NULL) { ++ crm_debug("Broadcasting local-only values"); + send_attrd_message(NULL, sync); ++ free_xml(sync); + } +- free_xml(sync); + } + + /*! +-- +1.8.3.1 + + +From ab90ffb785ea018556f216b8f540f8c3429a3947 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 11 Jun 2021 15:04:20 -0500 +Subject: [PATCH 10/11] Refactor: pacemaker-attrd: simplify attribute XML + creation function + +... and rename for clarity +--- + daemons/attrd/attrd_commands.c | 48 ++++++++++++++++++++++++------------------ + 1 file changed, 27 insertions(+), 21 deletions(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 356defb..5b32a77 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -125,25 +125,35 @@ cache_remote_node(const char *node_name) + CRM_ASSERT(crm_remote_peer_get(node_name) != NULL); + } + ++/*! ++ * \internal ++ * \brief Create an XML representation of an attribute for use in peer messages ++ * ++ * \param[in] parent Create attribute XML as child element of this element ++ * \param[in] a Attribute to represent ++ * \param[in] v Attribute value to represent ++ * \param[in] force_write If true, value should be written even if unchanged ++ * ++ * \return XML representation of attribute ++ */ + static xmlNode * +-build_attribute_xml( +- xmlNode *parent, const char *name, const char *set, const char *uuid, unsigned int timeout_ms, const char *user, +- gboolean is_private, const char *peer, uint32_t peerid, const char *value, gboolean is_force_write) ++add_attribute_value_xml(xmlNode *parent, attribute_t *a, attribute_value_t *v, ++ bool force_write) + { + xmlNode *xml = create_xml_node(parent, __func__); + +- crm_xml_add(xml, PCMK__XA_ATTR_NAME, name); +- crm_xml_add(xml, PCMK__XA_ATTR_SET, set); +- crm_xml_add(xml, PCMK__XA_ATTR_UUID, uuid); +- crm_xml_add(xml, PCMK__XA_ATTR_USER, user); +- crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, peer); +- if (peerid > 0) { +- crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, peerid); ++ crm_xml_add(xml, PCMK__XA_ATTR_NAME, a->id); ++ crm_xml_add(xml, PCMK__XA_ATTR_SET, a->set); ++ crm_xml_add(xml, PCMK__XA_ATTR_UUID, a->uuid); ++ crm_xml_add(xml, PCMK__XA_ATTR_USER, a->user); ++ crm_xml_add(xml, PCMK__XA_ATTR_NODE_NAME, v->nodename); ++ if (v->nodeid > 0) { ++ crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, v->nodeid); + } +- crm_xml_add(xml, PCMK__XA_ATTR_VALUE, value); +- crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, timeout_ms/1000); +- crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, is_private); +- crm_xml_add_int(xml, PCMK__XA_ATTR_FORCE, is_force_write); ++ crm_xml_add(xml, PCMK__XA_ATTR_VALUE, v->current); ++ crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, a->timeout_ms / 1000); ++ crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, a->is_private); ++ crm_xml_add_int(xml, PCMK__XA_ATTR_FORCE, force_write); + + return xml; + } +@@ -695,8 +705,7 @@ attrd_peer_sync(crm_node_t *peer, xmlNode *xml) + g_hash_table_iter_init(&vIter, a->values); + while (g_hash_table_iter_next(&vIter, NULL, (gpointer *) & v)) { + crm_debug("Syncing %s[%s] = %s to %s", a->id, v->nodename, v->current, peer?peer->uname:"everyone"); +- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, +- v->nodename, v->nodeid, v->current, FALSE); ++ add_attribute_value_xml(sync, a, v, false); + } + } + +@@ -788,8 +797,7 @@ broadcast_unseen_local_values(crm_node_t *peer, xmlNode *xml) + sync = create_xml_node(NULL, __func__); + crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); + } +- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, a->user, a->is_private, +- v->nodename, v->nodeid, v->current, (a->timeout_ms && a->timer ? TRUE : FALSE)); ++ add_attribute_value_xml(sync, a, v, a->timeout_ms && a->timer); + } + } + } +@@ -820,9 +828,7 @@ broadcast_local_value(attribute_t *a) + xmlNode *sync = create_xml_node(NULL, __func__); + + crm_xml_add(sync, PCMK__XA_TASK, PCMK__ATTRD_CMD_SYNC_RESPONSE); +- build_attribute_xml(sync, a->id, a->set, a->uuid, a->timeout_ms, +- a->user, a->is_private, v->nodename, v->nodeid, +- v->current, FALSE); ++ add_attribute_value_xml(sync, a, v, false); + attrd_xml_add_writer(sync); + send_attrd_message(NULL, sync); + free_xml(sync); +-- +1.8.3.1 + + +From 540d74130c5c8d9c626d6c50475e4dc4f64234e7 Mon Sep 17 00:00:00 2001 +From: Ken Gaillot <kgaillot(a)redhat.com> +Date: Fri, 4 Jun 2021 16:34:26 -0500 +Subject: [PATCH 11/11] Fix: pacemaker-attrd: avoid repeated unfencing of + remote nodes + +The attribute manager can't record a remote node's attributes to the CIB until +it knows the node is remote. Normally, this is learned when the remote node +starts, because the controller clears the CRM_OP_PROBED attribute and indicates +that it is for a remote node. + +However, if a cluster node is down when a remote node starts, and later comes +up, it learns the remote node's existing attributes as part of the attribute +sync. Previously, this did not include whether each value is for a cluster or +remote node, so the newly joined attribute manager couldn't write out remote +nodes' attributes until it learned that via some other event -- which might not +happen before the node becomes DC, in which case its scheduler will not see any +unfencing-related node attributes and may wrongly schedule unfencing. + +The sync response handling already calls attrd_lookup_or_create_value(), which +checks PCMK__XA_ATTR_IS_REMOTE, so all we need to do is add that to the sync +response. +--- + daemons/attrd/attrd_commands.c | 6 +++++- + 1 file changed, 5 insertions(+), 1 deletion(-) + +diff --git a/daemons/attrd/attrd_commands.c b/daemons/attrd/attrd_commands.c +index 5b32a77..0142383 100644 +--- a/daemons/attrd/attrd_commands.c ++++ b/daemons/attrd/attrd_commands.c +@@ -43,8 +43,9 @@ + * 1 1.1.15 PCMK__ATTRD_CMD_UPDATE_BOTH, + * PCMK__ATTRD_CMD_UPDATE_DELAY + * 2 1.1.17 PCMK__ATTRD_CMD_CLEAR_FAILURE ++ * 3 2.1.1 PCMK__ATTRD_CMD_SYNC_RESPONSE indicates remote nodes + */ +-#define ATTRD_PROTOCOL_VERSION "2" ++#define ATTRD_PROTOCOL_VERSION "3" + + int last_cib_op_done = 0; + GHashTable *attributes = NULL; +@@ -150,6 +151,9 @@ add_attribute_value_xml(xmlNode *parent, attribute_t *a, attribute_value_t *v, + if (v->nodeid > 0) { + crm_xml_add_int(xml, PCMK__XA_ATTR_NODE_ID, v->nodeid); + } ++ if (v->is_remote != 0) { ++ crm_xml_add_int(xml, PCMK__XA_ATTR_IS_REMOTE, 1); ++ } + crm_xml_add(xml, PCMK__XA_ATTR_VALUE, v->current); + crm_xml_add_int(xml, PCMK__XA_ATTR_DAMPENING, a->timeout_ms / 1000); + crm_xml_add_int(xml, PCMK__XA_ATTR_IS_PRIVATE, a->is_private); +-- +1.8.3.1 + diff --git a/gating.yaml