diff options
29 files changed, 1954 insertions, 69 deletions
diff --git a/ports/itk/CONTROL b/ports/itk/CONTROL index 282ac4b3c..d316675cb 100644 --- a/ports/itk/CONTROL +++ b/ports/itk/CONTROL @@ -1,9 +1,37 @@ Source: itk -Version: 5.0.1-2 +Version: 5.1.0 Description: Insight Segmentation and Registration Toolkit (ITK) is used for image processing and analysis. Homepage: https://github.com/InsightSoftwareConsortium/ITK -Build-Depends: double-conversion, libjpeg-turbo, zlib, libpng, tiff, expat, eigen3, hdf5[cpp], openjpeg +Build-Depends: double-conversion, libjpeg-turbo, zlib, libpng, tiff, expat, eigen3, hdf5[core,cpp], openjpeg[core], fftw3[core], gtest, gdcm, icu, minc Feature: vtk Description: Build ITKVtkGlue module. -Build-Depends: vtk +Build-Depends: vtk[core] + +Feature: python +Description: Python functionality for ITK +Build-Depends: python3 + +Feature: opencl +Description: Use OpenCL +Build-Depends: opencl + +Feature: cufftw +Description: Use CUDA FFTW +Build-Depends: cuda + +Feature: cuda +Description: Build CUDA module +Build-Depends: cuda, itk[core, opencl] + +Feature: tbb +Description: Build TBB Module +Build-Depends: tbb + +Feature: rtk +Description: Build RTK Module + +Feature: tools +Description: Build RTK with tools +Build-Depends: itk[core, rtk] + diff --git a/ports/itk/cufftw.patch b/ports/itk/cufftw.patch new file mode 100644 index 000000000..17365fb2f --- /dev/null +++ b/ports/itk/cufftw.patch @@ -0,0 +1,58 @@ +From 0f47aae05217884193a39690c2beef566f4ed3b1 Mon Sep 17 00:00:00 2001 +From: Stephen Aylward <stephen.aylward@kitware.com> +Date: Sat, 25 Apr 2020 20:15:21 -0400 +Subject: [PATCH] BUG: CUFFTW paths were not being set and unnecessary FFTW + files used + +FindFFTW sets the FFTW_INCLUDES variable. The FFTW_INCLUDE_PATH var is +specific to FFTW (not used by CUFFTW). + +FFTWGlobalConfiguration file is only needed if FFTW is being used, +not if CUFFT is being used. +--- + CMake/FindFFTW.cmake | 2 +- + Modules/Filtering/FFT/CMakeLists.txt | 2 +- + Modules/Filtering/FFT/src/CMakeLists.txt | 9 +++++---- + 3 files changed, 7 insertions(+), 6 deletions(-) + +diff --git a/CMake/FindFFTW.cmake b/CMake/FindFFTW.cmake +index 785edc2b628..e1935899cab 100644 +--- a/CMake/FindFFTW.cmake ++++ b/CMake/FindFFTW.cmake +@@ -62,7 +62,7 @@ if(ITK_USE_FFTWD OR ITK_USE_FFTWF) + find_path(FFTW_INCLUDE_PATH fftw3.h ${FFTW_INC_SEARCHPATH}) + endif() + +- if(FFTW_INCLUDE_PATH) ++ if(FFTW_INCLUDE_PATH OR CUFFTW_INCLUDE_PATH) + if(ITK_USE_CUFFTW) + file(TO_CMAKE_PATH "${CUFFTW_INCLUDE_PATH}" CUFFTW_INCLUDE_PATH) + set(FFTW_INCLUDE ${CUFFTW_INCLUDE_PATH}) +diff --git a/Modules/Filtering/FFT/CMakeLists.txt b/Modules/Filtering/FFT/CMakeLists.txt +index 7d9d1900b56..713530149cb 100644 +--- a/Modules/Filtering/FFT/CMakeLists.txt ++++ b/Modules/Filtering/FFT/CMakeLists.txt +@@ -5,5 +5,5 @@ if(ITK_USE_CUFFTW) + else() + set(ITKFFT_LIBRARIES ITKFFT) + endif() +-set(ITKFFT_INCLUDE_DIRS ${FFTW_INCLUDE_PATH}) ++set(ITKFFT_INCLUDE_DIRS ${FFTW_INCLUDE}) + itk_module_impl() +diff --git a/Modules/Filtering/FFT/src/CMakeLists.txt b/Modules/Filtering/FFT/src/CMakeLists.txt +index 3f3137b8cd4..bde3ee906f8 100644 +--- a/Modules/Filtering/FFT/src/CMakeLists.txt ++++ b/Modules/Filtering/FFT/src/CMakeLists.txt +@@ -1,7 +1,8 @@ +-set(ITKFFT_SRCS +- itkFFTWGlobalConfiguration.cxx +- itkComplexToComplexFFTImageFilter.cxx +- ) ++set(ITKFFT_SRCS itkComplexToComplexFFTImageFilter.cxx) ++ ++if( ITK_USE_FFTWF OR ITK_USE_FFTWD AND NOT ITK_USE_CUFFTW) ++ list(APPEND ITKFFT_SRCS itkFFTWGlobalConfiguration.cxx ) ++endif() + + itk_module_add_library(ITKFFT ${ITKFFT_SRCS}) + diff --git a/ports/itk/double-conversion.patch b/ports/itk/double-conversion.patch new file mode 100644 index 000000000..636dd8c4c --- /dev/null +++ b/ports/itk/double-conversion.patch @@ -0,0 +1,16 @@ +diff --git a/Modules/ThirdParty/DoubleConversion/CMakeLists.txt b/Modules/ThirdParty/DoubleConversion/CMakeLists.txt
+index 16c611fd3..13978724c 100644
+--- a/Modules/ThirdParty/DoubleConversion/CMakeLists.txt
++++ b/Modules/ThirdParty/DoubleConversion/CMakeLists.txt
+@@ -9,7 +9,10 @@ mark_as_advanced(ITK_USE_SYSTEM_DOUBLECONVERSION)
+ if(ITK_USE_SYSTEM_DOUBLECONVERSION)
+ find_package(double-conversion REQUIRED)
+ get_target_property(ITKDoubleConversion_INCLUDE_DIRS double-conversion::double-conversion INTERFACE_INCLUDE_DIRECTORIES)
+- get_target_property(ITKDoubleConversion_LIBRARIES double-conversion::double-conversion LOCATION)
++ get_target_property(ITKDoubleConversion_LIBRARY_RELEASE double-conversion::double-conversion LOCATION_RELEASE)
++ get_target_property(ITKDoubleConversion_LIBRARY_DEBUG double-conversion::double-conversion LOCATION_DEBUG)
++ include(SelectLibraryConfigurations)
++ select_library_configurations(ITKDoubleConversion)
+ else()
+ set(ITKDoubleConversion_INCLUDE_DIRS
+ ${ITKDoubleConversion_SOURCE_DIR}/src
diff --git a/ports/itk/fix_libminc_config_path.patch b/ports/itk/fix_libminc_config_path.patch deleted file mode 100644 index 3ff305d4b..000000000 --- a/ports/itk/fix_libminc_config_path.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/Modules/ThirdParty/MINC/src/libminc/CMakeLists.txt b/Modules/ThirdParty/MINC/src/libminc/CMakeLists.txt -index 305b2c63..63f81a53 100644 ---- a/Modules/ThirdParty/MINC/src/libminc/CMakeLists.txt -+++ b/Modules/ThirdParty/MINC/src/libminc/CMakeLists.txt -@@ -550,7 +550,7 @@ IF(LIBMINC_INSTALL_LIB_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT) - ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake - ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINCConfig.cmake - DESTINATION -- ${LIBMINC_INSTALL_LIB_DIR}/cmake -+ share/itk - COMPONENT Development) - ENDIF(LIBMINC_INSTALL_LIB_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT) - diff --git a/ports/itk/fix_openjpeg_search.patch b/ports/itk/fix_openjpeg_search.patch deleted file mode 100644 index d17a1ab84..000000000 --- a/ports/itk/fix_openjpeg_search.patch +++ /dev/null @@ -1,13 +0,0 @@ -diff --git a/Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt -index 6ac16ab6..4638f13c 100644 ---- a/Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt -+++ b/Modules/ThirdParty/GDCM/src/gdcm/CMakeLists.txt -@@ -373,7 +373,7 @@ else() - endif() - - if(GDCM_USE_SYSTEM_OPENJPEG) -- find_package(OpenJPEG 2.0.0 REQUIRED) -+ find_package(OpenJPEG REQUIRED) - set(GDCM_OPENJPEG_LIBRARIES ${OPENJPEG_LIBRARIES}) - else() - set(GDCM_OPENJPEG_LIBRARIES gdcmopenjp2) diff --git a/ports/itk/hdf5.patch b/ports/itk/hdf5.patch new file mode 100644 index 000000000..091594cda --- /dev/null +++ b/ports/itk/hdf5.patch @@ -0,0 +1,20 @@ +diff --git a/Modules/ThirdParty/HDF5/CMakeLists.txt b/Modules/ThirdParty/HDF5/CMakeLists.txt
+index a700ecdfb..0a683a52b 100644
+--- a/Modules/ThirdParty/HDF5/CMakeLists.txt
++++ b/Modules/ThirdParty/HDF5/CMakeLists.txt
+@@ -25,11 +25,11 @@ endif()
+ ")
+ endif()
+
+- set(ITKHDF5_LIBRARIES )
+- if(BUILD_SHARED_LIBS)
+- list(APPEND ITKHDF5_LIBRARIES ${HDF5_C_SHARED_LIBRARY} ${HDF5_CXX_SHARED_LIBRARY})
++ set(ITKHDF5_LIBRARIES)
++ if(HDF5_BUILD_SHARED_LIBS)
++ list(APPEND ITKHDF5_LIBRARIES hdf5::hdf5_cpp-shared hdf5::hdf5-shared)
+ else()
+- list(APPEND ITKHDF5_LIBRARIES ${HDF5_C_STATIC_LIBRARY} ${HDF5_CXX_STATIC_LIBRARY})
++ list(APPEND ITKHDF5_LIBRARIES hdf5::hdf5_cpp-static hdf5::hdf5-static)
+ endif()
+
+ set(ITKHDF5_INCLUDE_DIRS
diff --git a/ports/itk/opencl.patch b/ports/itk/opencl.patch new file mode 100644 index 000000000..f935d09d4 --- /dev/null +++ b/ports/itk/opencl.patch @@ -0,0 +1,176 @@ +diff --git a/Modules/Core/GPUCommon/CMakeLists.txt b/Modules/Core/GPUCommon/CMakeLists.txt +index da2d66b63..6fb476680 100644 +--- a/Modules/Core/GPUCommon/CMakeLists.txt ++++ b/Modules/Core/GPUCommon/CMakeLists.txt +@@ -24,9 +24,13 @@ if(ITK_USE_GPU AND APPLE AND NOT ITK_COMPILER_HAS_BLOCKS) + endif() + + if(ITK_USE_GPU) ++ message(STATUS "OPENCL_LIBRARIES:${OPENCL_LIBRARIES}") ++ if(TARGET OpenCL::OpenCL) ++ message(STATUS "OPENCL_LIBRARIES:${OpenCL_LIBRARIES}") ++ endif() + set(ITKGPUCommon_LIBRARIES ITKGPUCommon) +- set(ITKGPUCommon_SYSTEM_INCLUDE_DIRS ${OPENCL_INCLUDE_DIRS}) +- set(ITKGPUCommon_SYSTEM_LIBRARY_DIRS ${OPENCL_LIBRARIES}) ++ set(ITKGPUCommon_SYSTEM_INCLUDE_DIRS ${OpenCL_INCLUDE_DIRS}) ++ set(ITKGPUCommon_SYSTEM_LIBRARY_DIRS ${OpenCL_LIBRARIES}) + endif() + + if(NOT ITK_SOURCE_DIR) +diff --git a/Modules/Core/GPUCommon/src/CMakeLists.txt b/Modules/Core/GPUCommon/src/CMakeLists.txt +index 0b39f2a9a..160f7a752 100644 +--- a/Modules/Core/GPUCommon/src/CMakeLists.txt ++++ b/Modules/Core/GPUCommon/src/CMakeLists.txt +@@ -14,5 +14,5 @@ if (ITK_USE_GPU) + write_gpu_kernels("${ITKGPUCommon_Kernels}" ITKGPUCommon_SRCS) + + itk_module_add_library(ITKGPUCommon ${ITKGPUCommon_SRCS}) +- target_link_libraries(ITKGPUCommon LINK_PUBLIC ${OPENCL_LIBRARIES}) ++ target_link_libraries(ITKGPUCommon LINK_PUBLIC ${OpenCL_LIBRARIES}) + endif() +diff --git a/Modules/Core/GPUFiniteDifference/CMakeLists.txt b/Modules/Core/GPUFiniteDifference/CMakeLists.txt +index c1bfde450..a642d9230 100644 +--- a/Modules/Core/GPUFiniteDifference/CMakeLists.txt ++++ b/Modules/Core/GPUFiniteDifference/CMakeLists.txt +@@ -9,8 +9,8 @@ if(NOT ITK_SOURCE_DIR) + endif() + + if (ITK_USE_GPU) +- set(ITKGPUFiniteDifference_SYSTEM_INCLUDE_DIRS ${OPENCL_INCLUDE_DIRS}) +- set(ITKGPUFiniteDifference_SYSTEM_LIBRARY_DIRS ${OPENCL_LIBRARIES}) ++ set(ITKGPUFiniteDifference_SYSTEM_INCLUDE_DIRS ${OpenCL_INCLUDE_DIRS}) ++ set(ITKGPUFiniteDifference_SYSTEM_LIBRARY_DIRS ${OpenCL_LIBRARIES}) + set(ITKGPUFiniteDifference_LIBRARIES ITKGPUFiniteDifference) + endif() + +diff --git a/Modules/Core/GPUFiniteDifference/src/CMakeLists.txt b/Modules/Core/GPUFiniteDifference/src/CMakeLists.txt +index 8425cc025..8335c69a0 100644 +--- a/Modules/Core/GPUFiniteDifference/src/CMakeLists.txt ++++ b/Modules/Core/GPUFiniteDifference/src/CMakeLists.txt +@@ -9,5 +9,5 @@ if (ITK_USE_GPU) + write_gpu_kernels("${ITKGPUFiniteDifference_Kernels}" ITKGPUFiniteDifference_SRCS) + + itk_module_add_library(ITKGPUFiniteDifference ${ITKGPUFiniteDifference_SRCS}) +- target_link_libraries(ITKGPUFiniteDifference LINK_PUBLIC ${OPENCL_LIBRARIES}) ++ target_link_libraries(ITKGPUFiniteDifference LINK_PUBLIC ${OpenCL_LIBRARIES}) + endif() +diff --git a/Modules/Filtering/GPUAnisotropicSmoothing/CMakeLists.txt b/Modules/Filtering/GPUAnisotropicSmoothing/CMakeLists.txt +index f36fd887d..310d983fa 100644 +--- a/Modules/Filtering/GPUAnisotropicSmoothing/CMakeLists.txt ++++ b/Modules/Filtering/GPUAnisotropicSmoothing/CMakeLists.txt +@@ -10,8 +10,8 @@ endif() + + if (ITK_USE_GPU) + set(ITKGPUAnisotropicSmoothing_LIBRARIES ITKGPUAnisotropicSmoothing) +- set(ITKGPUAnisotropicSmoothing_SYSTEM_INCLUDE_DIRS ${OPENCL_INCLUDE_DIRS}) +- set(ITKGPUAnisotropicSmoothing_SYSTEM_LIBRARY_DIRS ${OPENCL_LIBRARIES}) ++ set(ITKGPUAnisotropicSmoothing_SYSTEM_INCLUDE_DIRS ${OpenCL_INCLUDE_DIRS}) ++ set(ITKGPUAnisotropicSmoothing_SYSTEM_LIBRARY_DIRS ${OpenCL_LIBRARIES}) + endif() + + if(NOT ITK_SOURCE_DIR) +diff --git a/Modules/Filtering/GPUImageFilterBase/CMakeLists.txt b/Modules/Filtering/GPUImageFilterBase/CMakeLists.txt +index 078905521..67fd7b832 100644 +--- a/Modules/Filtering/GPUImageFilterBase/CMakeLists.txt ++++ b/Modules/Filtering/GPUImageFilterBase/CMakeLists.txt +@@ -10,8 +10,8 @@ endif() + + if (ITK_USE_GPU) + set(ITKGPUImageFilterBase_LIBRARIES ITKGPUImageFilterBase) +- set(ITKGPUImageFilterBase_SYSTEM_INCLUDE_DIRS ${OPENCL_INCLUDE_DIRS}) +- set(ITKGPUImageFilterBase_SYSTEM_LIBRARY_DIRS ${OPENCL_LIBRARIES}) ++ set(ITKGPUImageFilterBase_SYSTEM_INCLUDE_DIRS ${OpenCL_INCLUDE_DIRS}) ++ set(ITKGPUImageFilterBase_SYSTEM_LIBRARY_DIRS ${OpenCL_LIBRARIES}) + endif() + + if(NOT ITK_SOURCE_DIR) +diff --git a/Modules/Filtering/GPUImageFilterBase/src/CMakeLists.txt b/Modules/Filtering/GPUImageFilterBase/src/CMakeLists.txt +index 251493f5e..6d33fa964 100644 +--- a/Modules/Filtering/GPUImageFilterBase/src/CMakeLists.txt ++++ b/Modules/Filtering/GPUImageFilterBase/src/CMakeLists.txt +@@ -10,5 +10,5 @@ if (ITK_USE_GPU) + write_gpu_kernels("${ITKGPUImageFilterBase_Kernels}" ITKGPUImageFilterBase_SRCS) + + itk_module_add_library(ITKGPUImageFilterBase ${ITKGPUImageFilterBase_SRCS}) +- target_link_libraries(ITKGPUImageFilterBase LINK_PUBLIC ${OPENCL_LIBRARIES}) ++ target_link_libraries(ITKGPUImageFilterBase LINK_PUBLIC ${OpenCL_LIBRARIES}) + endif() +diff --git a/Modules/Filtering/GPUSmoothing/CMakeLists.txt b/Modules/Filtering/GPUSmoothing/CMakeLists.txt +index 9bac40921..2ed493d40 100644 +--- a/Modules/Filtering/GPUSmoothing/CMakeLists.txt ++++ b/Modules/Filtering/GPUSmoothing/CMakeLists.txt +@@ -10,8 +10,8 @@ endif() + + if (ITK_USE_GPU) + set(ITKGPUSmoothing_LIBRARIES ITKGPUSmoothing) +- set(ITKGPUSmoothing_SYSTEM_INCLUDE_DIRS ${OPENCL_INCLUDE_DIRS}) +- set(ITKGPUSmoothing_SYSTEM_LIBRARY_DIRS ${OPENCL_LIBRARIES}) ++ set(ITKGPUSmoothing_SYSTEM_INCLUDE_DIRS ${OpenCL_INCLUDE_DIRS}) ++ set(ITKGPUSmoothing_SYSTEM_LIBRARY_DIRS ${OpenCL_LIBRARIES}) + endif() + + if(NOT ITK_SOURCE_DIR) +diff --git a/Modules/Filtering/GPUSmoothing/src/CMakeLists.txt b/Modules/Filtering/GPUSmoothing/src/CMakeLists.txt +index d2120e842..2c6ca4a4a 100644 +--- a/Modules/Filtering/GPUSmoothing/src/CMakeLists.txt ++++ b/Modules/Filtering/GPUSmoothing/src/CMakeLists.txt +@@ -9,5 +9,5 @@ if (ITK_USE_GPU) + write_gpu_kernels("${ITKGPUSmoothing_Kernels}" ITKGPUSmoothing_SRCS) + + itk_module_add_library(ITKGPUSmoothing ${ITKGPUSmoothing_SRCS}) +- target_link_libraries(ITKGPUSmoothing LINK_PUBLIC ${OPENCL_LIBRARIES}) ++ target_link_libraries(ITKGPUSmoothing LINK_PUBLIC ${OpenCL_LIBRARIES}) + endif() +diff --git a/Modules/Filtering/GPUThresholding/CMakeLists.txt b/Modules/Filtering/GPUThresholding/CMakeLists.txt +index 4390785f5..61786b7a8 100644 +--- a/Modules/Filtering/GPUThresholding/CMakeLists.txt ++++ b/Modules/Filtering/GPUThresholding/CMakeLists.txt +@@ -2,8 +2,8 @@ project(ITKGPUThresholding) + + if (ITK_USE_GPU) + set(ITKGPUThresholding_LIBRARIES ITKGPUThresholding) +- set(ITKGPUThresholding_SYSTEM_INCLUDE_DIRS ${OPENCL_INCLUDE_DIRS}) +- set(ITKGPUThresholding_SYSTEM_LIBRARY_DIRS ${OPENCL_LIBRARIES}) ++ set(ITKGPUThresholding_SYSTEM_INCLUDE_DIRS ${OpenCL_INCLUDE_DIRS}) ++ set(ITKGPUThresholding_SYSTEM_LIBRARY_DIRS ${OpenCL_LIBRARIES}) + endif() + + itk_module_impl() +diff --git a/Modules/Filtering/GPUThresholding/src/CMakeLists.txt b/Modules/Filtering/GPUThresholding/src/CMakeLists.txt +index 326c86859..c07c80414 100644 +--- a/Modules/Filtering/GPUThresholding/src/CMakeLists.txt ++++ b/Modules/Filtering/GPUThresholding/src/CMakeLists.txt +@@ -9,5 +9,5 @@ if (ITK_USE_GPU) + write_gpu_kernels("${ITKGPUThresholding_Kernels}" ITKGPUThresholding_SRCS) + + itk_module_add_library(ITKGPUThresholding ${ITKGPUThresholding_SRCS}) +- target_link_libraries(ITKGPUThresholding LINK_PUBLIC ${OPENCL_LIBRARIES}) ++ target_link_libraries(ITKGPUThresholding LINK_PUBLIC ${OpenCL_LIBRARIES}) + endif() +diff --git a/Modules/Registration/GPUPDEDeformable/CMakeLists.txt b/Modules/Registration/GPUPDEDeformable/CMakeLists.txt +index c8d70a423..097c974c5 100644 +--- a/Modules/Registration/GPUPDEDeformable/CMakeLists.txt ++++ b/Modules/Registration/GPUPDEDeformable/CMakeLists.txt +@@ -2,8 +2,8 @@ project(ITKGPUPDEDeformableRegistration) + + if (ITK_USE_GPU) + set(ITKGPUPDEDeformableRegistration_LIBRARIES ITKGPUPDEDeformableRegistration) +- set(ITKGPUPDEDeformableRegistration_SYSTEM_INCLUDE_DIRS ${OPENCL_INCLUDE_DIRS}) +- set(ITKGPUPDEDeformableRegistration_SYSTEM_LIBRARY_DIRS ${OPENCL_LIBRARIES}) ++ set(ITKGPUPDEDeformableRegistration_SYSTEM_INCLUDE_DIRS ${OpenCL_INCLUDE_DIRS}) ++ set(ITKGPUPDEDeformableRegistration_SYSTEM_LIBRARY_DIRS ${OpenCL_LIBRARIES}) + endif() + + itk_module_impl() +diff --git a/Modules/Registration/GPUPDEDeformable/src/CMakeLists.txt b/Modules/Registration/GPUPDEDeformable/src/CMakeLists.txt +index 28b1d194c..1a049bdde 100644 +--- a/Modules/Registration/GPUPDEDeformable/src/CMakeLists.txt ++++ b/Modules/Registration/GPUPDEDeformable/src/CMakeLists.txt +@@ -10,5 +10,5 @@ if (ITK_USE_GPU) + write_gpu_kernels("${ITKGPUPDEDeformableRegistration_Kernels}" ITKGPUPDEDeformableRegistration_SRCS) + + itk_module_add_library(ITKGPUPDEDeformableRegistration ${ITKGPUPDEDeformableRegistration_SRCS}) +- target_link_libraries(ITKGPUPDEDeformableRegistration LINK_PUBLIC ${OPENCL_LIBRARIES}) ++ target_link_libraries(ITKGPUPDEDeformableRegistration LINK_PUBLIC ${OpenCL_LIBRARIES}) + endif() diff --git a/ports/itk/openjpeg.patch b/ports/itk/openjpeg.patch new file mode 100644 index 000000000..0fe1f34c9 --- /dev/null +++ b/ports/itk/openjpeg.patch @@ -0,0 +1,548 @@ +diff --git a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+index 1b1fe9526..0da4aa0c4 100644
+--- a/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
++++ b/Modules/IO/JPEG2000/src/itkJPEG2000ImageIO.cxx
+@@ -26,9 +26,9 @@
+
+ extern "C"
+ {
+-#include "openjpeg.h"
+-#include "j2k.h"
+-#include "jp2.h"
++#include <openjpeg.h>
++//#include "j2k.h"
++//##include "jp2.h"
+ }
+
+
+@@ -62,8 +62,7 @@ public:
+ OPJ_UINT32 m_TileStartX;
+ OPJ_UINT32 m_TileStartY;
+
+- OPJ_UINT32 m_NumberOfTilesInX;
+- OPJ_UINT32 m_NumberOfTilesInY;
++ OPJ_UINT32 m_NumberOfTiles;
+
+ opj_dparameters_t m_DecompressionParameters; /* decompression parameters */
+ };
+@@ -86,8 +85,7 @@ JPEG2000ImageIO::JPEG2000ImageIO()
+ this->m_Internal->m_TileStartX = 0;
+ this->m_Internal->m_TileStartY = 0;
+
+- this->m_Internal->m_NumberOfTilesInX = 0;
+- this->m_Internal->m_NumberOfTilesInY = 0;
++ this->m_Internal->m_NumberOfTiles = 0;
+
+ const char * extensions[] = { ".j2k", ".jp2", ".jpt" };
+
+@@ -139,22 +137,16 @@ JPEG2000ImageIO::ReadImageInformation()
+ {
+ itkDebugMacro(<< "ReadImageInformation()");
+
+- FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+- /* decompression parameters */
++ /* set decoding parameters to default values */
++ opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+
+- if (!l_file)
++ opj_stream_t * cio = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
++ if (!cio)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+ << "Reason: "
+ << itksys::SystemTools::GetLastSystemError());
+ }
+-
+- /* set decoding parameters to default values */
+- opj_set_default_decoder_parameters(&(this->m_Internal->m_DecompressionParameters));
+-
+- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, true);
+-
+ this->m_Internal->m_Dinfo = nullptr; /* handle to a decompressor */
+
+ opj_image_t * l_image = nullptr;
+@@ -187,14 +179,14 @@ JPEG2000ImageIO::ReadImageInformation()
+ /* JPEG-2000 codestream */
+
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ // fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr");
++ << "Reason: opj_create_decompress(OPJ_CODEC_J2K) returns nullptr");
+ }
+ break;
+ }
+@@ -202,14 +194,14 @@ JPEG2000ImageIO::ReadImageInformation()
+ {
+ /* JPEG 2000 compressed image data */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ // fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr");
++ << "Reason: opj_create_decompress(OPJ_CODEC_JP2) returns nullptr");
+ }
+ break;
+ }
+@@ -217,20 +209,19 @@ JPEG2000ImageIO::ReadImageInformation()
+ {
+ /* JPEG 2000, JPIP */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+ if (!this->m_Internal->m_Dinfo)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
++ // fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr");
++ << "Reason: opj_create_decompress(OPJ_CODEC_JPT) returns nullptr");
+ }
+ break;
+ }
+ default:
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -247,27 +238,11 @@ JPEG2000ImageIO::ReadImageInformation()
+ << "Reason: opj_setup_decoder returns false");
+ }
+
+- // Image parameters - first tile
+- OPJ_INT32 l_tile_x0;
+- OPJ_INT32 l_tile_y0;
+
+- // Image parameters - tile width, height and number of tiles
+- OPJ_UINT32 l_tile_width;
+- OPJ_UINT32 l_tile_height;
+- OPJ_UINT32 l_nb_tiles_x;
+- OPJ_UINT32 l_nb_tiles_y;
+
+ itkDebugMacro(<< "Trying to read header now...");
+
+- bResult = opj_read_header(this->m_Internal->m_Dinfo,
+- &l_image,
+- &l_tile_x0,
+- &l_tile_y0,
+- &l_tile_width,
+- &l_tile_height,
+- &l_nb_tiles_x,
+- &l_nb_tiles_y,
+- cio);
++ bResult = opj_read_header(cio, this->m_Internal->m_Dinfo, &l_image);
+
+ if (!bResult)
+ {
+@@ -283,14 +258,22 @@ JPEG2000ImageIO::ReadImageInformation()
+ << "Reason: Error whle reading image header");
+ }
+
++ // Image parameters - first tile
++ OPJ_INT32 l_tile_x0=l_image->x0;
++ OPJ_INT32 l_tile_y0=l_image->y0;
++
++ // Image parameters - tile width, height and number of tiles
++ OPJ_UINT32 l_tile_width=l_image->x1;
++ OPJ_UINT32 l_tile_height=l_image->y1;
++ OPJ_UINT32 l_nb_tiles=l_image->numcomps;
++
+ this->m_Internal->m_TileStartX = l_tile_x0;
+ this->m_Internal->m_TileStartY = l_tile_y0;
+
+ this->m_Internal->m_TileWidth = l_tile_width;
+ this->m_Internal->m_TileHeight = l_tile_height;
