debian/0000775000000000000000000000000012265407332007174 5ustar debian/rules0000775000000000000000000000521512265407116010257 0ustar #!/usr/bin/make -f # -*- makefile -*- DISTDIR=$(CURDIR)/debian/cmtk # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 # custom option tests to provide build for validating unittests ifneq (,$(findstring docheck,$(DEB_BUILD_OPTIONS))) TESTING=ON DEB_HOST_ARCH=$(shell dpkg-architecture -qDEB_HOST_ARCH) ifeq ($(DEB_HOST_ARCH),i386) TFLAGS=-march=pentium4 endif ifeq ($(DEB_HOST_ARCH),amd64) TFLAGS=-march=nocona endif TFLAGS+=-mmmx -msse -msse2 -mfpmath=sse OPT_CMAKE_FLAGS=-DCMAKE_C_FLAGS:STRING="$(TFLAGS)" \ -DCMAKE_ANSI_CXXFLAGS:STRING="$(TFLAGS)" else TESTING=OFF export DEB_BUILD_OPTIONS += " nocheck" endif %: dh $@ --parallel override_dh_auto_configure: dh_auto_configure -- \ -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \ -DBUILD_APPS:BOOL=ON \ -DBUILD_DOCUMENTATION:BOOL=OFF \ -DBUILD_GUI:BOOL=ON \ -DBUILD_SHARED_LIBS:BOOL=ON \ -DBUILD_TESTING:BOOL=$(TESTING) \ -DCMTK_BUILD_DCMTK:BOOL=OFF \ -DCMTK_BUILD_MXML:BOOL=OFF \ -DCMTK_BUILD_NRRD:BOOL=ON \ -DCMTK_BUILD_SQLITE:BOOL=OFF \ -DCMTK_BUILD_ZLIB:BOOL=OFF \ -DCMTK_ROOT_PATH_SRI24:PATH=/usr/share/data/sri24-atlas \ -DCMTK_USE_DCMTK:BOOL=ON \ -DCMTK_USE_FFTW:BOOL=ON \ -DCMTK_USE_QT:BOOL=ON \ -DCMTK_USE_SMP:BOOL=ON \ -DCMTK_USE_SQLITE:BOOL=ON \ -DDART_TESTING_TIMEOUT:STRING=15000 \ -DMXML_INCLUDE_DIR:PATH=/usr/include \ -DLZMA_INCLUDE_DIRS:PATH=/usr/include/lzma \ -DCMAKE_SKIP_RPATH:BOOL=OFF \ -DCMTK_BUILD_WRAPPER:BOOL=ON \ $(OPT_CMAKE_FLAGS) override_dh_auto_test: ifneq (,$(findstring docheck,$(DEB_BUILD_OPTIONS))) xvfb-run --auto-servernum --server-num=20 \ dh_auto_test endif override_dh_auto_install: dh_auto_install : # Remove not needed headers, cmake files etc rm -fr $(DISTDIR)/usr/include -/usr/bin/find $(DISTDIR) -iname *.cmake -delete : # Prune duplicate docs rm -fr $(DISTDIR)/usr/share/cmtk/doc : # Generate manpages xvfb-run --auto-servernum --server-num=20 \ scripts/gen_manpages \ || dpkg -l xvfb | awk '/xvfb/{print $3;}' | grep -q ubuntu : # Above condition just to ignore unclean exit from xvfb on elderly broken ubuntus : # Cleaner solution patches are welcome! override_dh_installman: dh_installman debian/manpages/* override_dh_auto_clean: dh_auto_clean rm -rf debian/manpages get-orig-source: uscan --verbose --rename --force-download get-orig-source-svn: cd ../cmtk.gitsvn && \ git svn rebase && \ rev=$$(git show | sed -n -e '/git-svn-id/s/.*@\([0-9]*\) .*/\1/gp') && \ otgz=cmtk-2.1.0~svn$$rev.tar.gz && \ sh scripts/make_src_archive.sh && \ mv CMTK-2.1.0svn-Source.tar.gz $$otgz && \ cd - && \ git-import-orig ../cmtk.gitsvn/$$otgz || \ echo "Failed to git-import-orig ../cmtk.gitsvn/$$otgz" debian/watch0000664000000000000000000000032312265407116010223 0ustar # Compulsory line, this is a version 3 file version=3 opts="downloadurlmangle=s/$/\/?i_agree=1&download_now=1/" \ http://www.nitrc.org/frs/?group_id=212 \ .*/download\.php/.