[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>

1 files changed, 178 insertions, 0 deletions

diff --git a/ports/itk/python_gpu_wrapping.patch b/ports/itk/python_gpu_wrapping.patch
new file mode 100644
index 000000000..37367d979
--- /dev/null
+++ b/ports/itk/python_gpu_wrapping.patch
@@ -0,0 +1,178 @@
+diff --git a/CMake/itkOpenCL.cmake b/CMake/itkOpenCL.cmake
+index 0ccbe144d..fa381524f 100644
+--- a/CMake/itkOpenCL.cmake	
++++ b/CMake/itkOpenCL.cmake
+@@ -48,7 +48,7 @@ if(ITK_USE_GPU)
+                       )
+     set_source_files_properties(${CMAKE_CURRENT_BINARY_DIR}/${OUTPUT_FILE}
+                                 PROPERTIES GENERATED ON)
+-    set(${SRC_VAR} ${${SRC_VAR}} ${OUTPUT_FILE})
++    set(${SRC_VAR} ${${SRC_VAR}} ${CMAKE_CURRENT_BINARY_DIR}/${OUTPUT_FILE})
+   endmacro()
+ 
+   macro(write_gpu_kernels GPUKernels GPU_SRC)
+diff --git a/Modules/Core/Common/include/itkMacro.h b/Modules/Core/Common/include/itkMacro.h
+index 1816f722a..3a6a8aee5 100644
+--- a/Modules/Core/Common/include/itkMacro.h	
++++ b/Modules/Core/Common/include/itkMacro.h
+@@ -1141,7 +1141,7 @@ compilers.
+ #define itkGetVectorMacro(name, type, count)                                                                           \
+   virtual type * Get##name() const { return this->m_##name; }
+ 
+-/**\def itkGPUKernelClassMacro
++/**\def class itkGPUKernelClassMacro
+  * Construct a non-templatized helper class that
+  * provides the GPU kernel source code as a const char*
+  */
+@@ -1150,7 +1150,7 @@ compilers.
+    * Workaround KWstyle bug \                                                                                          \
+    * \ingroup ITKCommon \                                                                                              \
+    */                                                                                                                  \
+-  class kernel                                                                                                         \
++  kernel                                                                                                         \
+   {                                                                                                                    \
+   public:                                                                                                              \
+     static const char *                                                                                                \
+diff --git a/Modules/Core/GPUCommon/include/itkGPUImageOps.h b/Modules/Core/GPUCommon/include/itkGPUImageOps.h
+index f4eb8f33b..fbdf3d757 100644
+--- a/Modules/Core/GPUCommon/include/itkGPUImageOps.h	
++++ b/Modules/Core/GPUCommon/include/itkGPUImageOps.h
+@@ -23,7 +23,7 @@
+ namespace itk
+ {
+ /** Create a helper GPU Kernel class for GPUImageOps */
+-itkGPUKernelClassMacro(GPUImageOpsKernel);
++class itkGPUKernelClassMacro(GPUImageOpsKernel);
+ 
+ /** \class GPUImageOps
+  *
+diff --git a/Modules/Core/GPUCommon/include/itkGPUReduction.h b/Modules/Core/GPUCommon/include/itkGPUReduction.h
+index 524a5cd01..1b3ce91e9 100644
+--- a/Modules/Core/GPUCommon/include/itkGPUReduction.h	
++++ b/Modules/Core/GPUCommon/include/itkGPUReduction.h
+@@ -26,7 +26,7 @@
