debian/0000755000000000000000000000000011750765021007172 5ustar debian/source/0000755000000000000000000000000011750764074010501 5ustar debian/source/format0000644000000000000000000000001411750764074011707 0ustar 3.0 (quilt) debian/dirs0000644000000000000000000000002511750764074010062 0ustar usr/lib/ants usr/bin debian/watch0000644000000000000000000000015311750764074010231 0ustar version=3 opts="uversionmangle=s/pt/./g,dversionmangle=s/.dfsg$//" http://sf.net/advants/ants(.*)code\.zip debian/patches/0000755000000000000000000000000011750764074010630 5ustar debian/patches/series0000644000000000000000000000001511750764074012041 0ustar deb_antspath debian/patches/deb_antspath0000644000000000000000000000467211750764074013220 0ustar --- a/Scripts/antsaffine.sh +++ b/Scripts/antsaffine.sh @@ -1,5 +1,5 @@ #!/bin/sh -export ANTSPATH=${ANTSPATH:="$HOME/bin/ants/"} +export ANTSPATH=${ANTSPATH:="/usr/lib/ants/"} NUMPARAMS=$# --- a/Scripts/antsIntroduction.sh +++ b/Scripts/antsIntroduction.sh @@ -3,7 +3,7 @@ VERSION="0.0.7" # Uncomment the line below in case you have not set the ANTSPATH variable in your environment. -export ANTSPATH=${ANTSPATH:="$HOME/bin/ants/"} +export ANTSPATH=${ANTSPATH:="/usr/lib/ants/"} function Usage { cat < Uploaders: Yaroslav Halchenko , Michael Hanke -Build-Depends: debhelper (>= 7.0.50~), help2man, cmake, libgdcm2-dev, libopenjpeg-dev, libinsighttoolkit3-dev, libvtk5-dev, uuid-dev +Build-Depends: debhelper (>= 7.0.50~), help2man, cmake, libopenjpeg-dev, libinsighttoolkit3-dev, libvtk5-dev, uuid-dev Standards-Version: 3.9.1 Homepage: http://www.picsl.upenn.edu/ANTS/ Vcs-Git: git://git.debian.org/pkg-exppsy/ants.git debian/patches/jaunty-dsc-patch0000777000000000000000000000000011750764074016642 2lenny-dsc-patchustar debian/changelog0000644000000000000000000000604111750764074011054 0ustar ants (1.9.2+svn680.dfsg-4) unstable; urgency=low [ Matthias Klose ] * Fix build using GCC 4.7. Closes: #667099. -- Yaroslav Halchenko Fri, 04 May 2012 10:27:15 -0400 ants (1.9.2+svn680.dfsg-3) unstable; urgency=low * Seems to build fine now against available ITK 3.20 (Closes: #655306) * Boosting policy to 3.9.3 (no changes) * Version ITK build-depends >= 3.16~ * Placed build PATH ahead of system wide during tests so proper version of ants gets tested on systems with ants installed * (Temporarily) added a bulk of build-depends for wrapper bindings for vtk >= 5.8 to overcome #584300 -- Yaroslav Halchenko Fri, 09 Mar 2012 13:08:26 -0500 ants (1.9.2+svn680.dfsg-2) unstable; urgency=low * Upload to unstable version from experimental (forgotten there). Builds fine with ITK 3.20 (Closes: #614483) * New patch deb_antspath -- use default path on Debian systems (/usr/lib/ants) and do not override with hardcode custom upstream paths (Closes: #636529) * Boosting policy to 3.9.2 (no changes) -- Yaroslav Halchenko Fri, 23 Sep 2011 21:34:43 -0400 ants (1.9.2+svn680.dfsg-1) experimental; urgency=low * New upstream release * Adding .dfsg since Documentation/ is pruned from source trees due to incomplete set of building materials to reproduce PDFs -- Yaroslav Halchenko Sun, 14 Nov 2010 21:24:18 -0500 ants (1.9+svn532-5) unstable; urgency=low * Disable lengthy _SYN unittest to allow pass on slow archs (like sparc) (Closes: #594133). Added few other reasonably fast tests * Boosting policy to 3.9.1 -- including BSD-3 verbatim into copyright, updating copyright format according to DEP5 rev135 -- Yaroslav Halchenko Mon, 23 Aug 2010 17:53:32 -0400 ants (1.9+svn532-4) unstable; urgency=low * Cherry picking rev 581,589-590 from upstream to assure correct application of transformation while operating on 4D timeseries (Closes: #588195) -- Yaroslav Halchenko Tue, 06 Jul 2010 12:34:52 -0400 ants (1.9+svn532-3) unstable; urgency=low * Moving under NeuroDebian umbrella * Absorbed commits from upstream: - avoid division by 0 in progress meter (Closes: #586915) - initializer