debian/0000755000000000000000000000000012214773542007175 5ustar debian/watch0000644000000000000000000000010410762473345010225 0ustar version=3 http://packages.bic.mni.mcgill.ca/tgz/ minc-(.*)\.tar\.gz debian/compat0000644000000000000000000000000111716631150010364 0ustar 9debian/copyright0000644000000000000000000000152011026104403011106 0ustar This package was debianized by Steven Robbins in August 2001 It was downloaded from ftp://ftp.bic.mni.mcgill.ca/pub/minc/ Download site as of 2006-02-05 is http://packages.bic.mni.mcgill.ca/tgz/ Copyright 1993-2000 Peter Neelin and David MacDonald, McConnell Brain Imaging Centre, Montreal Neurological Institute, McGill University. Permission to use, copy, modify, and distribute this software and its documentation for any purpose and without fee is hereby granted, provided that the above copyright notice appear in all copies. The author and McGill University make no representations about the suitability of this software for any purpose. It is provided "as is" without express or implied warranty. Current upstream maintenance is done on the minc-development mailing list. http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-development debian/control0000644000000000000000000000641712036446075010610 0ustar Source: minc Homepage: http://www.bic.mni.mcgill.ca/ServicesSoftware/HomePage Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Steve M. Robbins Build-Depends: debhelper (>= 9), autotools-dev, dh-autoreconf, libnetcdf-dev, zlib1g-dev, texlive-latex-base, libhdf5-dev Standards-Version: 3.9.2 Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/minc/trunk/ Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/minc/trunk/ Package: minc-tools Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends}, netcdf-bin, libgetopt-tabular-perl, libtext-format-perl, imagemagick Description: MNI medical image format tools This package contains tools to manipulate MINC files. . The Minc file format is a highly flexible medical image file format built on top of the NetCDF generalized data format. The format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment: they are simple and powerful and make no attempt to provide a pretty interface to users. Package: libminc2-3 Section: libs Architecture: any Multi-Arch: same Pre-Depends: ${misc:Pre-Depends} Depends: ${shlibs:Depends}, ${misc:Depends} Description: MNI medical image format library This package contains the libraries libminc2 and libvolume_io2. . The Minc file format is a highly flexible medical image file format. Minc version 1 is built on top of the NetCDF generalized data format. Minc version 2 is built on top of the HDF data format. This library handles both formats. In each case the format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment : they are simple and powerful and make no attempt to provide a pretty interface to users. Package: libminc-dev Conflicts: libminc0-dev Replaces: libminc0-dev Section: libdevel Architecture: any Depends: ${misc:Depends}, libminc2-3 (= ${binary:Version}), libnetcdf-dev, libhdf5-dev Description: MNI medical image format development environment This package contains the library and headers for libminc2 and libvolume_io2. . The Minc file format is a highly flexible medical image file format. Minc version 1 is built on top of the NetCDF generalized data format. Minc version 2 is built on top of the HDF data format. This library handles both formats. In each case the format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. On top of the libraries is a suite of generic image-file manipulation tools. The format, libraries and tools are designed for use in a medical-imaging research environment : they are simple and powerful and make no attempt to provide a