*/CMTK-([.0-9]*)-Source\.tar\.gz debian/changelog0000664000000000000000000001071412265407311011046 0ustar cmtk (3.0.0-1ubuntu1) trusty; urgency=medium * Merge from Debian unstable. Remaining changes: - debian/control: Use libtiff-dev instead of libtiff4-dev build-dependency. * Drop cmake2.8.10-compat.patch, as it is no longer necessary. -- Logan Rosen Tue, 14 Jan 2014 23:29:16 -0500 cmtk (3.0.0-1) unstable; urgency=low * New major upstream bugfix release - see README and changelog for details: - affine transformation matrices (were broken when shear and non-isotropic scale were used) - handling of NIfTI qform and sform has changed - fit_spline_xform, xform2scalar etc. might produce different output now - should be compatible with cmake 2.8.10 (Closes: #697410) -- Yaroslav Halchenko Fri, 10 Jan 2014 09:34:59 -0500 cmtk (2.2.6-1ubuntu2) trusty; urgency=low * Use libtiff-dev instead of libtiff4-dev build-dependency. -- Dmitrijs Ledkovs Thu, 05 Dec 2013 22:48:25 +0000 cmtk (2.2.6-1ubuntu1) raring; urgency=low * cmake2.8.10-compat.patch: fix ftbfs due to new cmake -- Julian Taylor Sun, 06 Jan 2013 02:42:11 +0100 cmtk (2.2.6-1) experimental; urgency=low * New upstream release - includes freshier snapshot or nrrdio - addresses segfaults in dcm2image -- Yaroslav Halchenko Mon, 29 Oct 2012 19:16:13 -0400 cmtk (2.2.5-1) UNRELEASED; urgency=low * New upstream release - addresses bashism issues (Closes: #690930) -- Yaroslav Halchenko Tue, 23 Oct 2012 13:33:47 -0400 cmtk (2.2.4-1) experimental; urgency=low * New upstream bugfix release -- Yaroslav Halchenko Fri, 24 Aug 2012 19:45:29 -0400 cmtk (2.2.3-1) experimental; urgency=low * New upstream release - incorporates compatibility changes for older fftw (patch dropped) - requires mxml >= 2.7. Copy of it is now shipped along under Utilities/mxml -- amd built against when system-wide version is outdated. * debian/copyright: - added entry for Greg Jefferis's contributions -- Yaroslav Halchenko Fri, 10 Aug 2012 20:18:46 -0400 cmtk (2.2.2-2) unstable; urgency=low * Adding libfftw3-dev into build-depends and adding CMTK_USE_FFTW:BOOL=ON for cmake. Should make detect_adni_phantom referenced in a publication available. - for backports to older releases (e.g. squeeze) compatibility patch up_compat_older_fftw is provided and added to corresponding series * Added debian/upstream with a publication reference (added to debian/docs) -- Yaroslav Halchenko Wed, 18 Jul 2012 13:03:08 -0400 cmtk (2.2.2-1) unstable; urgency=low * Fresh upstream release - dropping 0001-FIX-remove-JPLS-header.patch -- Yaroslav Halchenko Mon, 18 Jun 2012 16:00:54 -0400 cmtk (2.2.1-1) unstable; urgency=low * New upstream release featuring MR unwarping using the ADNI phantom. - included post-release fix 0001-FIX-remove-JPLS-header.patch -- Yaroslav Halchenko Sat, 05 May 2012 21:35:22 -0400 cmtk (2.1.3-1) unstable; urgency=low * debian/control: - Boosted policy to 3.9.3 -- no changes - Removing versioned build-depend libpng12-dev in favor of upcoming meta package (previously purely virtual) libpng-dev (Closes: #662289) * debian/copyright: fixed url for DEP-5 Format: field -- Yaroslav Halchenko Sun, 04 Mar 2012 22:28:41 -0500 cmtk (2.1.2-1) unstable; urgency=low * New upstream release - fixes compatibility issue with zlib 1.2.6 (Closes: #660876) * Adjusted debian/watch to allow non-interactive download from NITRC -- Yaroslav Halchenko Wed, 29 Feb 2012 22:08:31 -0500 cmtk (2.1.1-2) unstable; urgency=low * Fixed path to sri24 atlas (should be /data/ not /doc/) -- Yaroslav Halchenko Tue, 24 Jan 2012 13:11:37 -0500 cmtk (2.1.1-1) unstable; urgency=low * New upstream release, features new tools: - "epiunwarp", for correction of B0-field distortion in echo-planar MR images without fieldmap image - "gmm", for tissue classification using a Gaussian mixture