[med-svn] [Git][med-team/minc-tools][master] 2 commits: Add manpages
Nilesh Patra
gitlab at salsa.debian.org
Thu Jul 30 15:34:43 BST 2020
Nilesh Patra pushed to branch master at Debian Med / minc-tools
Commits:
76b2aff2 by Nilesh Patra at 2020-07-30T14:33:56+00:00
Add manpages
- - - - -
474cd63c by Nilesh Patra at 2020-07-30T14:34:24+00:00
Update changelog
- - - - -
6 changed files:
- debian/changelog
- + debian/createmanpages
- + debian/manpages
- + debian/minchistory.1
- + debian/mincmorph.1
- + debian/mincpik.1
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,15 @@
+minc-tools (2.3.00+dfsg-4) unstable; urgency=medium
+
+ * Team Upload.
+ * Fix gcc-10 FTBFS (Closes: #957542)
+ * Add upstream/metadata
+ * Remove compat, switch to debhelper-compat version 13
+ * standards-version: 4.5.0
+ * Add "Rules-Requires-Root: no"
+ * Add manpages
+
+ -- Nilesh Patra <npatra974 at gmail.com> Thu, 30 Jul 2020 19:48:45 +0530
+
minc-tools (2.3.00+dfsg-3) unstable; urgency=medium
* Point watch file to Github
@@ -74,7 +86,7 @@ minc (2.2.00-2) unstable; urgency=low
stricter parsing of perl 5.18. Closes: #719502.
* rules: disable parallel build; causes tests to fail inexplicably.
-
+
-- Steve M. Robbins <smr at debian.org> Fri, 13 Sep 2013 23:22:53 -0500
minc (2.2.00-1) unstable; urgency=low
@@ -88,7 +100,7 @@ minc (2.2.00-1) unstable; urgency=low
* rules: Use "--with autoreconf" since new patches affect Makefile.am.
- * rules:
+ * rules:
* control: SOVERSION bump to 3; new package name libminc2-3.
-- Steve M. Robbins <smr at debian.org> Sat, 13 Oct 2012 23:09:25 -0500
@@ -96,16 +108,16 @@ minc (2.2.00-1) unstable; urgency=low
minc (2.1.10-1) unstable; urgency=low
* New upstream.
-
+
* patches/03_mincview.diff: Remove. Script mincview rewritten to use
Imagemagick
-
+
* patches/decompress-whole-file.diff:
* patches/read_file_names-refactor.patch: Remove. Applied upstream.
* rules: Remove use of dh_autoreconf.
* patches/hdfv2-fixes.patch: New. Ensure using HDF5 v2 API.
-
+
* control: Remove dependency and build-dependency on csh.
-- Steve M. Robbins <smr at debian.org> Sun, 26 Feb 2012 01:37:47 -0600
@@ -116,7 +128,7 @@ minc (2.1.00-5) unstable; urgency=low
* patches/read_file_names-refactor.patch: New. Refactored duplicated
PATH_MAX-using code into library. Need to run autoreconf because
Makefile.am changed.
-
+
* rules: Fix errors and really disable tests on sparc.
-- Steve M. Robbins <smr at debian.org> Mon, 20 Feb 2012 15:00:32 -0600
@@ -124,10 +136,10 @@ minc (2.1.00-5) unstable; urgency=low
minc (2.1.00-4) unstable; urgency=low
* source/format: Set to 3.0 (quilt), so that patches are applied.
-
+
* patches/mincaverage-pathmax.patch: New. Work around missing PATH_MAX
definition; fixes FTBFS on hurd.
-
+
* rules: Tests are buggy, but do work on most architectures. Disable on
sparc.
@@ -137,7 +149,7 @@ minc (2.1.00-3) unstable; urgency=low
* control: Switch to (serial) libhdf5-dev, to avoid conflict with serial
netcdf. Closes: #658307.
-
+
* control:
* rules: Switch from cdbs to debhelper's dh (compat level 9).
@@ -160,7 +172,7 @@ minc (2.0.18+cvs20100518-1) unstable; urgency=low
* Pull upstream CVS, contains fixes for netcdf 4. Closes: #577060,
#581296.
-
+
* control: replace libhdf5-*-dev (differing by architecture) by
libhdf5-mpi-dev.