+ namespace itk
+ {
+ /** Create a helper GPU Kernel class for GPUReduction */
+-itkGPUKernelClassMacro(GPUReductionKernel);
++class itkGPUKernelClassMacro(GPUReductionKernel);
+ 
+ /**
+  * \class GPUReduction
+diff --git a/Modules/Core/GPUFiniteDifference/include/itkGPUDenseFiniteDifferenceImageFilter.h b/Modules/Core/GPUFiniteDifference/include/itkGPUDenseFiniteDifferenceImageFilter.h
+index 853801cec..2fccf0bc5 100644
+--- a/Modules/Core/GPUFiniteDifference/include/itkGPUDenseFiniteDifferenceImageFilter.h	
++++ b/Modules/Core/GPUFiniteDifference/include/itkGPUDenseFiniteDifferenceImageFilter.h
+@@ -24,7 +24,7 @@
+ namespace itk
+ {
+ /** Create a helper GPU Kernel class for GPUDenseFiniteDifferenceImageFilter */
+-itkGPUKernelClassMacro(GPUDenseFiniteDifferenceImageFilterKernel);
++class ITKGPUFiniteDifference_EXPORT itkGPUKernelClassMacro(GPUDenseFiniteDifferenceImageFilterKernel);
+ 
+ /**
+  * \class GPUDenseFiniteDifferenceImageFilter
+diff --git a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientNDAnisotropicDiffusionFunction.h b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientNDAnisotropicDiffusionFunction.h
+index 4245ff914..1b21b709e 100644
+--- a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientNDAnisotropicDiffusionFunction.h	
++++ b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUGradientNDAnisotropicDiffusionFunction.h
+@@ -54,7 +54,7 @@ namespace itk
+  */
+ 
+ /** Create a helper GPU Kernel class for GPUGradientNDAnisotropicDiffusionFunction */
+-itkGPUKernelClassMacro(GPUGradientNDAnisotropicDiffusionFunctionKernel);
++class itkGPUKernelClassMacro(GPUGradientNDAnisotropicDiffusionFunctionKernel);
+ 
+ template <typename TImage>
+ class ITK_TEMPLATE_EXPORT GPUGradientNDAnisotropicDiffusionFunction
+diff --git a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUScalarAnisotropicDiffusionFunction.h b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUScalarAnisotropicDiffusionFunction.h
+index 305f6490e..d0d433080 100644
+--- a/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUScalarAnisotropicDiffusionFunction.h	
++++ b/Modules/Filtering/GPUAnisotropicSmoothing/include/itkGPUScalarAnisotropicDiffusionFunction.h
+@@ -32,7 +32,7 @@ namespace itk
+  * */
+ 
+ /** Create a helper GPU Kernel class for GPUScalarAnisotropicDiffusionFunction */
+-itkGPUKernelClassMacro(GPUScalarAnisotropicDiffusionFunctionKernel);
++class itkGPUKernelClassMacro(GPUScalarAnisotropicDiffusionFunctionKernel);
+ 
+ template <typename TImage>
+ class ITK_TEMPLATE_EXPORT GPUScalarAnisotropicDiffusionFunction : public GPUAnisotropicDiffusionFunction<TImage>
+diff --git a/Modules/Filtering/GPUImageFilterBase/include/itkGPUCastImageFilter.h b/Modules/Filtering/GPUImageFilterBase/include/itkGPUCastImageFilter.h
+index 23530ac5c..e1b83f696 100644
+--- a/Modules/Filtering/GPUImageFilterBase/include/itkGPUCastImageFilter.h	
++++ b/Modules/Filtering/GPUImageFilterBase/include/itkGPUCastImageFilter.h
+@@ -29,7 +29,7 @@ namespace itk
+ {
+ 
+ /** Create a helper GPU Kernel class for GPUCastImageFilter */
+-itkGPUKernelClassMacro(GPUCastImageFilterKernel);
++class itkGPUKernelClassMacro(GPUCastImageFilterKernel);
+ 
+ /** \class GPUCastImageFilter
+  * \brief GPU version of CastImageFilter.
