On Fri, 2010-12-24 at 16:53 -0600, Steve M. Robbins wrote: > Paul: I looked at your Ubuntu packages and modified the wrapping > options based on what I saw. Let me know if I have missed an > important option.
Looks good. Although a couple of the wrapping options were misspelled, also I don't think wrapping 4D data is necessary. I think it is pretty rare to need it and not having 4D significantly reduces the package sizes. These changes are in the attached patch file (0002-Fixed-some-things-in-the-rules-file.patch). > > Also, I created a couple of separate packages: > > python-insighttoolkit-numpy, python-insighttoolkit-vtk, and > > python-insighttoolkit-multithreader. These correspond to the projects in > > Wrapping/WrapITK/ExternalProjects. Very handy python modules that > > connect itk to vtk and itk to numpy. It would be nice to incorporate > > these projects too. > > Mmm. I overlooked these. Do you want to propose patches? :-) The "0001-Added-PyBuffer-and-ItkVtkGlue-to-build.patch" file does this. I didn't add the multithreader one, maybe I will add it later. The final patch file, adds a couple of registration optimizers I need wrapped. I hope these patch files are in a decent format, I use git-svn, and this is what git spit out when I asked for patch files. Let me know if I should use a different format. I think I might try adding the doxygen generated documentation next. IPython has a nice interface that will display these docs in the shell when you type something like "itk.Image?". I find it handy. Anyway, hope these help. -Paul
>From 9ac6d3461862f041ee663b086f7f239090909cbb Mon Sep 17 00:00:00 2001 From: Paul Novotny <[email protected]> Date: Tue, 18 Jan 2011 14:32:22 -0500 Subject: [PATCH 1/3] Added PyBuffer and ItkVtkGlue to build * This will add the two External Projects to the WrapITK build. PyBuffer provides easy interoperability with numpy. ItkVtkGlue makes it easy to convert from and to VTK. --- debian/control | 2 +- debian/patches/series | 1 + debian/patches/wrapitk-externalprojects.patch | 125 +++++++++++++++++++++++++ debian/rules | 1 + 4 files changed, 128 insertions(+), 1 deletions(-) create mode 100644 debian/patches/wrapitk-externalprojects.patch diff --git a/debian/control b/debian/control index fa098a6..3a18933 100644 --- a/debian/control +++ b/debian/control @@ -7,7 +7,7 @@ Uploaders: Steve M. Robbins <[email protected]> Build-Depends: cdbs (>= 0.4.49), debhelper (>= 7), cmake, cableswig (>= 0.1.0+cvs20100501), gccxml (>= 0.9.0+cvs20100501-2), zlib1g-dev (>= 1.2.2), libpng12-dev, libtiff4-dev (>= 3.7.3), - python-support (>= 0.6.4), python-dev, libfftw3-dev, + python-support (>= 0.6.4), python-dev, python-numpy, libfftw3-dev, tcl8.5-dev, tk8.5-dev, uuid-dev, libgdcm2-dev, libjpeg62-dev, libfreetype6-dev, libopenjpeg-dev, graphviz, libxext-dev, libxss-dev, libxft-dev, libpoppler-dev, libssl-dev, diff --git a/debian/patches/series b/debian/patches/series index a19dd25..b75b679 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -5,3 +5,4 @@ tcl-install.patch jni-dir.patch remove-cmake-export-build-settings.patch wrapitk.patch +wrapitk-externalprojects.patch diff --git a/debian/patches/wrapitk-externalprojects.patch b/debian/patches/wrapitk-externalprojects.patch new file mode 100644 index 0000000..28c37f0 --- /dev/null +++ b/debian/patches/wrapitk-externalprojects.patch @@ -0,0 +1,125 @@ +Index: insighttoolkit-3.20.0/Wrapping/WrapITK/CMakeLists.txt +=================================================================== +--- insighttoolkit-3.20.0.orig/Wrapping/WrapITK/CMakeLists.txt 2011-01-09 14:12:59.000000000 -0500 ++++ insighttoolkit-3.20.0/Wrapping/WrapITK/CMakeLists.txt 2011-01-11 10:19:08.000000000 -0500 +@@ -176,6 +176,17 @@ + SUBDIRS(Modules/${module}) + ENDFOREACH(module) + ++OPTION(BUILD_ITKVTKGLUE "Build WrapITK with ItkVtkGlue" ON) ++IF(BUILD_ITKVTKGLUE) ++ SUBDIRS(ExternalProjects/ItkVtkGlue) ++ENDIF(BUILD_ITKVTKGLUE) ++ ++OPTION(BUILD_PYBUFFER "Build WrapITK with Numpy support" ON) ++IF(BUILD_PYBUFFER) ++ SUBDIRS(ExternalProjects/PyBuffer) ++ENDIF(BUILD_PYBUFFER) ++ ++ + ############################################################################### + # Configure language-specific features + ############################################################################### +Index: insighttoolkit-3.20.0/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/CMakeLists.txt +=================================================================== +--- insighttoolkit-3.20.0.orig/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/CMakeLists.txt 2011-01-11 10:12:29.000000000 -0500 ++++ insighttoolkit-3.20.0/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/CMakeLists.txt 2011-01-17 18:14:17.000000000 -0500 +@@ -1,29 +1,3 @@ +-CMAKE_MINIMUM_REQUIRED(VERSION 2.4) +-IF(COMMAND CMAKE_POLICY) +- CMAKE_POLICY(SET CMP0003 NEW) +-ENDIF(COMMAND CMAKE_POLICY) +- +-PROJECT(ItkVtkGlue) +- +-OPTION(BUILD_WRAPPERS "Wrap library" OFF) +-OPTION(INSTALL_DEVEL_FILES "Install C++ headers" ON) +- +-FIND_PACKAGE(ITK REQUIRED) +-FIND_PACKAGE(VTK REQUIRED) +- +-INCLUDE_DIRECTORIES(${VTK_INCLUDE_DIRS} ${ITK_INCLUDE_DIRS} ${ItkVtkGlue_SOURCE_DIR}/src) +-LINK_DIRECTORIES(${VTK_LIBRARY_DIRS} ${ITK_LIBRARY_DIRS}) +- +-IF(BUILD_WRAPPERS) +- SUBDIRS(Wrapping) +-ENDIF(BUILD_WRAPPERS) +- +-# install devel files +-IF(INSTALL_DEVEL_FILES) +- FOREACH(f itkImageToVTKImageFilter.h itkImageToVTKImageFilter.txx itkVTKImageToImageFilter.h itkVTKImageToImageFilter.txx) +- INSTALL_FILES(/include/InsightToolkit/BasicFilters FILES ${CMAKE_CURRENT_SOURCE_DIR}/src/${f}) +- ENDFOREACH(f) +-ENDIF(INSTALL_DEVEL_FILES) +- +-ENABLE_TESTING() ++INCLUDE_DIRECTORIES(${CMAKE_CURRENT_SOURCE_DIR}/src) ++SUBDIRS(Wrapping) + +Index: insighttoolkit-3.20.0/Wrapping/WrapITK/ExternalProjects/PyBuffer/CMakeLists.txt +=================================================================== +--- insighttoolkit-3.20.0.orig/Wrapping/WrapITK/ExternalProjects/PyBuffer/CMakeLists.txt 2011-01-11 10:52:39.000000000 -0500 ++++ insighttoolkit-3.20.0/Wrapping/WrapITK/ExternalProjects/PyBuffer/CMakeLists.txt 2011-01-17 11:17:30.000000000 -0500 +@@ -1,11 +1,5 @@ +-PROJECT(PyBuffer) +-FIND_PACKAGE(WrapITK REQUIRED) +- + # Deal with numarray package Options +-SET(CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}") +-FIND_PACKAGE( NUMARRAY ) +- +-INCLUDE_DIRECTORIES( ${PYTHON_NUMARRAY_INCLUDE_DIR} ) ++INCLUDE_DIRECTORIES( ${PYTHON_NUMPY_INCLUDE_PATH} ) + + BEGIN_WRAPPER_LIBRARY("BufferConversion" Python) + +Index: insighttoolkit-3.20.0/Wrapping/WrapITK/ExternalProjects/PyBuffer/itkPyBuffer.txx +=================================================================== +--- insighttoolkit-3.20.0.orig/Wrapping/WrapITK/ExternalProjects/PyBuffer/itkPyBuffer.txx 2011-01-11 14:49:57.000000000 -0500 ++++ insighttoolkit-3.20.0/Wrapping/WrapITK/ExternalProjects/PyBuffer/itkPyBuffer.txx 2011-01-11 14:50:43.000000000 -0500 +@@ -49,7 +49,7 @@ + + char * data = (char *)( buffer ); + +- int dimensions[ ImageDimension ]; ++ npy_intp dimensions[ ImageDimension ]; + + SizeType size = image->GetBufferedRegion().GetSize(); + +Index: insighttoolkit-3.20.0/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/Wrapping/CMakeLists.txt +=================================================================== +--- insighttoolkit-3.20.0.orig/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/Wrapping/CMakeLists.txt 2011-01-11 15:14:29.000000000 -0500 ++++ insighttoolkit-3.20.0/Wrapping/WrapITK/ExternalProjects/ItkVtkGlue/Wrapping/CMakeLists.txt 2011-01-17 11:23:37.000000000 -0500 +@@ -1,23 +1,19 @@ +-FIND_PACKAGE(WrapITK REQUIRED) + +-BEGIN_WRAPPER_LIBRARY(${PROJECT_NAME}) ++BEGIN_WRAPPER_LIBRARY(ItkVtkGlue) + SET(WRAPPER_SWIG_LIBRARY_FILES ${WRAPPER_SWIG_LIBRARY_FILES} "${CMAKE_CURRENT_SOURCE_DIR}/itkvtk.swg") + SET(WRAPPER_LIBRARY_DEPENDS Base SimpleFilters) + +-WRAPPER_LIBRARY_CREATE_WRAP_FILES() +-WRAPPER_LIBRARY_CREATE_LIBRARY() +- + IF(WRAP_ITK_PYTHON) + # I can't manage to put that code in Python subdir :-( + SET(VTK_VERSION "${VTK_MAJOR_VERSION}.${VTK_MINOR_VERSION}.${VTK_BUILD_VERSION}") +- SET(MIN_ITK_VER "5.0.0") +- IF("${VTK_VERSION}" STRLESS "${MIN_ITK_VER}") +- TARGET_LINK_LIBRARIES(_${WRAPPER_LIBRARY_NAME}Python vtkImagingPython ITKCommon ITKBasicFilters) +- ELSE("${VTK_VERSION}" STRLESS "${MIN_ITK_VER}") +- TARGET_LINK_LIBRARIES(_${WRAPPER_LIBRARY_NAME}Python vtkImagingPythonD ITKCommon ITKBasicFilters) +- ENDIF("${VTK_VERSION}" STRLESS "${MIN_ITK_VER}") +- +- SUBDIRS(Python) ++ SET(MIN_VTK_VER "5.0.0") ++ IF("${VTK_VERSION}" STRLESS "${MIN_VTK_VER}") ++ SET(WRAPPER_LIBRARY_LINK_LIBRARIES vtkImagingPython ITKCommon ITKBasicFilters) ++ ELSE("${VTK_VERSION}" STRLESS "${MIN_VTK_VER}") ++ SET(WRAPPER_LIBRARY_LINK_LIBRARIES vtkImagingPythonD ITKCommon ITKBasicFilters) ++ ENDIF("${VTK_VERSION}" STRLESS "${MIN_VTK_VER}") + ENDIF(WRAP_ITK_PYTHON) + ++WRAPPER_LIBRARY_CREATE_WRAP_FILES() ++WRAPPER_LIBRARY_CREATE_LIBRARY() + diff --git a/debian/rules b/debian/rules index 8b0243a..f86a839 100755 --- a/debian/rules +++ b/debian/rules @@ -69,6 +69,7 @@ DEB_CMAKE_EXTRA_FLAGS = \ -DITK_USE_STRICT_CONCEPT_CHECKING:BOOL=ON \ -DPYTHON_EXECUTABLE:FILEPATH=/usr/bin/$(PYVERS) \ -DPYTHON_INCLUDE_PATH:PATH=/usr/include/$(PYVERS) \ + -DPYTHON_NUMPY_INCLUDE_PATH:PATH=/usr/include/$(PYVERS)/numpy \ -DPYTHON_LIBRARY:FILEPATH=/usr/lib/lib$(PYVERS).so \ -DTCL_INCLUDE_PATH:PATH=/usr/include/tcl$(TCLVERS) \ -DTCL_LIBRARY:FILEPATH=/usr/lib/libtcl$(TCLVERS).so \ -- 1.7.2.3
>From 303d21dba96ca878ef4121282c64c152c6050807 Mon Sep 17 00:00:00 2001 From: Paul Novotny <[email protected]> Date: Thu, 20 Jan 2011 13:48:28 -0500 Subject: [PATCH 2/3] Fixed some things in the rules file * get-orig-source was still deleting the Code/Review directory. This directory is needed for WrapITK now. * Some of the Wrap settings were misspelled. * Turned off wrapping of 4D images. I don't think this is needed by most people. This reduces the package size significantly --- debian/rules | 22 +++++++++++----------- 1 files changed, 11 insertions(+), 11 deletions(-) diff --git a/debian/rules b/debian/rules index f86a839..5945110 100755 --- a/debian/rules +++ b/debian/rules @@ -80,16 +80,16 @@ DEB_CMAKE_EXTRA_FLAGS = \ -DWRAP_ITK_JAVA:BOOL=ON \ -DWRAP_ITK_PYTHON:BOOL=ON \ -DWRAP_ITK_TCL:BOOL=ON \ - -DWRAP_ITK_DIMS:STRING='2;3;4' \ - -DWRAPcomplex_float:BOOL=ON \ - -DWRAPcovariant_vector_float:BOOL=ON \ - -DWRAPfloat:BOOL=ON \ - -DWRAPrgb_unsigned_char:BOOL=ON \ - -DWRAPrgb_unsigned_short:BOOL=ON \ - -DWRAPsigned_short:BOOL=ON \ - -DWRAPunsigned_char:BOOL=ON \ - -DWRAPunsigned_short:BOOL=ON \ - -DWRAPvector_float:BOOL=ON + -DWRAP_ITK_DIMS:STRING='2;3' \ + -DWRAP_complex_float:BOOL=ON \ + -DWRAP_covariant_vector_float:BOOL=ON \ + -DWRAP_float:BOOL=ON \ + -DWRAP_rgb_unsigned_char:BOOL=ON \ + -DWRAP_rgb_unsigned_short:BOOL=ON \ + -DWRAP_signed_short:BOOL=ON \ + -DWRAP_unsigned_char:BOOL=ON \ + -DWRAP_unsigned_short:BOOL=ON \ + -DWRAP_vector_float:BOOL=ON pre-build:: test -d Code/Review || mv review Code/Review @@ -150,7 +150,7 @@ $(UPSTREAM_SRC).tar.gz: get-orig-source: $(UPSTREAM_SRC).tar.gz tar xzf $(UPSTREAM_SRC).tar.gz find $(UPSTREAM_SRC) -name CVS -o -name Patented | xargs rm -rf - rm -rf $(UPSTREAM_SRC)/Code/Review + #rm -rf $(UPSTREAM_SRC)/Code/Review mv $(UPSTREAM_SRC) $(DEBIAN_SRC_DIR) GZIP=-9 tar czf $(DEBIAN_SRC_TAR) $(DEBIAN_SRC_DIR) -- 1.7.2.3
