[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>

2 files changed, 313 insertions, 0 deletions

diff --git a/ports/itk/rtk/already_defined.patch b/ports/itk/rtk/already_defined.patch
new file mode 100644
index 000000000..60b75e3eb
--- /dev/null
+++ b/ports/itk/rtk/already_defined.patch
@@ -0,0 +1,100 @@
+diff --git a/include/rtkProjectionGeometry.h b/include/rtkProjectionGeometry.h
+index e5831611f..73ed2b74f 100644
+--- a/include/rtkProjectionGeometry.h
++++ b/include/rtkProjectionGeometry.h
+@@ -23,6 +23,7 @@
+ 
+ #include <vector>
+ 
++#include "RTKExport.h"
+ #include "rtkMacro.h"
+ 
+ namespace rtk
+@@ -67,25 +68,18 @@ public:
+    * with the i-th matrix provides the physical coordinate on
+    * the i-th projection.
+    */
+-  const std::vector<MatrixType> &
+-  GetMatrices() const
+-  {
+-    return this->m_Matrices;
+-  }
++  itkGetConstReferenceMacro(Matrices,std::vector<MatrixType>)
+ 
+   /** Get the i-th projection matrix. */
+   MatrixType
+-  GetMatrix(const unsigned int i) const
+-  {
+-    return this->m_Matrices[i];
+-  }
++  GetMatrix(const unsigned int i) const;
+ 
+   /** Empty the geometry object. */
+   virtual void
+   Clear();
+ 
+ protected:
+-  ProjectionGeometry() = default;
++  ProjectionGeometry();
+   ~ProjectionGeometry() override = default;
+ 
+   void
+@@ -93,11 +87,7 @@ protected:
+ 
+   /** Add projection matrix */
+   virtual void
+-  AddMatrix(const MatrixType & m)
+-  {
+-    this->m_Matrices.push_back(m);
+-    this->Modified();
+-  }
++  AddMatrix(const MatrixType & m);
+ 
+ private:
+   /** Projection matrices */
+@@ -105,6 +95,9 @@ private:
+ };
+ } // namespace rtk
+ 
+-#include "rtkProjectionGeometry.hxx"
++#ifndef ITK_MANUAL_INSTANTIATION
++#   include "rtkProjectionGeometry.hxx"
++#endif
++
+ 
+ #endif // rtkProjectionGeometry_h
+diff --git a/include/rtkProjectionGeometry.hxx b/include/rtkProjectionGeometry.hxx
+index 192265812..97dfe8c3a 100644
+--- a/include/rtkProjectionGeometry.hxx
++++ b/include/rtkProjectionGeometry.hxx
+@@ -23,6 +23,8 @@
+ 
+ namespace rtk
+ {
++template <unsigned int TDimension>
++ProjectionGeometry<TDimension>::ProjectionGeometry() = default;
+ 
+ template <unsigned int TDimension>
+ void
+@@ -43,6 +45,21 @@ ProjectionGeometry<TDimension>::Clear()
+   this->Modified();
+ }
+ 
++template <unsigned int TDimension>
++typename ProjectionGeometry<TDimension>::MatrixType
++ProjectionGeometry<TDimension>::GetMatrix(const unsigned int i) const
++{
++  return this->m_Matrices[i];
++}
++
++template <unsigned int TDimension>
++void
++ProjectionGeometry<TDimension>::AddMatrix(const typename ProjectionGeometry<TDimension>::MatrixType & m)
++{
++  this->m_Matrices.push_back(m);
++  this->Modified();
++}
++
+ } // namespace rtk
+ 
+ #endif // rtkProjectionGeometry_hxx
diff --git a/ports/itk/rtk/unresolved.patch b/ports/itk/rtk/unresolved.patch