pretty interface to users. debian/source/0000755000000000000000000000000012214773313010471 5ustar debian/source/format0000644000000000000000000000001411720340777011704 0ustar 3.0 (quilt) debian/patches/0000755000000000000000000000000012214773313010620 5ustar debian/patches/series0000644000000000000000000000014412214773247012042 0ustar maxpathlen.patch makefile.patch 01_mincedit-sensible-viewer.diff acrnema-version.patch pod_fix.diff debian/patches/acrnema-version.patch0000644000000000000000000000046112036446045014734 0ustar --- minc-2.2.00.orig/Makefile.am +++ minc-2.2.00/Makefile.am @@ -555,6 +555,7 @@ volume_io/Volumes/volume_cache.c \ volume_io/Volumes/volumes.c +libacr_nema_la_LDFLAGS = -version-info 3:0:0 libacr_nema_la_SOURCES = \ conversion/Acr_nema/acr_io.c \ conversion/Acr_nema/dicom_client_routines.c \ debian/patches/maxpathlen.patch0000644000000000000000000000065412214773071014010 0ustar --- minc-2.2.00.orig/progs/mincmorph/mincmorph.c +++ minc-2.2.00/progs/mincmorph/mincmorph.c @@ -30,6 +30,11 @@ #define INTERNAL_PREC NC_FLOAT /* should be NC_FLOAT or NC_DOUBLE */ #define DEF_DOUBLE -DBL_MAX +#ifndef MAXPATHLEN +#define MAXPATHLEN 1024 +#endif + + /* function prototypes */ char *get_real_from_string(char *string, double *value); char *get_string_from_string(char *string, char **value); debian/patches/makefile.patch0000644000000000000000000000335412036446150013421 0ustar --- minc-2.2.00.orig/Makefile.am +++ minc-2.2.00/Makefile.am @@ -274,30 +274,30 @@ m4/smr_WITH_BUILD_PATH.m4 ezMINC_files = \ - ezminc/examples/volume_msq_dist.cpp - ezminc/examples/CMakeLists.txt - ezminc/examples/fuzzy_volume_similarity.cpp - ezminc/examples/trilinear_resample.cpp - ezminc/examples/volume_avg.cpp - ezminc/examples/volume_gtc_similarity.cpp - ezminc/examples/volume_similarity.cpp - ezminc/minc_1_simple_rw.cpp - ezminc/minc_1_simple_rw.h - ezminc/minc_io_4d_volume.h - ezminc/minc_io_fixed_vector.h - ezminc/minc_io_simple_volume.h - ezminc/tests/minc_rw_test2.cpp - ezminc/tests/minc_rw_test_4d.cpp - ezminc/tests/minc_rw_test_simple.cpp - ezminc/tests/CMakeLists.txt - ezminc/tests/ezminc_rw_test.cpp - ezminc/tests/ezminc_stats.cpp - ezminc/minc_1_simple.h - ezminc/CMakeLists.txt - ezminc/minc_1_rw.cpp - ezminc/minc_1_rw.h + ezminc/examples/volume_msq_dist.cpp \ + ezminc/examples/CMakeLists.txt \ + ezminc/examples/fuzzy_volume_similarity.cpp \ + ezminc/examples/trilinear_resample.cpp \ + ezminc/examples/volume_avg.cpp \ + ezminc/examples/volume_gtc_similarity.cpp \ + ezminc/examples/volume_similarity.cpp \ + ezminc/minc_1_simple_rw.cpp \ + ezminc/minc_1_simple_rw.h \ + ezminc/minc_io_4d_volume.h \ + ezminc/minc_io_fixed_vector.h \ + ezminc/minc_io_simple_volume.h \ + ezminc/tests/minc_rw_test2.cpp \ + ezminc/tests/minc_rw_test_4d.cpp \ + ezminc/tests/minc_rw_test_simple.cpp \ + ezminc/tests/CMakeLists.txt \ + ezminc/tests/ezminc_rw_test.cpp \ + ezminc/tests/ezminc_stats.cpp \ + ezminc/minc_1_simple.h \ + ezminc/CMakeLists.txt \ + ezminc/minc_1_rw.cpp \ + ezminc/minc_1_rw.h \ ezminc/minc_io_exceptions.h - + voxeltoworld_SOURCES = progs/coordinates/voxeltoworld.c worldtovoxel_SOURCES = progs/coordinates/worldtovoxel.c debian/patches/pod_fix.diff0000644000000000000000000000152312214750465013106 0ustar From: Dominic Hargreaves Subject: Fix POD syntax errors As of perl 5.18, pod2man aborts on POD syntax errors, so this patch fixes a FTBFS. Bug-Debian: http://bugs.debian.org/719502 Forwarded: no --- minc-2.2.00.orig/progs/mincpik/mincpik.in +++ minc-2.2.00/progs/mincpik/mincpik.in @@ -576,8 +576,11 @@ font point size for the title create an annotated bar to match the image (use height of the output image) +=back =head3 Image range and lookup table options + +=over 4 =item B<--range> @@ -595,8 +598,11 @@ automatically determine image range usin arguments to pass to minclookup +=back =head3 Slicing options + +=over 4 =item B<-s> B<--slice> @@ -614,8 +620,11 @@ get a coronal (y) slice get a sagital (x) slice +=back =head3 Triplanar options + +=over 4 =item B<-t> B<--triplanar> debian/patches/01_mincedit-sensible-viewer.diff0000644000000000000000000000041012036431502016633 0ustar --- minc-2.0.15.orig/progs/mincedit/mincedit +++ minc-2.0.15/progs/mincedit/mincedit @@ -109,7 +109,7 @@ then editor=${EDITOR} else - editor="emacs" + editor="sensible-editor" fi fi ;; debian/changelog0000644000000000000000000002660012214773172011052 0ustar minc (2.2.00-3) unstable; urgency=low * patches/maxpathlen.patch: New. Work around missing MAXPATHLEN on hurd. -- Steve M. Robbins Sat, 14 Sep 2013 00:39:06 -0500 minc (2.2.00-2) unstable; urgency=low * patches/pod_fix.diff: New. Fix POD documentation to comply with stricter parsing of perl 5.18. Closes: #719502. * rules: disable parallel build; causes tests to fail inexplicably. -- Steve M. Robbins Fri, 13 Sep 2013 23:22:53 -0500 minc (2.2.00-1) unstable; urgency=low * New upstream. * patches/hdfv2-fixes.patch: Remove. Applied upstream. * patches/makefile.patch: New. Fix build failure. * patches/acrnema-version.patch: New. Add proper versioning to libacr_nema. * rules: Use "--with autoreconf" since new patches affect Makefile.am. * rules: * control: SOVERSION bump to 3; new package name libminc2-3. -- Steve M. Robbins Sat, 13 Oct 2012 23:09:25 -0500 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 Sun, 26 Feb 2012 01:37:47 -0600 minc (2.1.00-5) unstable; urgency=low * patches/mincaverage-pathmax.patch: Remove. * 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 Mon, 20 Feb 2012 15:00:32 -0600 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. -- Steve M. Robbins Sun, 19 Feb 2012 21:58:51 -0600 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). -- Steve M. Robbins Sun, 19 Feb 2012 08:53:04 -0600 minc (2.1.00-2) unstable; urgency=low * patches/decompress-whole-file.diff: New. Always decompress entire file to support compressed MINC2 files. Closes: #585676. -- Steve M. Robbins Sun, 18 Dec 2011 20:47:03 -0600 minc (2.1.00-1) unstable; urgency=low * New upstream. -- Steve M. Robbins Tue, 17 Aug 2010 22:26:16 -0500 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. -- Steve M. Robbins Tue, 18 May 2010 22:53:30 -0500 minc (2.0.18-1) unstable; urgency=low * New upstream version. -- Steve M. Robbins Mon, 20 Jul 2009 05:24:57 -0500 minc (2.0.17-1) unstable; urgency=low * New upstream version. * patches/04_manpages.diff: * debian/patches/05_parseargv.diff: Remove; applied upstream. -- Steve M. Robbins Tue, 20 Jan 2009 19:37:41 -0600 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 Sat, 03 Jan 2009 16:29:06 -0600 minc (2.0.16-3) unstable; urgency=low * debian/control: Extend previous fix from build-depends to libminc-dev depends; i.e. use OpenMPI, except for certain architectures that it doesn't support; in the latter case, use LAM. -- Steve M. Robbins Thu, 30 Oct 2008 01:10:55 -0500 minc (2.0.16-2) unstable; urgency=low * debian/control: Use OpenMPI, except for certain architectures that it doesn't support; in the latter case, use LAM. -- Steve M. Robbins Mon, 27 Oct 2008 01:11:21 -0500 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 mpi.h is found. * 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 Sat, 11 Oct 2008 23:55:42 -0500 minc (2.0.15-3) unstable; urgency=low [ Charles Plessy ] * debian/copyright: added upstream contact information. [ Steve M. Robbins ] * debian/patches/02_mincedit-no-escape-chars.diff: New. Patch mincedit to remove extraneous \n strings. Closes: 486048. * debian/control: Replace depends on netcdfg-dev by