[med-svn] r1036 - in trunk/packages/minc/trunk: . debian progs progs/mincedit progs/mincview
smr at alioth.debian.org
smr at alioth.debian.org
Sat Dec 29 07:34:10 UTC 2007
Author: smr
Date: 2007-12-29 07:34:10 +0000 (Sat, 29 Dec 2007)
New Revision: 1036
Added:
trunk/packages/minc/trunk/Makefile.am
trunk/packages/minc/trunk/debian/
trunk/packages/minc/trunk/debian/changelog
trunk/packages/minc/trunk/debian/compat
trunk/packages/minc/trunk/debian/control
trunk/packages/minc/trunk/debian/copyright
trunk/packages/minc/trunk/debian/index.html
trunk/packages/minc/trunk/debian/libminc0-dev.doc-base
trunk/packages/minc/trunk/debian/rules
trunk/packages/minc/trunk/progs/
trunk/packages/minc/trunk/progs/mincedit/
trunk/packages/minc/trunk/progs/mincedit/mincedit
trunk/packages/minc/trunk/progs/mincview/
trunk/packages/minc/trunk/progs/mincview/mincview
Log:
[svn-inject] Applying Debian modifications to trunk
Added: trunk/packages/minc/trunk/Makefile.am
===================================================================
--- trunk/packages/minc/trunk/Makefile.am (rev 0)
+++ trunk/packages/minc/trunk/Makefile.am 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,454 @@
+# Makefile.am for MINC
+#
+AUTOMAKE_OPTIONS = check-news subdir-objects
+ACLOCAL_AMFLAGS = -I m4
+
+SUBDIRS = . volume_io testdir doc
+
+
+# Add these to the include searches.
+#
+INCLUDES = \
+ -I$(top_srcdir)/libsrc \
+ -I$(top_builddir)/volume_io/Include \
+ -I$(top_srcdir)/volume_io/Include \
+ -I$(top_srcdir)/progs/Proglib \
+ -I$(top_srcdir)/conversion/Acr_nema
+
+# Headers which must be installed.
+#
+include_HEADERS = \
+ libsrc/minc.h \
+ libsrc/ParseArgv.h \
+ libsrc/voxel_loop.h \
+ libsrc/nd_loop.h \
+ libsrc/time_stamp.h \
+ volume_io/Include/volume_io.h \
+ libsrc/minc_simple.h
+
+include_volume_iodir = $(includedir)/volume_io
+
+include_volume_io_HEADERS = \
+ volume_io/Include/volume_io/alloc.h \
+ volume_io/Include/volume_io/arrays.h \
+ volume_io/Include/volume_io/basic.h \
+ volume_io/Include/volume_io/def_math.h \
+ volume_io/Include/volume_io/files.h \
+ volume_io/Include/volume_io/geom_structs.h \
+ volume_io/Include/volume_io/geometry.h \
+ volume_io/Include/internal_volume_io.h \
+ volume_io/Include/volume_io/multidim.h \
+ volume_io/Include/volume_io/progress.h \
+ volume_io/Include/volume_io/string_funcs.h \
+ volume_io/Include/volume_io/system_dependent.h \
+ volume_io/Include/volume_io/transforms.h \
+ volume_io/Include/volume_io/vol_io_prototypes.h \
+ volume_io/Include/volume_io/volume.h \
+ volume_io/Include/volume_io/volume_cache.h
+
+# Header files which must be included in the distribution but which are
+# not part of the installation.
+#
+noinst_HEADERS = \
+ libsrc/minc_basic.h \
+ libsrc/minc_private.h \
+ libsrc/minc_routines.h \
+ libsrc/minc_structures.h \
+ libsrc/minc_useful.h \
+ libsrc/minc_varlists.h \
+ libsrc/type_limits.h \
+ progs/Proglib/convert_origin_to_start.h \
+ progs/Proglib/minc_def.h \
+ progs/minccalc/errx.h \
+ progs/minccalc/node.h \
+ progs/minccalc/y.tab.h \
+ progs/mincresample/mincresample.h \
+ progs/mincreshape/mincreshape.h \
+ conversion/ecattominc/ecat_file.h \
+ conversion/ecattominc/machine_indep.h \
+ conversion/ecattominc/ecat_header_definition.h \
+ conversion/minctoecat/ecat_write.h \
+ conversion/minctoecat/machine_indep.h \
+ conversion/nifti1/nifti1.h \
+ conversion/nifti1/nifti1_io.h \
+ conversion/nifti1/nifti1_local.h \
+ conversion/nifti1/analyze75.h \
+ conversion/dcm2mnc/acr_element_defs.h \
+ conversion/dcm2mnc/dcm2mnc.h \
+ conversion/dcm2mnc/dicom_read.h \
+ conversion/dcm2mnc/dicom_to_minc.h \
+ conversion/dcm2mnc/ext_element_defs.h \
+ conversion/dcm2mnc/minc_file.h \
+ conversion/dcm2mnc/progress.h \
+ conversion/dcm2mnc/siemens_to_dicom.h \
+ conversion/dcm2mnc/siemens_header_defs.h \
+ conversion/dcm2mnc/siemens_header_table.h \
+ conversion/dcm2mnc/spi_element_defs.h \
+ conversion/dcm2mnc/string_to_filename.h \
+ conversion/dcm2mnc/pms_element_defs.h \
+ conversion/dcm2mnc/gems_element_defs.h
+
+if ACR_NEMA_TOOLS
+include_HEADERS += conversion/Acr_nema/acr_nema.h
+
+include_acr_nemadir = $(includedir)/acr_nema
+
+include_acr_nema_HEADERS = \
+ conversion/Acr_nema/acr_nema/acr_io.h \
+ conversion/Acr_nema/acr_nema/dicom_client_routines.h \
+ conversion/Acr_nema/acr_nema/dicom_network.h \
+ conversion/Acr_nema/acr_nema/element.h \
+ conversion/Acr_nema/acr_nema/file_io.h \
+ conversion/Acr_nema/acr_nema/group.h \
+ conversion/Acr_nema/acr_nema/message.h \
+ conversion/Acr_nema/acr_nema/value_repr.h
+
+else
+#
+# If not installing the full ACR/NEMA package, just add these headers to
+# list of headers not to be installed.