b/gating.yaml index 9e15ced..e8aadb9 100644 --- a/gating.yaml +++ b/gating.yaml @@ -5,6 +5,7 @@ decision_context: bodhi_update_push_testing subject_type: koji_build rules: - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} + --- !Policy product_versions: - fedora-* @@ -13,3 +14,9 @@ subject_type: koji_build rules: - !PassingTestCaseRule {test_case_name: fedora-ci.koji-build.tier0.functional} +--- !Policy +product_versions: + - rhel-* +decision_context: osci_compose_gate +rules: + - !PassingTestCaseRule {test_case_name: osci.brew-build.tier0.functional} diff --git a/pacemaker.spec b/pacemaker.spec index 1f9dce2..48b6a44 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -1,9 +1,9 @@ -# Globals and defines to control package behavior (configure these as desired) +# User-configurable globals and defines to control package behavior +# (these should not test {with X} values, which are declared later) ## User and group to use for nonprivileged services %global uname hacluster %global gname haclient -%global hacluster_id 189 ## Where to install Pacemaker documentation %if 0%{?rhel} @@ -17,6 +17,13 @@ ## Where bug reports should be submitted ## Leave bug_url undefined to use ClusterLabs default, others define it here +%if 0%{?rhel} +%global bug_url https://bugzilla.redhat.com/ +%else +%if 0%{?fedora} +%global bug_url https://bugz.fedoraproject.org/%{name} +%endif +%endif ## What to use as the OCF resource agent root directory %global ocf_root %{_prefix}/lib/ocf @@ -25,19 +32,21 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.0 -%global specversion 4 +%global specversion 6 + +## Upstream commit (full commit ID, abbreviated commit ID, or tag) to build +%global commit 7c3f660707a495a1331716ad32cd3ac9d9f8ff58 -## Upstream commit (or git tag, such as "Pacemaker-" plus the -## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.1.0-rc3 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 + # Define conditionals so that "rpmbuild --with <feature>" and # "rpmbuild --without <feature>" can enable and disable specific features -## NOTE: skip --with stonithd +## Add option to enable support for stonith/external fencing agents +%bcond_with stonithd ## Add option for whether to support storing sensitive information outside CIB %if (0%{?fedora} && 0%{?fedora} <= 33) || (0%{?rhel} && 0%{?rhel} <= 8) @@ -52,8 +61,13 @@ ## Add option to create binaries with coverage analysis %bcond_with coverage -## Add option to skip/enable generating documentation +## Add option to skip (or enable, on RHEL) generating documentation +## (the build tools aren't available everywhere) +%if 0%{?rhel} +%bcond_with doc +%else %bcond_without doc +%endif ## Add option to default to start-up synchronization with SBD. ## @@ -66,16 +80,19 @@ ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) -%bcond_without pre_release +%bcond_with pre_release ## NOTE: skip --with upstart_job ## Add option to turn off hardening of libraries and daemon executables %bcond_without hardening -## Add option to enable links for legacy daemon names +## Add option to enable (or disable, on RHEL 8) links for legacy daemon names +%if 0%{?rhel} && 0%{?rhel} <= 8 +%bcond_without legacy_links +%else %bcond_with legacy_links - +%endif ## Nagios source control identifiers %global nagios_name nagios-agents-metadata @@ -94,29 +111,36 @@ ## Portion of export/dist tarball name after "pacemaker-", and release version %if 0%{tag_release} -%define archive_version %{commit} +%define archive_version %(c=%{commit}; echo ${c:10}) %define archive_github_url %{commit}#/%{name}-%{archive_version}.tar.gz -%define pcmk_release %(c=%{commit}; case $c in *-rc[[:digit:]]*%{rparen} - echo 0.%{specversion}.${c: -3} ;; - *%{rparen} echo %{specversion} ;; esac) %else %define archive_version %(c=%{commit}; echo ${c:0:%{commit_abbrev}}) %define archive_github_url %{archive_version}#/%{name}-%{archive_version}.tar.gz -%if %{with pre_release} -%define pcmk_release 0.%{specversion}.%{archive_version}.git -%else -%define pcmk_release %{specversion}.%{archive_version}.git -%endif %endif +### Always use a simple release number +%define pcmk_release %{specversion} ## Base GnuTLS cipher priorities (presumably only the initial, required keyword) ## overridable with "rpmbuild --define 'pcmk_gnutls_priorities PRIORITY-SPEC'" %define gnutls_priorities %{?pcmk_gnutls_priorities}%{!?pcmk_gnutls_priorities:@SYSTEM} +## Different distros name certain packages differently +## (note: corosync libraries also differ, but all provide corosync-devel) +%global pkgname_libtool_devel libtool-ltdl-devel +%global pkgname_libtool_devel_arch libtool-ltdl-devel%{?_isa} +%global pkgname_bzip2_devel bzip2-devel +%global pkgname_docbook_xsl docbook-style-xsl +%global pkgname_gnutls_devel gnutls-devel +%global pkgname_shadow_utils shadow-utils +%global pkgname_procps procps-ng +%global pkgname_glue_libs cluster-glue-libs +%global pkgname_pcmk_libs %{name}-libs +%global hacluster_id 189 + ## Distro-specific configuration choices ### Use 2.0-style output when other distro packages don't support current output -%if 0%{?fedora} +%if 0%{?fedora} || ( 0%{?rhel} && 0%{?rhel} <= 8 ) %global compat20 --enable-compat-2.0 %endif @@ -130,6 +154,7 @@ %global resource_stickiness --with-resource-stickiness-default=1 %endif + # Python-related definitions ## Turn off auto-compilation of Python files outside Python specific paths, @@ -145,13 +170,24 @@ sed -e 's!/usr/lib[^[:space:]]*/brp-python-bytecompile[[:space:]].*$!!g'; }) %endif -## Values that differ by Python major version +## Prefer Python 3 definitions explicitly, in case 2 is also available +%if %{defined __python3} %global python_name python3 -%global python_path %{?__python3}%{!?__python3:/usr/bin/python%{?python3_pkgversion}%{!?python3_pkgversion:3}} +%global python_path %{__python3} %define python_site %{?python3_sitelib}%{!?python3_sitelib:%( %{python_path} -c 'from distutils.sysconfig import get_python_lib as gpl; print(gpl(1))' 2>/dev/null)} -%global python_min 3.2 -# python_min still required? +%else +%if %{defined python_version} +%global python_name python%(echo %{python_version} | cut -d'.' -f1) +%define python_path %{?__python}%{!?__python:/usr/bin/%{python_name}} +%else +%global python_name python +%global python_path %{?__python}%{!?