[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, 100 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