+#
+noinst_HEADERS += \
+ conversion/Acr_nema/acr_nema.h \
+ conversion/Acr_nema/acr_nema/acr_io.h \
+ conversion/Acr_nema/acr_nema/dicom_client_routines.h \
+ conversion/Acr_nema/acr_nema/dicom_network.h \
+ conversion/Acr_nema/acr_nema/element.h \
+ conversion/Acr_nema/acr_nema/file_io.h \
+ conversion/Acr_nema/acr_nema/group.h \
+ conversion/Acr_nema/acr_nema/message.h \
+ conversion/Acr_nema/acr_nema/value_repr.h
+
+endif
+
+
+# Libraries which must be built and installed.
+#
+lib_LTLIBRARIES = libminc.la libvolume_io.la
+
+# Conditionally install the libacr_nema.la library. It must always be
+# built even if it is not installed.
+#
+if ACR_NEMA_TOOLS
+lib_LTLIBRARIES += libacr_nema.la
+else
+noinst_LTLIBRARIES = libacr_nema.la
+endif
+
+# Scripts we install: sh, csh, or perl.
+#
+dist_bin_SCRIPTS = \
+ progs/mincdiff/mincdiff \
+ progs/mincedit/mincedit \
+ progs/mincheader/mincheader \
+ progs/minchistory/minchistory \
+ progs/mincpik/mincpik \
+ progs/mincview/mincview
+
+
+# Programs we build and install.
+#
+bin_PROGRAMS = \
+ voxeltoworld \
+ worldtovoxel \
+ minc_modify_header \
+ mincaverage \
+ minccalc \
+ mincconcat \
+ minccopy \
+ mincexpand \
+ mincextract \
+ mincinfo \
+ minclookup \
+ mincmakescalar \
+ mincmakevector \
+ mincmath \
+ mincresample \
+ mincreshape \
+ mincstats \
+ minctoraw \
+ invert_raw_image \
+ mincwindow \
+ rawtominc \
+ transformtags \
+ xfmconcat \
+ xfminvert \
+ ecattominc \
+ minctoecat \
+ mnc2nii \
+ nii2mnc \
+ upet2mnc \
+ dcm2mnc
+
+if ACR_NEMA_TOOLS
+bin_PROGRAMS += \
+ mincexample1 \
+ mincexample2 \
+ acr_test \
+ dump_acr_nema \
+ extract_acr_nema \
+ read_acr_nema \
+ dicom_test \
+ copy_acr_nema
+endif
+
+noinst_PROGRAMS = \
+ mincexample1 \
+ mincexample2
+
+LDADD = libvolume_io.la libminc.la
+
+EXTRA_DIST = GETTING_STARTED \
+ $(m4_files) \
+ fortran \
+ libsrc/strdup.c \
+ progs/Get_image_offset/get_image_offset.c \
+ epm-header.in \
+ libsrc/config.h.msvc-win32 \
+ Makefile.msvc-win32 \
+ conversion/Acr_nema/dicom.txt
+
+# The fortran directory is not yet automakified, so it is just
+# listed in EXTRA_DIST. This will copy everything including CVS
+# files. We use this hook to get rid of the latter.