+
+- this->m_Internal->m_NumberOfTilesInX = l_nb_tiles_x;
+- this->m_Internal->m_NumberOfTilesInY = l_nb_tiles_y;
++ this->m_Internal->m_NumberOfTiles = l_nb_tiles;
+
+
+ itkDebugMacro(<< "Number of Components = " << l_image->numcomps);
+@@ -319,7 +302,7 @@ JPEG2000ImageIO::ReadImageInformation()
+ this->SetPixelType(IOPixelEnum::SCALAR);
+ break;
+ case 3:
+- if (l_image->color_space != CLRSPC_SRGB)
++ if (l_image->color_space != OPJ_CLRSPC_SRGB)
+ {
+ itkWarningMacro(<< "file does not specify color space, assuming sRGB");
+ }
+@@ -335,8 +318,7 @@ JPEG2000ImageIO::ReadImageInformation()
+ itkDebugMacro(<< "Tile Start Y = " << this->m_Internal->m_TileStartY);
+ itkDebugMacro(<< "Tile Width = " << this->m_Internal->m_TileWidth);
+ itkDebugMacro(<< "Tile Height = " << this->m_Internal->m_TileHeight);
+- itkDebugMacro(<< "Number of Tiles X = " << this->m_Internal->m_NumberOfTilesInX);
+- itkDebugMacro(<< "Number of Tiles Y = " << this->m_Internal->m_NumberOfTilesInY);
++ itkDebugMacro(<< "Number of Tiles = " << this->m_Internal->m_NumberOfTiles);
+
+ itkDebugMacro(<< "image->x1 = " << l_image->x1);
+ itkDebugMacro(<< "image->y1 = " << l_image->y1);
+@@ -349,7 +331,6 @@ JPEG2000ImageIO::ReadImageInformation()
+
+ /* close the byte stream */
+ opj_stream_destroy(cio);
+- fclose(l_file);
+
+ if (this->m_Internal->m_Dinfo)
+ {
+@@ -368,16 +349,7 @@ JPEG2000ImageIO::Read(void * buffer)
+ {
+ itkDebugMacro(<< "JPEG2000ImageIO::Read() Begin");
+
+- FILE * l_file = fopen(this->m_FileName.c_str(), "rb");
+-
+- if (!l_file)
+- {
+- itkExceptionMacro("JPEG2000ImageIO failed to open file for reading: " << this->GetFileName() << std::endl
+- << "Reason: "
+- << itksys::SystemTools::GetLastSystemError());
+- }
+-
+- opj_stream_t * l_stream = opj_stream_create_default_file_stream(l_file, true);
++ opj_stream_t * l_stream = opj_stream_create_default_file_stream(this->m_FileName.c_str(), true);
+ if (!l_stream)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+@@ -397,12 +369,13 @@ JPEG2000ImageIO::Read(void * buffer)
+ {
+ /* JPEG-2000 codestream */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_J2K);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_J2K);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_decompress(CODEC_J2K) returns nullptr");
++ << "Reason: opj_create_decompress(OPJ_CODEC_J2K) returns nullptr");
+ }
+ break;
+ }
+@@ -410,12 +383,13 @@ JPEG2000ImageIO::Read(void * buffer)
+ {
+ /* JPEG 2000 compressed image data */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JP2);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JP2);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_decompress(CODEC_JP2) returns nullptr");
++ << "Reason: opj_create_decompress(OPJ_CODEC_JP2) returns nullptr");
+ }
+ break;
+ }
+@@ -423,17 +397,18 @@ JPEG2000ImageIO::Read(void * buffer)
+ {
+ /* JPEG 2000, JPIP */
+ /* get a decoder handle */
+- this->m_Internal->m_Dinfo = opj_create_decompress(CODEC_JPT);
++ this->m_Internal->m_Dinfo = opj_create_decompress(OPJ_CODEC_JPT);
+ if (!this->m_Internal->m_Dinfo)
+ {
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_decompress(CODEC_JPT) returns nullptr");
++ << "Reason: opj_create_decompress(OPJ_CODEC_JPT) returns nullptr");
+ }
+ break;
+ }
+ default:
+- fclose(l_file);
++ opj_stream_destroy(l_stream);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: "
+ << this->GetFileName() << std::endl
+ << "Reason: "
+@@ -448,29 +423,13 @@ JPEG2000ImageIO::Read(void * buffer)
+ << "Reason: opj_setup_decoder returns false");
+ }
+
+- OPJ_INT32 l_tile_x0, l_tile_y0;
+-
+- OPJ_UINT32 l_tile_width;
+- OPJ_UINT32 l_tile_height;
+- OPJ_UINT32 l_nb_tiles_x;
+- OPJ_UINT32 l_nb_tiles_y;
+-
+- bool bResult = opj_read_header(this->m_Internal->m_Dinfo,
+- &l_image,
+- &l_tile_x0,
+- &l_tile_y0,
+- &l_tile_width,
+- &l_tile_height,
+- &l_nb_tiles_x,
+- &l_nb_tiles_y,
+- l_stream);
++ bool bResult = opj_read_header(l_stream, this->m_Internal->m_Dinfo,&l_image);
+
+ if (!bResult)
+ {
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: opj_read_header returns false");
+ }
+@@ -499,7 +458,7 @@ JPEG2000ImageIO::Read(void * buffer)
+ itkDebugMacro(<< "p_end_x = " << p_end_x);
+ itkDebugMacro(<< "p_end_y = " << p_end_y);
+
+- bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, p_start_x, p_start_y, p_end_x, p_end_y);
++ bResult = opj_set_decode_area(this->m_Internal->m_Dinfo, l_image, p_start_x, p_start_y, p_end_x, p_end_y);
+
+ itkDebugMacro(<< "opj_set_decode_area() after");
+
+@@ -508,7 +467,6 @@ JPEG2000ImageIO::Read(void * buffer)
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: opj_set_decode_area returns false");
+ }
+@@ -525,13 +483,13 @@ JPEG2000ImageIO::Read(void * buffer)
+
+ OPJ_UINT32 l_max_data_size = 1000;
+
+- bool l_go_on = true;
++ int l_go_on = true; // should be OBJ_BOOL
+
+ auto * l_data = (OPJ_BYTE *)malloc(1000);
+
+ while (l_go_on)
+ {
+- bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo,
++ bool tileHeaderRead = opj_read_tile_header(this->m_Internal->m_Dinfo, l_stream,
+ &l_tile_index,
+ &l_data_size,
+ &l_current_tile_x0,
+@@ -539,14 +497,12 @@ JPEG2000ImageIO::Read(void * buffer)
+ &l_current_tile_x1,
+ &l_current_tile_y1,
+ &l_nb_comps,
+- &l_go_on,
+- l_stream);
++ &l_go_on);
+
+ if (!tileHeaderRead)
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -571,7 +527,6 @@ JPEG2000ImageIO::Read(void * buffer)
+ if (!l_data)
+ {
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -590,7 +545,6 @@ JPEG2000ImageIO::Read(void * buffer)
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -654,7 +608,6 @@ JPEG2000ImageIO::Read(void * buffer)
+ {
+ free(l_data);
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ opj_image_destroy(l_image);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+@@ -666,14 +619,12 @@ JPEG2000ImageIO::Read(void * buffer)
+ opj_destroy_codec(this->m_Internal->m_Dinfo);
+ this->m_Internal->m_Dinfo = nullptr;
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to read file: " << this->GetFileName() << std::endl
+ << "Reason: error whle reading image");
+ }
+
+ /* close the byte stream */
+ opj_stream_destroy(l_stream);
+- fclose(l_file);
+
+ if (this->m_Internal->m_Dinfo)
+ {
+@@ -840,13 +791,13 @@ JPEG2000ImageIO ::Write(const void * buffer)
+
+ parameters.numresolution = numberOfResolutions;
+
+- OPJ_COLOR_SPACE color_space = CLRSPC_GRAY;
++ OPJ_COLOR_SPACE color_space = OPJ_CLRSPC_GRAY;
+ opj_image_cmptparm_t cmptparms[3];
+
+ if (this->GetNumberOfComponents() == 3)
+ {
+
+- color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? CLRSPC_SRGB : CLRSPC_UNSPECIFIED;
++ color_space = (this->GetPixelType() == IOPixelEnum::RGB) ? OPJ_CLRSPC_SRGB : OPJ_CLRSPC_UNSPECIFIED;
+
+ /* initialize image components */
+ memset(&cmptparms[0], 0, 3 * sizeof(opj_image_cmptparm_t));
+@@ -864,7 +815,7 @@ JPEG2000ImageIO ::Write(const void * buffer)
+
+ if (this->GetNumberOfComponents() == 1)
+ {
+- color_space = CLRSPC_GRAY;
++ color_space = OPJ_CLRSPC_GRAY;
+
+ /* initialize image components */
+ memset(&cmptparms[0], 0, sizeof(opj_image_cmptparm_t));
+@@ -940,32 +891,32 @@ JPEG2000ImageIO ::Write(const void * buffer)
+ opj_codec_t * cinfo = nullptr;
+ if (extension == ".j2k")
+ {
+- cinfo = opj_create_compress(CODEC_J2K);
++ cinfo = opj_create_compress(OPJ_CODEC_J2K);
+ if (!cinfo)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_compress(CODEC_J2K) returns nullptr");
++ << "Reason: opj_create_compress(OPJ_CODEC_J2K) returns nullptr");
+ }
+ }
+ else if (extension == ".jp2")
+ {
+- cinfo = opj_create_compress(CODEC_JP2);
++ cinfo = opj_create_compress(OPJ_CODEC_JP2);
+ if (!cinfo)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_compress(CODEC_JP2) returns nullptr");
++ << "Reason: opj_create_compress(OPJ_CODEC_JP2) returns nullptr");
+ }
+ }
+ else if (extension == ".jpt")
+ {
+- cinfo = opj_create_compress(CODEC_JPT);
++ cinfo = opj_create_compress(OPJ_CODEC_JPT);
+ if (!cinfo)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+ << this->GetFileName() << std::endl
+- << "Reason: opj_create_compress(CODEC_JPT) returns nullptr");
++ << "Reason: opj_create_compress(OPJ_CODEC_JPT) returns nullptr");
+ }
+ }
+ else
+@@ -989,17 +940,9 @@ JPEG2000ImageIO ::Write(const void * buffer)
+ << "Reason: opj_setup_encoder returns false");
+ }
+
+- FILE * l_file = fopen(parameters.outfile, "wb");
+- if (!l_file)
+- {
+- itkExceptionMacro("JPEG2000ImageIO failed to open file for writing: " << this->GetFileName() << std::endl
+- << "Reason: "
+- << itksys::SystemTools::GetLastSystemError());
+- }
+-
+ /* open a byte stream for writing */
+ /* allocate memory for all tiles */
+- opj_stream_t * cio = opj_stream_create_default_file_stream(l_file, false);
++ opj_stream_t * cio = opj_stream_create_default_file_stream(parameters.outfile, false);
+ if (!cio)
+ {
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: "
+@@ -1017,8 +960,7 @@ JPEG2000ImageIO ::Write(const void * buffer)
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+- itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
++ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_start_compress returns false");
+ }
+
+@@ -1026,7 +968,6 @@ JPEG2000ImageIO ::Write(const void * buffer)
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_encode returns false");
+ }
+@@ -1035,14 +976,12 @@ JPEG2000ImageIO ::Write(const void * buffer)
+ if (!bSuccess)
+ {
+ opj_stream_destroy(cio);
+- fclose(l_file);
+ itkExceptionMacro("JPEG2000ImageIO failed to write file: " << this->GetFileName() << std::endl
+ << "Reason: opj_end_compress returns false");
+ }
+
+ /* close and free the byte stream */
+ opj_stream_destroy(cio);
+- fclose(l_file);
+
+ /* free remaining compression structures */
+ opj_destroy_codec(cinfo);
+diff --git a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+index 103eaa9dd..eb8989135 100644
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -1,12 +1,25 @@
+ project(ITKOpenJPEG)
+ set(ITKOpenJPEG_THIRD_PARTY 1)
+
+-set(ITKOpenJPEG_INCLUDE_DIRS
+- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+- )
+-set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
+-set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
++if(ITK_USE_SYSTEM_OpenJPEG)
++ find_package(OpenJPEG REQUIRED)
++ if(TARGET openjp2)
++ set(ITKOpenJPEG_LIBRARIES ${OPENJPEG_LIBRARIES})
++ else()
++ message(FATAL_ERROR "OpenJPEG target openjp2 missing!")
