--- dicomnifti-2.28.10.orig/man/dicomhead.1 +++ dicomnifti-2.28.10/man/dicomhead.1 @@ -8,4 +8,4 @@ .SH "AUTHOR" \fBdicomhead\fR is written by Valerio Luccio (valerio.luccio@nyu.edu). .SH "SEE ALSO" -\fBHomepage:\fR https://cbi.nyu.edu/public/software/dinifti +\fBHomepage:\fR http://cbi.nyu.edu/software/dinifti.php --- dicomnifti-2.28.10.orig/debian/changelog +++ dicomnifti-2.28.10/debian/changelog @@ -0,0 +1,181 @@ +dicomnifti (2.28.10-1) unstable; urgency=low + + * New Upstream Version. + * Remove patch to prevent fixed sizes for 'int' and 'long' as upstream + switched to determine this with CMake dynamically (although it is still + not necessary for Debian's CTN library). + + -- Michael Hanke Fri, 30 Nov 2007 10:59:00 +0100 + +dicomnifti (2.28.8-1) unstable; urgency=low + + * New Upstream Version. Fixes a bug where dinifti did not respect the users + choice of number of slices (option -s). + + -- Michael Hanke Sun, 11 Nov 2007 11:20:07 +0100 + +dicomnifti (2.28.7-1) unstable; urgency=low + + * New Upstream Version. Changed license to a 3-clause BSD license. + + -- Michael Hanke Wed, 07 Nov 2007 09:38:35 +0100 + +dicomnifti (2.28.5-2) unstable; urgency=low + + * Updated Homepage info in debian/control using the new 'Homepage' field. + * Added VCS info to debian/control. + + -- Michael Hanke Thu, 18 Oct 2007 20:22:40 +0200 + +dicomnifti (2.28.5-1) unstable; urgency=low + + * New Upstream Version. Allows for custom naming schemes of image series. + (Closes: #446260) + + -- Michael Hanke Tue, 16 Oct 2007 00:46:55 +0200 + +dicomnifti (2.28.4-1) unstable; urgency=low + + * New Upstream bugfix release. + * Siemens Vision: fails to read the number of slices, now defaults 1 + and user can override this with the '-s' option (Closes: #442013). + * GE Elscint: fails to read series' description, only needed with + '-d' flag. Now defaults to "" + * Build-depend on libniftiio1-dev by default. + + -- Michael Hanke Mon, 17 Sep 2007 10:38:18 +0200 + +dicomnifti (2.28.2-1) unstable; urgency=low + + * New upstream release. NIfTI header value 'nu' is now always set to one + instead of the number of channels reported in the DICOMs. + * Updated upstream URL in manpages. + + -- Michael Hanke Wed, 12 Sep 2007 14:08:57 +0200 + +dicomnifti (2.28-1) unstable; urgency=low + + * New upstream release. Upstream switched from custom makefiles to + CMake-based build system. + * Converted NIfTI files now contain SPM5-like acquisition information. + (Closes: #431591) + * Bugfix: Wrong origin when converting sagital images (e.g. Siemens MPRAGE). + (Closes: #431652) + * Binaries are now build with -Wall -g -O2 by default (as it should be). + * debian/rules honours DEB_BUILD_OPTIONS='noopt' and sets -O0 accordingly. + * Removed dpatch build-dependency in favor of Git. + * Fixed member init order in dicomInfo class. + + -- Michael Hanke Sun, 15 Jul 2007 20:59:07 +0200 + +dicomnifti (2.27-1) unstable; urgency=low + + * New upstream release. Fix image pixel location (half-pixel shift) to + properly convert Siemens DICOMs. + + -- Michael Hanke Thu, 24 May 2007 06:45:08 +0200 + +dicomnifti (2.26.1-1) unstable; urgency=low + + * New upstream release. + * Merged all non-Debian-specific patches with upstream. This also fixes the + pending GCC 4.3 header issue that should have been fixed by the last + upload, but wasn't as the included patch was disabled by mistake. + (Closes: #417157) + * Fixed bug: wrong header information (dimensions, etc) (Closes: #420019) + + -- Michael Hanke Wed, 25 Apr 2007 18:25:23 +0200 + +dicomnifti (2.25-2) unstable; urgency=low + + * Added patch to check for duplicate image series names. dinifti now + modifies the series name and issues a warning instead of silently + overwriting the file. + * Added patch to add a --noact option to be able to quickly inspect the + content of a DICOM directory without having to actually write the NIfTI + files. + * Documented the new behavior and options in the manpage. + * Added patch to fix a missing header dependency which would result in a + FTBFS with the coming GCC 4.3. Thanks to Martin Michlmayr for providing + the