@@ -178,7 +190,7 @@ minc (2.0.17-1) unstable; urgency=low
* patches/04_manpages.diff:
* debian/patches/05_parseargv.diff: Remove; applied upstream.
-
+
-- Steve M. Robbins <smr at debian.org> Tue, 20 Jan 2009 19:37:41 -0600
minc (2.0.16-4) unstable; urgency=low
@@ -186,9 +198,9 @@ minc (2.0.16-4) unstable; urgency=low
* debian/patches/05_parseargv.diff: New. Patch from upstream to fix arg
parsing on 64bits. Closes: #510629. This was also the root cause of
mincheader and mincdiff failing. Closes: #506276.
-
+
* debian/control: Add ${misc:Depends}, since we use debhelper.
-
+
* debian/rules: Do not install test code acr_test, dicom_test.
-- Steve M. Robbins <smr at debian.org> Sat, 03 Jan 2009 16:29:06 -0600
@@ -212,7 +224,7 @@ minc (2.0.16-1) unstable; urgency=low
* New upstream release.
- debian/patches/02_mincedit-no-escape-chars: Remove. Applied upstream.
-
+
* debian/control: Switch dependencies from libhdf5-serial-dev to
libhdf5-openmpi-dev.
* debian/rules: Add CFLAGS=-I/usr/include/mpi to configure step so that
@@ -221,10 +233,10 @@ minc (2.0.16-1) unstable; urgency=low
* debian/control: Remove tetex-bin from build-depends (was alternative
to texlive-latex-base). Update Standards-Version to 3.8.0 (no
changes).
-
+
* debian/patches/04_manpages.diff: Fix errors in manpages, mainly
removal of trailing TAB characters.
-
+
* debian/rules: Adhere to parallel keyword in DEB_BUILD_OPTIONS.
-- Steve M. Robbins <smr at debian.org> Sat, 11 Oct 2008 23:55:42 -0500
@@ -246,12 +258,12 @@ minc (2.0.15-2) unstable; urgency=low
[ David Paleino ]
* debian/rules:
- conditionally add -mieee on Alpha (Closes: #368263)
-
+
[ Steve M. Robbins ]
* debian/rules: Do not run the tests, since they are broken in many
ways; e.g. int functions without a return statement, checking
floating-point values without a tolerance, and some that require a
- list of files on the command line but are given none.
+ list of files on the command line but are given none.
Closes: #475808.
-- Steve M. Robbins <smr at debian.org> Thu, 05 Jun 2008 09:24:59 -0500
@@ -273,7 +285,7 @@ minc (2.0.14-2) unstable; urgency=low
* rules: Don't install byte_swap or extract; can use "dd" instead of
these tools. Closes: #459834.
-
+
* control: Package minc-tools depends on libgetopt-tabular-perl.
* rules: Don't install Tabular.pm.
* Getopt-Tabular-0.3/Tabular.pm: Remove.
@@ -285,21 +297,21 @@ minc (2.0.14-2) unstable; urgency=low
minc (2.0.14-1) unstable; urgency=low
* New upstream version. Closes: #450922.
-
+
* control: Set Maintainer to debian-med-packaging.
Add build-depends for libhdf5-serial-dev, texlive-latex-base.
Rename package libminc0 --> libminc2-1.
Rename package libminc0-dev --> libminc-dev.
Package libminc-dev depends on libhdf5-serial-dev.
Package minc-tools depends on imagemagick.
-
+
* rules: Configure with --enable-minc2 and --enable-acr-nema.
* Getopt-Tabular-0.3/Tabular.pm: New. Perl module required
for mincpik and xfmflip. Closes: #457074.
* patches/02_testdir-runtests.diff: New. Fix test scripts.
-
+
* patches/03_mincview.diff: New. Use 'display' from ImageMagick rather
than 'xv' to view images. Closes: #457072.
@@ -313,7 +325,7 @@ minc (1.5-2) NEVER UPLOADED; urgency=low
* Rewrite build system using cdbs.
- patches/01_mincedit-sensible-viewer.diff: New. Obtained from
existing Debian diff.
-
+
* control: Build-depend on texlive-latex-base | tetex-bin, rather
than just tetex-bin. Update to Standards-Version 3.7.3 (no change
required). Use ${binary:Version} rather than ${Source-Version}
@@ -357,7 +369,7 @@ minc (1.4-2) unstable; urgency=low
minc (1.4-1) unstable; urgency=low
* New upstream version.