++ endif()
++ set(ITKOpenJPEG_INCLUDE_DIRS
++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++ )
++else()
++ set(ITKOpenJPEG_INCLUDE_DIRS
++ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++ ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++ )
++ set(ITKOpenJPEG_LIBRARIES itkopenjpeg)
++ set(ITK_LIBRARY_PROPERTIES WINDOWS_EXPORT_ALL_SYMBOLS FALSE)
++endif()
+
+ itk_module_impl()
+
diff --git a/ports/itk/openjpeg2.patch b/ports/itk/openjpeg2.patch new file mode 100644 index 000000000..86631f5f9 --- /dev/null +++ b/ports/itk/openjpeg2.patch @@ -0,0 +1,58 @@ +diff --git a/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/CMakeLists.txt +index 565cc338b..c061f0721 100644 +--- a/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/CMakeLists.txt ++++ b/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/CMakeLists.txt +@@ -194,7 +194,7 @@ mark_as_advanced(LIBRARY_OUTPUT_PATH EXECUTABLE_OUTPUT_PATH) + # configure name mangling to allow multiple libraries to coexist + # peacefully + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in) +-set(MANGLE_PREFIX ${OPENJPEG_LIBRARY_NAME}) ++set(MANGLE_PREFIX) + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in + ${CMAKE_CURRENT_BINARY_DIR}/openjpeg_mangle.h + @ONLY) +diff --git a/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt +index c4adb91a2..89b731d88 100644 +--- a/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt ++++ b/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt +@@ -3,7 +3,7 @@ include_regular_expression("^.*$") + # configure name mangling to allow multiple libraries to coexist + # peacefully + if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in) +-set(MANGLE_PREFIX ${OPENJPEG_LIBRARY_NAME}) ++set(MANGLE_PREFIX) + configure_file(${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in + ${CMAKE_CURRENT_BINARY_DIR}/openjpeg_mangle.h + @ONLY) +diff --git a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt +index 3811e52f4..a41e9264e 100644 +--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt ++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt +@@ -8,10 +8,10 @@ if(ITK_USE_SYSTEM_OpenJPEG) + else()
+ message(FATAL_ERROR "OpenJPEG target openjp2 missing!")
+ endif()
+- set(ITKOpenJPEG_INCLUDE_DIRS
+- ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+- ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
+- )
++ # set(ITKOpenJPEG_INCLUDE_DIRS
++ # ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
++ # ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg
++ # )
+ else()
+ set(ITKOpenJPEG_INCLUDE_DIRS
+ ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg
+diff --git a/Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeLists.txt b/Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeLists.txt +index e62e43eda..35dc89976 100644 +--- a/Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeLists.txt ++++ b/Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeLists.txt +@@ -68,7 +68,7 @@ CONFIGURE_FILE(${ITK3P_OpenJPEG_SOURCE_DIR}/opj_configure.h.in + # configure name mangling to allow multiple libraries to coexist + # peacefully + if(EXISTS ${ITK3P_OpenJPEG_SOURCE_DIR}/openjpeg_mangle.h.in) +-set(MANGLE_PREFIX itk) ++#set(MANGLE_PREFIX itk) + configure_file(${ITK3P_OpenJPEG_SOURCE_DIR}/openjpeg_mangle.h.in + ${ITK3P_OpenJPEG_BINARY_DIR}/openjpeg_mangle.h + @ONLY) diff --git a/ports/itk/portfile.cmake b/ports/itk/portfile.cmake index a666b5713..b16ba194a 100644 --- a/ports/itk/portfile.cmake +++ b/ports/itk/portfile.cmake @@ -1,22 +1,129 @@ -include(vcpkg_common_functions) - vcpkg_buildpath_length_warning(37) vcpkg_from_github( OUT_SOURCE_PATH SOURCE_PATH REPO InsightSoftwareConsortium/ITK - REF v5.0.1 - SHA512 242ce66cf83f82d26f20d2099108295e28c8875e7679126ba023834bf0e94454460ba86452a94c8ddaea93d2314befc399f2b151d7294370d4b47f0e9798e77f + REF d3286c9cc04ba16cc8f73de9a98fbcd7c02f3c7b + SHA512 c358449870d580aeb10e32f8be0ca39e8a76d8dc06fda973788fafb5971333e546611c399190be49d40f5f3c18a1105d9699eef271a560aff25ce168a396926e HEAD_REF master PATCHES - fix_openjpeg_search.patch - fix_libminc_config_path.patch + hdf5.patch + double-conversion.patch + openjpeg.patch + openjpeg2.patch + var_libraries.patch + wrapping.patch + python_gpu_wrapping.patch + opencl.patch + cufftw.patch +) + +vcpkg_check_features(OUT_FEATURE_OPTIONS FEATURE_OPTIONS + "vtk" Module_ITKVtkGlue + "cuda" Module_ITKCudaCommon # Requires RTK? + #"cuda" CUDA_HAVE_GPU # Automatically set by FindCUDA? + "cufftw" ITK_USE_CUFFTW + "opencl" ITK_USE_GPU + "tbb" Module_ITKTBB + "rtk" Module_RTK + "tools" RTK_BUILD_APPLICATIONS + # There are a lot of more (remote) modules and options in ITK + # feel free to add those as a feature ) -if ("vtk" IN_LIST FEATURES) - set(ITKVtkGlue ON) -else() - set(ITKVtkGlue OFF) +if("cufftw" IN_LIST FEATURES) + # Alternativly set CUFFT_LIB and CUFFTW_LIB + if(WIN32) + file(TO_CMAKE_PATH "$ENV{CUDA_PATH}" CUDA_PATH) + set(CUDA_LIB_PATH "${CUDA_PATH}") + + if(VCPKG_TARGET_ARCHITECTURE STREQUAL x64) + string(APPEND CUDA_LIB_PATH "/lib/x64") + elseif(VCPKG_TARGET_ARCHITECTURE STREQUAL x86) + string(APPEND CUDA_LIB_PATH "/lib/Win32") + message(FATAL_ERROR "CUFFTW is not supported on architecture ${VCPKG_TARGET_ARCHITECTURE}") + else() + message(FATAL_ERROR "Architecture ${VCPKG_TARGET_ARCHITECTURE} not supported !") + endif() + + list(APPEND ADDITIONAL_OPTIONS + "-DFFTW_LIB_SEARCHPATH=${CUDA_LIB_PATH}" + "-DFFTW_INCLUDE_PATH=${CUDA_PATH}/include" + "-DCUFFTW_INCLUDE_PATH=${CUDA_PATH}/include" + ) + endif() +endif() + +if("rtk" IN_LIST FEATURES) + if(VCPKG_TARGET_ARCHITECTURE STREQUAL x86) + message(FATAL_ERROR "RTK is not supported on architecture ${VCPKG_TARGET_ARCHITECTURE}") + endif() + SET(BUILD_RTK ON) + list(APPEND ADDITIONAL_OPTIONS + "-DModule_RTK_GIT_TAG=8099212f715231d093f7d6a1114daecf45d871ed" # RTK latest versions (11.05.2020) + ) + if("cuda" IN_LIST FEATURES) + list(APPEND ADDITIONAL_OPTIONS "-DRTK_USE_CUDA=ON") + #RTK + CUDA + PYTHON + dynamic library linkage will fail and needs upstream fixes. + endif() +endif() +file(REMOVE_RECURSE "${SOURCE_PATH}/Modules/Remote/RTK") + +if("opencl" IN_LIST FEATURES) + list(APPEND ADDITIONAL_OPTIONS # Wrapping options required by OpenCL if build with Python Wrappers + -DITK_WRAP_unsigned_long_long=ON + -DITK_WRAP_signed_long_long=ON + ) +endif() +if("tools" IN_LIST FEATURES) + + if("rtk" IN_LIST FEATURES) + list(APPEND TOOL_NAMES rtkadmmtotalvariation rtkadmmwavelets rtkamsterdamshroud rtkbackprojections rtkbioscangeometry rtkcheckimagequality rtkconjugategradient + rtkdigisensgeometry rtkdrawgeometricphantom rtkdrawshepploganphantom rtkdualenergysimplexdecomposition rtkelektasynergygeometry rtkextractphasesignal + rtkextractshroudsignal rtkfdk rtkfdktwodweights rtkfieldofview rtkforwardprojections rtkfourdconjugategradient rtkfourdfdk rtkfourdrooster rtkfourdsart + rtkgaincorrection rtki0estimation rtkimagxgeometry rtkiterativefdk rtklagcorrection rtklastdimensionl0gradientdenoising rtklut rtkmaskcollimation rtkmcrooster + rtkmotioncompensatedfourdconjugategradient rtkorageometry rtkosem rtkoverlayphaseandshroud rtkparkershortscanweighting rtkprojectgeometricphantom + rtkprojectionmatrix rtkprojections rtkprojectshepploganphantom rtkramp rtkrayboxintersection rtkrayquadricintersection rtkregularizedconjugategradient + rtksart rtkscatterglarecorrection rtksimulatedgeometry rtkspectraldenoiseprojections rtkspectralforwardmodel rtkspectralonestep rtkspectralrooster rtkspectralsimplexdecomposition + rtksubselect rtktotalnuclearvariationdenoising rtktotalvariationdenoising rtktutorialapplication rtkvarianobigeometry rtkvarianprobeamgeometry rtkvectorconjugategradient + rtkwangdisplaceddetectorweighting rtkwarpedbackprojectsequence rtkwarpedforwardprojectsequence rtkwaveletsdenoising rtkxradgeometry) + endif() +endif() +if("vtk" IN_LIST FEATURES) + vcpkg_find_acquire_program(PYTHON3) + list(APPEND ADDITIONAL_OPTIONS + "-DPython3_EXECUTABLE:PATH=${PYTHON3}" # Required by mvtk if vtk[python] was build + ) +endif() +if("python" IN_LIST FEATURES) + message(STATUS "${PORT} builds a long time (>1h) with python wrappers enabled!") + vcpkg_find_acquire_program(PYTHON3) + vcpkg_find_acquire_program(SWIG) # Swig is only required for wrapping! + get_filename_component(SWIG_DIR "${SWIG}" DIRECTORY) + list(APPEND ADDITIONAL_OPTIONS + -DITK_WRAP_PYTHON=ON + -DPython3_FIND_REGISTRY=NEVER + "-DPython3_EXECUTABLE:PATH=${PYTHON3}" # Required by more than one feature + "-DSWIG_EXECUTABLE=${SWIG}" + "-DSWIG_DIR=${SWIG_DIR}" + ) + # Due to ITKs internal shenanigans with the variables ...... + if(VCPKG_TARGET_IS_WINDOWS) + list(APPEND ADDITIONAL_OPTIONS "-DPython3_LIBRARY_RELEASE:PATH=${CURRENT_INSTALLED_DIR}/lib/python38.lib" + "-DPython3_LIBRARY_DEBUG:PATH=${CURRENT_INSTALLED_DIR}/debug/lib/python38_d.lib" + "-DPython3_INCLUDE_DIR:PATH=${CURRENT_INSTALLED_DIR}/include/python3.8") + list(APPEND OPTIONS_DEBUG "-DPython3_LIBRARY=${CURRENT_INSTALLED_DIR}/debug/lib/python38_d.lib") + list(APPEND OPTIONS_RELEASE "-DPython3_LIBRARY=${CURRENT_INSTALLED_DIR}/lib/python38.lib") + elseif(VCPKG_TARGET_IS_LINUX) + list(APPEND ADDITIONAL_OPTIONS "-DPython3_LIBRARY_RELEASE:PATH=${CURRENT_INSTALLED_DIR}/lib/libpython38m.a" + "-DPython3_LIBRARY_DEBUG:PATH=${CURRENT_INSTALLED_DIR}/debug/lib/libpython38md.a" + "-DPython3_INCLUDE_DIR:PATH=${CURRENT_INSTALLED_DIR}/include/python3.8m") + list(APPEND OPTIONS_DEBUG "-DPython3_LIBRARY=${CURRENT_INSTALLED_DIR}/debug/lib/libpython38md.a") + list(APPEND OPTIONS_RELEASE "-DPython3_LIBRARY=${CURRENT_INSTALLED_DIR}/lib/libpython38m.a") + elseif(VCPKG_TARGET_IS_OSX) + #Need Python3 information on OSX within VCPKG + endif() + #ITK_PYTHON_SITE_PACKAGES_SUFFIX should be set to the install dir of the site-packages within vcpkg endif() set(USE_64BITS_IDS OFF) @@ -24,6 +131,7 @@ if (VCPKG_TARGET_ARCHITECTURE STREQUAL x64 OR VCPKG_TARGET_ARCHITECTURE STREQUAL set(USE_64BITS_IDS ON) endif() +file(REMOVE_RECURSE "${SOURCE_PATH}/CMake/FindOpenCL.cmake") vcpkg_configure_cmake( SOURCE_PATH ${SOURCE_PATH} PREFER_NINJA @@ -31,7 +139,10 @@ vcpkg_configure_cmake( OPTIONS -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF + -DBUILD_PKGCONFIG_FILES=OFF + -DITK_DOXYGEN_HTML=OFF -DDO_NOT_INSTALL_ITK_TEST_DRIVER=ON + -DITK_SKIP_PATH_LENGTH_CHECKS=ON -DITK_INSTALL_DATA_DIR=share/itk/data -DITK_INSTALL_DOC_DIR=share/itk/doc -DITK_INSTALL_PACKAGE_DIR=share/itk @@ -45,31 +156,58 @@ vcpkg_configure_cmake( -DITK_USE_SYSTEM_TIFF=ON -DITK_USE_SYSTEM_ZLIB=ON -DITK_USE_SYSTEM_EIGEN=ON - # This should be turned on some day, however for now ITK does download specific versions so it shouldn't spontaneously break - -DITK_FORBID_DOWNLOADS=OFF - - -DITK_SKIP_PATH_LENGTH_CHECKS=ON - - # I haven't tried Python wrapping in vcpkg - #-DITK_WRAP_PYTHON=ON - #-DITK_PYTHON_VERSION=3 + -DITK_USE_SYSTEM_FFTW=ON + -DITK_USE_SYSTEM_HDF5=ON # HDF5 was problematic in the past and still