__python:/usr/bin/python%{?python_pkgversion}} +%endif +%define python_site %{?python_sitelib}%{!?python_sitelib:%( + %{python_name} -c 'from distutils.sysconfig import get_python_lib as gpl; print(gpl(1))' 2>/dev/null)} +%endif + # Keep sane profiling data if requested %if %{with profiling} @@ -165,25 +201,46 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ -Url: https://www.clusterlabs.org - -# Hint: use "spectool -s 0 pacemaker.spec" (rpmdevtools) to check the final URL +Url: https://www.clusterlabs.org/ + +# Example: https://codeload.github.com/ClusterLabs/pacemaker/tar.gz/e91769e +# will download pacemaker-e91769e.tar.gz +# +# The ending part starting with '#' is ignored by github but necessary for +# rpmbuild to know what the tar archive name is. (The downloaded file will be +# named correctly only for commit IDs, not tagged releases.) +# +# You can use "spectool -s 0 pacemaker.spec" (rpmdevtools) to show final URL. Source0: https://codeload.github.com/%{github_owner}/%{name}/tar.gz/%{archive_gith... Source1: https://codeload.github.com/%{github_owner}/%{nagios_name}/tar.gz/%{nagio... -# --- + +# upstream commits +Patch1: 001-ping-agent.patch +Patch2: 002-pacemakerd-options.patch +Patch3: 003-pacemakerd-output.patch +Patch4: 004-check-level.patch +Patch5: 005-crm_resource.patch +Patch6: 006-crm_simulate.patch +Patch7: 007-unfencing-loop.patch Requires: resource-agents -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Requires: %{name}-cluster-libs%{?_isa} = %{version}-%{release} Requires: %{name}-cli = %{version}-%{release} %{?systemd_requires} -# Pacemaker requires a minimum Python functionality -Requires: %{python_name} >= %{python_min} -BuildRequires: make -BuildRequires: %{python_name}-devel >= %{python_min} +%if %{defined centos} +ExclusiveArch: aarch64 i686 ppc64le s390x x86_64 %{arm} +%else +%if 0%{?rhel} +ExclusiveArch: aarch64 i686 ppc64le s390x x86_64 +%endif +%endif + +Requires: %{python_path} +BuildRequires: %{python_name}-devel # Pacemaker requires a minimum libqb functionality Requires: libqb >= 0.17.0 @@ -192,37 +249,41 @@ BuildRequires: libqb-devel >= 0.17.0 # Required basic build tools BuildRequires: coreutils findutils grep sed BuildRequires: autoconf automake gcc make pkgconfig -BuildRequires: libtool libtool-ltdl-devel +BuildRequires: libtool %{?pkgname_libtool_devel} # Required for core functionality BuildRequires: pkgconfig(glib-2.0) >= 2.42 BuildRequires: libxml2-devel libxslt-devel libuuid-devel -BuildRequires: bzip2-devel +BuildRequires: %{pkgname_bzip2_devel} # Enables optional functionality -BuildRequires: ncurses-devel docbook-style-xsl -BuildRequires: help2man gnutls-devel pam-devel pkgconfig(dbus-1) +BuildRequires: ncurses-devel %{pkgname_docbook_xsl} +BuildRequires: help2man %{pkgname_gnutls_devel} pam-devel pkgconfig(dbus-1) BuildRequires: pkgconfig(systemd) +# RH patches are created by git, so we need git to apply them +BuildRequires: git + Requires: corosync >= 2.0.0 BuildRequires: corosync-devel >= 2.0.0 -#XXX -#BuildRequires: pkgconfig(libcpg) -#BuildRequires: pkgconfig(libcfg) + +%if %{with stonithd} +BuildRequires: %{pkgname_glue_libs}-devel +%endif %if %{with doc} BuildRequires: asciidoc inkscape %{python_name}-sphinx %endif -# git-style patch application -#BuildRequires: git - Provides: pcmk-cluster-manager = %{version}-%{release} Provides: pcmk-cluster-manager%{?_isa} = %{version}-%{release} -# Pacemaker uses the crypto/md5 module from gnulib +# Bundled bits +## Pacemaker uses the crypto/md5-buffer module from gnulib +%if 0%{?fedora} || 0%{?rhel} Provides: bundled(gnulib) +%endif %description Pacemaker is an advanced, scalable High-Availability cluster resource @@ -236,18 +297,18 @@ when related resources fail and can be configured to periodically check resource health. Available rpmbuild rebuild options: - --with(out) : cibsecrets coverage doc hardening pre_release profiling + --with(out) : cibsecrets coverage doc hardening pre_release profiling stonithd %package cli License: GPLv2+ and LGPLv2+ Summary: Command line tools for controlling Pacemaker clusters -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Recommends: pcmk-cluster-manager = %{version}-%{release} # For crm_report Recommends: tar Recommends: bzip2 Requires: perl-TimeDate -Requires: procps-ng +Requires: %{pkgname_procps} Requires: psmisc Requires(post):coreutils @@ -259,28 +320,29 @@ The %{name}-cli package contains command line tools that can be used to query and control the cluster from machines that may, or may not, be part of the cluster. -%package libs +%package -n %{pkgname_pcmk_libs} License: GPLv2+ and LGPLv2+ Summary: Core Pacemaker libraries -Requires(pre): shadow-utils +Requires(pre): %{pkgname_shadow_utils} Requires: %{name}-schemas = %{version}-%{release} # sbd 1.4.0+ supports the libpe_status API for pe_working_set_t # sbd 1.4.2+ supports startup/shutdown handshake via pacemakerd-api # and handshake defaults to enabled for rhel builds -# sbd 1.4.3+ handshake defaults to enabled for fedora builds -Conflicts: sbd < 1.4.3 +# sbd 1.5.0+ handshake defaults to enabled with upstream sbd-release +# implicitly supports handshake defaults to enabled in this spec +Conflicts: sbd < 1.5.0 -%description libs +%description -n %{pkgname_pcmk_libs} Pacemaker is an advanced, scalable High-Availability cluster resource manager. -The %{name}-libs package contains shared libraries needed for cluster +The %{pkgname_pcmk_libs} package contains shared libraries needed for cluster nodes and those just running the CLI tools. %package cluster-libs License: GPLv2+ and LGPLv2+ Summary: Cluster Libraries used by Pacemaker -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} %description cluster-libs Pacemaker is an advanced, scalable High-Availability cluster resource @@ -292,7 +354,7 @@ libraries needed for nodes that will form part of the cluster nodes. %package remote License: GPLv2+ and LGPLv2+ Summary: Pacemaker remote executor daemon for non-cluster nodes -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Requires: %{name}-cli = %{version}-%{release} Requires: resource-agents # -remote can be fully independent of systemd @@ -308,35 +370,40 @@ The %{name}-remote package contains the Pacemaker Remote daemon which is capable of extending pacemaker functionality to remote nodes not running the full corosync/cluster stack. -%package libs-devel +%package -n %{pkgname_pcmk_libs}-devel License: GPLv2+ and LGPLv2+ Summary: Pacemaker development package -Requires: %{name}-libs%{?_isa} = %{version}-%{release} +Requires: %{pkgname_pcmk_libs}%{?_isa} = %{version}-%{release} Requires: %{name}-cluster-libs%{?_isa} = %{version}-%{release} -Requires: libtool-ltdl-devel%{?_isa} libuuid-devel%{?_isa} +Requires: %{?pkgname_libtool_devel_arch} libuuid-devel%{?_isa} Requires: libxml2-devel%{?_isa} libxslt-devel%{?_isa} -Requires: bzip2-devel%{?