Fix compatibility with latest ITK and RTK

applications/CMakeLists.txt

@@ -8,15 +8,23 @@ find_package(Gengetopt REQUIRED)
 if(NOT ITK_DIR)
   set(ITK_DIR ${ITK_BINARY_DIR}/CMakeTmp)
 endif()
-find_package(
-  ITK
-  REQUIRED
-  COMPONENTS
-    ${ITK_MODULE_PCT_DEPENDS}
-    ${ITK_MODULE_PCT-Test_DEPENDS}
-)
-include(${ITK_USE_FILE})
+find_package(ITK REQUIRED COMPONENTS ${ITK_MODULE_PCT_DEPENDS})
+include(itkVersion)
+if("${ITK_VERSION_MAJOR}" VERSION_LESS "6")
+  include(${ITK_USE_FILE})
+  set(PCT_APPLICATION_TARGETS ${PCT_LIBRARIES})
+else()
+  itk_generate_factory_registration()
+  set(
+    PCT_APPLICATION_TARGETS
+    ITK::PCTModule
+    ITK::ITKImageIO
+    ITK::ITKFFTImageFilterInit
+  )
+endif()
 
+#-----------------------------------------------------------------------------
+# Executables
 add_subdirectory(pctbackprojectionbinning)
 add_subdirectory(pctbinning)
 add_subdirectory(pctfdk)

applications/pctbackprojectionbinning/CMakeLists.txt

@@ -4,7 +4,7 @@ add_executable(
   pctbackprojectionbinning.cxx
   ${pctbackprojectionbinning_GGO_C}
 )
-target_link_libraries(pctbackprojectionbinning PCT)
+target_link_libraries(pctbackprojectionbinning ${PCT_APPLICATION_TARGETS})
 
 # Ensure binary is placed in the central PCT binary dir
 set_target_properties(

applications/pctbinning/CMakeLists.txt

@@ -4,7 +4,7 @@ add_executable(
   pctbinning.cxx
   ${pctbinning_GGO_C}
 )
-target_link_libraries(pctbinning PCT)
+target_link_libraries(pctbinning ${PCT_APPLICATION_TARGETS})
 
 # Ensure binary is placed in the central PCT binary dir
 set_target_properties(

applications/pctfdk/CMakeLists.txt

@@ -4,7 +4,7 @@ add_executable(
   pctfdk.cxx
   ${pctfdk_GGO_C}
 )
-target_link_libraries(pctfdk PCT)
+target_link_libraries(pctfdk ${PCT_APPLICATION_TARGETS})
 
 # Ensure binary is placed in the central PCT binary dir
 set_target_properties(

applications/pctpaircuts/CMakeLists.txt

@@ -4,7 +4,7 @@ add_executable(
   pctpaircuts.cxx
   ${pctpaircuts_GGO_C}
 )
-target_link_libraries(pctpaircuts PCT)
+target_link_libraries(pctpaircuts ${PCT_APPLICATION_TARGETS})
 
 # Ensure binary is placed in the central PCT binary dir
 set_target_properties(

applications/pctpairgeometry/CMakeLists.txt

@@ -4,7 +4,7 @@ add_executable(
   pctpairgeometry.cxx
   ${pctpairgeometry_GGO_C}
 )
-target_link_libraries(pctpairgeometry PCT)
+target_link_libraries(pctpairgeometry ${PCT_APPLICATION_TARGETS})
 
 # Ensure binary is placed in the central PCT binary dir
 set_target_properties(

applications/pctprojections/CMakeLists.txt

@@ -4,7 +4,7 @@ add_executable(
   pctprojections.cxx
   ${pctprojections_GGO_C}
 )
-target_link_libraries(pctprojections PCT)
+target_link_libraries(pctprojections ${PCT_APPLICATION_TARGETS})
 
 # Ensure binary is placed in the central PCT binary dir
 set_target_properties(

applications/pctzengbackprojections/CMakeLists.txt

@@ -4,7 +4,7 @@ add_executable(
   pctzengbackprojections.cxx
   ${pctzengbackprojections_GGO_C}
 )
-target_link_libraries(pctzengbackprojections PCT)
+target_link_libraries(pctzengbackprojections ${PCT_APPLICATION_TARGETS})
 
 # Ensure binary is placed in the central PCT binary dir
 set_target_properties(

include/pctDDParkerShortScanImageFilter.hxx

@@ -21,8 +21,8 @@ DDParkerShortScanImageFilter<TInputImage, TOutputImage>::DynamicThreadedGenerate
       maxAngularGapPos = iProj;
 
