COMP: Build the VTK examples against ITK 5.4, ITK 6, and VTK 9

.github/workflows/build-test-package.yml

@@ -12,7 +12,7 @@ on:
 
 jobs:
   cxx-build-workflow-itk5:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.6
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v5.4.7
 
   cxx-build-workflow-itk6:
     uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-cxx.yml@v6.0b02
@@ -21,7 +21,7 @@ jobs:
       itk-git-tag: '5d31af3cfdf2071d14dfc331d169111487b80597'
 
   python-build-workflow-itk5:
-    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.6
+    uses: InsightSoftwareConsortium/ITKRemoteModuleBuildTestPackageAction/.github/workflows/build-test-package-python.yml@v5.4.7
     with:
       test-notebooks: false
 

CMakeLists.txt

@@ -11,64 +11,37 @@ endif()
 
 option(LSTK_USE_VTK "Build visualization helper tools." OFF)
 if(LSTK_USE_VTK)
-  if(NOT COMMAND vtk_module_config)
-    macro(vtk_module_config ns)
-       foreach(arg ${ARGN})
-        if(${arg} MATCHES "^[Vv][Tt][Kk]")
-          string(REGEX REPLACE "^[Vv][Tt][Kk]" "" _arg ${arg})
-        else()
-          set(_arg ${arg})
-        endif()
-        set(${ns}_LIBRARIES ${${ns}_LIBRARIES} VTK::${_arg})
-       endforeach()
-    endmacro()
-
-    if(NOT VTK_RENDERING_BACKEND)
-      set(VTK_RENDERING_BACKEND OpenGL2)
-    endif()
-  endif()
-
-  if(NOT VTK_RENDERING_BACKEND)
-    if(NOT COMMAND vtk_module_config)
-      set(VTK_RENDERING_BACKEND OpenGL2)
-    else()
-      set(VTK_RENDERING_BACKEND OpenGL)
-    endif()
-  endif()
-
-  set(_target_freetypeopengl)
-  if(TARGET ${_target_prefix}RenderingFreeType${VTK_RENDERING_BACKEND})
-    set(_target_freetypeopengl ${_target_prefix}RenderingFreeType${VTK_RENDERING_BACKEND})
+  find_package(
+    VTK 9.0 REQUIRED
+    COMPONENTS
+      CommonCore
+      FiltersCore
+      FiltersGeneral
+      FiltersSources
+      ImagingCore
+      InteractionImage
+      InteractionStyle
+      InteractionWidgets
+      IOGeometry
+      IOImage
+      IOLegacy
+      RenderingCore
+      RenderingFreeType
+      RenderingOpenGL2
+      RenderingVolume
+      RenderingVolumeOpenGL2
+      vtksys
+  )
+  # ITK 6 exports one interface library per module; ITK 5.4 provides only the list variable.
+  if(TARGET ITK::LesionSizingToolkitModule)
+    set(_lstk_libraries ITK::LesionSizingToolkitModule)
+  elseif(TARGET LesionSizingToolkitModule)
+    set(_lstk_libraries LesionSizingToolkitModule)
+  else()
+    set(_lstk_libraries ${LesionSizingToolkit_LIBRARIES})
   endif()
-
-  set(_required_vtk_libraries
-    ${_target_prefix}RenderingVolume
-    #${_target_prefix}Rendering${VTK_RENDERING_BACKEND}
-    ${_target_prefix}IOGeometry
-    ${_target_prefix}IOLegacy
-    ${_target_prefix}IOImage
-    ${_target_prefix}InteractionWidgets
-    ${_target_prefix}InteractionImage
-    )
-
-  vtk_module_config(ITK_VTK_LSTK
-    ${_required_vtk_libraries}
-    )
-
-  set(ITK_VTK_LSTK_LIBRARIES ${LesionSizingToolkit_LIBRARIES} ${_required_vtk_libraries})
-
-  # The VTK DICOMParser and vtkmetaio includes conflict with the ITK
-  # versions. Here we remove them from the include directories.
-  #
-  string(REGEX REPLACE "[^;]*MetaIO;"
-           "" ITK_VTK_LSTK_INCLUDE_DIRS "${ITK_VTK_LSTK_INCLUDE_DIRS}")
-  string(REGEX REPLACE "[^;]*vtkmetaio;"
-           "" ITK_VTK_LSTK_INCLUDE_DIRS "${ITK_VTK_LSTK_INCLUDE_DIRS}")
-  string(REGEX REPLACE "[^;]*DICOMParser;"
-           "" ITK_VTK_LSTK_INCLUDE_DIRS "${ITK_VTK_LSTK_INCLUDE_DIRS}")
-
-  # Add preprocessor definitions needed to use VTK.
-  set_property(DIRECTORY APPEND PROPERTY COMPILE_DEFINITIONS ${ITK_VTK_LSTK_VTK_DEFINITIONS})
+  set(ITK_VTK_LSTK_LIBRARIES ${_lstk_libraries} ${ITK_LIBRARIES} ${VTK_LIBRARIES})
+  include_directories("${LesionSizingToolkit_SOURCE_DIR}/include")
 