+dist-hook:
+ rm -rf $(distdir)/fortran/CVS $(distdir)/fortran/vms/CVS
+
+m4_files = \
+ m4/mni_REQUIRE_LIB.m4 \
+ m4/smr_WITH_BUILD_PATH.m4
+
+
+voxeltoworld_SOURCES = progs/coordinates/voxeltoworld.c
+
+worldtovoxel_SOURCES = progs/coordinates/worldtovoxel.c
+
+minc_modify_header_SOURCES = progs/minc_modify_header/minc_modify_header.c
+
+mincaverage_SOURCES = progs/mincaverage/mincaverage.c
+
+minccalc_CFLAGS = -Iprogs/minccalc -I$(srcdir)/progs/minccalc
+minccalc_SOURCES = \
+ progs/minccalc/minccalc.c \
+ progs/minccalc/gram.y \
+ progs/minccalc/eval.c \
+ progs/minccalc/ident.c \
+ progs/minccalc/lex.l \
+ progs/minccalc/node.c \
+ progs/minccalc/optim.c \
+ progs/minccalc/scalar.c \
+ progs/minccalc/sym.c \
+ progs/minccalc/vector.c
+
+mincconcat_SOURCES = progs/mincconcat/mincconcat.c
+
+minccopy_SOURCES = progs/minccopy/minccopy.c
+
+mincexample1_SOURCES = progs/mincexample/mincexample1.c
+
+mincexample2_SOURCES = progs/mincexample/mincexample2.c
+
+mincexpand_SOURCES = progs/mincexpand/mincexpand.c
+
+mincextract_SOURCES = progs/mincextract/mincextract.c
+
+mincinfo_SOURCES = progs/mincinfo/mincinfo.c
+
+minclookup_SOURCES = progs/minclookup/minclookup.c
+
+mincmakescalar_SOURCES = progs/mincmakescalar/mincmakescalar.c
+
+mincmakevector_SOURCES = progs/mincmakevector/mincmakevector.c
+
+mincmath_SOURCES = progs/mincmath/mincmath.c
+
+mincresample_SOURCES = \
+ progs/mincresample/mincresample.c \
+ progs/mincresample/resample_volumes.c \
+ progs/Proglib/convert_origin_to_start.c
+
+mincreshape_SOURCES = \
+ progs/mincreshape/mincreshape.c \
+ progs/mincreshape/copy_data.c
+
+mincstats_SOURCES = progs/mincstats/mincstats.c
+
+minctoraw_SOURCES = progs/minctoraw/minctoraw.c
+
+invert_raw_image_SOURCES = progs/mincview/invert_raw_image.c
+
+mincwindow_SOURCES = progs/mincwindow/mincwindow.c
+
+rawtominc_SOURCES = \
+ progs/rawtominc/rawtominc.c \
+ progs/Proglib/convert_origin_to_start.c
+
+transformtags_SOURCES = progs/xfm/transformtags.c
+
+xfmconcat_SOURCES = progs/xfm/xfmconcat.c
+
+xfminvert_SOURCES = progs/xfm/xfminvert.c
+
+ecattominc_SOURCES = \
+ conversion/ecattominc/ecattominc.c \
+ conversion/ecattominc/insertblood.c \
+ conversion/ecattominc/ecat_file.c \
+ conversion/ecattominc/machine_indep.c
+
+minctoecat_SOURCES = \
+ conversion/minctoecat/minctoecat.c \
+ conversion/minctoecat/ecat_write.c \
+ conversion/minctoecat/machine_indep.c
+
+nii2mnc_SOURCES = \
+ conversion/nifti1/nii2mnc.c \
+ conversion/nifti1/nifti1_io.c
+
+mnc2nii_SOURCES = \
+ conversion/nifti1/mnc2nii.c \
+ conversion/nifti1/nifti1_io.c
+
+upet2mnc_SOURCES = \
+ conversion/micropet/upet2mnc.c
+
+dcm2mnc_LDADD = libacr_nema.la $(LDADD)
+
+dcm2mnc_SOURCES = \
+ conversion/dcm2mnc/dcm2mnc.c \
+ conversion/dcm2mnc/dicom_to_minc.c \
+ conversion/dcm2mnc/siemens_to_dicom.c \
+ conversion/dcm2mnc/dicom_read.c \
+ conversion/dcm2mnc/minc_file.c \
+ conversion/dcm2mnc/progress.c \
+ conversion/dcm2mnc/string_to_filename.c
+
+acr_test_LDADD = libacr_nema.la
+
+acr_test_SOURCES = conversion/Acr_nema/acr_test.c
+
+dump_acr_nema_LDADD = libacr_nema.la
+
+dump_acr_nema_SOURCES = conversion/Acr_nema/dump_acr_nema.c
+
+extract_acr_nema_LDADD = libacr_nema.la
+
+extract_acr_nema_SOURCES = conversion/Acr_nema/extract_acr_nema.c
+
+read_acr_nema_LDADD = libacr_nema.la
+
+read_acr_nema_SOURCES = conversion/Acr_nema/read_acr_nema.c
+
+dicom_test_LDADD = libacr_nema.la
+
+dicom_test_SOURCES = conversion/Acr_nema/dicom_test.c
+
+copy_acr_nema_LDADD = libacr_nema.la
+
+copy_acr_nema_SOURCES = conversion/Acr_nema/copy_acr_nema.c
+
+
+
+libminc_la_LDFLAGS = -version-info 1:0:1
+libminc_la_SOURCES = \
+ libsrc/ParseArgv.c \
+ libsrc/dim_conversion.c \
+ libsrc/image_conversion.c \
+ libsrc/minc_convenience.c \
+ libsrc/minc_error.c \