_isa} glib2-devel%{?_isa} +Requires: %{pkgname_bzip2_devel}%{?_isa} glib2-devel%{?_isa} Requires: libqb-devel%{?_isa} Requires: corosync-devel%{?_isa} >= 2.0.0 -%description libs-devel +%description -n %{pkgname_pcmk_libs}-devel Pacemaker is an advanced, scalable High-Availability cluster resource manager. -The %{name}-libs-devel package contains headers and shared libraries +The %{pkgname_pcmk_libs}-devel package contains headers and shared libraries for developing tools for Pacemaker. %package cts License: GPLv2+ and LGPLv2+ Summary: Test framework for cluster-related technologies like Pacemaker Requires: %{python_path} -Requires: %{python_name} >= %{python_min} -Requires: %{name}-libs = %{version}-%{release} -Requires: procps-ng +Requires: %{pkgname_pcmk_libs} = %{version}-%{release} +Requires: %{name}-cli = %{version}-%{release} +Requires: %{pkgname_procps} Requires: psmisc BuildArch: noarch +# systemd Python bindings are a separate package in some distros +%if %{defined systemd_requires} +%if %{defined fedora} || %{defined rhel} Requires: %{python_name}-systemd +%endif +%endif %description cts Test framework for cluster-related technologies like Pacemaker @@ -382,7 +449,10 @@ The metadata files required for Pacemaker to execute the nagios plugin monitor resources. %prep -%setup -q -a 1 -n %{name}-%{archive_version} +%autosetup -a 1 -n %{name}-%{archive_version} -S git_am -p 1 +# in f33 s390x complains but shouldn't hurt globally +# as configure.ac is checking for support +sed -i configure.ac -e "s/-Wall/-Wall -Wno-format-truncation/" %build @@ -420,11 +490,10 @@ export LDFLAGS_HARDENED_LIB="%{?_hardening_ldflags}" --with-initdir=%{_initrddir} \ --with-runstatedir=%{_rundir} \ --localstatedir=%{_var} \ - --with-version=%{version}-%{release} \ - --with-bug-url=https://bugz.fedoraproject.org/%{name} \ - --with-nagios \ - --with-nagios-metadata-dir=%{_datadir}/pacemaker/nagios/plugins-metadata/ \ - --with-nagios-plugin-dir=%{_libdir}/nagios/plugins/ + --with-nagios \ + --with-nagios-metadata-dir=%{_datadir}/pacemaker/nagios/plugins-metadata/ \ + --with-nagios-plugin-dir=%{_libdir}/nagios/plugins/ \ + --with-version=%{version}-%{release} make %{_smp_mflags} V=1 @@ -453,11 +522,7 @@ done mkdir -p ${RPM_BUILD_ROOT}%{_localstatedir}/lib/rpm-state/%{name} -# These are not actually scripts -find %{buildroot} -name '*.xml' -type f -print0 | xargs -0 chmod a-x - -# Don't package static libs -find %{buildroot} -name '*.a' -type f -print0 | xargs -0 rm -f +# Don't package libtool archives find %{buildroot} -name '*.la' -type f -print0 | xargs -0 rm -f # Do not package these either @@ -475,7 +540,7 @@ rm -f %{buildroot}/%{_initrddir}/pacemaker rm -f %{buildroot}/%{_initrddir}/pacemaker_remote # Byte-compile Python sources where suitable and the distro procedures known -%if %{defined py_byte_compile} && %{defined python_path} +%if %{defined py_byte_compile} %{py_byte_compile %{python_path} %{buildroot}%{_datadir}/pacemaker/tests} %if !%{defined _python_bytecompile_extra} %{py_byte_compile %{python_path} %{buildroot}%{python_site}/cts} @@ -552,15 +617,14 @@ fi %postun cli %systemd_postun_with_restart crm_mon.service -%pre libs -# XXX keep an eye on https://fedoraproject.org/wiki/Changes/SystemdSysusers -# reopened recently: -# https://lists.fedoraproject.org/archives/list/devel@lists.fedoraproject.o... +%pre -n %{pkgname_pcmk_libs} +# @TODO Use sysusers.d: +# https://fedoraproject.org/wiki/Changes/Adopting_sysusers.d_format getent group %{gname} >/dev/null || groupadd -r %{gname} -g %{hacluster_id} getent passwd %{uname} >/dev/null || useradd -r -g %{gname} -u %{hacluster_id} -s /sbin/nologin -c "cluster user" %{uname} exit 0 -%ldconfig_scriptlets libs +%ldconfig_scriptlets -n %{pkgname_pcmk_libs} %ldconfig_scriptlets cluster-libs %files @@ -667,7 +731,7 @@ exit 0 %dir %attr (770, %{uname}, %{gname}) %{_var}/log/pacemaker %dir %attr (770, %{uname}, %{gname}) %{_var}/log/pacemaker/bundles -%files libs +%files -n %{pkgname_pcmk_libs} %{_libdir}/libcib.so.* %{_libdir}/liblrmd.so.* %{_libdir}/libcrmservice.so.* @@ -716,7 +780,7 @@ exit 0 %doc COPYING %doc ChangeLog -%files libs-devel +%files -n %{pkgname_pcmk_libs}-devel %{_includedir}/pacemaker %{_libdir}/*.so %if %{with coverage} @@ -742,6 +806,12 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Jul 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-6 +- synced/merged with CS9 spec-file for current 2.1.0-release build + +* Tue Jun 8 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.5.rc3 +- silence f33 s390x build complaining about possible format-trucation + * Mon Jun 07 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.4.rc3.1 - Rebuilt for Python 3.10 @@ -753,7 +823,7 @@ exit 0 * Fri Jun 04 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.3.rc2.1 - Rebuilt for Python 3.10 -* Mon Jun 1 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 +* Mon May 31 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc2, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc2 diff --git a/sources b/sources index af5cd77..2ab7f32 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.1.0-rc3.tar.gz) = eb17566e079d313394dab509b055e326b642508844d974a21cde62509a3a526e44977a57c65f80d5094f085fec8ad92eda0deed4f4dfd32ecf0c3b80722e5504 +SHA512 (pacemaker-7c3f66070.tar.gz) = e1c53d019c965395affc1bd78358927617c9bc8572c405ee884737a8213455c5e85102e6f58bb5239ab23ebe5aa794f72c9cc0746900b7a6cc14fd3cf1879064 commit 5dc83e38659be95da4423eed082e2fb0029e2848 Author: Python Maint <python-maint(a)redhat.com> Date: Mon Jun 7 19:14:33 2021 +0200 Rebuilt for Python 3.10 diff --git a/pacemaker.spec b/pacemaker.spec index bf413b5..1f9dce2 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -165,7 +165,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist} +Release: %{pcmk_release}%{?dist}.1 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -742,6 +742,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Jun 07 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.4.rc3.1 +- Rebuilt for Python 3.10 + * Mon Jun 07 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.4.