[ITK] Update to 5.1

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]
+

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})
+

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

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

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()