   add_subdirectory(Examples)
   add_subdirectory(Utilities)

Examples/CMakeLists.txt

@@ -6,4 +6,5 @@ add_executable( LesionSegmentation
    LesionSegmentation.cxx
    itkLesionSegmentationCommandLineProgressReporter.cxx )
 target_link_libraries( LesionSegmentation ${ITK_VTK_LSTK_LIBRARIES} )
+vtk_module_autoinit( TARGETS LesionSegmentation MODULES ${VTK_LIBRARIES} )
 

Examples/LesionSegmentation.cxx

@@ -151,7 +151,7 @@ GetImage(std::string dir, bool ignoreDirection)
     catch (itk::ExceptionObject & ex)
     {
       std::cout << ex << std::endl;
-      return NULL;
+      return nullptr;
     }
 
 
@@ -172,10 +172,10 @@ GetImage(std::string dir, bool ignoreDirection)
   catch (itk::ExceptionObject & ex)
   {
     std::cout << ex << std::endl;
-    return NULL;
+    return nullptr;
   }
 
-  return NULL;
+  return nullptr;
 }
 
 // --------------------------------------------------------------------------

Examples/LesionSegmentationCLI.h

@@ -125,8 +125,8 @@ class LesionSegmentationCLI : public MetaCommand
       seeds[0];
       for (int i = 0; i < 3; i++)
       {
-        this->ROI[2 * i] = seeds[0].GetPosition()[i] - this->GetValueAsFloat("MaximumRadius");
-        this->ROI[2 * i + 1] = seeds[0].GetPosition()[i] + this->GetValueAsFloat("MaximumRadius");
+        this->ROI[2 * i] = seeds[0].GetPositionInObjectSpace()[i] - this->GetValueAsFloat("MaximumRadius");
+        this->ROI[2 * i + 1] = seeds[0].GetPositionInObjectSpace()[i] + this->GetValueAsFloat("MaximumRadius");
       }
     }
     return this->ROI;
@@ -252,7 +252,7 @@ class LesionSegmentationCLI : public MetaCommand
         exit(-1);
       }
 
-      seeds[i].SetPosition(sx, sy, sz);
+      seeds[i].SetPositionInObjectSpace(sx, sy, sz);
     }
     return seeds;
   }

Examples/itkLesionSegmentationCommandLineProgressReporter.h

@@ -17,11 +17,11 @@
  *=========================================================================*/
 
 #ifndef itkLesionSegmentationCommandLineProgressReporter_h
-#  define itkLesionSegmentatioCommandLineProgressReporter_h
+#define itkLesionSegmentationCommandLineProgressReporter_h
 
-#  include "itkLesionSegmentationImageFilter8.h"
-#  include "itkCommand.h"
-#  include <string>
+#include "itkLesionSegmentationImageFilter8.h"
+#include "itkCommand.h"
+#include <string>
 
 namespace itk
 {
@@ -45,10 +45,10 @@ class ITKCommon_EXPORT LesionSegmentationCommandLineProgressReporter : public Co
   // the instance invoking the event; eid is the event id (see
   // vtkCommand.h); and calldata is information sent when the callback
   // was invoked (e.g., progress value in the vtkCommand::ProgressEvent).
-  virtual void
-  Execute(const Object * caller, const EventObject & event);
-  virtual void
-  Execute(Object * caller, const EventObject & event);
+  void
+  Execute(const Object * caller, const EventObject & event) override;
+  void
+  Execute(Object * caller, const EventObject & event) override;
 
   void
   SetReportProgress(int i)

