[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>

3 files changed, 85 insertions, 0 deletions

diff --git a/ports/nifticlib/CONTROL b/ports/nifticlib/CONTROL
new file mode 100644
index 000000000..acd8aedaa
--- /dev/null
+++ b/ports/nifticlib/CONTROL
@@ -0,0 +1,25 @@
+Source: nifticlib
+Version: 2020-04-30
+Description: Nifticlib is a C I/O library for reading and writing files in the nifti-1 data format. 
+Homepage: NIFTI-Imaging/nifti_clib
+Build-Depends: zlib
+Default-Features: nifti2, nifticdf
+Supports: !uwp
+
+Feature: cifti
+Description: Build cifti libraries and tools
+
+Feature: fsl
+Description: Build fsl libraries and tools
+
+Feature: nifti2
+Description: Build nifti2 libraries and tools
+
+Feature: nifticdf
+Description: Build nifticdf libraries and tools
+
+Feature: tools
+Description: Build tools
+
+Feature: tests
+Description: Build tests
diff --git a/ports/nifticlib/portfile.cmake b/ports/nifticlib/portfile.cmake
new file mode 100644
index 000000000..c9d74a49e
--- /dev/null
+++ b/ports/nifticlib/portfile.cmake
@@ -0,0 +1,48 @@
+vcpkg_from_github(
+    OUT_SOURCE_PATH SOURCE_PATH
+    REPO    NIFTI-Imaging/nifti_clib 
+    REF 65f801b9c2f1f15f4de4a19d45e6595c25765632
+    SHA512 be03cdc6cf17fd9ff74c5ecc1f6b2132121bb4b7973a731da334af2a8428d1f0dbbf7b94b2511d1ff7e515b8cc4cf3316d62b189566fb6ffc88c6146eebd48ff
+    HEAD_REF master
+    PATCHES zlib_include.patch
+)
+
+if(VCPKG_TARGET_IS_WINDOWS)
+    vcpkg_check_linkage(ONLY_STATIC_LIBRARY)
+endif()
+
+vcpkg_check_features(OUT_FEATURE_OPTIONS FEATURE_OPTIONS
+    "cifti"         USE_CIFTI_CODE
+    "fsl"           USE_FSL_CODE
+    "nifti2"        USE_NIFTI2_CODE
+    "nifticdf"      USE_NIFTICDF_CODE
+    "tools"         NIFTI_BUILD_APPLICATIONS
+    "tests"         BUILD_TESTING
+)
+set(TOOL_NAMES)
+if("tools" IN_LIST FEATURES)
+    list(APPEND TOOL_NAMES nifti_stats nifti_tool nifti1_tool)
+endif()
+if("tests" IN_LIST FEATURES)
+    list(APPEND TOOL_NAMES nifit_test) 
+endif()
+
+vcpkg_configure_cmake(
+    SOURCE_PATH ${SOURCE_PATH}
+    PREFER_NINJA
+    OPTIONS
+        ${FEATURE_OPTIONS}
+)
+
+vcpkg_install_cmake()
+vcpkg_copy_pdbs()
+vcpkg_fixup_cmake_targets(CONFIG_PATH share/cmake TARGET_PATH share)
+
+if(TOOL_NAMES)
+    vcpkg_copy_tools(TOOL_NAMES ${TOOL_NAMES} AUTO_CLEAN)
+endif()
+
+file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/share")
+file(REMOVE_RECURSE "${CURRENT_PACKAGES_DIR}/debug/include")
+
+file(INSTALL ${SOURCE_PATH}/LICENSE DESTINATION ${CURRENT_PACKAGES_DIR}/share/${PORT} RENAME copyright)
diff --git a/ports/nifticlib/zlib_include.patch b/ports/nifticlib/zlib_include.patch
new file mode 100644
index 000000000..1ef462b7f
--- /dev/null
+++ b/ports/nifticlib/zlib_include.patch
@@ -0,0 +1,12 @@
+diff --git a/CMakeLists.txt b/CMakeLists.txt
+index 54150d739..c3ca8fe50 100644
+--- a/CMakeLists.txt	
++++ b/CMakeLists.txt
+@@ -77,6 +77,7 @@ set_if_not_defined(ZNZ_COMPILE_DEF "")
+ if(NOT NIFTI_ZLIB_LIBRARIES) # If using a custom zlib library, skip the find package
+   ###  USE AS STAND ALONE PACKAGE
+   find_package(ZLIB REQUIRED)
++  include_directories(${ZLIB_INCLUDE_DIRS})
+   set(NIFTI_ZLIB_LIBRARIES ${ZLIB_LIBRARIES})
+ endif()
+ #message(STATUS "---------------------ZLIB -${NIFTI_ZLIB_LIBRARIES}--")