is. ITK still has not figured out how to do it correctly! + -DITK_USE_SYSTEM_GDCM=ON + -DITK_USE_SYSTEM_OpenJPEG=ON # Added by VCPKG + -DITK_USE_SYSTEM_DCMTK=ON + -DDCMTK_USE_ICU=ON + -DITK_USE_SYSTEM_ICU=ON + #-DITK_USE_SYSTEM_VXL=ON + #-DITK_USE_SYSTEM_CASTXML=ON # needs to be added to vcpkg_find_acquire_program https://data.kitware.com/api/v1/file/hashsum/sha512/b8b6f0aff11fe89ab2fcd1949cc75f2c2378a7bc408827a004396deb5ff5a9976bffe8a597f8db1b74c886ea39eb905e610dce8f5bd7586a4d6c196d7349da8d/download + -DITK_USE_SYSTEM_MINC=ON + -DITK_USE_SYSTEM_SWIG=ON + -DITK_FORBID_DOWNLOADS=OFF # This should be turned on some day, however for now ITK does download specific versions so it shouldn't spontaneously break. Remote Modules would probably break with this! + -DINSTALL_GTEST=OFF + -DITK_USE_SYSTEM_GOOGLETEST=ON + -DEXECUTABLE_OUTPUT_PATH=tools/${PORT} + + # TODO + #-DVXL_USE_GEOTIFF=ON + -DVXL_USE_LFS=ON + + -DITK_MINIMUM_COMPLIANCE_LEVEL:STRING=1 # To Display all remote modules within cmake-gui + #-DModule_IOSTL=ON # example how to turn on a non-default module + #-DModule_MorphologicalContourInterpolation=ON # example how to turn on a remote module + #-DModule_RLEImage=ON # example how to turn on a remote module + + # Some additional wraping options + #-DITK_WRAP_double=ON + #-DITK_WRAP_complex_double=ON + #-DITK_WRAP_covariant_vector_double=ON + #-DITK_WRAP_vector_double=ON - -DITK_USE_SYSTEM_HDF5=ON # HDF5 was problematic in the past - -DModule_ITKVtkGlue=${ITKVtkGlue} # optional feature - - -DModule_IOSTL=ON # example how to turn on a non-default module - -DModule_MorphologicalContourInterpolation=ON # example how to turn on a remote module - -DModule_RLEImage=ON # example how to turn on a remote module - -DGDCM_USE_SYSTEM_OPENJPEG=ON #Use port openjpeg instead of own third-party + ${FEATURE_OPTIONS} ${ADDITIONAL_OPTIONS} + + OPTIONS_DEBUG ${OPTIONS_DEBUG} + OPTIONS_RELEASE ${OPTIONS_RELEASE} ) - +if(BUILD_RTK) # Remote Modules are only downloaded on configure. + # TODO: In the future try to download via vcpkg_from_github and move the files. That way patching does not need this workaround + vcpkg_apply_patches(SOURCE_PATH "${SOURCE_PATH}/Modules/Remote/RTK" QUIET PATCHES rtk/already_defined.patch rtk/unresolved.patch) +endif() vcpkg_install_cmake() vcpkg_copy_pdbs() vcpkg_fixup_cmake_targets() +if(TOOL_NAMES) + vcpkg_copy_tools(TOOL_NAMES ${TOOL_NAMES} AUTO_CLEAN) +endif() -file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/share) -file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/include) +file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/lib/cmake") +file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/lib/cmake") +file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/share") +file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/include") file(INSTALL ${SOURCE_PATH}/LICENSE DESTINATION ${CURRENT_PACKAGES_DIR}/share/${PORT} RENAME copyright) diff --git a/ports/itk/python_gpu_wrapping.patch b/ports/itk/python_gpu_wrapping.patch new file mode 100644 index 000000000..37367d979 --- /dev/null +++ b/ports/itk/python_gpu_wrapping.patch @@ -0,0 +1,178 @@ +diff --git a/CMake/itkOpenCL.cmake b/CMake/itkOpenCL.cmake +index 0ccbe144d..fa381524f 100644 +--- a/CMake/itkOpenCL.cmake ++++ b/CMake/itkOpenCL.cmake +@@ -48,7 +48,7 @@ if(ITK_USE_GPU) + ) + set_source_files_properties(${CMAKE_CURRENT_BINARY_DIR}/${OUTPUT_FILE} + PROPERTIES GENERATED ON) +- set(${SRC_VAR} ${${SRC_VAR}} ${OUTPUT_FILE}) ++ set(${SRC_VAR} ${${SRC_VAR}} ${CMAKE_CURRENT_BINARY_DIR}/${OUTPUT_FILE}) + endmacro() + + macro(write_gpu_kernels GPUKernels GPU_SRC) +diff --git a/Modules/Core/Common/include/itkMacro.h b/Modules/Core/Common/include/itkMacro.h +index 1816f722a..3a6a8aee5 100644 +--- a/Modules/Core/Common/include/itkMacro.h ++++ b/Modules/Core/Common/include/itkMacro.h +@@ -1141,7 +1141,7 @@ compilers. + #define itkGetVectorMacro(name, type, count) \ + virtual type * Get##name() const { return this->m_##name; } + +-/**\def itkGPUKernelClassMacro ++/**\def class itkGPUKernelClassMacro + * Construct a non-templatized helper class that + * provides the GPU kernel source code as a const char* + */ +@@ -1150,7 +1150,7 @@ compilers. + * Workaround KWstyle bug \ \ + * \ingroup ITKCommon \ \ + */ \ +- class kernel \ ++ kernel \ + { \ + public: \ + static const char * \ +diff --git a/Modules/Core/GPUCommon/include/itkGPUImageOps.h b/Modules/Core/GPUCommon/include/itkGPUImageOps.h +index f4eb8f33b..fbdf3d757 100644 +--- a/Modules/Core/GPUCommon/include/itkGPUImageOps.h ++++ b/Modules/Core/GPUCommon/include/itkGPUImageOps.h +@@ -23,7 +23,7 @@ + namespace itk + { + /** Create a helper GPU Kernel class for GPUImageOps */ +-itkGPUKernelClassMacro(GPUImageOpsKernel); ++class itkGPUKernelClassMacro(GPUImageOpsKernel); + + /** \class GPUImageOps + * +diff --git a/Modules/Core/GPUCommon/include/itkGPUReduction.h b/Modules/Core/GPUCommon/include/itkGPUReduction.h +index 524a5cd01..1b3ce91e9 100644 +--- a/Modules/Core/GPUCommon/include/itkGPUReduction.h ++++ b/Modules/Core/GPUCommon/include/itkGPUReduction.h +@@ -26,7 +26,7 @@ + namespace itk + { + /** Create a helper GPU Kernel class for GPUReduction */ +-itkGPUKernelClassMacro(GPUReductionKernel); ++class itkGPUKernelClassMacro(GPUReductionKernel); + + /** + * \class GPUReduction +diff --git a/Modules/Core/GPUFiniteDifference/include/itkGPUDenseFiniteDifferenceImageFilter.h b/Modules/Core/GPUFiniteDifference/include/itkGPUDenseFiniteDifferenceImageFilter.h +index 853801cec..2fccf0bc5 100644 +--- a/Modules/Core/GPUFiniteDifference/include/itkGPUDenseFiniteDifferenceImageFilter.h ++++ b/Modules/Core/GPUFiniteDifference/include/itkGPUDenseFiniteDifferenceImageFilter.h +@@ -24,7 +24,7 @@ + namespace itk + { + /** Create a helper GPU Kernel class for GPUDenseFiniteDifferenceImageFilter */ +-itkGPUKernelClassMacro(GPUDenseFiniteDifferenceImageFilterKernel); ++class ITKGPUFiniteDifference_EXPORT itkGPUKernelClassMacro(GPUDenseFiniteDifferenceImageFilterKernel); + + /** + * \class GPUDenseFiniteDifferenceImageFilter +diff --git a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientNDAnisotropicDiffusionFunction.h b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientNDAnisotropicDiffusionFunction.h +index 4245ff914..1b21b709e 100644 +--- a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientNDAnisotropicDiffusionFunction.h ++++ b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientNDAnisotropicDiffusionFunction.h +@@ -54,7 +54,7 @@ namespace itk + */ + + /** Create a helper GPU Kernel class for GPUGradientNDAnisotropicDiffusionFunction */ +-itkGPUKernelClassMacro(GPUGradientNDAnisotropicDiffusionFunctionKernel); ++class itkGPUKernelClassMacro(GPUGradientNDAnisotropicDiffusionFunctionKernel); + + template <typename TImage> + class ITK_TEMPLATE_EXPORT GPUGradientNDAnisotropicDiffusionFunction +diff --git a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUScalarAnisotropicDiffusionFunction.h b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUScalarAnisotropicDiffusionFunction.h +index 305f6490e..d0d433080 100644 +--- a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUScalarAnisotropicDiffusionFunction.h ++++ b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUScalarAnisotropicDiffusionFunction.h +@@ -32,7 +32,7 @@ namespace itk + * */ + + /** Create a helper GPU Kernel class for GPUScalarAnisotropicDiffusionFunction */ +-itkGPUKernelClassMacro(GPUScalarAnisotropicDiffusionFunctionKernel); ++class itkGPUKernelClassMacro(GPUScalarAnisotropicDiffusionFunctionKernel); + + template <typename TImage> + class ITK_TEMPLATE_EXPORT GPUScalarAnisotropicDiffusionFunction : public GPUAnisotropicDiffusionFunction<TImage> +diff --git a/Modules/Filtering/GPUImageFilterBase/include/itkGPUCastImageFilter.h b/Modules/Filtering/GPUImageFilterBase/include/itkGPUCastImageFilter.h +index 23530ac5c..e1b83f696 100644 +--- a/Modules/Filtering/GPUImageFilterBase/include/itkGPUCastImageFilter.h ++++ b/Modules/Filtering/GPUImageFilterBase/include/itkGPUCastImageFilter.h +@@ -29,7 +29,7 @@ namespace itk + { + + /** Create a helper GPU Kernel class for GPUCastImageFilter */ +-itkGPUKernelClassMacro(GPUCastImageFilterKernel); ++class itkGPUKernelClassMacro(GPUCastImageFilterKernel); + + /** \class GPUCastImageFilter + * \brief GPU version of CastImageFilter. +diff --git a/Modules/Filtering/GPUImageFilterBase/include/itkGPUNeighborhoodOperatorImageFilter.h b/Modules/Filtering/GPUImageFilterBase/include/itkGPUNeighborhoodOperatorImageFilter.h +index c4adc2967..69aeac6db 100644 +--- a/Modules/Filtering/GPUImageFilterBase/include/itkGPUNeighborhoodOperatorImageFilter.h ++++ b/Modules/Filtering/GPUImageFilterBase/include/itkGPUNeighborhoodOperatorImageFilter.h +@@ -41,7 +41,7 @@ namespace itk + */ + + /** Create a helper GPU Kernel class for GPUNeighborhoodOperatorImageFilter */ +-itkGPUKernelClassMacro(GPUNeighborhoodOperatorImageFilterKernel); ++class itkGPUKernelClassMacro(GPUNeighborhoodOperatorImageFilterKernel); + + template <typename TInputImage, + typename TOutputImage, +diff --git a/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h b/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h +index 57bc3ebb7..4ff98c665 100644 +--- a/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h ++++ b/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h +@@ -37,7 +37,7 @@ namespace itk + */ + + /** Create a helper GPU Kernel class for GPUMeanImageFilter */ +-itkGPUKernelClassMacro(GPUMeanImageFilterKernel); ++class itkGPUKernelClassMacro(GPUMeanImageFilterKernel); + + template <typename TInputImage, typename TOutputImage> + class ITK_TEMPLATE_EXPORT GPUMeanImageFilter +diff --git a/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h b/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h +index 8d26dcfc5..613bc623f 100644 +--- a/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h ++++ b/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h +@@ -85,7 +85,7 @@ private: + } // end of namespace Functor + + /** Create a helper GPU Kernel class for GPUBinaryThresholdImageFilter */ +-itkGPUKernelClassMacro(GPUBinaryThresholdImageFilterKernel); ++class itkGPUKernelClassMacro(GPUBinaryThresholdImageFilterKernel); + + /** + * \class GPUBinaryThresholdImageFilter +diff --git a/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h b/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h +index 28b21d592..0b46e27b8 100644 +--- a/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h ++++ b/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h +@@ -51,7 +51,7 @@ namespace itk + * \ingroup ITKGPUPDEDeformableRegistration + */ + /** Create a helper GPU Kernel class for GPUDemonsRegistrationFunction */ +-itkGPUKernelClassMacro(GPUDemonsRegistrationFunctionKernel); ++class itkGPUKernelClassMacro(GPUDemonsRegistrationFunctionKernel); + + template <typename TFixedImage, typename