Utilities/Visualization/CMakeLists.txt

@@ -4,16 +4,20 @@ include_directories(${Visualization_SOURCE_DIR})
 
 add_executable(ViewImageAndSegmentationSurface ViewImageAndSegmentationSurface.cxx )
 target_link_libraries(ViewImageAndSegmentationSurface ${ITK_VTK_LSTK_LIBRARIES})
+vtk_module_autoinit(TARGETS ViewImageAndSegmentationSurface MODULES ${VTK_LIBRARIES})
 
 add_executable(ViewImageSlicesAndSegmentationContours
   ViewImageSlicesAndSegmentationContours.cxx
   vtkContourVisualizationModule.cxx
   )
 target_link_libraries(ViewImageSlicesAndSegmentationContours ${ITK_VTK_LSTK_LIBRARIES})
+vtk_module_autoinit(TARGETS ViewImageSlicesAndSegmentationContours MODULES ${VTK_LIBRARIES})
 
 add_executable(LesionSurfaceExtraction LesionSurfaceExtraction.cxx )
 target_link_libraries(LesionSurfaceExtraction ${ITK_VTK_LSTK_LIBRARIES})
+vtk_module_autoinit(TARGETS LesionSurfaceExtraction MODULES ${VTK_LIBRARIES})
 
 add_executable(IsoSurfaceVolumeEstimation IsoSurfaceVolumeEstimation.cxx )
 target_link_libraries(IsoSurfaceVolumeEstimation ${ITK_VTK_LSTK_LIBRARIES})
+vtk_module_autoinit(TARGETS IsoSurfaceVolumeEstimation MODULES ${VTK_LIBRARIES})
 

Utilities/Visualization/LesionSurfaceExtraction.cxx

@@ -24,6 +24,8 @@
 #include "vtksys/SystemTools.hxx"
 #include "vtkVersion.h"
 
+#include <iostream>
+
 
 #define VTK_CREATE(type, name) vtkSmartPointer<type> name = vtkSmartPointer<type>::New()
 

Utilities/Visualization/ViewImageSlicesAndSegmentationContours.cxx

@@ -88,11 +88,11 @@ main(int argc, char * argv[])
       return EXIT_FAILURE;
     }
 
-    std::cout << "Number of objects in the group:" << group->GetNumberOfObjects(1) << std::endl;
+    std::cout << "Number of objects in the group:" << group->GetNumberOfChildren(1) << std::endl;
 
-    using ObjectListType = SpatialObjectReaderType::GroupType::ObjectListType;
+    using ObjectListType = SpatialObjectReaderType::GroupType::ChildrenListType;
 
-    ObjectListType * groupChildren = group->GetObjects(999999);
+    ObjectListType * groupChildren = group->GetChildren(999999);
 
     ObjectListType::const_iterator spatialObjectItr = groupChildren->begin();
 
@@ -119,7 +119,7 @@ main(int argc, char * argv[])
     const LandmarkPointListType & points = landmarkSpatialObject->GetPoints();
 
     // Grab the first point in the list of seed points
-    PointType point = points[0].GetPosition();
+    PointType point = points[0].GetPositionInObjectSpace();
 
     std::cout << "Seed point = " << point << std::endl;
 

include/itkFeatureAggregator.h

@@ -102,8 +102,6 @@ class ITK_TEMPLATE_EXPORT FeatureAggregator : public FeatureGenerator<NDimension
   const InputFeatureType *
   GetInputFeature(unsigned int featureId) const;
 
-  ProgressAccumulator::Pointer m_ProgressAccumulator;
-
 private:
   using FeatureGeneratorPointer = typename FeatureGeneratorType::Pointer;
   using FeatureGeneratorArrayType = std::vector<FeatureGeneratorPointer>;

include/itkFeatureAggregator.hxx

@@ -36,9 +36,6 @@ FeatureAggregator<NDimension>::FeatureAggregator()
   typename OutputImageSpatialObjectType::Pointer outputObject = OutputImageSpatialObjectType::New();
 
   this->ProcessObject::SetNthOutput(0, outputObject.GetPointer());
-
-  this->m_ProgressAccumulator = ProgressAccumulator::New();
-  this->m_ProgressAccumulator->SetMiniPipelineFilter(this);
 }
 
