Author: smr Date: 2014-03-30 20:45:13 +0000 (Sun, 30 Mar 2014) New Revision: 16541
Added: trunk/packages/insighttoolkit/trunk/debian/patches/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch trunk/packages/insighttoolkit/trunk/debian/patches/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch trunk/packages/insighttoolkit/trunk/debian/patches/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch trunk/packages/insighttoolkit/trunk/debian/patches/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch trunk/packages/insighttoolkit/trunk/debian/patches/0005-make-gdcm-helper-library-static.patch Modified: trunk/packages/insighttoolkit/trunk/debian/changelog trunk/packages/insighttoolkit/trunk/debian/control trunk/packages/insighttoolkit/trunk/debian/control.in trunk/packages/insighttoolkit/trunk/debian/copyright trunk/packages/insighttoolkit/trunk/debian/patches/bsd-hdf5.patch trunk/packages/insighttoolkit/trunk/debian/patches/series trunk/packages/insighttoolkit/trunk/debian/rules Log: Merge of Gert Wollny's itk4-enable-python branch into trunk. Modified: trunk/packages/insighttoolkit/trunk/debian/changelog =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/changelog 2014-03-28 18:55:33 UTC (rev 16540) +++ trunk/packages/insighttoolkit/trunk/debian/changelog 2014-03-30 20:45:13 UTC (rev 16541) @@ -1,3 +1,17 @@ +insighttoolkit4 (4.5.1-1) unstable; urgency=medium + + [Gert Wollny] + * new uptream + * enable python2.7 bindings + * update build dependencies to new wrapping method + * Add linker flags --as-needed to reduce dependencies + * make ITKGDCM a static library since it is only a dependency stub + + [ Steve M. Robbins ] + * Merged Gert's patches to main trunk for release. + + -- Steve M. Robbins <[email protected]> Sun, 30 Mar 2014 15:43:57 -0500 + insighttoolkit4 (4.5.0-3) unstable; urgency=low * Team upload. Modified: trunk/packages/insighttoolkit/trunk/debian/control =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/control 2014-03-28 18:55:33 UTC (rev 16540) +++ trunk/packages/insighttoolkit/trunk/debian/control 2014-03-30 20:45:13 UTC (rev 16541) @@ -5,11 +5,22 @@ Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Steve M. Robbins <[email protected]> Build-Depends: debhelper (>= 9), - cmake, cableswig (>= 0.1.0+cvs20110226), gccxml (>= 0.9.0+cvs20110723), - zlib1g-dev (>= 1.2.2), libpng12-dev, libtiff-dev, - libdcmtk2-dev, libgdcm2-dev, libdouble-conversion-dev, - uuid-dev, libminc-dev, libhdf5-dev, - libvtk5-dev, python-vtk + cmake, + swig (>= 2.0), + gccxml (>= 0.9.0+cvs20120420), + zlib1g-dev (>= 1.2.2), + libpng12-dev, + libtiff-dev, + libfftw3-dev, + libdcmtk2-dev, + libgdcm2-dev, + libdouble-conversion-dev, + uuid-dev, + libminc-dev, + libhdf5-dev, + python-all-dev, + libvtk5-dev, + python-vtk Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/insighttoolkit/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/insighttoolkit/trunk/ @@ -72,3 +83,22 @@ combine the information contained in both. . This package contains the source for example programs. + +Package: insighttoolkit4-python +Section: python +Architecture: amd64 i386 +Depends: ${misc:Depends}, ${shlibs:Depends} +Conflicts: insighttoolkit-python +Replaces: insighttoolkit-python +Description: Image processing toolkit for registration and segmentation - examples + ITK is an open-source software toolkit for performing registration and + segmentation. Segmentation is the process of identifying and + classifying data found in a digitally sampled + representation. Typically the sampled representation is an image + acquired from such medical instrumentation as CT or MRI + scanners. Registration is the task of aligning or developing + correspondences between data. For example, in the medical + environment, a CT scan may be aligned with