-
+
* Omit dependency on essential package debianutils (for sensible-editor).
Closes: #316425.
@@ -385,7 +397,7 @@ minc (1.3-1) unstable; urgency=low
* configure.in: Don't use AC_CONFIG_LINKS to generate link
volume_io/Include/volume_io to directory volume_io/Include as
autoconf 2.59 chokes on it. Use shell commands instead.
-
+
* volume_io/Include/internal_volume_io.h: Do not include "config.h".
* volume_io/Prog_utils/files.c: Do include "config.h".
* volume_io/Prog_utils/time.c: Restore call to sysconf( _SC_CLK_TCK ),
@@ -429,4 +441,3 @@ minc (1.0-1) unstable; urgency=low
- progs/mincstats/mincstats.c: fix segfault
-- Steve M. Robbins <smr at debian.org> Mon, 29 Jul 2002 16:06:56 -0400
-
=====================================
debian/createmanpages
=====================================
@@ -0,0 +1,60 @@
+#!/bin/sh
+MANDIR=debian
+mkdir -p $MANDIR
+
+VERSION=`dpkg-parsechangelog | awk '/^Version:/ {print $2}' | sed -e 's/^[0-9]*://' -e 's/-.*//' -e 's/[+~]dfsg$//'`
+NAME=`grep "^Description:" debian/control | sed 's/^Description: *//' | head -n1`
+PROGNAME=`grep "^Package:" debian/control | sed 's/^Package: *//' | head -n1`
+
+AUTHOR=".SH AUTHOR\n \
+This manpage was written by $DEBFULLNAME for the Debian distribution and\n \
+can be used for any other usage of the program.\
+"
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=minchistory
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=mincmorph
+help2man --no-info --no-discard-stderr --help-option="-help" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
+
+# If program name is different from package name or title should be
+# different from package short description change this here
+progname=mincpik
+help2man --no-info --no-discard-stderr --help-option="-h" \
+ --name="$NAME" \
+ --version-string="$VERSION" ${progname} > $MANDIR/${progname}.1
+echo $AUTHOR >> $MANDIR/${progname}.1
+
+echo "$MANDIR/*.1" > debian/manpages
+
+cat <<EOT
+Please enhance the help2man output.
+The following web page might be helpful in doing so:
+ http://liw.fi/manpages/
+EOT
=====================================
debian/manpages
=====================================
@@ -0,0 +1 @@
+debian/*.1
=====================================
debian/minchistory.1
=====================================
@@ -0,0 +1,28 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH MINCHISTORY "1" "July 2020" "minchistory 2.3.00" "User Commands"
+.SH NAME
+minchistory \- MNI medical image format tools
+.SH DESCRIPTION
+.SS "Usage:"
+.IP
+minchistory [options] <file1.mnc> [<file2.mnc> ... ]
+.IP
+minchistory will dump the internal history of one or more MINC files
+.SH OPTIONS
+.HP
+\fB\-v\fR, \fB\-\-verbose\fR
+.IP
+Be noisy when doing things
+.HP
+\fB\-\-version\fR
+.IP
+Print version number and exit
+.HP
+\fB\-h\fR, \fB\-\-help\fR
+.IP
+Dump some quick help output
+.HP
+\fB\-\-man\fR
+.IP
+Dump a man page
+.SH AUTHOR\n This manpage was written by Nilesh Patra for the Debian distribution and\n can be used for any other usage of the program.
=====================================
debian/mincmorph.1
=====================================
@@ -0,0 +1,158 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH MINCMORPH "1" "July 2020" "mincmorph 2.3.00" "User Commands"
+.SH NAME
+mincmorph \- MNI medical image format tools
+.SH SYNOPSIS
+.B mincmorph
+[\fI\,options\/\fR] \fI\,<in.mnc> <out.mnc>\/\fR
+.SH DESCRIPTION
+Command\-specific options:
+General options:
+.TP
+\fB\-verbose\fR:
+be verbose
+.TP
+\fB\-clobber\fR:
+clobber existing files
+.PP
+Outfile Options
+.TP
+\fB\-filetype\fR:
+Use data type of the input file.
+.TP
+\fB\-byte\fR:
+Write out byte data.