patch. (Closes: #417157) + + -- Michael Hanke Thu, 5 Apr 2007 15:27:38 +0200 + +dicomnifti (2.25-1) unstable; urgency=low + + * New upstream release. Fixes a bug when converting MOSAIC images with a + rectangular FOV. + + -- Michael Hanke Sat, 17 Mar 2007 07:47:01 +0100 + +dicomnifti (2.24-1) unstable; urgency=low + + * New upstream release. Fixes a problem when converting DICOMs from 3T GE + scanners. + + -- Michael Hanke Thu, 22 Feb 2007 08:11:08 +0100 + +dicomnifti (2.23-1) unstable; urgency=low + + * New upstream release. Fixes a bug that caused dinifti to crash if not all + DICOMs of an image series are available. + * Merged most patches with upstream. Thanks to Valerio Luccio. + * Added an additional space to the Homepage field in debian/control. + * Updated debian/copyright (year in the copyright statement). + + -- Michael Hanke Wed, 21 Feb 2007 10:20:24 +0100 + +dicomnifti (2.22-2) unstable; urgency=low + + * Fixed a number of memory leaks. I'm grateful to Yaroslav Halchenko + for pointing to a nasty STL-related bug. (Closes: #394834) + * Build-depend on ctn-dev >> 3.0.6-9 to finally solve the datatype size + issues on 64bit systems (see #387183). + * Added upstream homepage to the package description. + + -- Michael Hanke Sun, 28 Jan 2007 19:24:44 +0100 + +dicomnifti (2.22-1) unstable; urgency=low + + * New upstream release. + * Patches merged with upstream. + + -- Michael Hanke Thu, 5 Oct 2006 19:49:23 +0200 + +dicomnifti (2.21-3) unstable; urgency=low + + * Added --verbose option to enable a more verbose status output. This is + mostly useful to associate dinifti warnings with certain image series, + when converting directories containing multiple series. + + -- Michael Hanke Thu, 21 Sep 2006 19:50:56 +0200 + +dicomnifti (2.21-2) unstable; urgency=low + + * Added dependency to autotools-dev to get fresh copies of config.sub and + config.guess. This fixes a FTBFS on AMD64. + * Possible silent overwrite of converted files is noted in the manpage. + + -- Michael Hanke Mon, 4 Sep 2006 12:57:25 +0200 + +dicomnifti (2.21-1) unstable; urgency=low + + * New upstream release. + + -- Michael Hanke Tue, 29 Aug 2006 07:43:13 +0200 + +dicomnifti (2.20-1) unstable; urgency=low + + * New upstream release. + * Added minimal manpage for dicomhead, enhanced manpage for dinifti. Both + are forwarded to upstream and will become part of the next upstream + release. + + -- Michael Hanke Mon, 28 Aug 2006 16:11:43 +0200 + +dicomnifti (2.11-1) unstable; urgency=low + + * Initial release. (Closes: #383563) + + -- Michael Hanke Wed, 16 Aug 2006 02:11:44 +0200 + --- dicomnifti-2.28.10.orig/debian/compat +++ dicomnifti-2.28.10/debian/compat @@ -0,0 +1 @@ +5 --- dicomnifti-2.28.10.orig/debian/control +++ dicomnifti-2.28.10/debian/control @@ -0,0 +1,23 @@ +Source: dicomnifti +Section: science +Priority: optional +Maintainer: Michael Hanke +Build-Depends: debhelper (>= 5), ctn-dev (>> 3.0.6-9), libniftiio1-dev | libniftiio-dev, cmake, zlib1g-dev +Standards-Version: 3.7.2 +Homepage: http://cbi.nyu.edu/software/dinifti.php +Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/dicomnifti.git +Vcs-Git: git://git.debian.org/git/pkg-exppsy/dicomnifti.git + +Package: dicomnifti +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: converts DICOM files into the NIfTI format + The dinifti program converts MRI images stored in DICOM format to NIfTI + format. The NIfTI format is thought to be the new standard image format for + medical imaging and can be used with for example with FSL, AFNI, SPM, Caret + or Freesurfer. + . + dinifti converts single files, but also supports fully automatic batch + conversions of complete dicomdirs. Additionally, converted NIfTI files can + be properly named, using image series information from the DICOM files. + --- dicomnifti-2.28.10.orig/debian/copyright +++ dicomnifti-2.28.10/debian/copyright @@ -0,0 +1,47 @@ +This package was debianized by Michael Hanke on +Wed, 16 Aug 2006 02:11:44 +0200. + +It was downloaded from https://cbi.nyu.edu/public/software/dinifti/ + +Upstream Author: Valerio Luccio (valerio.luccio@nyu.edu) + +Copyright: 