[med-svn] r5628 - in trunk/packages/elastix/tags: . 4.4-1/debian 4.4-1/debian/patches
Steven Michael Robbins
smr at alioth.debian.org
Mon Dec 27 16:54:20 UTC 2010
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 <smr at debian.org> 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 <smr at debian.org> 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 <debian-med-packaging at lists.alioth.debian.org>
-Uploaders: Steve M. Robbins <smr at debian.org>
-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 <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Steve M. Robbins <smr at debian.org>
+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 elastix.support at gmail.com.
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 <smr at debian.org>
+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 elastix.support at gmail.com.
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