[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, 58 insertions, 0 deletions

diff --git a/ports/itk/openjpeg2.patch b/ports/itk/openjpeg2.patch
new file mode 100644
index 000000000..86631f5f9
--- /dev/null
+++ b/ports/itk/openjpeg2.patch
@@ -0,0 +1,58 @@
+diff --git a/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/CMakeLists.txt
+index 565cc338b..c061f0721 100644
+--- a/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/CMakeLists.txt
++++ b/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/CMakeLists.txt
+@@ -194,7 +194,7 @@ mark_as_advanced(LIBRARY_OUTPUT_PATH EXECUTABLE_OUTPUT_PATH)
+ # configure name mangling to allow multiple libraries to coexist
+ # peacefully
+ if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in)
+-set(MANGLE_PREFIX ${OPENJPEG_LIBRARY_NAME})
++set(MANGLE_PREFIX)
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in
+                ${CMAKE_CURRENT_BINARY_DIR}/openjpeg_mangle.h
+                @ONLY)
+diff --git a/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt b/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt
+index c4adb91a2..89b731d88 100644
+--- a/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt
++++ b/Modules/ThirdParty/GDCM/src/gdcm/Utilities/gdcmopenjpeg/src/lib/openjp2/CMakeLists.txt
+@@ -3,7 +3,7 @@ include_regular_expression("^.*$")
+ # configure name mangling to allow multiple libraries to coexist
+ # peacefully
+ if(EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in)
+-set(MANGLE_PREFIX ${OPENJPEG_LIBRARY_NAME})
++set(MANGLE_PREFIX)
+ configure_file(${CMAKE_CURRENT_SOURCE_DIR}/openjpeg_mangle.h.in
+                ${CMAKE_CURRENT_BINARY_DIR}/openjpeg_mangle.h
+                @ONLY)
+diff --git a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+index 3811e52f4..a41e9264e 100644
+--- a/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
++++ b/Modules/ThirdParty/OpenJPEG/CMakeLists.txt
+@@ -8,10 +8,10 @@ if(ITK_USE_SYSTEM_OpenJPEG)
+    else()

+         message(FATAL_ERROR "OpenJPEG target openjp2 missing!")

+    endif()

+-     set(ITKOpenJPEG_INCLUDE_DIRS

+-    ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg

+-    ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg

+-    )

++   #  set(ITKOpenJPEG_INCLUDE_DIRS

++   # ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg

++   # ${ITKOpenJPEG_SOURCE_DIR}/src/openjpeg

++   # )

+ else()

+   set(ITKOpenJPEG_INCLUDE_DIRS

+     ${ITKOpenJPEG_BINARY_DIR}/src/openjpeg

+diff --git a/Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeLists.txt b/Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeLists.txt
+index e62e43eda..35dc89976 100644
+--- a/Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeLists.txt
++++ b/Modules/ThirdParty/OpenJPEG/src/openjpeg/CMakeLists.txt
+@@ -68,7 +68,7 @@ CONFIGURE_FILE(${ITK3P_OpenJPEG_SOURCE_DIR}/opj_configure.h.in
+ # configure name mangling to allow multiple libraries to coexist
+ # peacefully
+ if(EXISTS ${ITK3P_OpenJPEG_SOURCE_DIR}/openjpeg_mangle.h.in)
+-set(MANGLE_PREFIX itk)
++#set(MANGLE_PREFIX itk)
+ configure_file(${ITK3P_OpenJPEG_SOURCE_DIR}/openjpeg_mangle.h.in
+                ${ITK3P_OpenJPEG_BINARY_DIR}/openjpeg_mangle.h
+              @ONLY)