debian/0000775000000000000000000000000012250204000007151 5ustar debian/upstream0000664000000000000000000000101712250201427010745 0ustar Contact: Stefan Klein and Marius Staring Homepage: http://elastix.isi.uu.nl/ Name: Elastix Reference: author: Stefan Klein and Marius Staring and Keelin Murphy and Max A. Viergever, Josien P. W. Pluim title: > elastix: A Toolbox for Intensity-Based Medical Image Registration journal: IEEE Transactions on Medical Imaging volume: 29 number: 1 pages: 196 - 205 year: 2010 PMID: 19923044 DOI: 10.1109/TMI.2009.2035616 URL: http://ieeexplore.ieee.org/xpls/abs_all.jsp?tp=&arnumber=5338015&isnumber=5371922 debian/source/0000775000000000000000000000000012250201427010463 5ustar debian/source/format0000664000000000000000000000001412250201427011671 0ustar 3.0 (quilt) debian/copyright0000664000000000000000000000612412250201427011121 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Upstream-Name: elastix Source: http://elastix.isi.uu.nl/ Upstream-Contacte: Stefan Klein and Marius Staring Files: * Copyright: 2004-2011 University Medical Center Utrecht, All rights reserved. Elastix Copyright Notice: . Elastix was initially developed by Stefan Klein and Marius Staring under contract to the Image Sciences Institute, University Medical Center Utrecht, The Netherlands. License: BSD-simplified Files: Common/KNN/ann_1.1/* Copyright: 1997-2005 University of Maryland and Sunil Arya and David Mount License: LGPL-2.1 This program 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 2.1 of the License, or (at your option) any later version. . On Debian systems this license may be found in file /usr/share/common-licenses/LGPL-2.1. Comment: In the Debian package of elastix, ANN is statically linked. Clause 3 of the LGPL is hereby invoked to re-license ANN under the GNU Public License, v2 (see /usr/share/common-licenses/GPL-2). The elastix package as a whole is therefore under the GPL v2 license. Files: debian/* Copyright: 2010-2011 Steve M. Robbins 2012 Andreas Tille License: BSD-simplified License: BSD-simplified 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 the University Medical Center Utrecht 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. Comment: The software is partially derived from the Insight Segmentation and Registration Toolkit (ITK), which is also distributed under the new and simplified BSD licence. The ITK is required by Elastix for compilation of the source code. debian/manpages0000664000000000000000000000004612250201427010701 0ustar debian/elastix.1 debian/transformix.1 debian/elastix.install0000664000000000000000000000002312250201427012217 0ustar debian/tmp/usr/bin debian/elastix.10000664000000000000000000000243712250201427010724 0ustar .TH ELASTIX "1" "December 2010" "elastix version: 4.400" "User Commands" .SH NAME elastix \- perform image registration .SH SYNOPSIS \fBelastix\fP \fImandatory-args\fR [\fIoptional-args\fR] .SH DESCRIPTION elastix registers a moving image to a fixed image. The registration\-process is specified in the parameter file. .PP .SH OPTIONS Call elastix from the command line with mandatory arguments: .TP \fB\-f\fR fixed image .TP \fB\-m\fR moving image .TP \fB\-out\fR output directory .TP \fB\-p\fR parameter file, elastix handles 1 or more "\-p" .PP Optional extra commands: .TP \fB\-fMask\fR mask for fixed image .TP \fB\-mMask\fR mask for moving image .TP \fB\-t0\fR parameter file for initial transform .TP \fB\-priority\fR set the process priority to high or belownormal (Windows only) .TP \fB\-threads\fR set the maximum number of threads of elastix .PP The parameter\-file must contain all the information necessary for elastix to run properly. That includes which metric to use, which optimizer, which transform, etc. It must also contain information specific for the metric, optimizer, transform, ... For a usable parameter\-file, see the website. .SH "SEE ALSO" .BR transformix (1) .PP Check the website http://elastix.isi.uu.nl, or mail elastix.support@gmail.com. debian/changelog0000664000000000000000000000416412250204000011030 