   // Input / ouput iterators
-  itk::ImageRegionConstIterator<InputImageType> itIn(this->GetInput(), outputRegionForThread);
-  itk::ImageRegionIterator<OutputImageType>     itOut(this->GetOutput(), outputRegionForThread);
+  itk::ImageRegionConstIteratorWithIndex<InputImageType> itIn(this->GetInput(), outputRegionForThread);
+  itk::ImageRegionIteratorWithIndex<OutputImageType>     itOut(this->GetOutput(), outputRegionForThread);
   itIn.GoToBegin();
   itOut.GoToBegin();
 

include/pctEnergyAdaptiveMLPFunction.h

@@ -113,12 +113,13 @@ class PCT_EXPORT EnergyAdaptiveMLPFunction : public MostLikelyPathFunction<doubl
   itkNewMacro(Self);
 
   /** Useful defines. */
+  using PointType = Superclass::PointType;
   using VectorType = Superclass::VectorType;
 
   /* Initialize the MLP estimator */
   virtual void
-  Init(const VectorType posIn,
-       const VectorType posOut,
+  Init(const PointType  posIn,
+       const PointType  posOut,
        const VectorType dirIn,
        const VectorType dirOut,
        double           eIn,

include/pctHoleFillingImageFilter.h

@@ -30,7 +30,7 @@ class HoleFillingImageFilter : public itk::ImageToImageFilter<TInputImage, TOutp
   using ConstPointer = itk::SmartPointer<const Self>;
 
   itkNewMacro(Self);
-  itkTypeMacro(HoleFillingImageFilter, ImageToImageFilter);
+  itkOverrideGetNameOfClassMacro(HoleFillingImageFilter);
 
   using InputImageType = TInputImage;
   using OutputImageType = TOutputImage;

include/pctMostLikelyPathFunction.h

@@ -10,6 +10,8 @@
 #  include <itkTimeProbe.h>
 #endif
 
+#include <rtkQuadricShape.h>
+
 namespace pct
 {
 
@@ -29,19 +31,21 @@ class ITK_TEMPLATE_EXPORT MostLikelyPathFunction : public itk::LightObject
   using ConstPointer = itk::SmartPointer<const Self>;
 
   /** Useful defines. */
+  // PointType definition based on rtk::QuadricShape to be compatible with RTK 2 and 3
+  using PointType = rtk::QuadricShape::PointType;
   using VectorType = itk::Vector<TCoordRep, 3>;
 
   /** Init the mlp parameters from the input and output directions and positions. */
   virtual void
-  Init(const VectorType posIn, const VectorType posOut, const VectorType dirIn, const VectorType dirOut)
+  Init(const PointType posIn, const PointType posOut, const VectorType dirIn, const VectorType dirOut)
   {
     itkGenericExceptionMacro("This version of the Init method not implemented for derived class.");
   }
 
   /** Init the mlp parameters from the input and output directions and positions, and energies. */
   virtual void
-  Init(const VectorType posIn,
-       const VectorType posOut,
+  Init(const PointType  posIn,
+       const PointType  posOut,
        const VectorType dirIn,
        const VectorType dirOut,
        double           eIn,
@@ -52,8 +56,8 @@ class ITK_TEMPLATE_EXPORT MostLikelyPathFunction : public itk::LightObject
 
   /** Init with additional parameters to consider tracker uncertainties */
   virtual void
-  InitUncertain(const VectorType posIn,
-                const VectorType posOut,
+  InitUncertain(const PointType  posIn,
+                const PointType  posOut,
                 const VectorType dirIn,
                 const VectorType dirOut,
                 double           dEntry,

include/pctPolynomialMLPFunction.h

@@ -149,11 +149,12 @@ class PCT_EXPORT PolynomialMLPFunction : public MostLikelyPathFunction<double>
   itkNewMacro(Self);
 
   /** Useful defines. */
+  using PointType = Superclass::PointType;
   using VectorType = Superclass::VectorType;
 
   /** Init the mlp parameters from the input and output directions and positions. */
   virtual void
-  Init(const VectorType posIn, const VectorType posOut, const VectorType dirIn, const VectorType dirOut) override;
+  Init(const PointType posIn, const PointType posOut, const VectorType dirIn, const VectorType dirOut) override;
 
   /* Vectorised version of Evaluate function. */
   virtual void

include/pctProtonPairsToBackProjection.hxx

@@ -1,5 +1,5 @@
 #include <itkImageFileReader.h>
-#include <itkImageRegionIterator.h>
+#include <itkImageRegionIteratorWithIndex.h>
 
 #include <rtkHomogeneousMatrix.h>
 
@@ -155,7 +155,7 @@ ProtonPairsToBackProjection<TInputImage, TOutputImage>::GenerateData()
           zmm.push_back(zmm.back() + minSpacing);
 
