[ITK] Update to 5.1 (#11208)

* [vtk-m] new port vtk-m

* [VTK] Update to 9.0

* include local buildtree changes

* [pcl] disable VTK due to API changes in VTK 9.0

* [vtk-m] add supports field to be only x64

* [vtk-dicom] add python executable.

* fix vtkm dependency

* [vtk-dicom] fix missing std:: namespace

* [vtk-m] add uwp to unsupported triplets

* [vtk] add pegtl include patch, reenable IOMotionFX

* remove hdf5 changes for testing

* use different pgetl patch which redirects to the installed config of pegtl

* [pegtl-2] version file needs renaming too

* [vtk] change dependency to pgetl-2 and fix the patch

* [vtk] put in hdf5 fix again and correct manually installed include files

* remove deprecated function to retrigger CI

* [lz4] correctly lowercase the lz4 config

* [vtk] remove unnecessary code

* [pegtl-2] add homepage

* [pegtl] modernize portfiles

* [vtk-dicom] add homepage

* [vtk-dicom] modernize portfile

* [vtk-m] remove empty build depends

* [vtk] try fixing the permission issue

* [vtk] minimal dependency correction

* [itk] update

* fix portfile errors

* WIP commit

* should make ITK green in VCPKG CI but there a still issues with features

* more dependencies and features....

* remove itk from baseline failure so the check can get green

* more dependency updating.

* minor build fixes

* [openjpeg] Fix dll location

* fix other issues

* add rtkcuda

* [openjpeg] remove default features to make arm and uwp platforms happy

* [itk] more dependency fixes

* [openjpeg] fix no tools case

* [itk] fix wip patch

* [itk] split up patches & cleanup & and move rtk tools if build

* [itk] fix patch and remove old and wip patch

* [nifticlib] Add new port required by minc

* [nifticlib] change repo and add features

* [nifticilib] add zlib dependency & cleanup

* [minc] add new port

* [vcpkg/scripts] add swig to find acquire programm

* [itk/minc] update for external minc

* add supports field for nifticlib

* [itk] make python a default feature for testing

* [itk] cleanup python vars a bit
[vcpkg/scripts] correct swig hash

* [vcpkg/scripts] fix swig

* [itk] fix python include path on unix system

* [itk] remove python as a default. A bit of feature cleanup

* [itk] update remote RTK

* [itk|rtk] remove RTK module before configure to allow patching

* [opencl] update opencl wrapper

* [itk] fix opencl static linkage

* [itk] add cufftw fix

* update baseline

* [itk] fix itk[tbb]

* [itk] update python paths to 3.8

* [itk] add failure messages for unsupported architectures for some features

* [vcpkg_find_acquire_program] update swig to 4.0.2

* Update portfile.cmake

* [itk] move the module removal out of the if for people reusing the old source tree

* [itk] add missing auto_clean to vcpkg_copy_tools

* Update ports/nifticlib/CONTROL

Co-authored-by: Robert Schumacher <roschuma@microsoft.com>

* Update ports/openjpeg/portfile.cmake

Co-authored-by: Robert Schumacher <roschuma@microsoft.com>

* Update scripts/cmake/vcpkg_find_acquire_program.cmake

Co-authored-by: Robert Schumacher <roschuma@microsoft.com>

* [openjpeg] pass OPTIONS to vcpkg_configure_cmake

* [itk] fix typo and leave a todo.

* use sourceforge args for swig

* Update ports/openjpeg/CONTROL

Co-authored-by: Jack·Boos·Yu <47264268+JackBoosY@users.noreply.github.com>

* Update ports/opencl/CONTROL

Co-authored-by: Jack·Boos·Yu <47264268+JackBoosY@users.noreply.github.com>

* [itk] remove debug msgs from patch

* pre-install yasm on OSX

Co-authored-by: Lily <47812810+LilyWangL@users.noreply.github.com>
Co-authored-by: Robert Schumacher <roschuma@microsoft.com>
Co-authored-by: Jack·Boos·Yu <47264268+JackBoosY@users.noreply.github.com>
Co-authored-by: JackBoosY <yuzaiyang@beyondsoft.com>

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/fix_libminc_config_path.patch

@@ -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)
- 

ports/itk/fix_openjpeg_search.patch

@@ -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)

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()

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()
+ 

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)