new file mode 100644
index 000000000..e2209ec75
--- /dev/null
+++ b/ports/itk/rtk/unresolved.patch
@@ -0,0 +1,213 @@
+diff --git a/include/rtkDCMImagXImageIO.h b/include/rtkDCMImagXImageIO.h
+index 2a70ae046..69abb409e 100644
+--- a/include/rtkDCMImagXImageIO.h
++++ b/include/rtkDCMImagXImageIO.h
+@@ -18,7 +18,7 @@
+ 
+ #ifndef rtkDCMImagXImageIO_h
+ #define rtkDCMImagXImageIO_h
+-
++#include "RTKExport.h"
+ #include <itkGDCMImageIO.h>
+ 
+ #include "rtkMacro.h"
+@@ -32,7 +32,7 @@ namespace rtk
+  *
+  * \ingroup RTK
+  */
+-class DCMImagXImageIO : public itk::GDCMImageIO
++class RTK_EXPORT DCMImagXImageIO : public itk::GDCMImageIO
+ {
+ public:
+   ITK_DISALLOW_COPY_AND_ASSIGN(DCMImagXImageIO);
+diff --git a/include/rtkEdfImageIO.h b/include/rtkEdfImageIO.h
+index 66499c56b..7b16fbc5a 100644
+--- a/include/rtkEdfImageIO.h
++++ b/include/rtkEdfImageIO.h
+@@ -18,7 +18,7 @@
+ 
+ #ifndef rtkEdfImageIO_h
+ #define rtkEdfImageIO_h
+-
++#include "RTKExport.h"
+ #include <itkImageIOBase.h>
+ #include <fstream>
+ #include <cstring>
+@@ -36,7 +36,7 @@ namespace rtk
+  *
+  * \ingroup RTK IOFilters
+  */
+-class EdfImageIO : public itk::ImageIOBase
++class RTK_EXPORT EdfImageIO : public itk::ImageIOBase
+ {
+ public:
+   ITK_DISALLOW_COPY_AND_ASSIGN(EdfImageIO);
+diff --git a/include/rtkHisImageIO.h b/include/rtkHisImageIO.h
+index 2ef2005dd..95449b8a6 100644
+--- a/include/rtkHisImageIO.h
++++ b/include/rtkHisImageIO.h
+@@ -19,6 +19,8 @@
+ #ifndef rtkHisImageIO_h
+ #define rtkHisImageIO_h
+ 
++#include "RTKExport.h"
++
+ // itk include
+ #include <itkImageIOBase.h>
+ #include "rtkMacro.h"
+@@ -35,7 +37,7 @@ namespace rtk
+  *
+  * \ingroup RTK IOFilters
+  */
+-class HisImageIO : public itk::ImageIOBase
++class RTK_EXPORT HisImageIO : public itk::ImageIOBase
+ {
+ public:
+   /** Standard class type alias. */
+diff --git a/include/rtkHncImageIO.h b/include/rtkHncImageIO.h
+index 7b9539bde..dc9dca759 100644
+--- a/include/rtkHncImageIO.h
++++ b/include/rtkHncImageIO.h
+@@ -19,9 +19,11 @@
+ #ifndef rtkHncImageIO_h
+ #define rtkHncImageIO_h
+ 
++#include "RTKExport.h"
++
+ // itk include
+ #include <itkImageIOBase.h>
+-#include "itksys/SystemTools.hxx"
++//#include "itksys/SystemTools.hxx"
+ 
+ #if defined(_MSC_VER) && (_MSC_VER < 1600)
+ // SR: taken from
+@@ -43,7 +45,7 @@ namespace rtk
+  *
+  * \ingroup RTK IOFilters
+  */
+-class HncImageIO : public itk::ImageIOBase
++class RTK_EXPORT HncImageIO : public itk::ImageIOBase
+ {
+ public:
+   /** Standard class type alias. */
+diff --git a/include/rtkHncImageIOFactory.h b/include/rtkHncImageIOFactory.h
+index 2bca8f77e..1d5a97938 100644
+--- a/include/rtkHncImageIOFactory.h
++++ b/include/rtkHncImageIOFactory.h
+@@ -38,7 +38,7 @@ namespace rtk
+  *
+  * \ingroup RTK IOFilters
+  */
+-class HncImageIOFactory : public itk::ObjectFactoryBase