TMovingImage, typename TDisplacementField> + class ITK_TEMPLATE_EXPORT GPUDemonsRegistrationFunction +diff --git a/Modules/Registration/GPUPDEDeformable/include/itkGPUPDEDeformableRegistrationFilter.h b/Modules/Registration/GPUPDEDeformable/include/itkGPUPDEDeformableRegistrationFilter.h +index 93ab975ec..0afd84871 100644 +--- a/Modules/Registration/GPUPDEDeformable/include/itkGPUPDEDeformableRegistrationFilter.h ++++ b/Modules/Registration/GPUPDEDeformable/include/itkGPUPDEDeformableRegistrationFilter.h +@@ -73,7 +73,7 @@ namespace itk + */ + + /** Create a helper GPU Kernel class for GPUPDEDeformableRegistrationFilter */ +-itkGPUKernelClassMacro(GPUPDEDeformableRegistrationFilterKernel); ++class itkGPUKernelClassMacro(GPUPDEDeformableRegistrationFilterKernel); + + template <typename TFixedImage, + typename TMovingImage, diff --git a/ports/itk/rtk/already_defined.patch b/ports/itk/rtk/already_defined.patch new file mode 100644 index 000000000..60b75e3eb --- /dev/null +++ b/ports/itk/rtk/already_defined.patch @@ -0,0 +1,100 @@ +diff --git a/include/rtkProjectionGeometry.h b/include/rtkProjectionGeometry.h +index e5831611f..73ed2b74f 100644 +--- a/include/rtkProjectionGeometry.h ++++ b/include/rtkProjectionGeometry.h +@@ -23,6 +23,7 @@ + + #include <vector> + ++#include "RTKExport.h" + #include "rtkMacro.h" + + namespace rtk +@@ -67,25 +68,18 @@ public: + * with the i-th matrix provides the physical coordinate on + * the i-th projection. + */ +- const std::vector<MatrixType> & +- GetMatrices() const +- { +- return this->m_Matrices; +- } ++ itkGetConstReferenceMacro(Matrices,std::vector<MatrixType>) + + /** Get the i-th projection matrix. */ + MatrixType +- GetMatrix(const unsigned int i) const +- { +- return this->m_Matrices[i]; +- } ++ GetMatrix(const unsigned int i) const; + + /** Empty the geometry object. */ + virtual void + Clear(); + + protected: +- ProjectionGeometry() = default; ++ ProjectionGeometry(); + ~ProjectionGeometry() override = default; + + void +@@ -93,11 +87,7 @@ protected: + + /** Add projection matrix */ + virtual void +- AddMatrix(const MatrixType & m) +- { +- this->m_Matrices.push_back(m); +- this->Modified(); +- } ++ AddMatrix(const MatrixType & m); + + private: + /** Projection matrices */ +@@ -105,6 +95,9 @@ private: + }; + } // namespace rtk + +-#include "rtkProjectionGeometry.hxx" ++#ifndef ITK_MANUAL_INSTANTIATION ++# include "rtkProjectionGeometry.hxx" ++#endif ++ + + #endif // rtkProjectionGeometry_h +diff --git a/include/rtkProjectionGeometry.hxx b/include/rtkProjectionGeometry.hxx +index 192265812..97dfe8c3a 100644 +--- a/include/rtkProjectionGeometry.hxx ++++ b/include/rtkProjectionGeometry.hxx +@@ -23,6 +23,8 @@ + + namespace rtk + { ++template <unsigned int TDimension> ++ProjectionGeometry<TDimension>::ProjectionGeometry() = default; + + template <unsigned int TDimension> + void +@@ -43,6 +45,21 @@ ProjectionGeometry<TDimension>::Clear() + this->Modified(); + } + ++template <unsigned int TDimension> ++typename ProjectionGeometry<TDimension>::MatrixType ++ProjectionGeometry<TDimension>::GetMatrix(const unsigned int i) const ++{ ++ return this->m_Matrices[i]; ++} ++ ++template <unsigned int TDimension> ++void ++ProjectionGeometry<TDimension>::AddMatrix(const typename ProjectionGeometry<TDimension>::MatrixType & m) ++{ ++ this->m_Matrices.push_back(m); ++ this->Modified(); ++} ++ + } // namespace rtk + + #endif // rtkProjectionGeometry_hxx diff --git a/ports/itk/rtk/unresolved.patch b/ports/itk/rtk/unresolved.patch new file mode 100644 index 000000000..e2209ec75 --- /dev/null +++ b/ports/itk/rtk/unresolved.patch @@ -0,0 +1,213 @@ +diff --git a/include/rtkDCMImagXImageIO.h b/include/rtkDCMImagXImageIO.h +index 2a70ae046..69abb409e 100644 +--- a/include/rtkDCMImagXImageIO.h ++++ b/include/rtkDCMImagXImageIO.h +@@ -18,7 +18,7 @@ + + #ifndef rtkDCMImagXImageIO_h + #define rtkDCMImagXImageIO_h +- ++#include "RTKExport.h" + #include <itkGDCMImageIO.h> + + #include "rtkMacro.h" +@@ -32,7 +32,7 @@ namespace rtk + * + * \ingroup RTK + */ +-class DCMImagXImageIO : public itk::GDCMImageIO ++class RTK_EXPORT DCMImagXImageIO : public itk::GDCMImageIO + { + public: + ITK_DISALLOW_COPY_AND_ASSIGN(DCMImagXImageIO); +diff --git a/include/rtkEdfImageIO.h b/include/rtkEdfImageIO.h +index 66499c56b..7b16fbc5a 100644 +--- a/include/rtkEdfImageIO.h ++++ b/include/rtkEdfImageIO.h +@@ -18,7 +18,7 @@ + + #ifndef rtkEdfImageIO_h + #define rtkEdfImageIO_h +- ++#include "RTKExport.h" + #include <itkImageIOBase.h> + #include <fstream> + #include <cstring> +@@ -36,7 +36,7 @@ namespace rtk + * + * \ingroup RTK IOFilters + */ +-class EdfImageIO : public itk::ImageIOBase ++class RTK_EXPORT EdfImageIO : public itk::ImageIOBase + { + public: + ITK_DISALLOW_COPY_AND_ASSIGN(EdfImageIO); +diff --git a/include/rtkHisImageIO.h b/include/rtkHisImageIO.h +index 2ef2005dd..95449b8a6 100644 +--- a/include/rtkHisImageIO.h ++++ b/include/rtkHisImageIO.h +@@ -19,6 +19,8 @@ + #ifndef rtkHisImageIO_h + #define rtkHisImageIO_h + ++#include "RTKExport.h" ++ + // itk include + #include <itkImageIOBase.h> + #include "rtkMacro.h" +@@ -35,7 +37,7 @@ namespace rtk + * + * \ingroup RTK IOFilters + */ +-class HisImageIO : public itk::ImageIOBase ++class RTK_EXPORT HisImageIO : public itk::ImageIOBase + { + public: + /** Standard class type alias. */ +diff --git a/include/rtkHncImageIO.h b/include/rtkHncImageIO.h +index 7b9539bde..dc9dca759 100644 +--- a/include/rtkHncImageIO.h ++++ b/include/rtkHncImageIO.h +@@ -19,9 +19,11 @@ + #ifndef rtkHncImageIO_h + #define rtkHncImageIO_h + ++#include "RTKExport.h" ++ + // itk include + #include <itkImageIOBase.h> +-#include "itksys/SystemTools.hxx" ++//#include "itksys/SystemTools.hxx" + + #if defined(_MSC_VER) && (_MSC_VER < 1600) + // SR: taken from +@@ -43,7 +45,7 @@ namespace rtk + * + * \ingroup RTK IOFilters + */ +-class HncImageIO : public itk::ImageIOBase ++class RTK_EXPORT HncImageIO : public itk::ImageIOBase + { + public: + /** Standard class type alias. */ +diff --git a/include/rtkHncImageIOFactory.h b/include/rtkHncImageIOFactory.h +index 2bca8f77e..1d5a97938 100644 +--- a/include/rtkHncImageIOFactory.h ++++ b/include/rtkHncImageIOFactory.h +@@ -38,7 +38,7 @@ namespace rtk + * + * \ingroup RTK IOFilters + */ +-class HncImageIOFactory : public itk::ObjectFactoryBase ++class RTK_EXPORT HncImageIOFactory : public itk::ObjectFactoryBase + { + public: + /** Standard class type alias. */ +diff --git a/include/rtkHndImageIO.h b/include/rtkHndImageIO.h +index 5a07897cc..5f843362a 100644 +--- a/include/rtkHndImageIO.h ++++ b/include/rtkHndImageIO.h +@@ -19,6 +19,8 @@ + #ifndef rtkHndImageIO_h + #define rtkHndImageIO_h + ++#include "RTKExport.h" ++ + // itk include + #include <itkImageIOBase.h> + +@@ -43,7 +45,7 @@ namespace rtk + * + * \ingroup RTK IOFilters + */ +-class HndImageIO : public itk::ImageIOBase ++class RTK_EXPORT HndImageIO : public itk::ImageIOBase + { + public: + /** Standard class type alias. */ +diff --git a/include/rtkImagXImageIO.h b/include/rtkImagXImageIO.h +index d69e9a790..d6cc8388e 100644 +--- a/include/rtkImagXImageIO.h ++++ b/include/rtkImagXImageIO.h +@@ -18,7 +18,7 @@ + + #ifndef rtkImagXImageIO_h + #define rtkImagXImageIO_h +- ++#include "RTKExport.h" + #include <itkImageIOBase.h> + #include <fstream> + #include <cstring> +@@ -34,7 +34,7 @@ namespace rtk + * + * \ingroup RTK + */ +-class ImagXImageIO : public itk::ImageIOBase ++class RTK_EXPORT ImagXImageIO : public itk::ImageIOBase + { + public: + /** Standard class type alias. */ +diff --git a/include/rtkOraImageIO.h b/include/rtkOraImageIO.h +index ece525a42..2d5332872 100644 +--- a/include/rtkOraImageIO.h ++++ b/include/rtkOraImageIO.h +@@ -19,6 +19,8 @@ + #ifndef rtkOraImageIO_h + #define rtkOraImageIO_h + ++#include "RTKExport.h" ++ + // This is done to avoid any interference with zlib + #ifdef OF + # undef OF +@@ -41,7 +43,7 @@ namespace rtk + * + * \ingroup RTK IOFilters + */ +-class OraImageIO : public itk::MetaImageIO ++class RTK_EXPORT OraImageIO : public itk::MetaImageIO + { + public: + /** Standard class type alias. */ +diff --git a/include/rtkXRadImageIO.h b/include/rtkXRadImageIO.h +index a72c934e4..0a92afa22 100644 +--- a/include/rtkXRadImageIO.h ++++ b/include/rtkXRadImageIO.h +@@ -19,6 +19,7 @@ + #ifndef rtkXRadImageIO_h + #define rtkXRadImageIO_h + ++#include "RTKExport.h" + #include <itkImageIOBase.h> + #include <fstream> + #include <cstring> +@@ -37,7 +38,7 @@ namespace rtk + * + * \ingroup RTK IOFilters + */ +-class XRadImageIO : public itk::ImageIOBase ++class RTK_EXPORT XRadImageIO : public itk::ImageIOBase + { + public: + /** Standard class type alias. */ +diff --git a/include/rtkXimImageIO.h b/include/rtkXimImageIO.h +index ae789dbf9..741f05183 100644 +--- a/include/rtkXimImageIO.h ++++ b/include/rtkXimImageIO.h +@@ -19,6 +19,7 @@ + #ifndef rtkXimImageIO_h + #define rtkXimImageIO_h + ++#include "RTKExport.h" + #include "rtkMacro.h" + + // itk include +@@ -43,7 +44,7 @@ namespace rtk + * + * \ingroup RTK IOFilters + */ +-class XimImageIO : public itk::ImageIOBase ++class RTK_EXPORT XimImageIO : public itk::ImageIOBase + { + public: + /** Standard class type alias. */ diff --git a/ports/itk/var_libraries.patch b/ports/itk/var_libraries.patch new file mode 100644 index 000000000..738fa980f --- /dev/null +++ b/ports/itk/var_libraries.patch @@ -0,0 +1,27 @@ +diff --git a/CMake/ITKModuleMacros.cmake b/CMake/ITKModuleMacros.cmake
+index da9f3a902..60420bb0a 100644
+--- a/CMake/ITKModuleMacros.cmake
++++ b/CMake/ITKModuleMacros.cmake
+@@ -162,9 +162,6 @@ macro(itk_module_impl)
+ foreach(dep IN LISTS ITK_MODULE_${itk-module}_DEPENDS)
+ list(APPEND ${itk-module}_LIBRARIES "${${dep}_LIBRARIES}")
+ endforeach()
+- if(${itk-module}_LIBRARIES)
+- list(REMOVE_DUPLICATES ${itk-module}_LIBRARIES)
+- endif()
+ endif()
+
+ if(EXISTS ${${itk-module}_SOURCE_DIR}/include)
+diff --git a/CMake/ITKModuleAPI.cmake b/CMake/ITKModuleAPI.cmake
+index af64d96dc..809335e6d 100644
+--- a/CMake/ITKModuleAPI.cmake
++++ b/CMake/ITKModuleAPI.cmake
+@@ -133,7 +133,7 @@ macro(itk_module_config ns)
+ endforeach()
+ unset(_${ns}_USED_MODULES)
+
+- foreach(v ${ns}_LIBRARIES ${ns}_INCLUDE_DIRS ${ns}_LIBRARY_DIRS
++ foreach(v ${ns}_INCLUDE_DIRS ${ns}_LIBRARY_DIRS
+ ${ns}_RUNTIME_LIBRARY_DIRS ${ns}_FACTORY_NAMES ${ns}_FACTORY_LIST)
+ if(${v})
+ list(REMOVE_DUPLICATES ${v})
diff --git a/ports/itk/wrapping.patch b/ports/itk/wrapping.patch new file mode 100644 index 000000000..1e2e53150 --- /dev/null +++ b/ports/itk/wrapping.patch @@ -0,0 +1,19 @@ +diff --git a/Wrapping/TypedefMacros.cmake b/Wrapping/TypedefMacros.cmake
+index e6f8d0bf3..6c000dba8 100644
+--- a/Wrapping/TypedefMacros.cmake
++++ b/Wrapping/TypedefMacros.cmake
+@@ -57,13 +57,12 @@ macro(itk_wrap_module library_name)
+
+ # WRAPPER_LIBRARY_DEPENDS. List of names of other wrapper libraries that
+ # define symbols used by this wrapper library.