2005-2007 Valerio Luccio (valerio.luccio@nyu.edu) + 2007 New York University + +License: + + All rights reserved. + + Redistribution and use in source and binary forms, with or without + modification, are permitted provided that the following conditions are + met: + + * Redistributions of source code must retain the above copyright + * notice, this list of conditions and the following disclaimer. + * Redistributions in binary form must reproduce the above + * copyright notice, this list of conditions and the following + * disclaimer in the documentation and/or other materials provided + * with the distribution. + * Neither the name of New York University nor the names of its + * contributors may be used to endorse or promote products derived + * from this software without specific prior written permission. + + THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS + "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT + LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR + A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT + OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, + SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT + LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, + DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY + THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT + (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE + OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. + + +The Debian packaging is (C) 2006-2007, Michael Hanke +and is licensed under the GPL, see above. + +On Debian systems, the complete text of the GNU General +Public License can be found in `/usr/share/common-licenses/GPL'. + --- dicomnifti-2.28.10.orig/debian/dirs +++ dicomnifti-2.28.10/debian/dirs @@ -0,0 +1 @@ +usr/bin --- dicomnifti-2.28.10.orig/debian/docs +++ dicomnifti-2.28.10/debian/docs @@ -0,0 +1 @@ +README --- dicomnifti-2.28.10.orig/debian/manpages +++ dicomnifti-2.28.10/debian/manpages @@ -0,0 +1,2 @@ +man/dicomhead.1 +man/dinifti.1 --- dicomnifti-2.28.10.orig/debian/rules +++ dicomnifti-2.28.10/debian/rules @@ -0,0 +1,89 @@ +#!/usr/bin/make -f +# -*- makefile -*- + +# Uncomment this to turn on verbose mode. +#export DH_VERBOSE=1 + +# path where binaries are built +pkg_buildpath=$(CURDIR)/build + +# default compiler flags +CXXFLAGS = -Wall -g + +# ease debugging +ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) + CXXFLAGS += -O0 +else + CXXFLAGS += -O2 +endif + +# default CMake flags: +# set manpage install dir to temp directory -- manpages will be installed +# by dh_installman +CMAKE_FLAGS = -DCMAKE_CXX_FLAGS:STRING="$(CXXFLAGS)" \ + -DCMAKE_INSTALL_PREFIX:PATH=/usr \ + -DDINIFTI_MAN_DIR:PATH=../../tmp/manpages + + +configure: configure-stamp +configure-stamp: + dh_testdir + # Add here commands to configure the package. + + if [ ! -d $(pkg_buildpath) ]; then mkdir $(pkg_buildpath); fi + cd $(pkg_buildpath) && cmake .. $(CMAKE_FLAGS) + + touch configure-stamp + + +build: build-stamp +build-stamp: configure + dh_testdir + # Add here commands to compile the package. + + cd $(pkg_buildpath) && $(MAKE) VERBOSE=1 + + touch build-stamp + +clean: + dh_testdir + dh_testroot + rm -f build-stamp configure-stamp + + -rm -rf $(pkg_buildpath) + + dh_clean + +install: build + dh_testdir + dh_testroot + dh_clean -k + dh_installdirs + + # Add here commands to install the package into debian/dicomnifti. + cd $(pkg_buildpath) && $(MAKE) install DESTDIR=$(CURDIR)/debian/dicomnifti + + +# Build architecture-independent files here. +binary-indep: install +# We have nothing to do by default. + +# Build architecture-dependent files here. +binary-arch: install + dh_testdir + dh_testroot + dh_installchangelogs + dh_installdocs + dh_installman + dh_link + dh_strip + dh_compress + dh_fixperms + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +binary: binary-indep binary-arch +.PHONY: build clean binary-indep binary-arch binary install configure --- dicomnifti-2.28.10.orig/debian/watch +++ dicomnifti-2.28.10/debian/watch @@ -0,0 +1,3 @@ +version=3 +http://cbi.nyu.edu/Downloads/DICOMNIfTI.([\d\.]+)\.tar\.gz +