model and atlas-based tissue priors -- Yaroslav Halchenko Sun, 22 Jan 2012 22:32:08 -0500 cmtk (2.1.0-1) unstable; urgency=low * Initial release (Closes: #626225) -- Yaroslav Halchenko Tue, 22 Nov 2011 20:00:37 -0500 debian/upstream0000664000000000000000000000037112265407116010760 0ustar Reference: Author: T. Rohlfing Title: User Guide to The Computational Morphometry Toolkit Journal: The Insight Journal Year: 2009 URL: http://hdl.handle.net/10380/3140 eprint: http://www.midasjournal.org/download/viewpdf/706/3/download debian/cmtk.sh0000664000000000000000000000054712265407116010474 0ustar # emacs: -*- mode: shell-script; c-basic-offset: 4; tab-width: 4; indent-tabs-mode: t -*- # ex: set sts=4 ts=4 sw=4 noet: # # Primitive script to assure presence of the path to CMTK binaries # Just source it if you are planing to use CMTK # addpath () { echo $PATH | tr ':' '\n' | grep -q "^$1\$" \ || export PATH=$1:$PATH; } addpath /usr/lib/cmtk/bin debian/compat0000664000000000000000000000000212265407116010372 0ustar 7 debian/cmtk.install0000664000000000000000000000003012265407116011513 0ustar debian/cmtk.sh etc/cmtk debian/README.source0000664000000000000000000000073512265407116011360 0ustar cmtk for Debian --------------- Upstream carries needed 3rd-part modules (DCMTK, mxml, etc) under Utilities. To reduce the size of the .orig.tar.gz and guarantee the use of system-wide available versions of those 3rd party libraries, .orig.tar.gz are stripped of them. CMTK package version though doesn't carry .dfsg suffix since per-se those removals are done not to achieve DFSG-compliance. -- Yaroslav Halchenko , Tue, 22 Nov 2011 20:06:58 -0500 debian/copyright0000664000000000000000000001372112265407116011133 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: cmtk Upstream-Contact: Torsten Rohlfing Source: http://www.nitrc.org/projects/cmtk Files: * Copyright: 1997-2012 Torsten Rohlfing 2004-2012 SRI International License: GPL-3.0+ Files: config/*OSX* libs/System/cmtkCompressedStreamFile.cxx Copyright: 2010-2012 Torsten Rohlfing 2010-2012 SRI International 2010-2011 Greg Jefferis License: GPL-3.0+ Files: Utilities/mxml Copyright: 2003-2011 Michael Sweet License: Mini-XML Files: Utilities/NrrdIO Copyright: 2005 Gordon Kindlmann 2004, 2003, 2002, 2001, 2000, 1999, 1998 University of Utah License: This software is provided 'as-is', without any express or implied warranty. In no event will the authors be held liable for any damages arising from the use of this software. . Permission is granted to anyone to use this software for any purpose, including commercial applications, and to alter it and redistribute it freely, subject to the following restrictions: . 1. The origin of this software must not be misrepresented; you must not claim that you wrote the original software. If you use this software in a product, an acknowledgment in the product documentation would be appreciated but is not required. 2. Altered source versions must be plainly marked as such, and must not be misrepresented as being the original software. 