         // Process pairs
-        itk::ImageRegionIterator<ProtonPairsImageType> it(m_ProtonPairs, outputRegionForThread);
+        itk::ImageRegionIteratorWithIndex<ProtonPairsImageType> it(m_ProtonPairs, outputRegionForThread);
         while (!it.IsAtEnd())
         {
           if (outputRegionForThread.GetIndex(1) == 0 && it.GetIndex()[1] % 1000 == 0)
@@ -165,9 +165,9 @@ ProtonPairsToBackProjection<TInputImage, TOutputImage>::GenerateData()
                       << 100 * it.GetIndex()[1] / outputRegionForThread.GetSize(1) << "%) in thread 1" << std::flush;
           }
 
-          VectorType pIn = it.Get();
+          RQIType::PointType pIn(it.Get());
           ++it;
-          VectorType pOut = it.Get();
+          RQIType::PointType pOut(it.Get());
           ++it;
           VectorType dIn = it.Get();
           ++it;
@@ -185,9 +185,9 @@ ProtonPairsToBackProjection<TInputImage, TOutputImage>::GenerateData()
           ++it;
 
           // Move straight to entrance and exit shapes
-          VectorType pSIn = pIn;
-          VectorType pSOut = pOut;
-          double     nearDistIn, nearDistOut, farDistIn, farDistOut;
+          RQIType::PointType pSIn = pIn;
+          RQIType::PointType pSOut = pOut;
+          double             nearDistIn, nearDistOut, farDistIn, farDistOut;
           if (m_QuadricIn.GetPointer() != NULL)
           {
             if (m_QuadricIn->IsIntersectedByRay(pIn, dIn, nearDistIn, farDistIn) &&

include/pctProtonPairsToDistanceDrivenProjection.hxx

@@ -1,5 +1,5 @@
 #include <itkImageFileReader.h>
-#include <itkImageRegionIterator.h>
+#include <itkImageRegionIteratorWithIndex.h>
 
 #include "pctThirdOrderPolynomialMLPFunction.h"
 #include "pctSchulteMLPFunction.h"
@@ -169,9 +169,9 @@ ProtonPairsToDistanceDrivenProjection<TInputImage, TOutputImage>::ThreadedGenera
   using VectorType = itk::Vector<double, 3>;
 
   // Create zmm and magnitude lut (look up table)
-  itk::ImageRegionIterator<ProtonPairsImageType> it(m_ProtonPairs, region);
-  std::vector<double>                            zmm(imgSize[2]);
-  std::vector<double>                            zmag(imgSize[2]);
+  itk::ImageRegionIteratorWithIndex<ProtonPairsImageType> it(m_ProtonPairs, region);
+  std::vector<double>                                     zmm(imgSize[2]);
+  std::vector<double>                                     zmag(imgSize[2]);
   ++it;
   const double zPlaneOutInMM = it.Get()[2];
   --it;
@@ -190,9 +190,9 @@ ProtonPairsToDistanceDrivenProjection<TInputImage, TOutputImage>::ThreadedGenera
                 << 100 * it.GetIndex()[1] / region.GetSize(1) << "%) in thread 1" << std::flush;
     }
 
-    VectorType pIn = it.Get();
+    RQIType::PointType pIn(it.Get());
     ++it;
-    VectorType pOut = it.Get();
+    RQIType::PointType pOut(it.Get());
     ++it;
     VectorType dIn = it.Get();
     ++it;
@@ -257,11 +257,11 @@ ProtonPairsToDistanceDrivenProjection<TInputImage, TOutputImage>::ThreadedGenera
     // Move straight to entrance and exit shapes
 
 
-    VectorType pSIn = pIn;
-    VectorType pSOut = pOut;
-    double     nearDistIn, nearDistOut, farDistIn, farDistOut;
-    double     distanceEntry, distanceExit;
-    bool       QuadricIntersected = false;
+    RQIType::PointType pSIn = pIn;
+    RQIType::PointType pSOut = pOut;
+    double             nearDistIn, nearDistOut, farDistIn, farDistOut;
+    double             distanceEntry, distanceExit;
+    bool               QuadricIntersected = false;
     if (m_QuadricIn.GetPointer() != NULL)
     {
       if (m_QuadricIn->IsIntersectedByRay(pIn, dIn, nearDistIn, farDistIn) &&

include/pctSchulteMLPFunction.h

@@ -150,16 +150,17 @@ class PCT_EXPORT SchulteMLPFunction : public MostLikelyPathFunction<double>
   itkNewMacro(Self);
 
   /** Useful defines. */
+  using PointType = Superclass::PointType;
   using VectorType = Superclass::VectorType;
 
