[VTK/vtk-m] Update VTK to 9.0 and add vtk-m (#11148)

* [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

* bump control

* Update FindHDF5.cmake

* Update pegtl.patch

* Update ports/vtk/pegtl.patch

Co-authored-by: nicole mazzuca <mazzucan@outlook.com>

* [vtk] refactor portfile, added a few deps on [core] and added feature cuda

* [vtk] pegtl.patch: Add additional found message

* [vtk-m] add more documentation comments

* [vtk] fix string replacement

Co-authored-by: nicole mazzuca <mazzucan@outlook.com>

3 files changed, 82 insertions, 7 deletions

diff --git a/ports/vtk-dicom/CONTROL b/ports/vtk-dicom/CONTROL
index 2041f21e1..e8e3494d8 100644
--- a/ports/vtk-dicom/CONTROL
+++ b/ports/vtk-dicom/CONTROL
@@ -1,7 +1,8 @@
 Source: vtk-dicom

-Version: 0.8.12
+Version: 0.8.12-1
 Description: DICOM for VTK

-Build-Depends: vtk, zlib

+Homepage: https://github.com/dgobbi/vtk-dicom

+Build-Depends: vtk[core], zlib

 

 Feature: gdcm

 Description: Use gdcm for decompressing DICOM files.

diff --git a/ports/vtk-dicom/portfile.cmake b/ports/vtk-dicom/portfile.cmake
index bd137e61e..171a046a2 100644
--- a/ports/vtk-dicom/portfile.cmake
+++ b/ports/vtk-dicom/portfile.cmake
@@ -1,11 +1,10 @@
-include(vcpkg_common_functions)

-

 vcpkg_from_github(

     OUT_SOURCE_PATH SOURCE_PATH

     REPO dgobbi/vtk-dicom

     REF 5034c68450de857b70fbe4a4b9f8dddb62badef3 # v0.8.12
     SHA512 bad1ed6a4a412402a2cd69e5f85b2b73f1ee7ea46a6bbcac31c5f66d07ae006679ffbd9a3c70f9baa1b05b1af0a2d4ca0efc34ec0a85a92f5116b900e81635cd

     HEAD_REF master

+    PATCHES std.patch # similar patch is already in master

 )

 

 if ("gdcm" IN_LIST FEATURES)

@@ -21,22 +20,23 @@ if(USE_GDCM)
         -DUSE_DCMTK=OFF

     )

 endif()

-

+vcpkg_find_acquire_program(PYTHON3)

 vcpkg_configure_cmake(

     SOURCE_PATH ${SOURCE_PATH}

     PREFER_NINJA

     OPTIONS

         -DBUILD_PROGRAMS=OFF

         -DBUILD_EXAMPLES=OFF

+        "-DPython3_EXECUTABLE=${PYTHON3}"

         ${ADDITIONAL_OPTIONS}

 )

 

 vcpkg_install_cmake()

+vcpkg_fixup_cmake_targets(CONFIG_PATH lib/cmake)

 vcpkg_copy_pdbs()

 

 file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/include)

 file(REMOVE_RECURSE ${CURRENT_PACKAGES_DIR}/debug/share)

 

 # Handle copyright

-file(COPY ${SOURCE_PATH}/Copyright.txt DESTINATION ${CURRENT_PACKAGES_DIR}/share/vtk-dicom)

-file(RENAME ${CURRENT_PACKAGES_DIR}/share/vtk-dicom/Copyright.txt ${CURRENT_PACKAGES_DIR}/share/vtk-dicom/copyright)

+file(INSTALL ${SOURCE_PATH}/Copyright.txt DESTINATION ${CURRENT_PACKAGES_DIR}/share/${PORT} RENAME copyright)

diff --git a/ports/vtk-dicom/std.patch b/ports/vtk-dicom/std.patch
new file mode 100644
index 000000000..59160f089
--- /dev/null
+++ b/ports/vtk-dicom/std.patch
@@ -0,0 +1,74 @@
+diff --git a/Source/vtkScancoCTReader.cxx b/Source/vtkScancoCTReader.cxx
+index a71f2e46e..afe202ffc 100644
+--- a/Source/vtkScancoCTReader.cxx	
++++ b/Source/vtkScancoCTReader.cxx
+@@ -176,7 +176,7 @@ int vtkScancoCTReader::CheckVersion(const char header[16])
+ //----------------------------------------------------------------------------
+ int vtkScancoCTReader::CanReadFile(const char *filename)
+ {
+-  ifstream infile(filename, ios::in | ios::binary);
++  std::ifstream infile(filename, ios::in | ios::binary);
+ 
+   bool canRead = false;
+   if (infile.good())
+@@ -409,7 +409,7 @@ void vtkScancoCTReader::StripString(char *dest, const char *cp, size_t l)
+ }
+ 
+ //----------------------------------------------------------------------------
+-int vtkScancoCTReader::ReadISQHeader(ifstream *file, unsigned long bytesRead)
++int vtkScancoCTReader::ReadISQHeader(std::ifstream *file, unsigned long bytesRead)
+ {
+   if (bytesRead < 512)
+   {
+@@ -620,7 +620,7 @@ int vtkScancoCTReader::ReadISQHeader(ifstream *file, unsigned long bytesRead)
+ }
+ 
+ //----------------------------------------------------------------------------
+-int vtkScancoCTReader::ReadAIMHeader(ifstream *file, unsigned long bytesRead)
++int vtkScancoCTReader::ReadAIMHeader(std::ifstream *file, unsigned long bytesRead)
+ {
+   if (bytesRead < 160)
+   {
+@@ -987,7 +987,7 @@ int vtkScancoCTReader::RequestInformation(
+   const char *ufilename = filename;
+ #endif
+ 
+-  ifstream infile(ufilename, ios::in | ios::binary);
++  std::ifstream infile(ufilename, ios::in | ios::binary);
+   if (!infile.good())
+   {
+     vtkErrorMacro("Cannot open file " << filename);
+@@ -1115,7 +1115,7 @@ int vtkScancoCTReader::RequestData(
+     static_cast<unsigned char *>(data->GetScalarPointer());
+ 
+   // open the file
+-  ifstream infile(filename, ios::in | ios::binary);
++  std::ifstream infile(filename, ios::in | ios::binary);
+   if (!infile.good())
+   {
+     vtkErrorMacro("Cannot open file " << filename);
+diff --git a/Source/vtkScancoCTReader.h b/Source/vtkScancoCTReader.h
+index ca31d7572..240d532f2 100644
+--- a/Source/vtkScancoCTReader.h	
++++ b/Source/vtkScancoCTReader.h
+@@ -34,6 +34,7 @@
+ #ifndef vtkScancoCTReader_h
+ #define vtkScancoCTReader_h
+ 
++#include <iosfwd>
+ #include "vtkImageReader2.h"
+ #include "vtkDICOMModule.h" // For export macro
+ #include "vtkDICOMConfig.h" // For configuration details
+@@ -185,10 +186,10 @@ protected:
+   void InitializeHeader();
+ 
+   //! Read an ISQ header.
+-  int ReadISQHeader(ifstream *file, unsigned long bytesRead);
++  int ReadISQHeader(std::ifstream *file, unsigned long bytesRead);
+ 
+   //! Read AIM header.
+-  int ReadAIMHeader(ifstream *file, unsigned long bytesRead);
++  int ReadAIMHeader(std::ifstream *file, unsigned long bytesRead);
+ 
+   //! Check the file header to see what type of file it is.
+   /*!