3. This notice may not be removed or altered from any source distribution. Files: libs/Numerics Copyright: 1984-2000 Stephen L. Moshier 1992-2007 The University of Tennessee 2005-2008 Sergey Bochkanov (ALGLIB project) License: BSD-3 Files: debian/* Copyright: 2011-2012, Yaroslav Halchenko License: GPL-3.0+ License: GPL-3.0+ This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . . On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". License: BSD-3 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 listed in this license in the documentation and/or other materials provided with the distribution. . - Neither the name of the copyright holders 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. License: Mini-XML Mini-XML License October 18, 2005 . The Mini-XML library and included programs are provided under the terms of the GNU Library General Public License (LGPL) with the following exceptions: . 1. Static linking of applications to the Mini-XML library does not constitute a derivative work and does not require the author to provide source code for the application, use the shared Mini-XML libraries, or link their applications against a user-supplied version of Mini-XML. If you link the application to a modified version of Mini-XML, then the changes to Mini-XML must be provided under the terms of the LGPL in sections 1, 2, and 4. 2. You do not have to provide a copy of the Mini-XML license with programs that are linked to the Mini-XML library, nor do you have to identify the Mini-XML license in your program or documentation as required by section 6 of the LGPL. GNU LIBRARY GENERAL PUBLIC LICENSE Version 2, June 1991 This package is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more details. . You should have received a copy of the GNU Lesser General Public License along with this package; if not, write to the Free Software Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA . On Debian systems, the complete text of the GNU Lesser General Public License can be found in `/usr/share/common-licenses/LGPL-2'. debian/source/0000775000000000000000000000000012265407331010473 5ustar debian/source/format0000664000000000000000000000001412265407116011702 0ustar 3.0 (quilt) debian/README.Debian0000664000000000000000000000156112265407116011240 0ustar CMTK for Debian --------------- CMTK provides a collection of command line tools which are not installed directly into /usr/bin/ by this package but rather located under /usr/lib/cmtk/bin to avoid possible naming conflicts with other software packages. There are two possible ways to invoke those tools: - /usr/bin/cmtk helper script serves as an entry point to the toolkit. Just prepend with it any call to the CMTK command, e.g.: > cmtk glm --help - /etc/cmtk/cmtk.sh provides necessary tune up to the PATH environment variable so all CMTK command line tools become available and take precedence over possibly similarly named system-wide available tools under /usr/bin. To use it, just source it from your ~/.bashrc or ~/.profile, e.g.: . /etc/cmtk/cmtk.sh Enjoy -- Yaroslav Halchenko , Fri, 4 Nov 2011 23:00:11 -0400 debian/TODO0000664000000000000000000000051712265407116007667 0ustar # emacs: -*- mode: org; -*- * LZMA checks and cmtkCompressedStream.h looking for absent in distribution lzmadec.h (seems to be coming from the original LZMA SDK) ** still misses mxml while building testing/libs/System * package atlas and provide path to it * For testing needs - data/testing from SVN (111 MB) - sqlite3 - xvfb debian/control0000664000000000000000000000342012265407116010576 0ustar Source: cmtk Section: science Priority: extra Maintainer: Ubuntu Developers XSBC-Original-Maintainer: NeuroDebian Team Uploaders: Yaroslav Halchenko , Michael