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
+    REF d3286c9cc04ba16cc8f73de9a98fbcd7c02f3c7b
-    SHA512 242ce66cf83f82d26f20d2099108295e28c8875e7679126ba023834bf0e94454460ba86452a94c8ddaea93d2314befc399f2b151d7294370d4b47f0e9798e77f
+    SHA512 c358449870d580aeb10e32f8be0ca39e8a76d8dc06fda973788fafb5971333e546611c399190be49d40f5f3c18a1105d9699eef271a560aff25ce168a396926e
     HEAD_REF master
     PATCHES
-        fix_openjpeg_search.patch
+        hdf5.patch
-        fix_libminc_config_path.patch
+        double-conversion.patch 
+        openjpeg.patch
+        openjpeg2.patch
+        var_libraries.patch
+        wrapping.patch
+        python_gpu_wrapping.patch
+        opencl.patch
+        cufftw.patch
 )
 
-if ("vtk" IN_LIST FEATURES)
+vcpkg_check_features(OUT_FEATURE_OPTIONS FEATURE_OPTIONS
-    set(ITKVtkGlue ON)
+    "vtk"          Module_ITKVtkGlue
-else()
+    "cuda"         Module_ITKCudaCommon # Requires RTK?
-    set(ITKVtkGlue OFF)
+    #"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("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 ${SOURCE_PATH}
     PREFER_NINJA
@@ -31,7 +139,10 @@ vcpkg_configure_cmake(
     OPTIONS
         -DBUILD_TESTING=OFF
         -DBUILD_EXAMPLES=OFF
+        -DBUILD_PKGCONFIG_FILES=OFF 
+        -DITK_DOXYGEN_HTML=OFF
         -DDO_NOT_INSTALL_ITK_TEST_DRIVER=ON
+        -DITK_SKIP_PATH_LENGTH_CHECKS=ON
         -DITK_INSTALL_DATA_DIR=share/itk/data
         -DITK_INSTALL_DOC_DIR=share/itk/doc
         -DITK_INSTALL_PACKAGE_DIR=share/itk
@@ -45,31 +156,58 @@ vcpkg_configure_cmake(
         -DITK_USE_SYSTEM_TIFF=ON
         -DITK_USE_SYSTEM_ZLIB=ON
         -DITK_USE_SYSTEM_EIGEN=ON
-        # This should be turned on some day, however for now ITK does download specific versions so it shouldn't spontaneously break
+        -DITK_USE_SYSTEM_FFTW=ON
-        -DITK_FORBID_DOWNLOADS=OFF
+        -DITK_USE_SYSTEM_HDF5=ON # HDF5 was problematic in the past and still is. ITK still has not figured out how to do it correctly!
+        -DITK_USE_SYSTEM_GDCM=ON
+        -DITK_USE_SYSTEM_OpenJPEG=ON # Added by VCPKG
+        -DITK_USE_SYSTEM_DCMTK=ON 
+        -DDCMTK_USE_ICU=ON
+        -DITK_USE_SYSTEM_ICU=ON
+        #-DITK_USE_SYSTEM_VXL=ON
+        #-DITK_USE_SYSTEM_CASTXML=ON # needs to be added to vcpkg_find_acquire_program https://data.kitware.com/api/v1/file/hashsum/sha512/b8b6f0aff11fe89ab2fcd1949cc75f2c2378a7bc408827a004396deb5ff5a9976bffe8a597f8db1b74c886ea39eb905e610dce8f5bd7586a4d6c196d7349da8d/download
+        -DITK_USE_SYSTEM_MINC=ON
+        -DITK_USE_SYSTEM_SWIG=ON
+        -DITK_FORBID_DOWNLOADS=OFF # This should be turned on some day, however for now ITK does download specific versions so it shouldn't spontaneously break. Remote Modules would probably break with this!
+        -DINSTALL_GTEST=OFF
+        -DITK_USE_SYSTEM_GOOGLETEST=ON
+        -DEXECUTABLE_OUTPUT_PATH=tools/${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_SKIP_PATH_LENGTH_CHECKS=ON
+        ${FEATURE_OPTIONS}
-
-        # I haven't tried Python wrapping in vcpkg
-        #-DITK_WRAP_PYTHON=ON
-        #-DITK_PYTHON_VERSION=3
-
-        -DITK_USE_SYSTEM_HDF5=ON # HDF5 was problematic in the past
-        -DModule_ITKVtkGlue=${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
         ${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}/lib/cmake")
-file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/include)
+file(REMOVE_RECURSE "${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)

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,

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

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. */

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})

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.

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]

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",

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

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)

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

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)

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}--")

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
 

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)

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

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

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 ${CURRENT_PACKAGES_DIR}/share/openjpeg)
+file(INSTALL "${SOURCE_PATH}/LICENSE" DESTINATION "${CURRENT_PACKAGES_DIR}/share/${PORT}" RENAME copyright)
-file(RENAME ${CURRENT_PACKAGES_DIR}/share/openjpeg/LICENSE ${CURRENT_PACKAGES_DIR}/share/openjpeg/copyright)
 
 vcpkg_copy_pdbs()

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

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)