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc3, for full details, see included ChangeLog file or commit e52de4390a10fcc15efd749a705386ea8b46e0b4 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Mon Jun 7 15:55:07 2021 +0200 * Mon Jun 07 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.4.rc3 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc3, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc3 diff --git a/pacemaker.spec b/pacemaker.spec index a6800fc..bf413b5 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -25,11 +25,11 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.0 -%global specversion 3 +%global specversion 4 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.1.0-rc2 +%global commit Pacemaker-2.1.0-rc3 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -165,7 +165,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -742,6 +742,11 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Jun 07 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.4.rc3 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc3, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc3 + * Fri Jun 04 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.3.rc2.1 - Rebuilt for Python 3.10 diff --git a/sources b/sources index 76e3c9a..af5cd77 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.1.0-rc2.tar.gz) = 01396cd23b0cb49cab40b870e227b132f1e0c9b94cf6ac29d58e61bd3ff4ee4ea95fa6509c9a4a09179284b8fdbdba8319ceb46e8f94ce9cea92cf13832f9f4d +SHA512 (pacemaker-Pacemaker-2.1.0-rc3.tar.gz) = eb17566e079d313394dab509b055e326b642508844d974a21cde62509a3a526e44977a57c65f80d5094f085fec8ad92eda0deed4f4dfd32ecf0c3b80722e5504 commit 172718bb48a11ed751025770698e5452ae20a815 Author: Python Maint <python-maint(a)redhat.com> Date: Fri Jun 4 20:14:25 2021 +0200 Rebuilt for Python 3.10 diff --git a/pacemaker.spec b/pacemaker.spec index 979a0e0..a6800fc 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -165,7 +165,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist} +Release: %{pcmk_release}%{?dist}.1 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -742,6 +742,9 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Fri Jun 04 2021 Python Maint <python-maint(a)redhat.com> - 2.1.0-0.3.rc2.1 +- Rebuilt for Python 3.10 + * Mon Jun 1 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc2, for full details, see included ChangeLog file or commit 595ee6bf2a7d18022e3d17a40b07aafea1960ecf Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Tue Jun 1 13:50:20 2021 +0200 * Mon Jun 1 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc2, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc2 - merge changes in upstream specfile sind Pacemaker-2.1.0-rc1 add configurable ocf_root enable cibsecrets for > f33 require libqb >= 0.17.0 instead of 0.13.0 default to syncing with sbd conflict all sbd < 1.4.3 to enforce sbd-build has the same default diff --git a/pacemaker.spec b/pacemaker.spec index 885a70e..979a0e0 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -15,15 +15,21 @@ ## GitHub entity that distributes source (for ease of using a fork) %global github_owner ClusterLabs +## Where bug reports should be submitted +## Leave bug_url undefined to use ClusterLabs default, others define it here + +## What to use as the OCF resource agent root directory +%global ocf_root %{_prefix}/lib/ocf + ## Upstream pacemaker version, and its package version (specversion ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.0 -%global specversion 2 +%global specversion 3 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.1.0-rc1 +%global commit Pacemaker-2.1.0-rc2 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -33,8 +39,12 @@ ## NOTE: skip --with stonithd -## Add option to enable support for storing sensitive information outside CIB +## Add option for whether to support storing sensitive information outside CIB +%if (0%{?fedora} && 0%{?fedora} <= 33) || (0%{?rhel} && 0%{?rhel} <= 8) %bcond_with cibsecrets +%else +%bcond_without cibsecrets +%endif ## Add option to create binaries suitable for use with profiling tools %bcond_with profiling @@ -45,6 +55,15 @@ ## Add option to skip/enable generating documentation %bcond_without doc +## Add option to default to start-up synchronization with SBD. +## +## If enabled, SBD *MUST* be built to default similarly, otherwise data +## corruption could occur. Building both Pacemaker and SBD to default +## to synchronization improves safety, without requiring higher-level tools +## to be aware of the setting or requiring users to modify configurations +## after upgrading to versions that support synchronization. +%bcond_without sbd_sync + ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) %bcond_without pre_release @@ -167,14 +186,15 @@ BuildRequires: make BuildRequires: %{python_name}-devel >= %{python_min} # Pacemaker requires a minimum libqb functionality -Requires: libqb >= 0.13.0 -BuildRequires: libqb-devel >= 0.13.0 +Requires: libqb >= 0.17.0 +BuildRequires: libqb-devel >= 0.17.0 -# Basics required for the build (even if usually satisfied through other BRs) +# Required basic build tools BuildRequires: coreutils findutils grep sed +BuildRequires: autoconf automake gcc make pkgconfig +BuildRequires: libtool libtool-ltdl-devel # Required for core functionality -BuildRequires: automake autoconf gcc libtool pkgconfig libtool-ltdl-devel BuildRequires: pkgconfig(glib-2.0) >= 2.42 BuildRequires: libxml2-devel libxslt-devel libuuid-devel BuildRequires: bzip2-devel @@ -245,7 +265,10 @@ Summary: Core Pacemaker libraries Requires(pre): shadow-utils Requires: %{name}-schemas = %{version}-%{release} # sbd 1.4.0+ supports the libpe_status API for pe_working_set_t -Conflicts: sbd < 1.4.0 +# sbd 1.4.2+ supports startup/shutdown handshake via pacemakerd-api +# and handshake defaults to enabled for rhel builds +# sbd 1.4.3+ handshake defaults to enabled for fedora builds +Conflicts: sbd < 1.4.3 %description libs Pacemaker is an advanced, scalable High-Availability cluster resource @@ -268,7 +291,7 @@ libraries needed for nodes that will form part of the cluster nodes. %package remote License: GPLv2+ and LGPLv2+ -Summary: Pacemaker remote daemon for non-cluster nodes +Summary: Pacemaker remote executor daemon for non-cluster nodes Requires: %{name}-libs%{?_isa} = %{version}-%{release} Requires: %{name}-cli = %{version}-%{release} Requires: resource-agents @@ -386,7 +409,10 @@ export LDFLAGS_HARDENED_LIB="%{?