 
@@ -143,14 +140,17 @@ template <unsigned int NDimension>
 void
 FeatureAggregator<NDimension>::UpdateAllFeatureGenerators()
 {
+  ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+  progress->SetMiniPipelineFilter(this);
+
   auto gitr = this->m_FeatureGenerators.begin();
   auto gend = this->m_FeatureGenerators.end();
 
   while (gitr != gend)
   {
     // Assuming that most of the time is spent in generating the features and
     // hardly negligible time is spent in consolidating the features
-    this->m_ProgressAccumulator->RegisterInternalFilter(*gitr, 1.0 / this->m_FeatureGenerators.size());
+    progress->RegisterInternalFilter(*gitr, 1.0 / this->m_FeatureGenerators.size());
 
     (*gitr)->Update();
     ++gitr;

include/itkLesionSegmentationMethod.h

@@ -125,12 +125,10 @@ class ITK_TEMPLATE_EXPORT LesionSegmentationMethod : public ProcessObject
 
   SegmentationModulePointer m_SegmentationModule;
 
-  ProgressAccumulator::Pointer m_ProgressAccumulator;
-
 
   /** This method calls the Update() method of each one of the feature generators */
   void
-  UpdateAllFeatureGenerators();
+  UpdateAllFeatureGenerators(ProgressAccumulator * progress);
 
   /** This method compares the number of available features against the number
    * of expected features, and it will throw an exception if they do not match.
@@ -143,7 +141,7 @@ class ITK_TEMPLATE_EXPORT LesionSegmentationMethod : public ProcessObject
   ConnectFeaturesToSegmentationModule();
 
   void
-  ExecuteSegmentationModule();
+  ExecuteSegmentationModule(ProgressAccumulator * progress);
 };
 
 } // end namespace itk

include/itkLesionSegmentationMethod.hxx

@@ -42,9 +42,6 @@ LesionSegmentationMethod<NDimension>::LesionSegmentationMethod()
   typename OutputSpatialObjectType::Pointer outputObject = OutputSpatialObjectType::New();
 
   this->ProcessObject::SetNthOutput(0, outputObject.GetPointer());
-
-  this->m_ProgressAccumulator = ProgressAccumulator::New();
-  this->m_ProgressAccumulator->SetMiniPipelineFilter(this);
 }
 
 
@@ -105,13 +102,16 @@ LesionSegmentationMethod<NDimension>::GenerateData()
     itkExceptionMacro("Segmentation Module has not been connected");
   }
 
-  this->UpdateAllFeatureGenerators();
+  ProgressAccumulator::Pointer progress = ProgressAccumulator::New();
+  progress->SetMiniPipelineFilter(this);
+
+  this->UpdateAllFeatureGenerators(progress);
 
   this->VerifyNumberOfAvailableFeaturesMatchedExpectations();
 
   this->ConnectFeaturesToSegmentationModule();
 
-  this->ExecuteSegmentationModule();
+  this->ExecuteSegmentationModule(progress);
 }
 
 
@@ -120,14 +120,14 @@ LesionSegmentationMethod<NDimension>::GenerateData()
  */
 template <unsigned int NDimension>
 void
-LesionSegmentationMethod<NDimension>::UpdateAllFeatureGenerators()
+LesionSegmentationMethod<NDimension>::UpdateAllFeatureGenerators(ProgressAccumulator * progress)
 {
   auto gitr = this->m_FeatureGenerators.begin();
   auto gend = this->m_FeatureGenerators.end();
 
   while (gitr != gend)
   {
-    this->m_ProgressAccumulator->RegisterInternalFilter(*gitr, 0.5 / this->m_FeatureGenerators.size());
+    progress->RegisterInternalFilter(*gitr, 0.5 / this->m_FeatureGenerators.size());
     (*gitr)->Update();
     ++gitr;
   }
@@ -164,9 +164,9 @@ LesionSegmentationMethod<NDimension>::ConnectFeaturesToSegmentationModule()
 
 template <unsigned int NDimension>
 void
-LesionSegmentationMethod<NDimension>::ExecuteSegmentationModule()
+LesionSegmentationMethod<NDimension>::ExecuteSegmentationModule(ProgressAccumulator * progress)
 {
-  this->m_ProgressAccumulator->RegisterInternalFilter(this->m_SegmentationModule, 0.5);
+  progress->RegisterInternalFilter(this->m_SegmentationModule, 0.5);
   this->m_SegmentationModule->SetInput(this->m_InitialSegmentation);
   this->m_SegmentationModule->Update();
 }