libnetcdf-dev. -- Steve M. Robbins Thu, 19 Jun 2008 07:40:18 -0500 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. Closes: #475808. -- Steve M. Robbins Thu, 05 Jun 2008 09:24:59 -0500 minc (2.0.15-1) unstable; urgency=low [ Charles Plessy ] * Changed the doc-base section according to the new policy. [ David Paleino ] * New upstream release * debian/patches/: - 01_mincedit-sensible-viewer.diff updated - 02_testdir-runtests.diff removed, it has been merged upstream -- Steve M. Robbins Sat, 31 May 2008 05:53:26 -0500 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. * patches/04_progs-use-lib.diff: Remove. * copyright: Remove Getopt-Tabular license text. -- Steve M. Robbins Fri, 11 Jan 2008 00:30:23 -0600 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. * patches/04_progs-use-lib.diff: New. Add "use lib" declaration to find the private Getopt::Tabular. -- Steve M. Robbins Sun, 06 Jan 2008 20:40:29 -0600 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} for libminc0-dev dependency on libminc0. Add Homepage and Vcs-Svn header fields. -- Steve M. Robbins Sat, 29 Dec 2007 15:10:53 -0600 minc (1.5-1) unstable; urgency=low * New upstream. -- Steve M. Robbins Mon, 13 Nov 2006 23:26:13 -0600 minc (1.4.1-1) unstable; urgency=low * New upstream. -- Steve M. Robbins Sat, 11 Nov 2006 22:14:54 -0600 minc (1.4-4) unstable; urgency=low * testdir/create_grid_xfm.c: initialize minc_input_options properly. Closes: #352183. -- Steve M. Robbins Sat, 18 Feb 2006 17:33:37 -0500 minc (1.4-3) unstable; urgency=low * Build-depend on csh. Closes: #351826. -- Steve M. Robbins Tue, 7 Feb 2006 20:02:56 -0500 minc (1.4-2) unstable; urgency=low * Rebuild to pick up new netcdf library, which changed due to C++ ABI transition (#346312). -- Steve M. Robbins Sun, 5 Feb 2006 13:45:22 -0500 minc (1.4-1) unstable; urgency=low * New upstream version. * Omit dependency on essential package debianutils (for sensible-editor). Closes: #316425. -- Steve M. Robbins Sun, 3 Jul 2005 20:31:25 -0400 minc (1.3-3) unstable; urgency=low * progs/mincedit/mincedit: use "sensible-editor" rather than "emacs". Closes: #292194. -- Steve M. Robbins Thu, 27 Jan 2005 22:21:22 -0500 minc (1.3-2) unstable; urgency=low * debian/rules: package minc-tools depends on libtext-format-perl Closes: #278840. -- Steve M. Robbins Sun, 28 Nov 2004 14:33:06 -0500 minc (1.3-1) unstable; urgency=low * New upstream version. Re-ran all auto*-tools machinery, as upstream used fairly old versions. * 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 ), wrapped in #if HAVE_SYSCONF. -- Steve M. Robbins Sun, 28 Nov 2004 14:22:03 -0500 minc (1.2-1) unstable; urgency=low * New upstream version. * debian/control: minc-tools depend on netcdf-bin (for ncdump). -- Steve M. Robbins Sat, 20 Dec 2003 11:22:09 -0500 minc (1.1-1) unstable; urgency=low * New upstream. - build shared lib package - rename devel package to libminc0-dev -- Steve M. Robbins Sat, 25 Jan 2003 18:25:04 -0500 minc (1.0-2) unstable; urgency=low * libminc-dev: Depend on netcdfg-dev. * minc-tools: Use "csh|c-shell" in dependency line, remove dependency on "awk" on advice from lintian. * Update from upstream CVS. -- Steve M. Robbins Wed, 11 Dec 2002 12:27:36 -0500 minc (1.0-1) unstable; urgency=low * Initial Debian package. Closes: #153629. * Patches from upstream CVS: - libsrc/ParseArgv.h: declare as "extern C" - progs/mincstats/mincstats.c: fix segfault -- Steve M. Robbins Mon, 29 Jul 2002 16:06:56 -0400 debian/index.html0000644000000000000000000000177110735374212011175 0ustar MINC Documentation

MINC Library Documentation

The MINC library is used to deal with large files typically encountered in medical imaging. A programmer's guide and a programmer's reference manual are available.