warper ones (prior to the loop) in WarpTimeSeriesImageMultiTransform -- Yaroslav Halchenko Wed, 23 Jun 2010 11:25:16 -0400 ants (1.9+svn532-2) unstable; urgency=low * Placing all binaries and scripts under /usr/lib/ants, since many scripts rely on binaries to be in the same directory, and ftp-master raised concern about some names for the binaries. ANTS binary only gets symlinked under /usr/bin * Initial Debian release (Closes: #579569) * Added fsl and gridengine-client into suggests -- Yaroslav Halchenko Tue, 01 Jun 2010 13:11:44 -0400 ants (1.9+svn532-1) UNRELEASED; urgency=low * Initial packaging -- Yaroslav Halchenko Wed, 28 Apr 2010 13:29:29 -0400 debian/README.Debian0000644000000000000000000000062511750764074011245 0ustar ANTS for Debian --------------- ANTS binaries, shell and perl scripts under are distributed all under /usr/lib/ants, so you might adjust your PATH if you intend to use those directly. Only ANTS binary itself is symlinked into /usr/bin. Moreover many scripts rely on ANTSPATH variable, point it to the same /usr/lib/ants. -- Yaroslav Halchenko , Tue, 1 Jun 2010 13:09:19 -0400 debian/copyright0000644000000000000000000000543211750764074011140 0ustar Format-Specification: http://svn.debian.org/wsvn/dep/web/deps/dep5.mdwn?op=file&rev=135 Name: ANTs (AKA Advants) Maintainer: Brian Avants Source: https://advants.svn.sourceforge.net/svnroot/advants Files: * Copyright: Copyright (C) 2009, 2010 ConsortiumOfANTS Authors: Brian Avants, Sandhitsu Das, Jeff Duda, John Pluta, Gang Song, Nick Tustison License: BSD-3 Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. 2. 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. 3. Neither the name of the consortium 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 CONSORTIUM 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 REGENTS 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. Files: Examples/ConformalMapping.cxx ImageRegistration/itkSpatialMutualInformationRegistrationFunction.h ImageRegistration/itkSpatialMutualInformationRegistrationFunction.cxx Temporary/itkFEMElement3DC0LinearTriangularLaplaceBeltrami.cxx Temporary/itkFEMElement3DC0LinearTriangular.cxx Temporary/itkFEMConformalMap.cxx Temporary/itkFEMElement3DC0LinearTriangularMembrane.h Temporary/itkFEMDiscConformalMap.h Temporary/itkFEMElement3DC0LinearTriangularLaplaceBeltrami.h Temporary/itkFEMConformalMap.h Temporary/itkFEMElement3DMembrane1DOF.h Temporary/itkFEMElement3DC0LinearTriangular.h Temporary/itkFEMElement3DC0LinearTriangularMembrane.cxx Temporary/itkDijkstrasAlgorithm.h Temporary/itkFEMDiscConformalMap.cxx Temporary/itkManifoldIntegrationAlgorithm.h Copyright: 2001, 2002 (C) Insight Consortium License: mix of BSD-2 and BSD-3 Files: debian/* Copyright: Copyright (C) 2010, Yaroslav Halchenko License: BSD-3 debian/rules0000755000000000000000000000357511750764074010273 0ustar #!/usr/bin/make -f # -*- makefile -*- # Build directory, to don't dig them out later # on from the bulk since there is no install target in upstream build system BUILDDIR=$(CURDIR)/build DESTBINDIR=$(BUILDDIR)/bin export CFLAGS = -Wall -g export LDFLAGS = -Wl,--as-needed ifneq (,$(findstring noopt,$(DEB_BUILD_OPTIONS))) export CFLAGS += -O0 else export CFLAGS += -O2 endif export CXXFLAGS = $(CFLAGS) -fpermissive # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 # Default mega-rule %: dh -DExamples $@ override_dh_auto_configure: dh_auto_configure -- \ -DCOPY_SCRIPT_FILES_TO_BIN_DIR:BOOL=OFF \ -DCMAKE_SKIP_RPATH:BOOL=ON \ -DEXECUTABLE_OUTPUT_PATH:PATH=$(DESTBINDIR) override_dh_auto_build: dh_auto_build : Build manpages cd $(DESTBINDIR) && mkdir ../man && \ for f in *; do \ help2man --name="part of ANTS registration suite" --version-string 1.9 \ --no-info --no-discard-stderr ./$$f >| ../man/$$f.1; \ done # For now perform only some small subselection of tests since some # tests are very CPU intensive and some fail and there is no clean way # to select "good" and quick ones override_dh_auto_test: # debhelper just calls make test so no -R could be passed # PATH=$$PATH:$(DESTBINDIR) dh_auto_test -- -R "ANTS_(CC_1|...