++class RTK_EXPORT HncImageIOFactory : public itk::ObjectFactoryBase
+ {
+ public:
+   /** Standard class type alias. */
+diff --git a/include/rtkHndImageIO.h b/include/rtkHndImageIO.h
+index 5a07897cc..5f843362a 100644
+--- a/include/rtkHndImageIO.h
++++ b/include/rtkHndImageIO.h
+@@ -19,6 +19,8 @@
+ #ifndef rtkHndImageIO_h
+ #define rtkHndImageIO_h
+ 
++#include "RTKExport.h"
++
+ // itk include
+ #include <itkImageIOBase.h>
+ 
+@@ -43,7 +45,7 @@ namespace rtk
+  *
+  * \ingroup RTK IOFilters
+  */
+-class HndImageIO : public itk::ImageIOBase
++class RTK_EXPORT HndImageIO : public itk::ImageIOBase
+ {
+ public:
+   /** Standard class type alias. */
+diff --git a/include/rtkImagXImageIO.h b/include/rtkImagXImageIO.h
+index d69e9a790..d6cc8388e 100644
+--- a/include/rtkImagXImageIO.h
++++ b/include/rtkImagXImageIO.h
+@@ -18,7 +18,7 @@
+ 
+ #ifndef rtkImagXImageIO_h
+ #define rtkImagXImageIO_h
+-
++#include "RTKExport.h"
+ #include <itkImageIOBase.h>
+ #include <fstream>
+ #include <cstring>
+@@ -34,7 +34,7 @@ namespace rtk
+  *
+  * \ingroup RTK
+  */
+-class ImagXImageIO : public itk::ImageIOBase
++class RTK_EXPORT ImagXImageIO : public itk::ImageIOBase
+ {
+ public:
+   /** Standard class type alias. */
+diff --git a/include/rtkOraImageIO.h b/include/rtkOraImageIO.h
+index ece525a42..2d5332872 100644
+--- a/include/rtkOraImageIO.h
++++ b/include/rtkOraImageIO.h
+@@ -19,6 +19,8 @@
+ #ifndef rtkOraImageIO_h
+ #define rtkOraImageIO_h
+ 
++#include "RTKExport.h"
++
+ // This is done to avoid any interference with zlib
+ #ifdef OF
+ #  undef OF
+@@ -41,7 +43,7 @@ namespace rtk
+  *
+  * \ingroup RTK IOFilters
+  */
+-class OraImageIO : public itk::MetaImageIO
++class RTK_EXPORT OraImageIO : public itk::MetaImageIO
+ {
+ public:
+   /** Standard class type alias. */
+diff --git a/include/rtkXRadImageIO.h b/include/rtkXRadImageIO.h
+index a72c934e4..0a92afa22 100644
+--- a/include/rtkXRadImageIO.h
++++ b/include/rtkXRadImageIO.h
+@@ -19,6 +19,7 @@
+ #ifndef rtkXRadImageIO_h
+ #define rtkXRadImageIO_h
+ 
++#include "RTKExport.h"
+ #include <itkImageIOBase.h>
+ #include <fstream>
+ #include <cstring>
+@@ -37,7 +38,7 @@ namespace rtk
+  *
+  * \ingroup RTK IOFilters
+  */
+-class XRadImageIO : public itk::ImageIOBase
++class RTK_EXPORT XRadImageIO : public itk::ImageIOBase
+ {
+ public:
+   /** Standard class type alias. */
+diff --git a/include/rtkXimImageIO.h b/include/rtkXimImageIO.h
+index ae789dbf9..741f05183 100644
+--- a/include/rtkXimImageIO.h
++++ b/include/rtkXimImageIO.h
+@@ -19,6 +19,7 @@
+ #ifndef rtkXimImageIO_h
+ #define rtkXimImageIO_h
+ 
++#include "RTKExport.h"
+ #include "rtkMacro.h"
+ 
+ // itk include
+@@ -43,7 +44,7 @@ namespace rtk
+  *
+  * \ingroup RTK IOFilters
+  */
+-class XimImageIO : public itk::ImageIOBase
++class RTK_EXPORT XimImageIO : public itk::ImageIOBase
+ {
+ public:
+   /** Standard class type alias. */