+.TP
+\fB\-short\fR:
+Write out short integer data. (Default)
+.TP
+\fB\-int\fR:
+Write out long integer data.
+.TP
+\fB\-float\fR:
+Write out single\-precision data.
+.TP
+\fB\-double\fR:
+Write out double\-precision data.
+.TP
+\fB\-signed\fR:
+Write signed integer data.
+.TP
+\fB\-unsigned\fR:
+Write unsigned integer data.
+.PP
+Kernel Options
+.TP
+\fB\-2D04\fR:
+Use a 2D 4\-connectivity kernel.
+.TP
+\fB\-2D08\fR:
+Use a 2D 8\-connectivity kernel.
+.TP
+\fB\-3D06\fR:
+Use a 3D 6\-connectivity kernel. (default)
+.TP
+\fB\-3D26\fR:
+Use a 3D 26\-connectivity kernel.
+.TP
+\fB\-kernel\fR:
+<kernel.kern> read in a custom kernel file
+.PP
+Morphology Options
+.TP
+\fB\-floor\fR:
+lowwer value for binarising or clamping
+.IP
+Default value: \fB\-1\fR.79769e+308
+.TP
+\fB\-ceil\fR:
+upper value for binarising or clamping (incl)
+.IP
+Default value: 1.79769e+308
+.TP
+\fB\-range\fR:
+range for binarising or clamping (incl)
+.IP
+Default value: \fB\-1\fR.79769e+308 1.79769e+308
+.TP
+\fB\-foreground\fR:
+foreground value
+.IP
+Default value: 1
+.TP
+\fB\-background\fR:
+background value
+.IP
+Default value: 0
+.SS "Single morphological operations:"
+.TP
+\fB\-binarise\fR:
+binarise volume using the input range
+.TP
+\fB\-clamp\fR:
+clamp volume using the input range
+.TP
+\fB\-pad\fR:
+pad volume with respect to the current kernel (\fB\-background\fR to specify value)
+.TP
+\fB\-erosion\fR:
+do a single erosion
+.TP
+\fB\-dilation\fR:
+do a single dilation
+.TP
+\fB\-median_dilation\fR:
+do a single median dilation (note: this is not a median filter!)
+.TP
+\fB\-open\fR:
+open: dilation(erosion(X))
+.TP
+\fB\-close\fR:
+close: erosion(dilation(X))
+.TP
+\fB\-lowpass\fR:
+lowpass filter: close(open(X))
+.TP
+\fB\-highpass\fR:
+highpass filter: X \- lowpass(X)
+.TP
+\fB\-convolve\fR:
+convolve file with kernel
+.TP
+\fB\-distance\fR:
+distance transform
+.TP
+\fB\-group\fR:
+label groups in ascending order
+.SS "Successive morphological operations:"
+.TP
+\fB\-successive\fR:
+Successive operations (Maximum: 100)
+.IP
+B[floor:ceil:fg:bg] \- binarise in the range, using foreground and background
+K[floor:ceil:bg] \- clamp between the specified range. Set other voxels to 'bg' (default: 0)
+P[bg] \- pad volume with respect to the current kernel using 'bg' (default: 0)
+E \- erosion
+D \- dilation
+M \- median dilation
+O \- open
+C \- close
+L \- lowpass filter
+H \- highpass filter
+X \- convolve
+F \- distance transform (binary input only \- not checked)
+G \- Label the groups in the volume in ascending order
+R[TYPE|file.kern] \- (2D04|2D08|3D06|3D26) or read in a kernel file
+W[file.mnc] \- write out current results
+I[cmp.mnc] \- local xcorr between current file and cmp.mnc
+Default: "B"
+.SS "Generic options for all commands:"
+.TP
+\fB\-help\fR:
+Print summary of command\-line options and abort
+.TP
+\fB\-version\fR:
+Print version number of program and exit
+.IP
+mincmorph \fB\-help\fR
+.SH AUTHOR\n This manpage was written by Nilesh Patra for the Debian distribution and\n can be used for any other usage of the program.
=====================================
debian/mincpik.1
=====================================
@@ -0,0 +1,135 @@
+.\" DO NOT MODIFY THIS FILE! It was generated by help2man 1.47.12.