a MRI scan in order to + combine the information contained in both. + . + This package contains the python bindings. Modified: trunk/packages/insighttoolkit/trunk/debian/control.in =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/control.in 2014-03-28 18:55:33 UTC (rev 16540) +++ trunk/packages/insighttoolkit/trunk/debian/control.in 2014-03-30 20:45:13 UTC (rev 16541) @@ -5,11 +5,22 @@ Maintainer: Debian Med Packaging Team <[email protected]> Uploaders: Steve M. Robbins <[email protected]> Build-Depends: debhelper (>= 9), - cmake, cableswig (>= 0.1.0+cvs20110226), gccxml (>= 0.9.0+cvs20110723), - zlib1g-dev (>= 1.2.2), libpng12-dev, libtiff-dev, - libdcmtk2-dev, libgdcm2-dev, libdouble-conversion-dev, - uuid-dev, libminc-dev, libhdf5-dev, - libvtk5-dev, python-vtk + cmake, + swig (>= 2.0), + gccxml (>= 0.9.0+cvs20120420), + zlib1g-dev (>= 1.2.2), + libpng12-dev, + libtiff-dev, + libfftw3-dev, + libdcmtk2-dev, + libgdcm2-dev, + libdouble-conversion-dev, + uuid-dev, + libminc-dev, + libhdf5-dev, + python-all-dev, + libvtk5-dev, + python-vtk Standards-Version: 3.9.5 Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/insighttoolkit/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/insighttoolkit/trunk/ @@ -72,3 +83,22 @@ combine the information contained in both. . This package contains the source for example programs. + +Package: insighttoolkit@VER_MAJOR@-python +Section: python +Architecture: amd64 i386 +Depends: ${misc:Depends}, ${shlibs:Depends} +Conflicts: insighttoolkit-python +Replaces: insighttoolkit-python +Description: Image processing toolkit for registration and segmentation - examples + ITK is an open-source software toolkit for performing registration and + segmentation. Segmentation is the process of identifying and + classifying data found in a digitally sampled + representation. Typically the sampled representation is an image + acquired from such medical instrumentation as CT or MRI + scanners. Registration is the task of aligning or developing + correspondences between data. For example, in the medical + environment, a CT scan may be aligned with a MRI scan in order to + combine the information contained in both. + . + This package contains the python bindings. Modified: trunk/packages/insighttoolkit/trunk/debian/copyright =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/copyright 2014-03-28 18:55:33 UTC (rev 16540) +++ trunk/packages/insighttoolkit/trunk/debian/copyright 2014-03-30 20:45:13 UTC (rev 16541) @@ -65,7 +65,7 @@ 1) DICOMParser: Copyright by Matt Turek. Distributed under a BSD-Like license. [This work was funded by NLM so its copyright - should probably be transfered to the ISC.] + should probably be transferred to the ISC.] 2) AnalyzeDB.h: The Mayo Clinic aggreed to distribute this file with ITK. Point of contact: Vincent Magnotta. Added: trunk/packages/insighttoolkit/trunk/debian/patches/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/patches/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch (rev 0) +++ trunk/packages/insighttoolkit/trunk/debian/patches/0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch 2014-03-30 20:45:13 UTC (rev 16541) @@ -0,0 +1,50 @@ +From d069b7b94287dae15fcaf707775f5dd2bbebcc38 Mon Sep 17 00:00:00 2001 +From: Matt McCormick <[email protected]> +Date: Wed, 5 Feb 2014 15:52:34 -0500 +Subject: [PATCH 1/3] BUG: Wrap TransformFileReader, TransformFileWriter. + +Missing CMakeLists.txt in the wrapping directory. Need to explicitly include +the headers after "Template" was appended to the class name. + +Suggested-by: Sami Koho <[email protected]> + +Change-Id: I6f994bb18f37d5adf1d0f0311fa73506c41239a7 +--- + Modules/IO/TransformBase/wrapping/CMakeLists.txt | 3 +++ + Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap | 2 ++ + Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap | 2 ++ + 3 files changed, 7 insertions(+) + create mode 100644 Modules/IO/TransformBase/wrapping/CMakeLists.txt + +diff --git a/Modules/IO/TransformBase/wrapping/CMakeLists.txt b/Modules/IO/TransformBase/wrapping/CMakeLists.txt +new file mode 100644 +index 0000000..6072567 +--- /dev/null ++++ b/Modules/IO/TransformBase/wrapping/CMakeLists.txt +@@ -0,0 +1,3 @@ ++itk_wrap_module(ITKIOTransformBase) ++itk_auto_load_submodules() ++itk_end_wrap_module() +diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap +index 9b52fbc..662df9e 100644 +--- a/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap ++++ b/Modules/IO/TransformBase/wrapping/itkTransformFileReader.wrap +@@ -1,3 +1,5 @@ ++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) ++itk_wrap_include("itkTransformFileReader.h") + itk_wrap_class("itk::TransformFileReaderTemplate" POINTER) + foreach(t ${WRAP_ITK_REAL}) + itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") +diff --git a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap +index 4f1ac4a..356aaf3 100644 +--- a/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap ++++ b/Modules/IO/TransformBase/wrapping/itkTransformFileWriter.wrap +@@ -1,3 +1,5 @@ ++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) ++itk_wrap_include("itkTransformFileWriter.h") + itk_wrap_class("itk::TransformFileWriterTemplate" POINTER) + foreach(t ${WRAP_ITK_REAL}) + itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") +-- +1.8.5.3 + Added: trunk/packages/insighttoolkit/trunk/debian/patches/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/patches/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch (rev 0) +++ trunk/packages/insighttoolkit/trunk/debian/patches/0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch 2014-03-30 20:45:13 UTC (rev 16541) @@ -0,0 +1,28 @@ +From 66d2955fbe5528d9df216c639277d1d2686447e5 Mon Sep 17 00:00:00 2001 +From: Michka Popoff <[email protected]> +Date: Fri, 7 Feb 2014 19:24:49 +0100 +Subject: [PATCH 2/3] COMP: Fixed itkQuasiNewtonOptimizerv4 wrapping warnings + +The warning : +/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(5): Unknown type type: itk::QuasiNewtonOptimizerv4 [typedef] +/scratch/dashboards/Linux-x86_64-gcc4.4-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkQuasiNewtonOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::QuasiNewtonOptimizerv4Template< double > +--- + .../Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap | 8 +++++++- + 1 file changed, 7 insertions(+), 1 deletion(-) + +diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap +index 4a43dd4..7eed11c 100644 +--- a/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap ++++ b/Modules/Numerics/Optimizersv4/wrapping/itkQuasiNewtonOptimizerv4.wrap +@@ -1 +1,7 @@ +-itk_wrap_simple_class("itk::QuasiNewtonOptimizerv4" POINTER) ++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) ++itk_wrap_include("itkQuasiNewtonOptimizerv4.h") ++itk_wrap_class("itk::QuasiNewtonOptimizerv4Template" POINTER) ++ foreach(t ${WRAP_ITK_REAL}) ++ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") ++ endforeach(t) ++itk_end_wrap_class() +-- +1.8.5.3 + Added: trunk/packages/insighttoolkit/trunk/debian/patches/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/patches/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch (rev 0) +++ trunk/packages/insighttoolkit/trunk/debian/patches/0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch 2014-03-30 20:45:13 UTC (rev 16541) @@ -0,0 +1,73 @@ +From fced46ce8769b4edc7971ea0928045390b5c3f84 Mon Sep 17 00:00:00 2001 +From: Michka Popoff <[email protected]> +Date: Mon, 10 Feb 2014 09:41:42 +0100 +Subject: [PATCH 3/3] COMP: Fixed itkGradientDescentOptimizerv4 wrapping + warnings + +I splitted the 3 wrapping