+ libsrc/minc_globdef.c \
+ libsrc/nd_loop.c \
+ libsrc/netcdf_convenience.c \
+ libsrc/time_stamp.c \
+ libsrc/value_conversion.c \
+ libsrc/voxel_loop.c \
+ libsrc/minc_simple.c
+
+libvolume_io_la_LDFLAGS = -version-info 0:1:0
+libvolume_io_la_SOURCES = \
+ volume_io/Geometry/colour.c \
+ volume_io/Geometry/colour_def.c \
+ volume_io/Geometry/gaussian.c \
+ volume_io/Geometry/inverse.c \
+ volume_io/Geometry/newton.c \
+ volume_io/Geometry/points.c \
+ volume_io/Geometry/splines.c \
+ volume_io/Geometry/tensors.c \
+ volume_io/Geometry/transforms.c \
+ volume_io/MNI_formats/gen_xf_io.c \
+ volume_io/MNI_formats/gen_xfs.c \
+ volume_io/MNI_formats/grid_transforms.c \
+ volume_io/MNI_formats/mni_io.c \
+ volume_io/MNI_formats/tag_points.c \
+ volume_io/MNI_formats/thin_plate_spline.c \
+ volume_io/Prog_utils/alloc.c \
+ volume_io/Prog_utils/alloc_check.c \
+ volume_io/Prog_utils/arrays.c \
+ volume_io/Prog_utils/files.c \
+ volume_io/Prog_utils/print.c \
+ volume_io/Prog_utils/progress.c \
+ volume_io/Prog_utils/string.c \
+ volume_io/Prog_utils/time.c \
+ volume_io/Volumes/evaluate.c \
+ volume_io/Volumes/get_hyperslab.c \
+ volume_io/Volumes/input_free.c \
+ volume_io/Volumes/input_mnc.c \
+ volume_io/Volumes/input_volume.c \
+ volume_io/Volumes/multidim_arrays.c \
+ volume_io/Volumes/output_mnc.c \
+ volume_io/Volumes/output_volume.c \
+ volume_io/Volumes/set_hyperslab.c \
+ volume_io/Volumes/volume_cache.c \
+ volume_io/Volumes/volumes.c
+
+libacr_nema_la_SOURCES = \
+ conversion/Acr_nema/acr_io.c \
+ conversion/Acr_nema/dicom_client_routines.c \
+ conversion/Acr_nema/dicom_network.c \
+ conversion/Acr_nema/element.c \
+ conversion/Acr_nema/file_io.c \
+ conversion/Acr_nema/globals.c \
+ conversion/Acr_nema/group.c \
+ conversion/Acr_nema/message.c \
+ conversion/Acr_nema/value_repr.c
+
+# MAN pages go here. The "dist_" prefix signals that they files
+# are to be included in source distribution.
+#
+dist_man1_MANS = \
+ progs/coordinates/voxeltoworld.man1 \
+ progs/minc_modify_header/minc_modify_header.man1 \
+ progs/mincaverage/mincaverage.man1 \
+ progs/minccalc/minccalc.man1 \
+ progs/mincconcat/mincconcat.man1 \
+ progs/minccopy/minccopy.man1 \
+ progs/mincdiff/mincdiff.man1 \
+ progs/mincedit/mincedit.man1 \
+ progs/mincexpand/mincexpand.man1 \
+ progs/mincextract/mincextract.man1 \
+ progs/mincheader/mincheader.man1 \
+ progs/minchistory/minchistory.man1 \
+ progs/mincinfo/mincinfo.man1 \
+ progs/minclookup/minclookup.man1 \
+ progs/mincmakescalar/mincmakescalar.man1 \
+ progs/mincmakevector/mincmakevector.man1 \
+ progs/mincmath/mincmath.man1 \
+ progs/mincpik/mincpik.man1 \
+ progs/mincresample/mincresample.man1 \
+ progs/mincreshape/mincreshape.man1 \
+ progs/mincstats/mincstats.man1 \
+ progs/minctoraw/minctoraw.man1 \
+ progs/mincview/invert_raw_image.man1 \
+ progs/mincview/mincview.man1 \
+ progs/mincwindow/mincwindow.man1 \
+ progs/rawtominc/rawtominc.man1 \
+ progs/xfm/transformtags.man1 \
+ progs/xfm/xfmconcat.man1 \
+ progs/xfm/xfminvert.man1 \
+ conversion/ecattominc/ecattominc.man1 \
+ conversion/minctoecat/minctoecat.man1 \
+ conversion/nifti1/nii2mnc.man1 \
+ conversion/nifti1/mnc2nii.man1 \
+ conversion/micropet/upet2mnc.man1 \
+ conversion/dcm2mnc/dcm2mnc.man1
+
+dist_man3_MANS = libsrc/ParseArgv.man3
Property changes on: trunk/packages/minc/trunk/debian
___________________________________________________________________
Name: mergeWithUpstream
+ 1
Added: trunk/packages/minc/trunk/debian/changelog
===================================================================
--- trunk/packages/minc/trunk/debian/changelog (rev 0)
+++ trunk/packages/minc/trunk/debian/changelog 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,108 @@
+minc (1.5-1) unstable; urgency=low
+
+ * New upstream.