_hardening_ldflags}" %{?with_profiling: --with-profiling} \ %{?with_coverage: --with-coverage} \ %{?with_cibsecrets: --with-cibsecrets} \ + %{?with_sbd_sync: --with-sbd-sync-default="true"} \ %{?gnutls_priorities: --with-gnutls-priorities="%{gnutls_priorities}"} \ + %{?bug_url: --with-bug-url=%{bug_url}} \ + %{?ocf_root: --with-ocfdir=%{ocf_root}} \ %{?concurrent_fencing} \ %{?resource_stickiness} \ %{?compat20} \ @@ -572,8 +598,8 @@ exit 0 %dir %attr (750, %{uname}, %{gname}) %{_var}/lib/pacemaker/cib %dir %attr (750, %{uname}, %{gname}) %{_var}/lib/pacemaker/pengine -/usr/lib/ocf/resource.d/pacemaker/controld -/usr/lib/ocf/resource.d/pacemaker/remote +%{ocf_root}/resource.d/pacemaker/controld +%{ocf_root}/resource.d/pacemaker/remote %files cli %dir %attr (750, root, %{gname}) %{_sysconfdir}/pacemaker @@ -609,13 +635,13 @@ exit 0 # XXX "dirname" is not owned by any prerequisite %{_datadir}/snmp/mibs/PCMK-MIB.txt -%exclude /usr/lib/ocf/resource.d/pacemaker/controld -%exclude /usr/lib/ocf/resource.d/pacemaker/o2cb -%exclude /usr/lib/ocf/resource.d/pacemaker/remote +%exclude %{ocf_root}/resource.d/pacemaker/controld +%exclude %{ocf_root}/resource.d/pacemaker/o2cb +%exclude %{ocf_root}/resource.d/pacemaker/remote -%dir /usr/lib/ocf -%dir /usr/lib/ocf/resource.d -/usr/lib/ocf/resource.d/pacemaker +%dir %{ocf_root} +%dir %{ocf_root}/resource.d +%{ocf_root}/resource.d/pacemaker %doc %{_mandir}/man7/* %exclude %{_mandir}/man7/pacemaker-controld.* @@ -716,6 +742,17 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Mon Jun 1 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.3.rc2 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc2, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc2 +- merge changes in upstream specfile sind Pacemaker-2.1.0-rc1 + add configurable ocf_root + enable cibsecrets for > f33 + require libqb >= 0.17.0 instead of 0.13.0 + default to syncing with sbd + conflict all sbd < 1.4.3 to enforce sbd-build has the same default + * Wed May 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.2.rc1 - remove PCMK_TIME_EMERGENCY_CGT not present in pacemaker codebase anymore - enable Pacemaker-2.0-compatibility for a fedora versions diff --git a/sources b/sources index a976443..76e3c9a 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.1.0-rc1.tar.gz) = 64fef270ac0f0df63a2ac974c4467dfb6a646cbe2089c6b523f14311bf236653caa75cd9e2851af7882057d63651ecd3c9d40647349a76619c4522c938063acf +SHA512 (pacemaker-Pacemaker-2.1.0-rc2.tar.gz) = 01396cd23b0cb49cab40b870e227b132f1e0c9b94cf6ac29d58e61bd3ff4ee4ea95fa6509c9a4a09179284b8fdbdba8319ceb46e8f94ce9cea92cf13832f9f4d commit e7aab8014f11ec96139f581de2cfe66c85975ed0 Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Fri May 7 11:11:12 2021 +0200 * Wed May 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.2.rc1 - remove PCMK_TIME_EMERGENCY_CGT not present in pacemaker codebase anymore - enable Pacemaker-2.0-compatibility for a fedora versions diff --git a/pacemaker.spec b/pacemaker.spec index 676075c..885a70e 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -19,7 +19,7 @@ ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) %global pcmkversion 2.1.0 -%global specversion 1 +%global specversion 2 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package @@ -97,7 +97,7 @@ ## Distro-specific configuration choices ### Use 2.0-style output when other distro packages don't support current output -%if 0%{?fedora} && 0%{?fedora} <= 34 +%if 0%{?fedora} %global compat20 --enable-compat-2.0 %endif @@ -379,9 +379,6 @@ export LDFLAGS_HARDENED_LIB="%{?_hardening_ldflags}" ./autogen.sh -# Rawhide glibc doesn't like ftime at all -export CPPFLAGS="-UPCMK_TIME_EMERGENCY_CGT $CPPFLAGS" - %{configure} \ PYTHON=%{python_path} \ %{!?with_hardening: --disable-hardening} \ @@ -719,6 +716,10 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Wed May 5 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.2.rc1 +- remove PCMK_TIME_EMERGENCY_CGT not present in pacemaker codebase anymore +- enable Pacemaker-2.0-compatibility for a fedora versions + * Tue May 4 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc1, for full details, see included ChangeLog file or commit c8cc15254d66b4d69d4d3eb547808fcfd172662a Author: Klaus Wenninger <klaus.wenninger(a)aon.at> Date: Tue May 4 22:24:44 2021 +0200 * Tue May 4 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.1.rc1 - Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc1, for full details, see included ChangeLog file or https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc1 - merge changes in upstream spec-file since Pacemaker-2.0.5 - disable legacy-links diff --git a/pacemaker.spec b/pacemaker.spec index b786f9c..676075c 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -18,12 +18,12 @@ ## Upstream pacemaker version, and its package version (specversion ## can be incremented to build packages reliably considered "newer" ## than previously built packages with the same pcmkversion) -%global pcmkversion 2.0.5 -%global specversion 10 +%global pcmkversion 2.1.0 +%global specversion 1 ## Upstream commit (or git tag, such as "Pacemaker-" plus the ## {pcmkversion} macro for an official release) to use for this package -%global commit Pacemaker-2.0.5 +%global commit Pacemaker-2.1.0-rc1 ## Since git v2.11, the extent of abbreviation is autoscaled by default ## (used to be constant of 7), so we need to convey it for non-tags, too. %global commit_abbrev 9 @@ -43,24 +43,19 @@ %bcond_with coverage ## Add option to skip/enable generating documentation -## (the build tools aren't available everywhere) -%if 0%{?rhel} - %bcond_with doc -%else - %bcond_without doc -%endif +%bcond_without doc ## Add option to prefix package version with "0." ## (so later "official" packages will be considered updates) -%bcond_with pre_release +%bcond_without pre_release ## NOTE: skip --with upstart_job ## Add option to turn off hardening of libraries and daemon executables %bcond_without hardening -## Add option to disable links for legacy daemon names -%bcond_without legacy_links +## Add option to enable links for legacy daemon names +%bcond_with legacy_links ## Nagios source control identifiers @@ -95,14 +90,27 @@ %endif %endif -## Heuristic used to infer bleeding-edge deployments that are -## less likely to have working versions of the documentation tools -%define bleeding %(test ! -e /etc/yum.repos.d/fedora-rawhide.repo; echo $?) - ## Base GnuTLS cipher priorities (presumably only the initial, required keyword) ## overridable with "rpmbuild --define 'pcmk_gnutls_priorities PRIORITY-SPEC'" %define gnutls_priorities %{?pcmk_gnutls_priorities}%{!?pcmk_gnutls_priorities:@SYSTEM} +## Distro-specific configuration choices + +### Use 2.0-style output when other distro packages don't support current output +%if 0%{?fedora} && 0%{?fedora} <= 34 +%global compat20 --enable-compat-2.0 +%endif + +### Default concurrent-fencing to true when distro prefers that +%if 0%{?rhel} +%global concurrent_fencing --with-concurrent-fencing-default=true +%endif + +### Default resource-stickiness to 1 when distro prefers that +%if 0%{?fedora} >= 35 || 0%{?rhel} >= 9 +%global resource_stickiness --with-resource-stickiness-default=1 +%endif + # Python-related definitions ## Turn off auto-compilation of Python files outside Python specific paths, @@ -138,7 +146,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.2 +Release: %{pcmk_release}%{?dist} License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -167,7 +175,7 @@ BuildRequires: coreutils findutils grep sed # Required for core functionality BuildRequires: automake autoconf gcc libtool pkgconfig libtool-ltdl-devel -BuildRequires: pkgconfig(glib-2.0) >= 2.16 +BuildRequires: pkgconfig(glib-2.0) >= 2.42 BuildRequires: libxml2-devel libxslt-devel libuuid-devel BuildRequires: bzip2-devel @@ -183,11 +191,8 @@ BuildRequires: corosync-devel >= 2.0.0 #BuildRequires: pkgconfig(libcpg) #BuildRequires: pkgconfig(libcfg) -## (note no avoiding effect when building through non-customized mock) -%if !