+ INTERSECTION(WRAPPER_LIBRARY_DEPENDS "${ITK_MODULE_${library_name}_DEPENDS}" "${WRAP_ITK_MODULES}")
+ # set(WRAPPER_LIBRARY_DEPENDS ${ITK_MODULE_${library_name}_DEPENDS})
+
+ # WRAPPER_LIBRARY_LINK_LIBRARIES. List of other libraries that should
+ # be linked to the wrapper library.
+- set(WRAPPER_LIBRARY_LINK_LIBRARIES ${ITK_LIBRARIES} ${${itk-module}_LIBRARIES})
+-
++ set(WRAPPER_LIBRARY_LINK_LIBRARIES ${ITK_LIBRARIES} ${${library_name}_LIBRARIES})
+ # WRAPPER_SUBMODULE_ORDER. List of *.wrap submodules in the source dir
+ # that should be included/wrapped before the rest in the given order.
+ # Just the submodule group name is needed, not the full path or file name.
diff --git a/ports/minc/CONTROL b/ports/minc/CONTROL new file mode 100644 index 000000000..6cd1d5499 --- /dev/null +++ b/ports/minc/CONTROL @@ -0,0 +1,9 @@ +Source: minc +Version: 2.4.03 +Description: MINC - Medical Image NetCDF or MINC isn't netCDF +Homepage: https://github.com/BIC-MNI/libminc +Build-Depends: nifticlib, hdf5[core], zlib + +Feature: minc1 +Description: Support minc1 file format, requires NETCDF +Build-Depends: netcdf[core]
\ No newline at end of file diff --git a/ports/minc/build.patch b/ports/minc/build.patch new file mode 100644 index 000000000..d0275c20d --- /dev/null +++ b/ports/minc/build.patch @@ -0,0 +1,67 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 52cc81ace..d7a1f63f8 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -403,9 +404,11 @@ ENDIF(LIBMINC_MINC1_SUPPORT) + # Keep this variable for compatibility + SET(VOLUME_IO_LIBRARY ${LIBMINC_EXTERNAL_LIB_PREFIX}minc2) + SET(CMAKE_INSTALL_RPATH ${CMAKE_INSTALL_PREFIX}/lib${LIB_SUFFIX}) + + ADD_LIBRARY(${LIBMINC_LIBRARY} ${LIBRARY_TYPE} ${minc_LIB_SRCS} ${minc_HEADERS} ${volume_io_LIB_SRCS} ${volume_io_HEADERS} ) +- ++if(WIN32) ++ target_link_libraries(${LIBMINC_LIBRARY} ws2_32) ++endif() + IF(NIFTI_FOUND AND NOT LIBMINC_USE_SYSTEM_NIFTI) + ADD_DEPENDENCIES(${LIBMINC_LIBRARY} NIFTI) + ENDIF() +@@ -453,7 +456,7 @@ IF( LIBMINC_INSTALL_LIB_DIR ) + ${LIBMINC_EXPORTED_TARGETS} + LIBRARY DESTINATION ${LIBMINC_INSTALL_LIB_DIR} COMPONENT libraries + ARCHIVE DESTINATION ${LIBMINC_INSTALL_LIB_DIR} COMPONENT libraries +- RUNTIME DESTINATION ${LIBMINC_INSTALL_LIB_DIR} COMPONENT libraries ++ RUNTIME DESTINATION ${LIBMINC_INSTALL_BIN_DIR} COMPONENT libraries + ) + ENDIF( LIBMINC_INSTALL_LIB_DIR ) + +@@ -538,7 +541,7 @@ IF(LIBMINC_INSTALL_LIB_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT) + ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/Use${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINC.cmake + ${CMAKE_CURRENT_BINARY_DIR}/CMakeFiles/${LIBMINC_EXTERNAL_LIB_PREFIX}LIBMINCConfig.cmake + DESTINATION +- ${LIBMINC_INSTALL_LIB_DIR} ++ ${LIBMINC_INSTALL_LIB_DIR}/cmake + COMPONENT Development) + + ENDIF(LIBMINC_INSTALL_LIB_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT) +diff --git a/config.h.cmake b/config.h.cmake +index 9ceffa8fc..21c2f3baf 100644 +--- a/config.h.cmake ++++ b/config.h.cmake +@@ -1,4 +1,8 @@ + /* various defines */ ++#ifdef _MSC_VER ++#define strcasecmp _stricmp ++#define strncasecmp _strnicmp ++#endif + + #ifndef MINC2 + #define MINC2 @MINC2@ +diff --git a/libcommon/minc_config.c b/libcommon/minc_config.c +index 531ef108e..5472d9274 100644 +--- a/libcommon/minc_config.c ++++ b/libcommon/minc_config.c +@@ -20,14 +20,6 @@ + + #include "minc_config.h" + +-#ifdef _MSC_VER +-#define snprintf _snprintf +-#define vsnprintf _vsnprintf +-#define strcasecmp _stricmp +-#define strncasecmp _strnicmp +-#endif +- +- + static const char *_CONFIG_VAR[]= + { + "MINC_FORCE_V2", diff --git a/ports/minc/config.patch b/ports/minc/config.patch new file mode 100644 index 000000000..a726b9a57 --- /dev/null +++ b/ports/minc/config.patch @@ -0,0 +1,15 @@ +diff --git a/LIBMINCConfig.cmake.in b/LIBMINCConfig.cmake.in +index 7790597b2..c041b685a 100644 +--- a/LIBMINCConfig.cmake.in ++++ b/LIBMINCConfig.cmake.in +@@ -1,3 +1,4 @@ ++set(_IMPORT_PREFIX "${CMAKE_CURRENT_LIST_DIR}/../../") + # LIBMINC CMake configuration file + + get_filename_component(LIBMINC_CMAKE_DIR "${CMAKE_CURRENT_LIST_FILE}" PATH ) +@@ -37,3 +38,4 @@ set( LIBMINC_FOUND 1 ) + # set( LIBMINC_TARGETS_IMPORTED 1 ) + # include( "${LIBMINC_CMAKE_DIR}/@LIBMINC_EXPORTED_TARGETS@.cmake" ) + #endif() ++unset(_IMPORT_PREFIX) +\ No newline at end of file diff --git a/ports/minc/portfile.cmake b/ports/minc/portfile.cmake new file mode 100644 index 000000000..4b9ff63b1 --- /dev/null +++ b/ports/minc/portfile.cmake @@ -0,0 +1,47 @@ +vcpkg_from_github( + OUT_SOURCE_PATH SOURCE_PATH + REPO BIC-MNI/libminc + REF e75a936c12a305b596d743c26a5437196ebce2a4 + SHA512 744f879ac8f0594c310d1c1b7fe67543c5feeb3e5a0979035918dbb2bf1d0973fbd389e5357a75631e618cc614b648c21179f7467576bd68e3522e63f21451b0 + HEAD_REF master + PATCHES build.patch + config.patch +) + +vcpkg_check_features(OUT_FEATURE_OPTIONS FEATURE_OPTIONS + "minc1" LIBMINC_MINC1_SUPPORT +) + +if(VCPKG_TARGET_IS_WINDOWS) + vcpkg_check_linkage(ONLY_STATIC_LIBRARY) # Symbols are not properly exported +endif() + +set(OPTIONS) +if(VCPKG_LIBRARY_LINKAGE STREQUAL "dynamic") + list(APPEND OPTIONS "-DLIBMINC_BUILD_SHARED_LIBS=ON") +else() + list(APPEND OPTIONS "-DLIBMINC_BUILD_SHARED_LIBS=OFF") +endif() + +vcpkg_configure_cmake( + SOURCE_PATH ${SOURCE_PATH} + PREFER_NINJA + DISABLE_PARALLEL_CONFIGURE + OPTIONS + "-DBUILD_TESTING=OFF" + "-DLIBMINC_USE_SYSTEM_NIFTI=ON" + ${OPTIONS} + ${FEATURE_OPTIONS} +) + +vcpkg_install_cmake() +vcpkg_copy_pdbs() +vcpkg_fixup_cmake_targets(CONFIG_PATH lib/cmake TARGET_PATH share/libminc) + +if(VCPKG_LIBRARY_LINKAGE STREQUAL "static") + file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/bin" "${CURRENT_PACKAGES_DIR}/debug/bin") +endif() +file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/share") +file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/include") + +file(INSTALL ${SOURCE_PATH}/COPYING DESTINATION ${CURRENT_PACKAGES_DIR}/share/${PORT} RENAME copyright) diff --git a/ports/nifticlib/CONTROL b/ports/nifticlib/CONTROL new file mode 100644 index 000000000..acd8aedaa --- /dev/null +++ b/ports/nifticlib/CONTROL @@ -0,0 +1,25 @@ +Source: nifticlib +Version: 2020-04-30 +Description: Nifticlib is a C I/O library for reading and writing files in the nifti-1 data format. +Homepage: NIFTI-Imaging/nifti_clib +Build-Depends: zlib +Default-Features: nifti2, nifticdf +Supports: !uwp + +Feature: cifti +Description: Build cifti libraries and tools + +Feature: fsl +Description: Build fsl libraries and tools + +Feature: nifti2 +Description: Build nifti2 libraries and tools + +Feature: nifticdf +Description: Build nifticdf libraries and tools + +Feature: tools +Description: Build tools + +Feature: tests +Description: Build tests diff --git a/ports/nifticlib/portfile.cmake b/ports/nifticlib/portfile.cmake new file mode 100644 index 000000000..c9d74a49e --- /dev/null +++ b/ports/nifticlib/portfile.cmake @@ -0,0 +1,48 @@ +vcpkg_from_github( + OUT_SOURCE_PATH SOURCE_PATH + REPO NIFTI-Imaging/nifti_clib + REF 65f801b9c2f1f15f4de4a19d45e6595c25765632 + SHA512 be03cdc6cf17fd9ff74c5ecc1f6b2132121bb4b7973a731da334af2a8428d1f0dbbf7b94b2511d1ff7e515b8cc4cf3316d62b189566fb6ffc88c6146eebd48ff + HEAD_REF master + PATCHES zlib_include.patch +) + +if(VCPKG_TARGET_IS_WINDOWS) + vcpkg_check_linkage(ONLY_STATIC_LIBRARY) +endif() + +vcpkg_check_features(OUT_FEATURE_OPTIONS FEATURE_OPTIONS + "cifti" USE_CIFTI_CODE + "fsl" USE_FSL_CODE + "nifti2" USE_NIFTI2_CODE + "nifticdf" USE_NIFTICDF_CODE + "tools" NIFTI_BUILD_APPLICATIONS + "tests" BUILD_TESTING +) +set(TOOL_NAMES) +if("tools" IN_LIST FEATURES) + list(APPEND TOOL_NAMES nifti_stats nifti_tool nifti1_tool) +endif() +if("tests" IN_LIST FEATURES) + list(APPEND TOOL_NAMES nifit_test) +endif() + +vcpkg_configure_cmake( + SOURCE_PATH ${SOURCE_PATH} + PREFER_NINJA + OPTIONS + ${FEATURE_OPTIONS} +) + +vcpkg_install_cmake() +vcpkg_copy_pdbs() +vcpkg_fixup_cmake_targets(CONFIG_PATH share/cmake TARGET_PATH share) + +if(TOOL_NAMES) + vcpkg_copy_tools(TOOL_NAMES ${TOOL_NAMES} AUTO_CLEAN) +endif() + +file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/share") +file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/include") + +file(INSTALL ${SOURCE_PATH}/LICENSE DESTINATION ${CURRENT_PACKAGES_DIR}/share/${PORT} RENAME copyright) diff --git a/ports/nifticlib/zlib_include.patch b/ports/nifticlib/zlib_include.patch new file mode 100644 index 000000000..1ef462b7f --- /dev/null +++ b/ports/nifticlib/zlib_include.patch @@ -0,0 +1,12 @@ +diff --git a/CMakeLists.txt b/CMakeLists.txt +index 54150d739..c3ca8fe50 100644 +--- a/CMakeLists.txt ++++ b/CMakeLists.txt +@@ -77,6 +77,7 @@ set_if_not_defined(ZNZ_COMPILE_DEF "") + if(NOT NIFTI_ZLIB_LIBRARIES) # If using a custom zlib library, skip the find package + ### USE AS STAND ALONE PACKAGE + find_package(ZLIB REQUIRED) ++ include_directories(${ZLIB_INCLUDE_DIRS}) + set(NIFTI_ZLIB_LIBRARIES ${ZLIB_LIBRARIES}) + endif() + #message(STATUS "---------------------ZLIB -${NIFTI_ZLIB_LIBRARIES}--") diff --git a/ports/opencl/CONTROL b/ports/opencl/CONTROL index 9ad614bbf..41069be82 100644 --- a/ports/opencl/CONTROL +++ b/ports/opencl/CONTROL @@ -1,5 +1,6 @@ Source: opencl -Version: 2.2-2-1 +Version: 2.2 +Port-Version: 3 Homepage: https://github.com/KhronosGroup/OpenCL-Headers Description: C/C++ headers and ICD loader (Installable Client Driver) for OpenCL diff --git a/ports/opencl/vcpkg-cmake-wrapper.cmake b/ports/opencl/vcpkg-cmake-wrapper.cmake index 73c9da576..0893710ff 100644 --- a/ports/opencl/vcpkg-cmake-wrapper.cmake +++ b/ports/opencl/vcpkg-cmake-wrapper.cmake @@ -4,6 +4,9 @@ if(NOT BUILD_SHARED_LIBS AND (NOT CMAKE_SYSTEM_NAME MATCHES "Darwin")) set(OpenCL_Extra_Libs ${CMAKE_DL_LIBS} ${CMAKE_THREAD_LIBS_INIT})