calls in 3 separate files and fixed the wrapping. + +The warnings : +/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerBasev4 [typedef] +/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::GradientDescentOptimizerv4 [typedef] +/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(5): Unknown type type: itk::ObjectToObjectOptimizerBase [typedef] +/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerBasev4Template< double > +/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::GradientDescentOptimizerv4Template< double > +/home/kevin/kitware/ITK_Build/Wrapping/Modules/ITKOptimizersv4/itkGradientDescentOptimizerv4.xml: warning(4): ITK type not wrapped, or currently not known: itk::ObjectToObjectOptimizerBaseTemplate< double > + +Should also hopefully fix the new error on the dashboard I introduced by fixing the itkQuasiNewtonOptimizerv4 warnings (http://review.source.kitware.com/#/c/14317/) +/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Nothing known about base class 'itk::GradientDescentOptimizerv4Template< float >'. Ignored. +/home/kevin/kitware/ITK_Build/Wrapping/Typedefs/itkQuasiNewtonOptimizerv4.i:87: Warning 401: Maybe you forgot to instantiate 'itk::GradientDescentOptimizerv4Template< float >' using %template. + +Change-Id: I15b6af11690ed6efeaced68f73af5212ab5dc364 +--- + .../wrapping/itkGradientDescentOptimizerBasev4.wrap | 7 +++++++ + .../Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap | 10 +++++++--- + .../Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap | 7 +++++++ + 3 files changed, 21 insertions(+), 3 deletions(-) + create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap + create mode 100644 Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap + +diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap +new file mode 100644 +index 0000000..74f5a6c +--- /dev/null ++++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerBasev4.wrap +@@ -0,0 +1,7 @@ ++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) ++itk_wrap_include("itkGradientDescentOptimizerBasev4.h") ++itk_wrap_class("itk::GradientDescentOptimizerBasev4Template" POINTER) ++ foreach(t ${WRAP_ITK_REAL}) ++ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") ++ endforeach(t) ++itk_end_wrap_class() +diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap +index d53a176..3236448 100644 +--- a/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap ++++ b/Modules/Numerics/Optimizersv4/wrapping/itkGradientDescentOptimizerv4.wrap +@@ -1,3 +1,7 @@ +-itk_wrap_simple_class("itk::ObjectToObjectOptimizerBase" POINTER) +-itk_wrap_simple_class("itk::GradientDescentOptimizerBasev4" POINTER) +-itk_wrap_simple_class("itk::GradientDescentOptimizerv4" POINTER) ++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) ++itk_wrap_include("itkGradientDescentOptimizerv4.h") ++itk_wrap_class("itk::GradientDescentOptimizerv4Template" POINTER) ++ foreach(t ${WRAP_ITK_REAL}) ++ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") ++ endforeach(t) ++itk_end_wrap_class() +diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap +new file mode 100644 +index 0000000..61b2c44 +--- /dev/null ++++ b/Modules/Numerics/Optimizersv4/wrapping/itkObjectToObjectOptimizerBase.wrap +@@ -0,0 +1,7 @@ ++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) ++itk_wrap_include("itkObjectToObjectOptimizerBase.h") ++itk_wrap_class("itk::ObjectToObjectOptimizerBaseTemplate" POINTER) ++ foreach(t ${WRAP_ITK_REAL}) ++ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") ++ endforeach(t) ++itk_end_wrap_class() +-- +1.8.5.3 + Added: trunk/packages/insighttoolkit/trunk/debian/patches/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/patches/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch (rev 0) +++ trunk/packages/insighttoolkit/trunk/debian/patches/0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch 2014-03-30 20:45:13 UTC (rev 16541) @@ -0,0 +1,30 @@ +Author: Matt McCormick <[email protected]> +Date: Thu Feb 6 10:26:49 2014 -0500 + + COMP: Wrap OptimizerParameterScalesEstimatorTemplate. + + The class name changed and it became templated. Fixes: + + /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: + warning(5): Unknown type type: itk::OptimizerParameterScalesEstimator + [typedef] + /playpen/blowekamp/MacOSX-WrapITK/ITK-build/Wrapping/Modules/ITKOptimizersv4/itkOptimizerParameterScalesEstimator.xml: + warning(4): ITK type not wrapped, or currently not known: + itk::OptimizerParameterScalesEstimatorTemplate< double > + + Change-Id: Ic6b4d6fba10d5d6c7b58de8d842bad6511e1ae7b + +diff --git a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap b/Modules/Numerics/Optimizersv4/wrapping/itkOptim +index efd6a8c..a647ee4 100644 +--- a/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap ++++ b/Modules/Numerics/Optimizersv4/wrapping/itkOptimizerParameterScalesEstimator.wrap +@@ -1 +1,7 @@ +-itk_wrap_simple_class("itk::OptimizerParameterScalesEstimator" POINTER) ++set(WRAPPER_AUTO_INCLUDE_HEADERS OFF) ++itk_wrap_include("itkOptimizerParameterScalesEstimator.h") ++itk_wrap_class("itk::OptimizerParameterScalesEstimatorTemplate" POINTER) ++ foreach(t ${WRAP_ITK_REAL}) ++ itk_wrap_template("${ITKM_${t}}" "${ITKT_${t}}") ++ endforeach(t) ++itk_end_wrap_class() + Added: trunk/packages/insighttoolkit/trunk/debian/patches/0005-make-gdcm-helper-library-static.patch =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/patches/0005-make-gdcm-helper-library-static.patch (rev 0) +++ trunk/packages/insighttoolkit/trunk/debian/patches/0005-make-gdcm-helper-library-static.patch 2014-03-30 20:45:13 UTC (rev 16541) @@ -0,0 +1,11 @@ +diff --git a/Modules/ThirdParty/GDCM/src/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/CMakeLists.txt +index e98077c..70f4286 100644 +--- a/Modules/ThirdParty/GDCM/src/CMakeLists.txt ++++ b/Modules/ThirdParty/GDCM/src/CMakeLists.txt +@@ -1,5 +1,5 @@ + if(ITK_USE_SYSTEM_GDCM) +- add_library(ITKGDCM ITK-GDCM.cxx) ++ add_library(ITKGDCM STATIC ITK-GDCM.cxx) + target_link_libraries(ITKGDCM gdcmDICT gdcmMSFF) + itk_module_target(ITKGDCM) + return() Modified: trunk/packages/insighttoolkit/trunk/debian/patches/bsd-hdf5.patch =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/patches/bsd-hdf5.patch 2014-03-28 18:55:33 UTC (rev 16540) +++ trunk/packages/insighttoolkit/trunk/debian/patches/bsd-hdf5.patch 2014-03-30 20:45:13 UTC (rev 16541) @@ -10,7 +10,7 @@ #----------------------------------------------------------------------------- IF (CMAKE_COMPILER_IS_GNUCC) SET (CMAKE_C_FLAGS "${CMAKE_ANSI_CFLAGS} ${CMAKE_C_FLAGS} -std=c99 -finline-functions -fno-common") -+ IF ($ENV{DEB_HOST_ARCH_OS} STREQUAL "kfreebsd") ++ IF ("x$ENV{DEB_HOST_ARCH_OS}" STREQUAL "xkfreebsd") + SET (CMAKE_C_FLAGS "${CMAKE_C_FLAGS} -D_BSD_SOURCE") + ENDIF () ENDIF (CMAKE_COMPILER_IS_GNUCC) Modified: trunk/packages/insighttoolkit/trunk/debian/patches/series =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/patches/series 2014-03-28 18:55:33 UTC (rev 16540) +++ trunk/packages/insighttoolkit/trunk/debian/patches/series 2014-03-30 20:45:13 UTC (rev 16541) @@ -1,3 +1,8 @@ nrrdio-linking.patch bsd-hdf5.patch #doubleconv.patch +0001-BUG-Wrap-TransformFileReader-TransformFileWriter.patch +0002-COMP-Fixed-itkQuasiNewtonOptimizerv4-wrapping-warnin.patch +0003-COMP-Fixed-itkGradientDescentOptimizerv4-wrapping-wa.patch +0004-COMP-Warp-OptimizerParameterScalesEstimatorTemplate.patch +0005-make-gdcm-helper-library-static.patch Modified: trunk/packages/insighttoolkit/trunk/debian/rules =================================================================== --- trunk/packages/insighttoolkit/trunk/debian/rules 