$$)" # thus lets do it manually cd obj-*; PATH=$(DESTBINDIR):$$PATH ctest --force-new-ctest-process -R "ANTS_(CC_1|SYN_|EXP|...$$)" -E "(ANTS_SYN|ANTS_SYN_WITH_TIME)$$" override_dh_auto_install: dh_auto_install : Install binaries install -t debian/ants/usr/lib/ants $(DESTBINDIR)/* : Symlink binaries of primary importance into /usr/bin for f in ANTS WarpImageMultiTransform; do \ dh_link usr/lib/ants/$$f usr/bin/$$f; \ done : Install shell scripts install -t debian/ants/usr/lib/ants Scripts/* : Install manpages dh_installman $(BUILDDIR)/man/* override_dh_auto_clean: dh_auto_clean rm -rf $(BUILDDIR) debian/README.source0000644000000000000000000000063611750764074011365 0ustar ANTS for Debian --------------- Source package is built out of SVN source tree (cloned via git-svn) to facilitate easier adoption of upstream patches and release of snapshots if necessary. Unfortunately components/copyright information of the Documentation/ is not cleared up, so they are excluded from Debian release of ANTs. -- Yaroslav Halchenko , Mon, 17 May 2010 18:00:28 -0400 debian/docs0000644000000000000000000000001311750764074010046 0ustar README.txt debian/gbp.conf0000644000000000000000000000115511750764074010622 0ustar [DEFAULT] # the default build command: builder = debuild -i'\.(git\.*|gbp.conf|gitignore)' # the default branch for upstream sources: upstream-branch = dfsg # the default branch for the debian patch: debian-branch = debian-release # the default tag formats used: upstream-tag = upstream/%(version)s debian-tag = debian/%(version)s # Options only affecting git-buildpackage [git-buildpackage] # ignore some any non-gitted files ignore-new = True # uncomment this to automatically GPG sign tags sign-tags = True # use this for more svn-buildpackage like bahaviour: export-dir = ../build-area/ tarball-dir = ../tarballs/ debian/ants.lintian-overrides0000644000000000000000000000041211750764074013523 0ustar # Manpages are generated from --help using help2man. # Some formatting issues are yet to be addressed, # upstream was informed and working toward it ants binary: manpage-has-errors-from-man usr/share/man/man1/Atropos.1.gz 26: warning [p 1, 4.7i]: cannot adjust line debian/control0000644000000000000000000000300611750764074010603 0ustar Source: ants Section: science Priority: extra Maintainer: NeuroDebian Team Uploaders: Yaroslav Halchenko , Michael Hanke Build-Depends: debhelper (>= 7.0.50~), help2man, cmake, libgdcm2-dev, libopenjpeg-dev, libinsighttoolkit3-dev (>= 3.16~), libvtk5-dev, uuid-dev, tcl-vtk | libvtk5-dev (<< 5.8), python-vtk | libvtk5-dev (<< 5.8), libvtk-java | libvtk5-dev (<< 5.8), libvtk5.8-qt4 | libvtk5-dev (<< 5.8) Standards-Version: 3.9.3 Homepage: http://www.picsl.upenn.edu/ANTS/ Vcs-Git: git://git.debian.org/pkg-exppsy/ants.git Vcs-Browser: http://git.debian.org/?p=pkg-exppsy/ants.git;a=summary Package: ants Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: fsl, gridengine-client Description: advanced normalization tools for brain and image analysis Advanced Normalization Tools (ANTS) is an ITK-based suite of normalization, segmentation and template-building tools for quantitative morphometric analysis. Many of the ANTS registration tools are diffeomorphic, but deformation (elastic and BSpline) transformations are available. Unique components of ANTS include multivariate similarity metrics, landmark guidance, the ability to use label images to guide the mapping and both greedy and space-time optimal implementations of diffeomorphisms. The symmetric normalization (SyN) strategy is a part of the ANTS toolkit as is directly manipulated free form deformation (DMFFD). debian/compat0000644000000000000000000000000211750764074010377 0ustar 7