Hanke Build-Depends: debhelper (>= 7.0.50~), cmake, libmxml-dev, libsqlite3-dev, zlib1g-dev | libz-dev, libdcmtk2-dev | libdcmtk1-dev | libdcmtk-dev, libbz2-dev, libfftw3-dev, liblzma-dev, libqt4-dev, qt4-qmake, libpng-dev, libtiff-dev, libwrap0-dev, libcharls-dev | libdcmtk1-dev | libdcmtk2-dev (<< 3.6.0-8~), libxml2-dev, libssl-dev, xvfb, xauth, Standards-Version: 3.9.3 Homepage: http://www.nitrc.org/projects/cmtk/ Vcs-Git: git://git.debian.org/pkg-exppsy/cmtk.git Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/cmtk.git;a=summary Package: cmtk Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: sri24-atlas Suggests: numdiff Description: Computational Morphometry Toolkit A software toolkit for computational morphometry of biomedical images, CMTK comprises a set of command line tools and a back-end general-purpose library for processing and I/O. . The command line tools primarily provide the following functionality: registration (affine and nonrigid; single and multi-channel; pairwise and groupwise), image correction (MR bias field estimation; interleaved image artifact correction), processing (filters; combination of segmentations via voting and STAPLE; shape-based averaging), statistics (t-tests; general linear regression). debian/cmtk.dirs0000664000000000000000000000001112265407116011005 0ustar etc/cmtk debian/docs0000664000000000000000000000003312265407116010043 0ustar README.txt debian/upstream debian/gbp.conf0000664000000000000000000000027412265407116010616 0ustar [DEFAULT] debian-tag = debian/%(version)s upstream-tag = upstream/%(version)s [git-import-orig] filter = [ 'Utilities/dcmtk', 'Utilities/sqlite3', 'Utilities/zlib', 'Utilities/numdiff*'] debian/patches/0000775000000000000000000000000012265407331010622 5ustar debian/patches/series0000664000000000000000000000004712265407226012043 0ustar up_assure_no_as_needed_for_checklibdep debian/patches/up_assure_no_as_needed_for_checklibdep0000664000000000000000000000111512265407116020420 0ustar --- a/CMake/FindConfigDCMTK.cmake +++ b/CMake/FindConfigDCMTK.cmake @@ -238,7 +238,7 @@ FUNCTION(CheckLibraryDependency _require ${CMAKE_BINARY_DIR} ${CMAKE_BINARY_DIR}${CMAKE_FILES_DIRECTORY}/CMakeTmp/src.cxx COMPILE_DEFINITIONS ${CMAKE_REQUIRED_DEFINITIONS} - CMAKE_FLAGS -DCOMPILE_DEFINITIONS:STRING=${MACRO_CHECK_FUNCTION_DEFINITIONS} + CMAKE_FLAGS -DCMAKE_EXE_LINKER_FLAGS:STRING=-Wl,--no-as-needed -DCOMPILE_DEFINITIONS:STRING=${MACRO_CHECK_FUNCTION_DEFINITIONS} "${CHECK_CXX_SOURCE_COMPILES_ADD_LIBRARIES}" OUTPUT_VARIABLE OUTPUT) debian/patches/deb_noCharLS0000664000000000000000000000122212265407116013026 0ustar --- a/CMake/FindConfigDCMTK.cmake +++ b/CMake/FindConfigDCMTK.cmake @@ -61,7 +61,7 @@ dcmimage dcmimgle dcmjpeg - dcmjpls +## dcmjpls ## dcmnet ## dcmpstat ## dcmqrdb @@ -214,7 +214,7 @@ ## CheckLibraryDependency(DCMTK_LIBRARIES wrap hosts_access) CheckLibraryDependency(DCMTK_LIBRARIES png png_write_image) CheckLibraryDependency(DCMTK_LIBRARIES tiff TIFFGetVersion) - CheckLibraryDependency(DCMTK_LIBRARIES CharLS JpegLsReadHeader) + ## CheckLibraryDependency(DCMTK_LIBRARIES CharLS JpegLsReadHeader) ## CheckLibraryDependency(DCMTK_LIBRARIES xml2 xmlGetProp) FIND_PATH(DCMTK_DCMDICTPATH debian/patches/series-oneiric0000664000000000000000000000001512265407116013462 0ustar deb_noCharLS debian/patches/series-natty0000664000000000000000000000001512265407116013171 0ustar deb_noCharLS