%{bleeding} %if %{with doc} -BuildRequires: asciidoc inkscape publican -%endif +BuildRequires: asciidoc inkscape %{python_name}-sphinx %endif # git-style patch application @@ -380,12 +385,14 @@ export CPPFLAGS="-UPCMK_TIME_EMERGENCY_CGT $CPPFLAGS" %{configure} \ PYTHON=%{python_path} \ %{!?with_hardening: --disable-hardening} \ - %{!?with_legacy_links: --disable-legacy-links} \ + %{?with_legacy_links: --enable-legacy-links} \ %{?with_profiling: --with-profiling} \ %{?with_coverage: --with-coverage} \ %{?with_cibsecrets: --with-cibsecrets} \ - %{!?with_doc: --with-brand=} \ %{?gnutls_priorities: --with-gnutls-priorities="%{gnutls_priorities}"} \ + %{?concurrent_fencing} \ + %{?resource_stickiness} \ + %{?compat20} \ --disable-static \ --with-initdir=%{_initrddir} \ --with-runstatedir=%{_rundir} \ @@ -415,10 +422,6 @@ make install \ DESTDIR=%{buildroot} V=1 docdir=%{pcmk_docdir} \ %{?_python_bytecompile_extra:%{?py_byte_compile:am__py_compile=true}} -mkdir -p ${RPM_BUILD_ROOT}%{_sysconfdir}/sysconfig -install -m 644 daemons/pacemakerd/pacemaker.sysconfig ${RPM_BUILD_ROOT}%{_sysconfdir}/sysconfig/pacemaker -install -m 644 tools/crm_mon.sysconfig ${RPM_BUILD_ROOT}%{_sysconfdir}/sysconfig/crm_mon - mkdir -p %{buildroot}%{_datadir}/pacemaker/nagios/plugins-metadata for file in $(find %{nagios_name}-%{nagios_hash}/metadata -type f); do install -m 644 $file %{buildroot}%{_datadir}/pacemaker/nagios/plugins-metadata @@ -549,9 +552,7 @@ exit 0 %exclude %{_libexecdir}/pacemaker/cts-log-watcher %exclude %{_libexecdir}/pacemaker/cts-support %exclude %{_sbindir}/pacemaker-remoted -%if %{with legacy_links} %exclude %{_sbindir}/pacemaker_remoted -%endif %{_libexecdir}/pacemaker/* %{_sbindir}/crm_attribute @@ -671,9 +672,7 @@ exit 0 %{_unitdir}/pacemaker_remote.service %{_sbindir}/pacemaker-remoted -%if %{with legacy_links} %{_sbindir}/pacemaker_remoted -%endif %{_mandir}/man8/pacemaker-remoted.* %license licenses/GPLv2 %doc COPYING @@ -720,6 +719,13 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Tue May 4 2021 Klaus Wenninger <kwenning(a)redhat.com> - 2.1.0-0.1.rc1 +- Update for new upstream tarball for release candidate: Pacemaker-2.1.0-rc1, + for full details, see included ChangeLog file or + https://github.com/ClusterLabs/pacemaker/releases/tag/Pacemaker-2.1.0-rc1 +- merge changes in upstream spec-file since Pacemaker-2.0.5 +- disable legacy-links + * Tue Mar 02 2021 Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> - 2.0.5-10.2 - Rebuilt for updated systemd-rpm-macros See https://pagure.io/fesco/issue/2583. diff --git a/sources b/sources index b19a593..a976443 100644 --- a/sources +++ b/sources @@ -1,2 +1,2 @@ SHA512 (nagios-agents-metadata-105ab8a7b2c16b9a29cf1c1596b80136eeef332b.tar.gz) = 11ddeb48a4929e7642b6dfa9c7962aa1d7a1af1c569830f55ed6cd6773abac13377317327bc1db8411c8077884f83f81cc54d746c834b63a99fa6dc219b5caad -SHA512 (pacemaker-Pacemaker-2.0.5.tar.gz) = 5fd3614f0284297babb66ea2dc567583315052fcf77f49107c52161e8e8c164ae3169d98528fdc1316d8eabaacc98ed24e9c6e6c90b3286f2f012a4ee874bbba +SHA512 (pacemaker-Pacemaker-2.1.0-rc1.tar.gz) = 64fef270ac0f0df63a2ac974c4467dfb6a646cbe2089c6b523f14311bf236653caa75cd9e2851af7882057d63651ecd3c9d40647349a76619c4522c938063acf commit 3978725c064d9bf7d504f7c8118f3c9d34bfb715 Author: Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> Date: Tue Mar 2 16:13:07 2021 +0100 Rebuilt for updated systemd-rpm-macros See https://pagure.io/fesco/issue/2583. diff --git a/pacemaker.spec b/pacemaker.spec index 8f15ea0..b786f9c 100644 --- a/pacemaker.spec +++ b/pacemaker.spec @@ -138,7 +138,7 @@ Name: pacemaker Summary: Scalable High-Availability cluster resource manager Version: %{pcmkversion} -Release: %{pcmk_release}%{?dist}.1 +Release: %{pcmk_release}%{?dist}.2 License: GPLv2+ and LGPLv2+ Url: https://www.clusterlabs.org @@ -720,6 +720,10 @@ exit 0 %license %{nagios_name}-%{nagios_hash}/COPYING %changelog +* Tue Mar 02 2021 Zbigniew Jędrzejewski-Szmek <zbyszek(a)in.waw.pl> - 2.0.5-10.2 +- Rebuilt for updated systemd-rpm-macros + See https://pagure.io/fesco/issue/2583. + * Tue Jan 26 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 2.0.5-10.1 - Rebuilt for https://fedoraproject.org/wiki/Fedora_34_Mass_Rebuild

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Architecture specific change in rpms/wabt.git

by githook-noreply＠fedoraproject.org

The package rpms/wabt.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/wabt.git/commit/?id=a5b8120bc45b3.... Change: -%ifarch s390x Thanks. Full change: ============ commit 9ac7663c7233185f239259091aa5c7616602dfdf Merge: 584973c a5b8120 Author: Dominik 'Rathann' Mierzejewski <dominik(a)greysector.net> Date: Fri Aug 20 11:09:21 2021 +0200 Merge branch 'f34' into f35 diff --cc wabt.spec index a5831d6,2610d9a..ebc8d6f --- a/wabt.spec +++ b/wabt.spec @@@ -125,9 -114,10 +114,13 @@@ test/run-tests.py -v --bindir %{_vpath_ %{_mandir}/man1/wat2wasm.1* %changelog + * Fri Aug 20 2021 Dominik Mierzejewski <rpm(a)greysector.net> 1.0.24-1 + - update to 1.0.24 (#1993479) + - enable skipped tests on s390x (fixed upstream) + +* Fri Jul 23 2021 Fedora Release Engineering <releng(a)fedoraproject.org> - 1.0.23-2 +- Rebuilt for https://fedoraproject.org/wiki/Fedora_35_Mass_Rebuild + * Fri May 14 2021 Dominik Mierzejewski <rpm(a)greysector.net> 1.0.23-1 - update to 1.0.23 (#1934466) - drop obsolete patch commit a5b8120bc45b3ab5979a70b73af3d8a011a25856 Author: Dominik 'Rathann' Mierzejewski <dominik(a)greysector.net> Date: Fri Aug 20 11:08:36 2021 +0200 update to 1.0.24 (#1993479) enable skipped tests on s390x (fixed upstream) diff --git a/.gitignore b/.gitignore index 746c0e9..797a8f7 100644 --- a/.gitignore +++ b/.gitignore @@ -18,3 +18,5 @@ /wabt-09ac53e41d959ce8e14e703e627327971e67f6d3.tar.gz /wabt-1.0.23.tar.gz /wabt-testsuite-9994915.tar.gz +/wabt-1.0.24.tar.gz +/wabt-testsuite-01efde8.tar.gz diff --git a/sources b/sources index 17e65a7..7becfb5 100644 --- a/sources +++ b/sources @@ -1,3 +1,3 @@ -SHA512 (wabt-1.0.23.tar.gz) = caa11433d850d6d3117a6fd6b16fe8c41a8813052dd79f99b7b2e5f97720e806cf41c3aed109e25683bb1da1fa94ff9f8d8248bcd0e293b1bac9854c90338595 -SHA512 (wabt-testsuite-9994915.tar.gz) = c8b9a6cfbfc438932b294eb71f1c2813a8607afd5c7762a3f2f73b33a68ea1f7ec17083b8ef97e9219797ba6d2cf01b12c62692472820ee350f902437444f468 +SHA512 (wabt-1.0.24.tar.gz) = 6257702f06baace7eded7fd4890cbf23e533f20ee6c40de82a7a4cd32fe931a49efd3cbfc1355c4da49e6fbd3b62b1cf05edf1699313840d4825a2165a3928a8 +SHA512 (wabt-testsuite-01efde8.tar.gz) = 549c2e13ebbd7d87013426d8cdeaa0a6177928307b688e1b90026e79683f7964f09dfb47294b34ba9190d0f3acb279f6d0a924e1f1a9112fc9d89637b8cb9efd SHA512 (wabt-wasm-c-api-d9a8009.tar.gz) = b6ee7d2d83a3ca7b3cb3ee110282f7d32eada1d9020cadd3fdec58f40478879fd9ac9fada526021d8f6e8a26e1df7353df313d4149be2ffe4aea3a28f856fd89 diff --git a/wabt.spec b/wabt.spec index a1db44a..2610d9a 100644 --- a/wabt.spec +++ b/wabt.spec @@ -1,15 +1,15 @@ %undefine __cmake_in_source_build %bcond_without check -%global commit aa0515b3c808da880942db8658abeaa969534667 +%global commit 21279a861fa3dbac9af9d2bab16c741df17a86af %global shortcommit %(c=%{commit}; echo ${c:0:7}) -%global ts_commit 9994915e0cca8b42a16c577e4c85491822367dde +%global ts_commit 01efde81028c5b0d099eb836645a2dc5e7755449 %global ts_shortcommit %(c=%{ts_commit}; echo ${c:0:7}) %global wc_commit d9a80099d496b5cdba6f3fe8fc77586e0e505ddc %global wc_shortcommit %(c=%{wc_commit}; echo ${c:0:7}) Summary: The WebAssembly Binary Toolkit Name: wabt -Version: 1.0.23 +Version: 1.0.24 Release: 1%{?dist} URL: https://github.com/WebAssembly/wabt Source0: https://github.com/WebAssembly/wabt/archive/%{version}/%{name}-%{version}... @@ -67,17 +67,6 @@ rm spec/conversions.txt rm spec/simd/simd_conversions.txt rm wasm2c/spec/conversions.txt %endif -# https://github.com/WebAssembly/wabt/issues/1670 -%ifarch s390x -rm spec/simd/simd_load16_lane.txt -rm spec/simd/simd_load32_lane.txt -rm spec/simd/simd_load64_lane.txt -rm spec/simd/simd_load8_lane.txt -rm spec/simd/simd_store16_lane.txt -rm spec/simd/simd_store32_lane.txt -rm spec/simd/simd_store64_lane.txt -rm spec/simd/simd_store8_lane.txt -%endif popd %endif @@ -125,6 +114,10 @@ test/run-tests.py -v --bindir %{_vpath_builddir} --timeout=80 %{?_smp_mflags} %{_mandir}/man1/wat2wasm.1* %changelog +* Fri Aug 20 2021 Dominik Mierzejewski <rpm(a)greysector.net> 1.0.24-1 +- update to 1.0.24 (#1993479) +- enable skipped tests on s390x (fixed upstream) + * Fri May 14 2021 Dominik Mierzejewski <rpm(a)greysector.net> 1.0.23-1 - update to 1.0.23 (#1934466) - drop obsolete patch

2 years, 9 months

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Architecture specific change in rpms/wabt.git

by githook-noreply＠fedoraproject.org

The package rpms/wabt.git has added or updated architecture specific content in its spec file (ExclusiveArch/ExcludeArch or %ifarch/%ifnarch) in commit(s): https://src.fedoraproject.org/cgit/rpms/wabt.git/commit/?id=a5b8120bc45b3.... Change: -%ifarch s390x Thanks. Full change: ============ commit a5b8120bc45b3ab5979a70b73af3d8a011a25856 Author: Dominik 'Rathann' Mierzejewski <dominik(a)greysector.net> Date: Fri Aug 20 11:08:36 2021 +0200 update to 1.0.24 (#1993479) enable skipped tests on s390x (fixed upstream) diff --git a/.gitignore b/.gitignore index 746c0e9..797a8f7 100644 --- a/.gitignore +++ b/.gitignore @@ -18,3 +18,5 @@ /wabt-09ac53e41d959ce8e14e703e627327971e67f6d3.tar.gz /wabt-1.0.23.tar.gz /wabt-testsuite-9994915.tar.gz +/wabt-1.0.24.tar.gz +/wabt-testsuite-01efde8.tar.gz diff --git a/sources b/sources index 17e65a7..7becfb5 100644 --- a/sources +++ b/sources @@ -1,3 +1,3 @@ -SHA512 (wabt-1.0.23.tar.gz) = caa11433d850d6d3117a6fd6b16fe8c41a8813052dd79f99b7b2e5f97720e806cf41c3aed109e25683bb1da1fa94ff9f8d8248bcd0e293b1bac9854c90338595 -SHA512 (wabt-testsuite-9994915.tar.gz) = c8b9a6cfbfc438932b294eb71f1c2813a8607afd5c7762a3f2f73b33a68ea1f7ec17083b8ef97e9219797ba6d2cf01b12c62692472820ee350f902437444f468 +SHA512 (wabt-1.0.24.tar.gz) = 6257702f06baace7eded7fd4890cbf23e533f20ee6c40de82a7a4cd32fe931a49efd3cbfc1355c4da49e6fbd3b62b1cf05edf1699313840d4825a2165a3928a8 +SHA512 (wabt-testsuite-01efde8.tar.gz) = 549c2e13ebbd7d87013426d8cdeaa0a6177928307b688e1b90026e79683f7964f09dfb47294b34ba9190d0f3acb279f6d0a924e1f1a9112fc9d89637b8cb9efd SHA512 (wabt-wasm-c-api-d9a8009.tar.gz) = b6ee7d2d83a3ca7b3cb3ee110282f7d32eada1d9020cadd3fdec58f40478879fd9ac9fada526021d8f6e8a26e1df7353df313d4149be2ffe4aea3a28f856fd89 diff --git a/wabt.spec b/wabt.spec index a1db44a..2610d9a 100644 --- a/wabt.spec +++ b/wabt.spec @@ -1,15 +1,15 @@ %undefine __cmake_in_source_build %bcond_without check -%global commit aa0515b3c808da880942db8658abeaa969534667 +%global commit 21279a861fa3dbac9af9d2bab16c741df17a86af %global shortcommit %(c=%{commit}; echo ${c:0:7}) -%global ts_commit 9994915e0cca8b42a16c577e4c85491822367dde +%global ts_commit 01efde81028c5b0d099eb836645a2dc5e7755449 %global ts_shortcommit %(c=%{ts_commit}; echo ${c:0:7}) %global wc_commit d9a80099d496b5cdba6f3fe8fc77586e0e505ddc %global wc_shortcommit %(c=%{wc_commit}; echo ${c:0:7}) Summary: The WebAssembly Binary Toolkit Name: wabt -Version: 1.0.23 +Version: 1.0.24 Release: 1%{?dist} URL: https://github.com/WebAssembly/wabt Source0: https://github.com/WebAssembly/wabt/archive/%{version}/%{name}-%{version}... @@ -67,17 +67,6 @@ rm spec/conversions.txt rm spec/simd/simd_conversions.txt rm wasm2c/spec/conversions.txt %endif -# https://github.com/WebAssembly/wabt/issues/1670 -%ifarch s390x -rm spec/simd/simd_load16_lane.txt -rm spec/simd/simd_load32_lane.txt -rm spec/simd/simd_load64_lane.txt -rm spec/simd/simd_load8_lane.txt -rm spec/simd/simd_store16_lane.txt -rm spec/simd/simd_store32_lane.txt -rm spec/simd/simd_store64_lane.txt -rm spec/simd/simd_store8_lane.txt -%endif popd %endif @@ -125,6 +114,10 @@ test/run-tests.py -v --bindir %{_vpath_builddir} --timeout=80 %{?_smp_mflags} %{_mandir}/man1/wat2wasm.1* %changelog +* Fri Aug 20 2021 Dominik Mierzejewski <rpm(a)greysector.net> 1.0.24-1 +- update to 1.0.24 (#1993479) +- enable skipped tests on s390x (fixed upstream) + * Fri May 14 2021 Dominik Mierzejewski <rpm(a)greysector.net> 1.0.23-1 - update to 1.0.23 (#1934466) - drop obsolete patch

2 years, 9 months

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