>From 3f213a7daef265ddb789b3e8636d03c8d6bbb772 Mon Sep 17 00:00:00 2001 From: Paul Novotny <[email protected]> Date: Fri, 21 Jan 2011 16:26:49 -0500 Subject: [PATCH 3/3] Added a few Registration Optimizers for Wrapping * Added a couple new registration optimizers, including LBFGSBOptimizer used for B-spline 3D registratoin. * Also needed to add a few array types to use the optimizers correctly --- debian/patches/add-registration-optimizers.patch | 28 ++++++++++++++++++++++ debian/patches/series | 1 + 2 files changed, 29 insertions(+), 0 deletions(-) create mode 100644 debian/patches/add-registration-optimizers.patch diff --git a/debian/patches/add-registration-optimizers.patch b/debian/patches/add-registration-optimizers.patch new file mode 100644 index 0000000..15a9173 --- /dev/null +++ b/debian/patches/add-registration-optimizers.patch @@ -0,0 +1,28 @@ +Index: insighttoolkit-3.20.0/Wrapping/WrapITK/WrapITKTypes.cmake +=================================================================== +--- insighttoolkit-3.20.0.orig/Wrapping/WrapITK/WrapITKTypes.cmake 2011-01-21 12:36:35.000000000 -0500 ++++ insighttoolkit-3.20.0/Wrapping/WrapITK/WrapITKTypes.cmake 2011-01-21 12:38:05.000000000 -0500 +@@ -80,6 +80,8 @@ + WRAP_TYPE("itk::Array" "A") + WRAP_TEMPLATE("${ITKM_D}" "${ITKT_D}") + WRAP_TEMPLATE("${ITKM_F}" "${ITKT_F}") ++ WRAP_TEMPLATE("${ITKM_UL}" "${ITKT_UL}") ++ WRAP_TEMPLATE("${ITKM_SL}" "${ITKT_SL}") + END_WRAP_TYPE() + SET(itk_Wrap_Array ${WRAPPER_TEMPLATES}) + +Index: insighttoolkit-3.20.0/Wrapping/WrapITK/Modules/BaseNumerics/wrap_ITKOptimizers.cmake +=================================================================== +--- insighttoolkit-3.20.0.orig/Wrapping/WrapITK/Modules/BaseNumerics/wrap_ITKOptimizers.cmake 2011-01-21 12:38:49.000000000 -0500 ++++ insighttoolkit-3.20.0/Wrapping/WrapITK/Modules/BaseNumerics/wrap_ITKOptimizers.cmake 2011-01-21 12:39:15.000000000 -0500 +@@ -14,3 +14,10 @@ + WRAP_NON_TEMPLATE_CLASS("itk::RegularStepGradientDescentOptimizer" POINTER) + WRAP_NON_TEMPLATE_CLASS("itk::VersorTransformOptimizer" POINTER) + WRAP_NON_TEMPLATE_CLASS("itk::AmoebaOptimizer" POINTER) ++WRAP_NON_TEMPLATE_CLASS("itk::CumulativeGaussianOptimizer" POINTER) ++WRAP_NON_TEMPLATE_CLASS("itk::ExhaustiveOptimizer" POINTER) ++WRAP_NON_TEMPLATE_CLASS("itk::FRPROptimizer" POINTER) ++WRAP_NON_TEMPLATE_CLASS("itk::LBFGSBOptimizer" POINTER) ++WRAP_NON_TEMPLATE_CLASS("itk::PowellOptimizer" POINTER) ++WRAP_NON_TEMPLATE_CLASS("itk::SPSAOptimizer" POINTER) ++WRAP_NON_TEMPLATE_CLASS("itk::VersorRigid3DTransformOptimizer" POINTER) diff --git a/debian/patches/series b/debian/patches/series index b75b679..eca545d 100644 --- a/debian/patches/series +++ b/debian/patches/series @@ -6,3 +6,4 @@ jni-dir.patch remove-cmake-export-build-settings.patch wrapitk.patch wrapitk-externalprojects.patch +add-registration-optimizers.patch -- 1.7.2.3