+diff --git a/Modules/Filtering/GPUImageFilterBase/include/itkGPUNeighborhoodOperatorImageFilter.h b/Modules/Filtering/GPUImageFilterBase/include/itkGPUNeighborhoodOperatorImageFilter.h
+index c4adc2967..69aeac6db 100644
+--- a/Modules/Filtering/GPUImageFilterBase/include/itkGPUNeighborhoodOperatorImageFilter.h	
++++ b/Modules/Filtering/GPUImageFilterBase/include/itkGPUNeighborhoodOperatorImageFilter.h
+@@ -41,7 +41,7 @@ namespace itk
+  */
+ 
+ /** Create a helper GPU Kernel class for GPUNeighborhoodOperatorImageFilter */
+-itkGPUKernelClassMacro(GPUNeighborhoodOperatorImageFilterKernel);
++class itkGPUKernelClassMacro(GPUNeighborhoodOperatorImageFilterKernel);
+ 
+ template <typename TInputImage,
+           typename TOutputImage,
+diff --git a/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h b/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h
+index 57bc3ebb7..4ff98c665 100644
+--- a/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h	
++++ b/Modules/Filtering/GPUSmoothing/include/itkGPUMeanImageFilter.h
+@@ -37,7 +37,7 @@ namespace itk
+  */
+ 
+ /** Create a helper GPU Kernel class for GPUMeanImageFilter */
+-itkGPUKernelClassMacro(GPUMeanImageFilterKernel);
++class itkGPUKernelClassMacro(GPUMeanImageFilterKernel);
+ 
+ template <typename TInputImage, typename TOutputImage>
+ class ITK_TEMPLATE_EXPORT GPUMeanImageFilter
+diff --git a/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h b/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h
+index 8d26dcfc5..613bc623f 100644
+--- a/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h	
++++ b/Modules/Filtering/GPUThresholding/include/itkGPUBinaryThresholdImageFilter.h
+@@ -85,7 +85,7 @@ private:
+ } // end of namespace Functor
+ 
+ /** Create a helper GPU Kernel class for GPUBinaryThresholdImageFilter */
+-itkGPUKernelClassMacro(GPUBinaryThresholdImageFilterKernel);
++class itkGPUKernelClassMacro(GPUBinaryThresholdImageFilterKernel);
+ 
+ /**
+  * \class GPUBinaryThresholdImageFilter
+diff --git a/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h b/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h
+index 28b21d592..0b46e27b8 100644
+--- a/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h	
++++ b/Modules/Registration/GPUPDEDeformable/include/itkGPUDemonsRegistrationFunction.h
+@@ -51,7 +51,7 @@ namespace itk
+  * \ingroup ITKGPUPDEDeformableRegistration
+  */
+ /** Create a helper GPU Kernel class for GPUDemonsRegistrationFunction */
+-itkGPUKernelClassMacro(GPUDemonsRegistrationFunctionKernel);
++class itkGPUKernelClassMacro(GPUDemonsRegistrationFunctionKernel);
+ 
+ template <typename TFixedImage, typename TMovingImage, typename TDisplacementField>
+ class ITK_TEMPLATE_EXPORT GPUDemonsRegistrationFunction
+diff --git a/Modules/Registration/GPUPDEDeformable/include/itkGPUPDEDeformableRegistrationFilter.h b/Modules/Registration/GPUPDEDeformable/include/itkGPUPDEDeformableRegistrationFilter.h
+index 93ab975ec..0afd84871 100644
+--- a/Modules/Registration/GPUPDEDeformable/include/itkGPUPDEDeformableRegistrationFilter.h	
++++ b/Modules/Registration/GPUPDEDeformable/include/itkGPUPDEDeformableRegistrationFilter.h
+@@ -73,7 +73,7 @@ namespace itk
+  */
+ 
+ /** Create a helper GPU Kernel class for GPUPDEDeformableRegistrationFilter */
+-itkGPUKernelClassMacro(GPUPDEDeformableRegistrationFilterKernel);
++class itkGPUKernelClassMacro(GPUPDEDeformableRegistrationFilterKernel);
+ 
+ template <typename TFixedImage,
+           typename TMovingImage,