[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>

4 files changed, 138 insertions, 0 deletions

diff --git a/ports/minc/CONTROL b/ports/minc/CONTROL
new file mode 100644
index 000000000..6cd1d5499
--- /dev/null
+++ b/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]
\ No newline at end of file
diff --git a/ports/minc/build.patch b/ports/minc/build.patch
new file mode 100644
index 000000000..d0275c20d
--- /dev/null
+++ b/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}
++     ${LIBMINC_INSTALL_LIB_DIR}/cmake
+     COMPONENT Development)
+   
+ ENDIF(LIBMINC_INSTALL_LIB_DIR AND NOT LIBMINC_INSTALL_NO_DEVELOPMENT)
+diff --git a/config.h.cmake b/config.h.cmake
+index 9ceffa8fc..21c2f3baf 100644
+--- a/config.h.cmake	
++++ b/config.h.cmake
+@@ -1,4 +1,8 @@
+ /* various defines */
++#ifdef _MSC_VER
++#define strcasecmp _stricmp 
++#define strncasecmp _strnicmp 
++#endif
+ 
+ #ifndef MINC2
+ #define MINC2 @MINC2@
+diff --git a/libcommon/minc_config.c b/libcommon/minc_config.c
+index 531ef108e..5472d9274 100644
+--- a/libcommon/minc_config.c	
++++ b/libcommon/minc_config.c
+@@ -20,14 +20,6 @@
+ 
+ #include "minc_config.h"
+ 
+-#ifdef _MSC_VER
+-#define snprintf _snprintf 
+-#define vsnprintf _vsnprintf 
+-#define strcasecmp _stricmp 
+-#define strncasecmp _strnicmp 
+-#endif
+-
+-
+ static const char *_CONFIG_VAR[]=
+   {
+       "MINC_FORCE_V2",
diff --git a/ports/minc/config.patch b/ports/minc/config.patch
new file mode 100644
index 000000000..a726b9a57
--- /dev/null
+++ b/ports/minc/config.patch
@@ -0,0 +1,15 @@
+diff --git a/LIBMINCConfig.cmake.in b/LIBMINCConfig.cmake.in
+index 7790597b2..c041b685a 100644
+--- a/LIBMINCConfig.cmake.in	
++++ b/LIBMINCConfig.cmake.in
+@@ -1,3 +1,4 @@
++set(_IMPORT_PREFIX "${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
diff --git a/ports/minc/portfile.cmake b/ports/minc/portfile.cmake
new file mode 100644
index 000000000..4b9ff63b1
--- /dev/null
+++ b/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)