   /** Init the mlp parameters from the input and output directions and positions. */
   virtual void
-  Init(const VectorType posIn, const VectorType posOut, const VectorType dirIn, const VectorType dirOut) override;
+  Init(const PointType posIn, const PointType posOut, const VectorType dirIn, const VectorType dirOut) override;
 
   /** Init with additional parameters to consider tracker uncertainties */
   virtual void
-  InitUncertain(const VectorType posIn,
-                const VectorType posOut,
+  InitUncertain(const PointType  posIn,
+                const PointType  posOut,
                 const VectorType dirIn,
                 const VectorType dirOut,
                 double           dEntry,

include/pctThirdOrderPolynomialMLPFunction.h

@@ -25,11 +25,12 @@ class ITK_TEMPLATE_EXPORT ThirdOrderPolynomialMLPFunction : public MostLikelyPat
   itkNewMacro(Self);
 
   /** Useful defines. */
+  using PointType = typename Superclass::PointType;
   using VectorType = typename Superclass::VectorType;
 
   /** Init the mlp parameters from the input and output directions and positions. */
   virtual void
-  Init(const VectorType posIn, const VectorType posOut, const VectorType dirIn, const VectorType dirOut) override;
+  Init(const PointType posIn, const PointType posOut, const VectorType dirIn, const VectorType dirOut) override;
 
   /** Evaluate the coordinates (x,y) at depth z. */
   virtual void

include/pctThirdOrderPolynomialMLPFunction.hxx

@@ -3,8 +3,8 @@ namespace pct
 
 template <class TCoordRep>
 void
-ThirdOrderPolynomialMLPFunction<TCoordRep>::Init(const VectorType posIn,
-                                                 const VectorType posOut,
+ThirdOrderPolynomialMLPFunction<TCoordRep>::Init(const PointType  posIn,
+                                                 const PointType  posOut,
                                                  const VectorType dirIn,
                                                  const VectorType dirOut)
 {

src/pctEnergyAdaptiveMLPFunction.cxx

@@ -29,8 +29,8 @@ EnergyAdaptiveMLPFunction ::EnergyAdaptiveMLPFunction()
 }
 
 void
-EnergyAdaptiveMLPFunction ::Init(const VectorType posIn,
-                                 const VectorType posOut,
+EnergyAdaptiveMLPFunction ::Init(const PointType  posIn,
+                                 const PointType  posOut,
                                  const VectorType dirIn,
                                  const VectorType dirOut,
                                  double           eIn,

src/pctPolynomialMLPFunction.cxx

@@ -76,8 +76,8 @@ PolynomialMLPFunction ::SetPolynomialDegree(const int polydeg)
 }
 
 void
-PolynomialMLPFunction ::Init(const VectorType posIn,
-                             const VectorType posOut,
+PolynomialMLPFunction ::Init(const PointType  posIn,
+                             const PointType  posOut,
                              const VectorType dirIn,
                              const VectorType dirOut)
 {

src/pctSchulteMLPFunction.cxx

@@ -46,8 +46,8 @@ SchulteMLPFunction ::SchulteMLPFunction()
 
 // Initialize terms needed to include tracker uncertainties
 void
-SchulteMLPFunction ::InitUncertain(const VectorType posIn,
-                                   const VectorType posOut,
+SchulteMLPFunction ::InitUncertain(const PointType  posIn,
+                                   const PointType  posOut,
                                    const VectorType dirIn,
                                    const VectorType dirOut,
                                    double           dEntry,
@@ -97,8 +97,8 @@ SchulteMLPFunction ::InitUncertain(const VectorType posIn,
 
 // standard part of the Initialization
 void
-SchulteMLPFunction ::Init(const VectorType posIn,
-                          const VectorType posOut,
+SchulteMLPFunction ::Init(const PointType  posIn,
+                          const PointType  posOut,
                           const VectorType dirIn,
                           const VectorType dirOut)
 {

test/pctHoleFillingImageFilterTest.cxx

@@ -1,7 +1,7 @@
 #include "pctHoleFillingImageFilter.h"
 
 #include "itkImage.h"
-#include "itkImageRegionIterator.h"
+#include "itkImageRegionIteratorWithIndex.h"
 #include "itkTestingMacros.h"
 
 int
@@ -19,7 +19,7 @@ pctHoleFillingImageFilterTest(int argc, char * argv[])
   img->FillBuffer(42);
 
   // Insert some holes (use 0 as hole value)
-  itk::ImageRegionIterator<ImageType> it(img, region);
+  itk::ImageRegionIteratorWithIndex<ImageType> it(img, region);
   for (it.GoToBegin(); !it.IsAtEnd(); ++it)
   {
     ImageType::IndexType idx = it.GetIndex();