+
+ -- Steve M. Robbins <smr at debian.org> Mon, 13 Nov 2006 23:26:13 -0600
+
+minc (1.4.1-1) unstable; urgency=low
+
+ * New upstream.
+
+ -- Steve M. Robbins <smr at debian.org> 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 <smr at debian.org> Sat, 18 Feb 2006 17:33:37 -0500
+
+minc (1.4-3) unstable; urgency=low
+
+ * Build-depend on csh. Closes: #351826.
+
+ -- Steve M. Robbins <smr at debian.org> 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 <smr at debian.org> 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 <smr at debian.org> 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 <smr at debian.org> 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 <smr at debian.org> 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 <smr at debian.org> 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 <smr at debian.org> 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 <smr at debian.org> 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 <smr at debian.org> 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 <smr at debian.org> Mon, 29 Jul 2002 16:06:56 -0400
+
Added: trunk/packages/minc/trunk/debian/compat
===================================================================
--- trunk/packages/minc/trunk/debian/compat (rev 0)
+++ trunk/packages/minc/trunk/debian/compat 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1 @@
+5
Added: trunk/packages/minc/trunk/debian/control
===================================================================
--- trunk/packages/minc/trunk/debian/control (rev 0)
+++ trunk/packages/minc/trunk/debian/control 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,59 @@
+Source: minc
+Section: science
+Priority: optional
+Maintainer: Steve M. Robbins <smr at debian.org>
+Build-Depends: debhelper (>= 5), csh, netcdfg-dev, tetex-bin
+Standards-Version: 3.6.2.0
+
+Package: minc-tools
+Architecture: any
+Depends: ${shlibs:Depends}, csh | c-shell, netcdf-bin, libtext-format-perl
+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: libminc0
+Section: libs
+Architecture: any
+Depends: ${shlibs:Depends}
+Description: MNI medical image format library
+ This package contains the libraries libminc and libvolume_io.
+ .
+ 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: libminc0-dev
+Provides: libminc-dev
+Conflicts: libminc-dev
+Section: libdevel
+Architecture: any
+Depends: libminc0 (= ${Source-Version}), netcdfg-dev
+Description: MNI medical image format development environment
+ This package contains the library and headers for libminc and
+ libvolume_io.
+ .
+ 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.
Added: trunk/packages/minc/trunk/debian/copyright
===================================================================
--- trunk/packages/minc/trunk/debian/copyright (rev 0)
+++ trunk/packages/minc/trunk/debian/copyright 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,14 @@
+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.
Added: trunk/packages/minc/trunk/debian/index.html
===================================================================
--- trunk/packages/minc/trunk/debian/index.html (rev 0)
+++ trunk/packages/minc/trunk/debian/index.html 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,38 @@
+<html>
+<head>
+<title>MINC Documentation</title>
+</head>
+
+<body>
+
+<h1>MINC Library Documentation</h1>
+
+The MINC library is used to deal with large files typically encountered
+in medical imaging. A
+<a href="prog_guide.ps.gz">programmer's guide</a>
+and a
+<a href="prog_ref.ps.gz">programmer's reference manual</a>
+are available.
+
+<p> The <a href="volume_io.ps.gz">volume_io library</a>, also included
+in the MINC package, provides a simpler programming interface to MINC.
+</p>
+
+<h1>Additional Links</h1>
+
+<p>For other tools that work well with MINC, check
+out the <a href="http://www.bic.mni.mcgill.ca/software/">MNI Brain
+Imaging Centre software toolbox</a>.
+</p>
+
+<p>There are two mailing lists for MINC: <a
+href="http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-users">minc
+users</a> and <a
+href="http://www.bic.mni.mcgill.ca/mailman/listinfo/minc-development">minc
+development</a>.
+</p>
+
+<hr>
+<address></address>
+<!-- hhmts start -->Last modified: Sat Dec 20 09:27:53 EST 2003 <!-- hhmts end -->
+</body> </html>
Added: trunk/packages/minc/trunk/debian/libminc0-dev.doc-base
===================================================================
--- trunk/packages/minc/trunk/debian/libminc0-dev.doc-base (rev 0)
+++ trunk/packages/minc/trunk/debian/libminc0-dev.doc-base 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,13 @@
+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
+ 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.