if(CMAKE_SYSTEM_NAME MATCHES "Windows")
list(APPEND OpenCL_Extra_Libs cfgmgr32)
+ if($ENV{WindowsSDKVersion} MATCHES "^10")
+ list(APPEND OpenCL_Extra_Libs OneCoreUAP)
+ endif()
endif(CMAKE_SYSTEM_NAME MATCHES "Windows")
if(TARGET OpenCL::OpenCL)
diff --git a/ports/openjpeg/CONTROL b/ports/openjpeg/CONTROL index 0fd7d64a6..07afd75f1 100644 --- a/ports/openjpeg/CONTROL +++ b/ports/openjpeg/CONTROL @@ -1,4 +1,17 @@ Source: openjpeg -Version: 2.3.1-1 +Version: 2.3.1 +Port-Version: 2 Homepage: https://github.com/uclouvain/openjpeg Description: JPEG 2000 image library + +Feature: jpwl +Description: Build optional component jpwl + +Feature: mj2 +Description: Build optional component mj2 + +Feature: jpip +Description: Build optional component jpip + +Feature: jp3d +Description: Build optional component jp3d diff --git a/ports/openjpeg/dll.location.patch b/ports/openjpeg/dll.location.patch new file mode 100644 index 000000000..bdc77a542 --- /dev/null +++ b/ports/openjpeg/dll.location.patch @@ -0,0 +1,32 @@ +diff --git a/src/lib/openjp3d/CMakeLists.txt b/src/lib/openjp3d/CMakeLists.txt +index b0469af1f..75048ef13 100644 +--- a/src/lib/openjp3d/CMakeLists.txt ++++ b/src/lib/openjp3d/CMakeLists.txt +@@ -34,8 +34,9 @@ endif() + # Install library + install(TARGETS ${OPENJP3D_LIBRARY_NAME} + EXPORT OpenJP3DTargets +- DESTINATION ${OPENJPEG_INSTALL_LIB_DIR} +- COMPONENT Libraries ++ RUNTIME DESTINATION ${OPENJPEG_INSTALL_BIN_DIR} COMPONENT Applications ++ LIBRARY DESTINATION ${OPENJPEG_INSTALL_LIB_DIR} COMPONENT Libraries ++ ARCHIVE DESTINATION ${OPENJPEG_INSTALL_LIB_DIR} COMPONENT Libraries + ) + + # Install includes files +diff --git a/src/lib/openmj2/CMakeLists.txt b/src/lib/openmj2/CMakeLists.txt +index 25294b20e..e3acfe8e7 100644 +--- a/src/lib/openmj2/CMakeLists.txt ++++ b/src/lib/openmj2/CMakeLists.txt +@@ -53,8 +53,9 @@ endif() + # Install library + install(TARGETS ${OPENMJ2_LIBRARY_NAME} + EXPORT OpenMJ2Targets +- DESTINATION ${OPENJPEG_INSTALL_LIB_DIR} +- COMPONENT Libraries ++ RUNTIME DESTINATION ${OPENJPEG_INSTALL_BIN_DIR} COMPONENT Applications ++ LIBRARY DESTINATION ${OPENJPEG_INSTALL_LIB_DIR} COMPONENT Libraries ++ ARCHIVE DESTINATION ${OPENJPEG_INSTALL_LIB_DIR} COMPONENT Libraries + ) + + # Install includes files diff --git a/ports/openjpeg/portfile.cmake b/ports/openjpeg/portfile.cmake index 2296734ad..c6d854490 100644 --- a/ports/openjpeg/portfile.cmake +++ b/ports/openjpeg/portfile.cmake @@ -1,27 +1,65 @@ -include(vcpkg_common_functions) - vcpkg_from_github( OUT_SOURCE_PATH SOURCE_PATH REPO uclouvain/openjpeg REF v2.3.1 SHA512 339fbc899bddf2393d214df71ed5d6070a3a76b933b1e75576c8a0ae9dfcc4adec40bdc544f599e4b8d0bc173e4e9e7352408497b5b3c9356985605830c26c03 HEAD_REF master + PATCHES dll.location.patch ) +if(VCPKG_LIBRARY_LINKAGE STREQUAL "static") + list(APPEND OPTIONS "-DBUILD_SHARED_LIBS=OFF" + "-DBUILD_STATIC_LIBS=ON") +else() + list(APPEND OPTIONS "-DBUILD_SHARED_LIBS=ON" + "-DBUILD_STATIC_LIBS=OFF") +endif() + +vcpkg_check_features(OUT_FEATURE_OPTIONS FEATURE_OPTIONS + "jpwl" BUILD_JPWL + "mj2" BUILD_MJ2 + "jpip" BUILD_JPIP + "jp3d" BUILD_JP3D + ) + vcpkg_configure_cmake( SOURCE_PATH ${SOURCE_PATH} PREFER_NINJA OPTIONS -DBUILD_CODEC:BOOL=OFF + -DBUILD_DOC:BOOL=OFF -DOPENJPEG_INSTALL_PACKAGE_DIR=share/openjpeg -DOPENJPEG_INSTALL_INCLUDE_DIR=include + -DEXECUTABLE_OUTPUT_PATH=tools/${PORT} + -DBUILD_PKGCONFIG_FILES=ON + ${FEATURE_OPTIONS} + ${OPTIONS} ) vcpkg_install_cmake() +vcpkg_fixup_cmake_targets() +if(VCPKG_TARGET_IS_WINDOWS) + # TODO: remove -lm from *.pc files +endif() +vcpkg_fixup_pkgconfig(SYSTEM_LIBRARIES m) file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/include) -vcpkg_fixup_cmake_targets() - +set(TOOL_NAMES) +if("jpwl" IN_LIST FEATURES) + list(APPEND TOOL_NAMES opj_dec_server opj_jpwl_compress opj_jpwl_decompress) +endif() +if("mj2" IN_LIST FEATURES) + list(APPEND TOOL_NAMES opj_compress opj_decompress opj_dump opj_mj2_compress opj_mj2_decompress opj_mj2_extract opj_mj2_wrap) +endif() +if("jpip" IN_LIST FEATURES) + list(APPEND TOOL_NAMES opj_jpip_addxml opj_jpip_test opj_jpip_transcode) +endif() +if("jp3d" IN_LIST FEATURES) + list(APPEND TOOL_NAMES opj_jp3d_compress opj_jp3d_decompress) +endif() +if(TOOL_NAMES) + vcpkg_copy_tools(TOOL_NAMES ${TOOL_NAMES} AUTO_CLEAN) +endif() file(READ ${CURRENT_PACKAGES_DIR}/include/openjpeg.h OPENJPEG_H) if(VCPKG_LIBRARY_LINKAGE STREQUAL "static") string(REPLACE "defined(OPJ_STATIC)" "1" OPENJPEG_H "${OPENJPEG_H}") @@ -32,7 +70,6 @@ string(REPLACE "defined(DLL_EXPORT)" "0" OPENJPEG_H "${OPENJPEG_H}") file(WRITE ${CURRENT_PACKAGES_DIR}/include/openjpeg.h "${OPENJPEG_H}") # Handle copyright -file(COPY ${SOURCE_PATH}/LICENSE DESTINATION ${CURRENT_PACKAGES_DIR}/share/openjpeg) -file(RENAME ${CURRENT_PACKAGES_DIR}/share/openjpeg/LICENSE ${CURRENT_PACKAGES_DIR}/share/openjpeg/copyright) +file(INSTALL "${SOURCE_PATH}/LICENSE" DESTINATION "${CURRENT_PACKAGES_DIR}/share/${PORT}" RENAME copyright) vcpkg_copy_pdbs() diff --git a/scripts/ci.baseline.txt b/scripts/ci.baseline.txt index dc9a44ffb..8b1c6b31c 100644 --- a/scripts/ci.baseline.txt +++ b/scripts/ci.baseline.txt @@ -614,9 +614,6 @@ isal:x64-uwp=fail isal:x64-windows=fail isal:x64-windows-static=fail isal:x86-windows=fail -itk:x64-windows=fail -itk:x64-windows-static=fail -itk:x86-windows=fail jack2:arm-uwp=fail jack2:x64-uwp=fail jaeger-client-cpp:arm64-windows=fail diff --git a/scripts/cmake/vcpkg_find_acquire_program.cmake b/scripts/cmake/vcpkg_find_acquire_program.cmake index ff50f6548..8b006990a 100644 --- a/scripts/cmake/vcpkg_find_acquire_program.cmake +++ b/scripts/cmake/vcpkg_find_acquire_program.cmake @@ -33,6 +33,7 @@ ## - NINJA ## - NUGET ## - SCONS +## - SWIG ## - YASM ## ## Note that msys2 has a dedicated helper function: [`vcpkg_acquire_msys`](vcpkg_acquire_msys.md). @@ -309,7 +310,32 @@ function(vcpkg_find_acquire_program VAR) set(PATHS ${DOWNLOADS}/tools/scons) set(URL "https://sourceforge.net/projects/scons/files/scons-local-3.0.1.zip/download") set(ARCHIVE "scons-local-3.0.1.zip") - set(HASH fe121b67b979a4e9580c7f62cfdbe0c243eba62a05b560d6d513ac7f35816d439b26d92fc2d7b7d7241c9ce2a49ea7949455a17587ef53c04a5f5125ac635727) + set(HASH fe121b67b979a4e9580c7f62cfdbe0c243eba62a05b560d6d513ac7f35816d439b26d92fc2d7b7d7241c9ce2a49ea7949455a17587ef53c04a5f5125ac635727) + elseif(VAR MATCHES "SWIG") + set(VERSION 4.0.2) + set(PROGNAME swig) + if(CMAKE_HOST_WIN32) + set(URL "https://sourceforge.net/projects/swig/files/swigwin/swigwin-${VERSION}/swigwin-${VERSION}.zip/download") + set(ARCHIVE "swigwin-${VERSION}.zip") + set(HASH b8f105f9b9db6acc1f6e3741990915b533cd1bc206eb9645fd6836457fd30789b7229d2e3219d8e35f2390605ade0fbca493ae162ec3b4bc4e428b57155db03d) + set(SUBDIR "swigwin-${VERSION}") + set(PATHS "${DOWNLOADS}/tools/swig/${SUBDIR}/${SUBDIR}") + else() + #Not used + set(_vfa_SUPPORTED TRUE) + set(URL https://sourceforge.net/projects/swig/files/swig/swig-${VERSION}/swig-${VERSION}.tar.gz/download) + set(ARCHIVE "swig-${VERSION}.tar.gz") + set(HASH 05e7da70ce6d9a733b96c0bcfa3c1b82765bd859f48c74759bbf4bb1467acb1809caa310cba5e2b3280cd704fca249eaa0624821dffae1d2a75097c7f55d14ed) + set(SUBDIR "swig-${VERSION}") + set(PATHS "${DOWNLOADS}/tools/swig/${SUBDIR}") + endif() + set(SOURCEFORGE_ARGS + REPO swig + FILENAME "${ARCHIVE}" + SHA512 "${HASH}" + NO_REMOVE_ONE_LEVEL + WORKING_DIRECTORY "${DOWNLOADS}/tools/swig" + ) elseif(VAR MATCHES "DOXYGEN") set(PROGNAME doxygen) set(DOXYGEN_VERSION 1.8.17) |