0ustar elastix (4.5-4) unstable; urgency=low * Team upload. * Build-depend on libtiff-dev, instead of libtiff4-dev. -- Dmitrijs Ledkovs Thu, 05 Dec 2013 23:10:56 +0000 elastix (4.5-3) unstable; urgency=low * debian/control: - cme fix dpkg-copyright - debhelper 9 - Build-Depends-Indep: latex-xcolor Closes: #713280 - Remove duplicated "Section: science" - Duplicated long description * debian/rules: use xz compression * debian/copyright: s/GNU Lesser Public License/GNU Lesser General Public License/ -- Andreas Tille Tue, 25 Jun 2013 08:14:19 +0200 elastix (4.5-2) unstable; urgency=low * debian/control: - Standards-Version: 3.9.3 (no changes needed) - Fixed Vcs fields - Build-Depends: s/libpng12-dev/libpng-dev/ Closes: 662311 * debian/upstream: - Tasks file had a slightly more precise information about author - Valid BibTeX authors field - More precise information (authors, pmid, doi) * debian/copyright: Rewritten to match DEP5. verified using cme fix dpkg-copyright * Note: Tried debhelper 9 (control+compat) but failed for a reason which is totally unclear to me. There seems to be an error return code in the middle of the build process without any visible error message -- Andreas Tille Fri, 11 May 2012 13:50:29 +0200 elastix (4.5-1) unstable; urgency=low * New upstream. -- Steve M. Robbins Thu, 13 Oct 2011 01:52:26 -0500 elastix (4.4-2) unstable; urgency=low [ Andreas Tille ] * debian/control: - Fix name of Debian Med team (without '-') - Added Vcs fields - Fix typo in description Closes: #613621 * Added debian/upstream-metadata.yaml * Added debian/watch (Thanks to Paul Wise and Daniel Leidert ) [ Steve M. Robbins ] * target upload to unstable. -- Steve M. Robbins Mon, 21 Feb 2011 10:30:55 -0600 elastix (4.4-1) experimental; urgency=low * New package. Closes: #607030. -- Steve M. Robbins Mon, 27 Dec 2010 06:01:00 -0600 debian/elastix-doc.docs0000664000000000000000000000003312250201427012245 0ustar dox/manual/manual.pdf help debian/control0000664000000000000000000000436212250201462010572 0ustar Source: elastix Maintainer: Debian Med Packaging Team Uploaders: Steve M. Robbins , Andreas Tille Section: science Priority: optional Build-Depends: debhelper (>= 9), cmake, libinsighttoolkit3-dev (>= 3.20.0-5), libgdcm2-dev, zlib1g-dev, libpng-dev, libtiff-dev Build-Depends-Indep: doxygen, graphviz, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended, ghostscript, latex-xcolor Standards-Version: 3.9.4 Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/elastix/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/elastix/trunk/ Homepage: http://elastix.isi.uu.nl/ Package: elastix Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Suggests: elastix-doc Description: toolbox for rigid and nonrigid registration of images Image registration based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. Package: elastix-doc Architecture: all Section: doc Depends: ${shlibs:Depends}, ${misc:Depends} Description: toolbox for rigid and nonrigid registration of images - docs Image registration based on the well-known Insight Segmentation and Registration Toolkit (ITK). The software consists of a collection of algorithms that are commonly used to solve (medical) image registration problems. The modular design of elastix allows the user to quickly configure, test, and compare different registration methods for a specific application. A command-line interface enables automated processing of large numbers of data sets, by means of scripting. . This package contains the elastix documentation. debian/transformix.10000664000000000000000000000323312250201427011622 0ustar .TH TRANSFORMIX "1" "December 2010" "transformix version: 4.400" "User Commands" .SH NAME transformix \- apply geometric transform to an image .SH SYNOPSIS \fBtransformix\fP \fImandatory-args\fR [\fIoptional-args\fR] .SH DESCRIPTION transformix applies a transform on an input image and/or generates a deformation field. The transform is specified in the transform\-parameter file. .PP .SH OPTIONS Call transformix from the command line with mandatory