+Section: Science
+
+Format: HTML
+Index: /usr/share/doc/libminc0-dev/index.html
+Files: /usr/share/doc/libminc0-dev/index.html
Added: trunk/packages/minc/trunk/debian/rules
===================================================================
--- trunk/packages/minc/trunk/debian/rules (rev 0)
+++ trunk/packages/minc/trunk/debian/rules 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,101 @@
+#!/usr/bin/make -f
+# Sample debian/rules that uses debhelper.
+# This file is public domain software, originally written by Joey Hess.
+#
+# This version is for a multibinary package. It also allows you to build any
+# of the binary packages independantly, via binary-<package> targets.
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+# This has to be exported to make some magic below work.
+export DH_OPTIONS
+
+# Handle optimization per debian policy.
+#
+export CFLAGS=-g
+ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS)))
+CFLAGS += -O0
+else
+CFLAGS += -O2
+endif
+
+
+# Suppress accidental execution of the auto-* tools
+# http://lists.debian.org/debian-devel/2001/debian-devel-200111/msg01416.html
+#
+missing=$(shell pwd)/ac_config_aux/missing
+no_auto_tools = ACLOCAL="$(missing) aclocal" \
+ AUTOCONF="$(missing) autoconf" \
+ AUTOMAKE="$(missing) automake" \
+ AUTOHEADER="$(missing) autoheader"
+no_auto_tools=
+
+build: build-stamp
+build-stamp:
+ dh_testdir
+ ./configure --prefix=/usr --mandir=/usr/share/man --enable-shared
+ $(MAKE) $(no_auto_tools)
+ $(MAKE) $(no_auto_tools) check
+ $(MAKE) $(no_auto_tools) -C doc docs
+ $(MAKE) $(no_auto_tools) -C volume_io/Documentation docs
+ touch build-stamp
+
+clean:
+ dh_testdir
+ dh_testroot
+ rm -f build-stamp
+ -$(MAKE) distclean
+ dh_clean
+
+install: DH_OPTIONS=
+install: build
+ dh_testdir
+ dh_testroot
+ dh_clean -k
+ dh_installdirs
+ $(MAKE) DESTDIR=`pwd`/debian/tmp install
+ rm -f debian/tmp/usr/bin/mincexample?
+ dh_movefiles -pminc-tools usr/bin usr/share/man/man1
+ dh_install -plibminc0 --autodest debian/tmp/usr/lib/*.so.0*
+ rm -f debian/tmp/usr/lib/*.so.0*
+ dh_movefiles -plibminc0-dev usr/include usr/lib
+ dh_movefiles
+ dh_installdocs -plibminc0-dev doc/prog_ref.ps doc/prog_guide.ps \
+ volume_io/Documentation/volume_io.ps debian/index.html
+
+# This single target is used to build all the packages, all at once, or
+# one at a time. So keep in mind: any options passed to commands here will
+# affect _all_ packages. Anything you want to only affect one package
+# should be put in another target, such as the install target.
+binary-common:
+ dh_testdir
+ dh_testroot
+ dh_installdocs -plibminc0-dev GETTING_STARTED
+ dh_installdocs
+ dh_installchangelogs ChangeLog
+ dh_link usr/share/man/man1/voxeltoworld.1 usr/share/man/man1/worldtovoxel.1
+ dh_compress
+ dh_fixperms
+ dh_strip
+ dh_makeshlibs
+ dh_shlibdeps -L libminc0 -l debian/libminc0/usr/lib
+ dh_installdeb
+ dh_gencontrol
+ dh_md5sums
+ dh_builddeb
+
+# Build architecture independant packages using the common target.
+binary-indep: build install
+# $(MAKE) -f debian/rules DH_OPTIONS=-i binary-common
+
+# Build architecture dependant packages using the common target.
+binary-arch: build install
+ $(MAKE) -f debian/rules DH_OPTIONS=-a binary-common
+
+# Any other binary targets build just one binary package at a time.
+binary-%: build install
+ make -f debian/rules binary-common DH_OPTIONS=-p$*
+
+binary: binary-indep binary-arch
+.PHONY: build clean binary-indep binary-arch binary install
Property changes on: trunk/packages/minc/trunk/debian/rules
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/minc/trunk/progs/mincedit/mincedit
===================================================================
--- trunk/packages/minc/trunk/progs/mincedit/mincedit (rev 0)
+++ trunk/packages/minc/trunk/progs/mincedit/mincedit 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,159 @@
+#! /bin/csh -f
+#
+# Script to allow editing of minc files
+#
+# Usage: mincedit <minc file> [<editor>]
+#
+# Modifications:
+# $Log: mincedit,v $
+# Revision 6.2 2000/09/12 15:43:37 neelin
+# Changed default TMPDIR to look for /var/tmp, /usr/tmp, /tmp.