+.TH MINCPIK "1" "July 2020" "mincpik 2.3.00" "User Commands"
+.SH NAME
+mincpik \- MNI medical image format tools
+.SH DESCRIPTION
+Option h is ambiguous (help, horizontal)
+Usage:
+.IP
+mincpik [options] <infile>.mnc [<image.type>]
+.IP
+mincpik generates image files from MINC volumes using the Imagemagick
+convert utility. Use \fB\-help\fR or \fB\-man\fR for more information and examples
+.SH OPTIONS
+.HP
+\fB\-v\fR, \fB\-\-verbose\fR
+.IP
+Be noisy when doing things
+.HP
+\fB\-\-version\fR
+.IP
+Print version number and exit
+.HP
+\-?, \fB\-\-help\fR
+.IP
+Dump some quick help output
+.HP
+\fB\-\-man\fR
+.IP
+Dump a man page
+.HP
+\fB\-c\fR \fB\-\-clobber\fR
+.IP
+overwrite the output file if it exists already
+.HP
+\fB\-f\fR \fB\-\-fake\fR
+.IP
+do a dry run, (echo cmds only). This is usually used in combination
+with \fB\-verbose\fR to echo commands only
+.HP
+\fB\-\-scale\fR
+.IP
+scaling factor for resulting image, by default images are output at
+twice their original resolution
+.HP
+\fB\-\-width\fR
+.IP
+autoscale the resulting image to have a fixed image width (in
+pixels)
+.HP
+\fB\-\-depth\fR
+.IP
+bitdepth for resulting image 8 or 16 (MSB machines only!)
+.HP
+\fB\-\-title\fR
+.IP
+add a title to the resulting image, if just this option is specified
+the text used for the title is the name of the input image file.
+.HP
+\fB\-\-title_text\fR
+.IP
+use the input string for the title [default: input\-filename]. This
+option must be used in conjunction with \fB\-title\fR
+.HP
+\fB\-\-title_size\fR
+.IP
+font point size for the title
+.HP
+\fB\-\-anot_bar\fR
+.IP
+create an annotated bar to match the image (use height of the output
+image)
+.IP
+Image range and lookup table options:
+.HP
+\fB\-\-range\fR
+.IP
+valid range of values for MINC file
+.HP
+\fB\-\-image_range\fR
+.IP
+range of image values to use for pixel intensity
+.HP
+\fB\-\-auto_range\fR
+.IP
+automatically determine image range using a 5 and 95% PcT.
+(histogram)
+.HP
+\fB\-\-lookup\fR
+.IP
+arguments to pass to minclookup
+.IP
+Slicing options:
+.HP
+\fB\-s\fR \fB\-\-slice\fR
+.IP
+slice number to get. (note this is in voxel co\-ordinates)
+.HP
+\fB\-z\fR \fB\-\-axial\fR \fB\-\-transverse\fR
+.IP
+get an axial/transverse (z) slice
+.HP
+\fB\-y\fR \fB\-\-coronal\fR
+.IP
+get a coronal (y) slice
+.HP
+\fB\-x\fR \fB\-\-sagittal\fR
+.IP
+get a sagital (x) slice
+.IP
+Triplanar options:
+.HP
+\fB\-t\fR \fB\-\-triplanar\fR
+.IP
+create a triplanar view of the input file
+.HP
+\fB\-\-tilesize\fR
+.IP
+pixel size for each image in a triplanar
+.HP
+\fB\-\-sagittal_offset\fR
+.IP
+offset the sagittal slice from the centre
+.HP
+\fB\-\-sagittal_offset_perc\fR
+.IP
+offset the sagittal slice by a percentage from the centre
+.HP
+\fB\-\-vertical\fR
+.IP
+create a vertical triplanar view (Default)
+.HP
+\fB\-\-horizontal\fR
+.IP
+create a horizontal triplanar view
+.SH AUTHOR\n This manpage was written by Nilesh Patra for the Debian distribution and\n can be used for any other usage of the program.
View it on GitLab: https://salsa.debian.org/med-team/minc-tools/-/compare/69e6ca35676370c7f7ef725ad356a3481c8d18d6...474cd63c198cdf848b1b16fa24f8988de4798bb0
--
View it on GitLab: https://salsa.debian.org/med-team/minc-tools/-/compare/69e6ca35676370c7f7ef725ad356a3481c8d18d6...474cd63c198cdf848b1b16fa24f8988de4798bb0
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