2014-03-28 18:55:33 UTC (rev 16540) +++ trunk/packages/insighttoolkit/trunk/debian/rules 2014-03-30 20:45:13 UTC (rev 16541) @@ -3,16 +3,31 @@ VER_MAJOR = 4 VER_MINOR = 5 +export DEB_LDFLAGS_MAINT_APPEND = -Wl,--as-needed + # TODO: turn on the following: # # system HDF5 (omits C++ bindings; Bug #660547) # system FFTW (test failures; see http://lists.debian.org/debian-med/2012/04/msg00064.html) +# ( __float128 not parsed by gccxml on i386 +# http://public.kitware.com/pipermail/gccxml/2011-December/thread.html#1470 +# http://www.gccxml.org/Bug/view.php?id=14794) +# # system VXL (Bug #656837) # Module_ITKLevelSetsv4Visualization (https://issues.itk.org/jira/browse/ITK-2856) # Module_ITKVideoBridgeOpenCV (undiagnosed build error) # Module_ITKVideoBridgeVXL (undiagnosed build error) # Module_ITKVtkGlue (https://issues.itk.org/jira/browse/ITK-2856) +# multi-python, no idea how to do this without re-compiling all and everything for +# each python version + +ifeq ($(DEB_BUILD_ARCH),i386) + ENABLE_FFTW=OFF +else + ENABLE_FFTW=ON +endif + CMAKE_FLAGS = \ -DBUILD_EXAMPLES:BOOL=ON \ -DBUILD_SHARED_LIBS:BOOL=ON \ @@ -21,11 +36,12 @@ -DCMAKE_EXPORT_COMPILE_COMMANDS:BOOL=ON \ -DCMAKE_SKIP_RPATH:BOOL=ON \ -DCMAKE_VERBOSE_MAKEFILE:BOOL=ON \ - -DITK_USE_FFTWD:BOOL=OFF \ - -DITK_USE_FFTWF:BOOL=OFF \ + -DUSE_FFTWF=$(ENABLE_FFTW) \ + -DITK_USE_FFTWD:BOOL=$(ENABLE_FFTW) \ + -DITK_USE_FFTWF:BOOL=$(ENABLE_FFTW) \ + -DITK_USE_SYSTEM_FFTW:BOOL=$(ENABLE_FFTW) \ -DITK_USE_STRICT_CONCEPT_CHECKING:BOOL=ON \ -DITK_USE_SYSTEM_DCMTK:BOOL=ON \ - -DITK_USE_SYSTEM_FFTW:BOOL=OFF \ -DITK_USE_SYSTEM_GDCM:BOOL=ON \ -DITK_USE_SYSTEM_DOUBLECONVERSION:BOOL=OFF \ -DITK_USE_SYSTEM_HDF5:BOOL=OFF \ @@ -34,6 +50,7 @@ -DITK_USE_SYSTEM_TIFF:BOOL=ON \ -DITK_USE_SYSTEM_VXL:BOOL=OFF \ -DITK_USE_SYSTEM_ZLIB:BOOL=ON \ + -DITK_USE_SYSTEM_GCCXML:BOOL=ON \ -DModule_ITKDCMTK:BOOL=ON \ -DModule_ITKIOPhilipsREC:BOOL=OFF \ -DModule_ITKLevelSetsv4Visualization:BOOL=OFF \ @@ -41,13 +58,24 @@ -DModule_ITKVideoBridgeOpenCV:BOOL=OFF \ -DModule_ITKVideoBridgeVXL:BOOL=OFF \ -DModule_ITKVtkGlue:BOOL=OFF \ - -DVCL_INCLUDE_CXX_0X:BOOL=ON + -DVCL_INCLUDE_CXX_0X:BOOL=ON \ + -DITK_USE_SYSTEM_SWIG:BOOL=ON \ + -DITK_WRAP_DIMS="2;3;4" \ + -DITK_WRAP_double:BOOL=ON \ + -DITK_WRAP_vector_double:BOOL=ON \ + -DITK_WRAP_covariant_vector_double:BOOL=ON \ + -DITK_WRAP_complex_double:BOOL=ON \ + -DITK_WRAPPING:BOOL=ON \ + -DITK_WRAP_PYTHON:BOOL=ON \ + -DPython_ADDITIONAL_VERSIONS=2.7 + SOVERSION = $(VER_MAJOR).$(VER_MINOR) pkg_lib = libinsighttoolkit$(SOVERSION) pkg_dev = libinsighttoolkit$(VER_MAJOR)-dev pkg_examples = insighttoolkit$(VER_MAJOR)-examples +pkg_python = insighttoolkit$(VER_MAJOR)-python %: @@ -78,10 +106,21 @@ dh_installman -p$(pkg_dev) debian/insighttoolkit.3 dh_installdocs -p$(pkg_dev) Documentation/* dh_install -p$(pkg_dev) -XJava -XPython -XTcl debian/tmp/usr/lib/lib*.so usr/lib + + # this is only for libITKGDCM which is a stub + dh_install -p$(pkg_dev) -XJava -XPython -XTcl debian/tmp/usr/lib/lib*.a usr/lib + dh_install -p$(pkg_dev) --autodest debian/tmp/usr/include/ITK-$(SOVERSION)/* + dh_install -p$(pkg_dev) --autodest debian/tmp/usr/bin/itkTestDriver + + # remove wrapping related cmake files, and tools. They should not be needed. + rm -r debian/tmp/usr/lib/cmake/ITK-$(SOVERSION)/WrapITK dh_install -p$(pkg_dev) --autodest debian/tmp/usr/lib/cmake - dh_install -p$(pkg_dev) --autodest debian/tmp/usr/bin/itkTestDriver # dh_install -p$(pkg_dev) Wrapping/WrapITK /usr/src + # + # pkg_python + dh_install -p$(pkg_python) debian/tmp/usr/lib/python2.7/* usr/lib/python2.7/ + dh_install -p$(pkg_python) usr/lib/ITK-$(SOVERSION)/Python usr/lib/ITK-$(SOVERSION) override_dh_installexamples: # pkg_examples _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