+#
+# Revision 6.1 1999/10/19 14:45:21 neelin
+# Fixed Log subsitutions for CVS
+#
+# Revision 6.0 1997/09/12 13:23:34 neelin
+# Release of minc version 0.6
+#
+# Revision 5.0 1997/08/21 13:24:35 neelin
+# Release of minc version 0.5
+#
+# Revision 4.0 1997/05/07 20:00:36 neelin
+# Release of minc version 0.4
+#
+# Revision 3.0 1995/05/15 19:31:09 neelin
+# Release of minc version 0.3
+#
+# Revision 2.0 1994/09/28 10:33:58 neelin
+# Release of minc version 0.2
+#
+# Revision 1.6 94/09/28 10:33:55 neelin
+# Pre-release
+#
+# Revision 1.5 93/08/25 11:24:48 neelin
+# Added checking for -h or -help options.
+#
+# Revision 1.4 93/08/11 15:19:09 neelin
+# Added RCS logging in source.
+#
+#
+#
+# Copyright 1993 Peter Neelin, 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.
+
+# Create temporary directory
+if (! $?TMPDIR) then
+ if (-d /var/tmp) then
+ set TMPDIR = /var/tmp
+ else if (-d /usr/tmp) then
+ set TMPDIR = /usr/tmp
+ else
+ set TMPDIR = /tmp
+ endif
+endif
+if (! -d $TMPDIR) then
+ echo "Working directory $TMPDIR does not exist."
+ exit 1
+endif
+set working_dir = $TMPDIR
+
+# Set default editor
+set editor = sensible-editor
+
+# Check arguments
+switch ("$#argv")
+case 1:
+ if (("$1" == "-help") || ("$1" == "-h") || ("$1" == "")) then
+ echo "Usage: $0 <minc file> [<editor>]"
+ exit
+ endif
+ if ($?EDITOR) then
+ set editor = $EDITOR
+ endif
+ breaksw
+case 2:
+ set editor = "$2"
+ breaksw
+default:
+ echo "Usage: $0 <minc file> [<editor>]"
+ exit
+endsw
+
+# Set up the file names
+set filename = $1
+set backup_filename = ${filename}~
+set cdl_prefix = mincedit-$$
+set cdl_orig = $working_dir/${cdl_prefix}-orig.cdl
+set cdl_edit = $working_dir/${cdl_prefix}-edit.cdl
+
+# Set interrupt handling
+onintr cleanup
+
+# Dump the file
+mincheader $filename > $cdl_orig
+if ($status) then
+ echo "${0}: Error reading file '$filename'"
+ goto cleanup
+endif
+cp $cdl_orig $cdl_edit
+
+# Loop until successful file generation
+set do_edit = 1
+while ($do_edit)
+
+# Edit the cdl file
+ $editor $cdl_edit
+ if ($status) then
+ echo "${0}: Error editing with editor '$editor'"
+ goto cleanup
+ endif
+ set do_edit = 0
+
+# Compare the files for difference
+ diff $cdl_orig $cdl_edit >& /dev/null
+ if ($status == 0) then
+ echo "File $filename not modified"
+ goto cleanup
+ endif
+
+# Rename the original file and generate a new one
+ mv $filename $backup_filename
+ ncgen -o $filename $cdl_edit
+ if ($status) then
+ mv $backup_filename $filename
+ echo -n "Error generating new file. Redit the file (y/n)? (def=n):"
+ set answer = $<
+ if ("$answer" =~ y*) then
+ set do_edit = 1
+ continue
+ endif
+ goto cleanup
+ endif
+
+# Copy the data
+ minccopy $backup_filename $filename
+ if ($status) then
+ mv $backup_filename $filename
+ echo -n "Error copying image data. Redit the file (y/n)? (def=n):"
+ set answer = $<
+ if ("$answer" =~ y*) then
+ set do_edit = 1
+ continue
+ endif
+ goto cleanup
+ endif
+
+# End while loop
+end
+
+cleanup:
+ rm -f $working_dir/*${cdl_prefix}*
+ exit
+
Property changes on: trunk/packages/minc/trunk/progs/mincedit/mincedit
___________________________________________________________________
Name: svn:executable
+ *
Added: trunk/packages/minc/trunk/progs/mincview/mincview
===================================================================
--- trunk/packages/minc/trunk/progs/mincview/mincview (rev 0)
+++ trunk/packages/minc/trunk/progs/mincview/mincview 2007-12-29 07:34:10 UTC (rev 1036)
@@ -0,0 +1,151 @@
+#! /bin/csh -f
+# Script for viewing a minc file.
+# Requires a pnm file viewer such as xv or display from ImageMagick,
+# as wells as the filter invert_raw_image.
+#
+# Displays images with patient left on left side of the screen.