The volume_io library, also included in the MINC package, provides a simpler programming interface to MINC.

Additional Links

For other tools that work well with MINC, check out the MNI Brain Imaging Centre software toolbox.

There are two mailing lists for MINC: minc users and minc development.

Last modified: Sat Dec 20 09:27:53 EST 2003 debian/rules0000755000000000000000000000253712214761477010270 0ustar #! /usr/bin/make -f %: dh $@ --with autoreconf --with autotools_dev ARCH := $(shell dpkg-architecture -qDEB_BUILD_ARCH) # Tests are buggy; disable test on sparc ifeq ($(ARCH),sparc) DEB_BUILD_OPTIONS += nocheck endif DEB_CONFIGURE_EXTRA_FLAGS = --enable-shared --enable-minc2 --enable-acr-nema CFLAGS="$(CFLAGS)" override_dh_auto_configure: dh_auto_configure -- $(DEB_CONFIGURE_EXTRA_FLAGS) ps_docs = doc/prog_ref.ps doc/prog_guide.ps volume_io/Documentation/volume_io.ps doc/prog_ref.ps doc/prog_guide.ps: $(MAKE) -C doc docs volume_io/Documentation/volume_io.ps: $(MAKE) -C volume_io/Documentation docs override_dh_install: $(ps_docs) # minc-tools rm -f debian/tmp/usr/bin/byte_swap rm -f debian/tmp/usr/bin/extract rm -f debian/tmp/usr/bin/acr_test rm -f debian/tmp/usr/bin/dicom_test dh_install -pminc-tools --autodest debian/tmp/usr/bin dh_install -pminc-tools --autodest debian/tmp/usr/share/man dh_link -pminc-tools \ /usr/share/man/man1/voxeltoworld.1 \ /usr/share/man/man1/worldtovoxel.1 # libminc2-3 dh_install -plibminc2-3 --autodest debian/tmp/usr/lib/*/lib*.so.* # libminc-dev dh_install -plibminc-dev --autodest debian/tmp/usr/lib/*/lib*.so dh_install -plibminc-dev --autodest debian/tmp/usr/lib/*/lib*.a dh_install -plibminc-dev --autodest debian/tmp/usr/include dh_installdocs -plibminc-dev $(ps_docs) debian/index.html debian/libminc-dev.doc-base0000644000000000000000000000121410774061645012766 0ustar Document: minc Title: MINC Medical Image Format Library Reference Author: Peter Neelin Abstract: The Minc file format is a highly flexible medical image file format. Minc version 1 is built on top of the NetCDF generalized data format. Minc version 2 is built on top of the HDF data format. This library handles both formats. In each case the format is simple, self-describing, extensible, portable and N-dimensional, with programming interfaces for both low-level data access and high-level volume manipulation. Section: Science/Biology Format: HTML Index: /usr/share/doc/libminc-dev/index.html Files: /usr/share/doc/libminc-dev/index.html