Author: smr Date: 2010-12-27 16:54:19 +0000 (Mon, 27 Dec 2010) New Revision: 5628
Added: trunk/packages/elastix/tags/4.4-1/ trunk/packages/elastix/tags/4.4-1/debian/changelog trunk/packages/elastix/tags/4.4-1/debian/compat trunk/packages/elastix/tags/4.4-1/debian/control trunk/packages/elastix/tags/4.4-1/debian/copyright trunk/packages/elastix/tags/4.4-1/debian/elastix-doc.docs trunk/packages/elastix/tags/4.4-1/debian/elastix.1 trunk/packages/elastix/tags/4.4-1/debian/elastix.install trunk/packages/elastix/tags/4.4-1/debian/manpages trunk/packages/elastix/tags/4.4-1/debian/patches/build-static-ann.patch trunk/packages/elastix/tags/4.4-1/debian/patches/series trunk/packages/elastix/tags/4.4-1/debian/rules trunk/packages/elastix/tags/4.4-1/debian/transformix.1 Removed: trunk/packages/elastix/tags/4.4-1/debian/changelog trunk/packages/elastix/tags/4.4-1/debian/compat trunk/packages/elastix/tags/4.4-1/debian/control trunk/packages/elastix/tags/4.4-1/debian/patches/install-dir.patch trunk/packages/elastix/tags/4.4-1/debian/patches/series trunk/packages/elastix/tags/4.4-1/debian/rules Log: [svn-buildpackage] Tagging elastix 4.4-1 Deleted: trunk/packages/elastix/tags/4.4-1/debian/changelog =================================================================== --- trunk/packages/elastix/trunk/debian/changelog 2010-12-24 02:20:56 UTC (rev 5618) +++ trunk/packages/elastix/tags/4.4-1/debian/changelog 2010-12-27 16:54:19 UTC (rev 5628) @@ -1,6 +0,0 @@ -elastix (4.3-1) UNRELEASED; urgency=low - - * New package. Closes: #607030. - - -- Steve M. Robbins <[email protected]> Mon, 13 Dec 2010 22:42:52 -0600 - Copied: trunk/packages/elastix/tags/4.4-1/debian/changelog (from rev 5625, trunk/packages/elastix/trunk/debian/changelog) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/changelog (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/changelog 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,6 @@ +elastix (4.4-1) experimental; urgency=low + + * New package. Closes: #607030. + + -- Steve M. Robbins <[email protected]> Mon, 27 Dec 2010 06:01:00 -0600 + Deleted: trunk/packages/elastix/tags/4.4-1/debian/compat =================================================================== --- trunk/packages/elastix/trunk/debian/compat 2010-12-24 02:20:56 UTC (rev 5618) +++ trunk/packages/elastix/tags/4.4-1/debian/compat 2010-12-27 16:54:19 UTC (rev 5628) @@ -1 +0,0 @@ -7 Copied: trunk/packages/elastix/tags/4.4-1/debian/compat (from rev 5620, trunk/packages/elastix/trunk/debian/compat) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/compat (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/compat 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1 @@ +8 Deleted: trunk/packages/elastix/tags/4.4-1/debian/control =================================================================== --- trunk/packages/elastix/trunk/debian/control 2010-12-24 02:20:56 UTC (rev 5618) +++ trunk/packages/elastix/tags/4.4-1/debian/control 2010-12-27 16:54:19 UTC (rev 5628) @@ -1,23 +0,0 @@ -Source: elastix -Homepage: http://elastix.isi.uu.nl/ -Section: science -Priority: optional -Maintainer: Debian-Med Packaging Team <[email protected]> -Uploaders: Steve M. Robbins <[email protected]> -Build-Depends: quilt, debhelper (>= 7), cmake, libinsighttoolkit3-dev, doxygen -Standards-Version: 3.7.3 - -Package: elastix -Section: science -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends} -Description: toolbox for rigid and nonrigid registration of images - Image reigstration 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. - Copied: trunk/packages/elastix/tags/4.4-1/debian/control (from rev 5626, trunk/packages/elastix/trunk/debian/control) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/control (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/control 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,40 @@ +Source: elastix +Homepage: http://elastix.isi.uu.nl/ +Section: science +Priority: optional +Maintainer: Debian-Med Packaging Team <[email protected]> +Uploaders: Steve M. Robbins <[email protected]> +Build-Depends: quilt, debhelper (>= 8), cmake, + libinsighttoolkit3-dev (>= 3.20.0-5), libgdcm2-dev, zlib1g-dev, libpng12-dev, libtiff4-dev +Build-Depends-Indep: doxygen, graphviz, texlive-latex-base, texlive-latex-extra, texlive-latex-recommended, ghostscript +Standards-Version: 3.9.1 + +Package: elastix +Section: science +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +Suggests: elastix-doc +Description: toolbox for rigid and nonrigid registration of images + Image reigstration 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 +Section: doc +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends} +Description: toolbox for rigid and nonrigid registration of images - docs + Image reigstration 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. + Copied: trunk/packages/elastix/tags/4.4-1/debian/copyright (from rev 5623, trunk/packages/elastix/trunk/debian/copyright) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/copyright (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/copyright 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,62 @@ +Name: elastix +Maintainer: Stefan Klein and Marius Staring +Source: http://elastix.isi.uu.nl/ + + +Elastix Copyright Notice: + + Copyright (c) 2004-2010 University Medical Center Utrecht + All rights reserved. + + +Elastix was initially developed by Stefan Klein and Marius Staring +under contract to the Image Sciences Institute, University Medical +Center Utrecht, The Netherlands. + + +Elastix is distributed under the new and simplified BSD license +approved by the Open Source Initiative (OSI) +[http://www.opensource.org/licenses/bsd-license.php]: + +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. + + +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. + +The copyright of the files in the Common/KNN/ann_1.1 subdirectory is +held by a third party, the University of Maryland. The ANN package is +distributed under the GNU Lesser Public Licence v2.1. This license +may be found in file /usr/share/common-licenses/LGPL-2.1. + + +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. + Copied: trunk/packages/elastix/tags/4.4-1/debian/elastix-doc.docs (from rev 5625, trunk/packages/elastix/trunk/debian/elastix-doc.docs) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/elastix-doc.docs (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/elastix-doc.docs 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,2 @@ +dox/manual/manual.pdf +help Copied: trunk/packages/elastix/tags/4.4-1/debian/elastix.1 (from rev 5624, trunk/packages/elastix/trunk/debian/elastix.1) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/elastix.1 (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/elastix.1 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,39 @@ +.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 [email protected]. Copied: trunk/packages/elastix/tags/4.4-1/debian/elastix.install (from rev 5625, trunk/packages/elastix/trunk/debian/elastix.install) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/elastix.install (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/elastix.install 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1 @@ +debian/tmp/usr/bin Copied: trunk/packages/elastix/tags/4.4-1/debian/manpages (from rev 5623, trunk/packages/elastix/trunk/debian/manpages) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/manpages (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/manpages 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,2 @@ +debian/elastix.1 +debian/transformix.1 Copied: trunk/packages/elastix/tags/4.4-1/debian/patches/build-static-ann.patch (from rev 5620, trunk/packages/elastix/trunk/debian/patches/build-static-ann.patch) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/patches/build-static-ann.patch (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/patches/build-static-ann.patch 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,39 @@ +Description: Build convenience static ANN library +Author: Steve Robbins <[email protected]> +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() +- Deleted: trunk/packages/elastix/tags/4.4-1/debian/patches/install-dir.patch =================================================================== --- trunk/packages/elastix/trunk/debian/patches/install-dir.patch 2010-12-24 02:20:56 UTC (rev 5618) +++ trunk/packages/elastix/tags/4.4-1/debian/patches/install-dir.patch 2010-12-27 16:54:19 UTC (rev 5628) @@ -1,20 +0,0 @@ ---- elastix-4.3.orig/src/Common/KNN/ann_1.1/CMakeLists.txt -+++ elastix-4.3/src/Common/KNN/ann_1.1/CMakeLists.txt -@@ -33,6 +33,6 @@ - - # Install - INSTALL(TARGETS ANNlib -- RUNTIME DESTINATION . -- LIBRARY DESTINATION . ) -+ RUNTIME DESTINATION lib -+ LIBRARY DESTINATION lib ) - ---- elastix-4.3.orig/src/Core/CMakeLists.txt -+++ elastix-4.3/src/Core/CMakeLists.txt -@@ -167,5 +167,5 @@ - #--------------------------------------------------------------------- - # Define the install directory. - --INSTALL( TARGETS elastix transformix RUNTIME DESTINATION . ) -+INSTALL( TARGETS elastix transformix RUNTIME DESTINATION bin ) - Deleted: trunk/packages/elastix/tags/4.4-1/debian/patches/series =================================================================== --- trunk/packages/elastix/trunk/debian/patches/series 2010-12-24 02:20:56 UTC (rev 5618) +++ trunk/packages/elastix/tags/4.4-1/debian/patches/series 2010-12-27 16:54:19 UTC (rev 5628) @@ -1 +0,0 @@ -install-dir.patch Copied: trunk/packages/elastix/tags/4.4-1/debian/patches/series (from rev 5620, trunk/packages/elastix/trunk/debian/patches/series) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/patches/series (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/patches/series 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1 @@ +build-static-ann.patch Deleted: trunk/packages/elastix/tags/4.4-1/debian/rules =================================================================== --- trunk/packages/elastix/trunk/debian/rules 2010-12-24 02:20:56 UTC (rev 5618) +++ trunk/packages/elastix/tags/4.4-1/debian/rules 2010-12-27 16:54:19 UTC (rev 5628) @@ -1,13 +0,0 @@ -#!/usr/bin/make -f - -%: - dh $@ --sourcedirectory=src --parallel - -DEB_CMAKE_EXTRA_FLAGS += \ - -DCMAKE_INSTALL_PREFIX=/usr \ - -DCMAKE_BUILD_TYPE=RELEASE \ - -DCMAKE_SKIP_RPATH=ON - -override_dh_auto_configure: - dh_auto_configure -- $(DEB_CMAKE_EXTRA_FLAGS) - Copied: trunk/packages/elastix/tags/4.4-1/debian/rules (from rev 5625, trunk/packages/elastix/trunk/debian/rules) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/rules (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/rules 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,37 @@ +#!/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) + +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 + + + Copied: trunk/packages/elastix/tags/4.4-1/debian/transformix.1 (from rev 5624, trunk/packages/elastix/trunk/debian/transformix.1) =================================================================== --- trunk/packages/elastix/tags/4.4-1/debian/transformix.1 (rev 0) +++ trunk/packages/elastix/tags/4.4-1/debian/transformix.1 2010-12-27 16:54:19 UTC (rev 5628) @@ -0,0 +1,41 @@ +.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 [email protected]. _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