+
+# Constants
+set xv_visual = `xdpyinfo | awk '($1=="class:"){visual=$2};(($1=="depth:") && (visual=="TrueColor") && ($2==24)) {found=1}; END {if (found) print "-visual TrueColor"}'`
+set VIEWER = "xv" # Any pnm display program that handles a list of files
+set VIEWER_OPTIONS = "-geometry 512x512 -fixed -cmap -raw $xv_visual"
+
+#set VIEWER = "display"
+#set VIEWER_OPTIONS = "-geometry 512x512"
+
+set PGM_CODE = "P5"
+set PPM_CODE = "P6"
+set usage = "Usage: $0 <filename.mnc> [<slice number>]"
+set exit_status = 0
+
+# Check arguments
+if (($#argv < 1) || ($#argv > 2) || ("$1" == "-help") || ("$1" == "-h")) then
+ echo "$usage"
+ exit -1
+endif
+set filename = "$1"
+set slice = `awk "BEGIN{print $2+0}" < /dev/null`
+@ slice_specified = ( $#argv >= 2 )
+
+# Create temporary directory
+if (! $?TMPDIR) then
+ if (-d /var/tmp) then
+ set TMPDIR = /var/tmp
+ else if (-d /usr/tmp) then
+ set TMPDIR = /usr/tmp
+ else
+ set TMPDIR = /tmp
+ endif
+endif
+if (! -d $TMPDIR) then
+ echo "Working directory $TMPDIR does not exist."
+ exit 1
+endif
+set workingdir = $TMPDIR
+
+set workingparent = $workingdir/mincview-$$
+set childdir = $filename:t
+set workingdir = $workingparent/$childdir
+onintr cleanup
+mkdir $workingparent
+mkdir $workingdir
+
+# Expand the file if needed
+set newfilename = $filename:t
+set newfilename = $workingdir/temp_$newfilename:r
+set filename = `mincexpand $filename $newfilename -name_only`
+
+# Get dimension names
+set dims = `mincinfo $filename -vardims image`
+
+# Check for vector dimension
+set pnm_code = $PGM_CODE
+set bytes_per_pixel = 1
+if ("$dims[$#dims]" == "vector_dimension") then
+ @ ndims = $#dims - 1
+ set nvec = `mincinfo $filename -dimlength $dims[$#dims]`
+ set start_suffix = ",0"
+ if ($nvec != 3) then
+ set count_suffix = ",1"
+ else
+ set count_suffix = ",3"
+ set pnm_code = $PPM_CODE
+ set bytes_per_pixel = 3
+ endif
+else
+ set ndims = $#dims
+ set start_suffix = ""
+ set count_suffix = ""
+endif
+
+if ($ndims > 3) then
+ @ nprefix = $ndims - 3
+ set start_prefix = \
+ "`awk 'BEGIN{for (i=0;i<$nprefix;i++) print "'"'"0,"'"'"}' < /dev/null`"
+ set count_prefix = \
+ "`awk 'BEGIN{for (i=0;i<$nprefix;i++) print "'"'"1,"'"'"}' < /dev/null`"
+else if ($ndims < 2) then
+ echo "No image found in file $filename"
+ set exit_status = -1
+ goto cleanup
+else
+ set start_prefix = ""
+ set count_prefix = ""
+endif
+
+# Get number of slices and image dimensions
+@ ind1 = $ndims - 2
+@ ind2 = $ndims - 1
+@ ind3 = $ndims
+if ($ind1 > 0) then
+ set nslices = `mincinfo $filename -dimlength $dims[$ind1]`
+else
+ set nslices = 1
+endif
+set imgsize = `mincinfo $filename -dimlength $dims[$ind2] -dimlength $dims[$ind3]`
+if ($slice_specified) then
+ if (($slice >= $nslices) || ($slice < 0)) then
+ echo "Slice number out of range"
+ set exit_status = -1
+ goto cleanup
+ endif
+ @ nslices = $slice + 1
+endif
+
+# Check for inverting images to get standard orientation
+set rows = -$imgsize[1]
+set cols = $imgsize[2]
+
+# Loop through slices, if needed
+echo -n Loading slices
+while ($slice < $nslices)
+ echo -n .
+ if ($ndims > 2) then
+ set start = "$start_prefix $slice,0,0 $start_suffix"
+ set count = "$count_prefix 1,$imgsize[1],$imgsize[2] $count_suffix"
+ else
+ set start = "0,0 $start_suffix"
+ set count = "$imgsize[1],$imgsize[2] $count_suffix"
+ endif
+ set output_file = $workingdir/$slice
+ echo "$pnm_code" >! $output_file
+ echo "$imgsize[2] $imgsize[1]" >> $output_file
+ echo "255" >> $output_file
+ mincextract $filename -byte -start "$start" -count "$count" \
+ -positive_direction |\
+ invert_raw_image $cols $rows $bytes_per_pixel >> $output_file
+ @ slice++
+end
+echo Done
+
+# Remove the temporary file
+rm -f $newfilename
+
+# Display the images
+cd $workingparent
+$VIEWER $VIEWER_OPTIONS $childdir/{?,??,???,????}
+
+cleanup:
+ cd /
+ rm -rf $workingparent
+ exit $exit_status
Property changes on: trunk/packages/minc/trunk/progs/mincview/mincview
___________________________________________________________________
Name: svn:executable
+ *
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