arguments: .TP \fB\-out\fR output directory .TP \fB\-tp\fR transform\-parameter file, only 1 .PP Optional extra commands: .TP \fB\-in\fR input image to deform .TP \fB\-def\fR file containing input\-image points .IP the point are transformed according to the specified transform\-parameter file use "\-def all" to transform all points from the input\-image, which effectively generates a deformation field. .PP .TP \fB\-jac\fR use "\-jac all" to generate an image with the determinant of the spatial Jacobian .TP \fB\-jacmat\fR use "\-jacmat all" to generate an image with the spatial Jacobian matrix at each voxel .TP \fB\-priority\fR set the process priority to high or belownormal (Windows only) .TP \fB\-threads\fR set the maximum number of threads of transformix At least one of the options "\-in", "\-def", "\-jac", or "\-jacmat" should be given. .PP The transform\-parameter file must contain all the information necessary for transformix to run properly. That includes which transform to use, with which parameters, etc. For a usable transform\-parameter file, see the output of elastix. .SH "SEE ALSO" .BR elastix (1) .PP Check the website http://elastix.isi.uu.nl, or mail elastix.support@gmail.com. debian/rules0000775000000000000000000000151712250201427010247 0ustar #!/usr/bin/make -f %: dh $@ --sourcedirectory=src --parallel binary: binary-arch binary-indep binary-indep: doc-stamp dh $@ --sourcedirectory=src --parallel # Need -DUSE_KNNGraphAlphaMutualInformationMetric:BOOL=ON, otherwise # KNN is not built, and link of elastix fails. # DEB_CMAKE_EXTRA_FLAGS += \ -DCMAKE_INSTALL_PREFIX=/usr \ -DCMAKE_BUILD_TYPE=RELEASE \ -DCMAKE_SKIP_RPATH=ON \ -DUSE_KNNGraphAlphaMutualInformationMetric:BOOL=ON override_dh_auto_configure: dh_auto_configure -- $(DEB_CMAKE_EXTRA_FLAGS) override_dh_builddeb: dh_builddeb -- -Z xz doc: doc-stamp doc-stamp: help/html/index.html dox/manual/manual.pdf touch $@ # build-deps: doxygen, latex, dot help/html/index.html: help/doxyfile.out doxygen $< dox/manual/manual.pdf: dox/manual/manual.tex cd dox/manual && latex manual && latex manual && dvipdf manual debian/watch0000664000000000000000000000103212250201427010210 0ustar version=3 # Author: Daniel Leidert opts=downloadurlmangle=s/whatsnew_0(\d+)_(\d+)\.php$/download\/elastix_sources_v$1.$2.tar.bz2/,filenamemangle=s/whatsnew_0(\d+)_(\d+)\.php$/elastix_sources_v$1.$2.tar.bz2/ \ http://elastix.isi.uu.nl/news.php whatsnew_0(\d+)_(\d+).php ## This works only if the about.php page will be properly maintained ## Author: Paul Wise #opts=downloadurlmangle=s/example/sources/ \ # http://elastix.isi.uu.nl/about.php \ # .*/elastix_example_v([\d\.]+)\.tar\.bz2 debian/patches/0000775000000000000000000000000012250201427010612 5ustar debian/patches/build-static-ann.patch0000664000000000000000000000214712250201427014775 0ustar Description: Build convenience static ANN library Author: Steve Robbins Forwarded: no The ANN library sources are included with elastix to implement KNNGraphAlphaMutualInformationMetric. The ANN library reported isn't meant to be shared (c.f. #602582) so we change the build procedure to NOT install it, and therefore it must be built statically. --- elastix-4.4.orig/src/Common/KNN/ann_1.1/CMakeLists.txt +++ elastix-4.4/src/Common/KNN/ann_1.1/CMakeLists.txt @@ -25,7 +25,7 @@ ) # Create the ANNlib library -ADD_LIBRARY( ANNlib SHARED ${ANN_SRCS} ) +ADD_LIBRARY( ANNlib STATIC ${ANN_SRCS} ) # Necessary, because in windows dll_export is needed for creating the # dll, but dll_import for using it in a program. @@ -34,16 +34,3 @@ # Group in IDE's like Visual Studio SET_PROPERTY( TARGET ANNlib PROPERTY FOLDER "libraries" ) -# Install -IF( WIN32 ) - INSTALL( TARGETS ANNlib - RUNTIME DESTINATION . - LIBRARY DESTINATION . ) - #COMPONENT libraries ) -ELSE() - INSTALL( TARGETS ANNlib - RUNTIME DESTINATION bin - LIBRARY DESTINATION lib ) - #COMPONENT libraries ) -ENDIF() - debian/patches/series0000664000000000000000000000002712250201427012026 0ustar build-static-ann.patch debian/compat0000664000000000000000000000000212250201427010361 0ustar 9