Debug RTStruct conversion with empty struc

[clitk.git] / registration / clitkBLUTDIRGenericFilter.cxx

diff --git a/registration/clitkBLUTDIRGenericFilter.cxx b/registration/clitkBLUTDIRGenericFilter.cxx
index c786eeb59dedbd6e1c50d48799e632af63dd126f..24d461361f9e27a232e54a9e3fcfd757de02f8db 100644 (file)
--- a/registration/clitkBLUTDIRGenericFilter.cxx
+++ b/registration/clitkBLUTDIRGenericFilter.cxx
@@ -30,7 +30,13 @@ It is distributed under dual licence
 #include "clitkBLUTDIRGenericFilter.h"
 #include "clitkBLUTDIRCommandIterationUpdateDVF.h"
 #include "itkCenteredTransformInitializer.h"
-  
+#include "itkLabelStatisticsImageFilter.h"
+#if (ITK_VERSION_MAJOR == 4) && (ITK_VERSION_MINOR < 6)
+# include "itkTransformToDisplacementFieldSource.h"
+#else
+# include "itkTransformToDisplacementFieldFilter.h"
+#endif
+
 namespace clitk
 {
 
@@ -240,7 +246,7 @@ namespace clitk
           m_CommandIterationUpdate->SetOptimizer(m_GenericOptimizer);
 
           // Set the previous transform parameters to the registration
-          // if(m_Initializer->m_Parameters!=NULL )delete m_Initializer->m_Parameters;
+          // if(m_Initializer->m_Parameters!=ITK_NULLPTR )delete m_Initializer->m_Parameters;
           m_Initializer->SetInitialParameters(currentCoefficientImages, *newParameters);
           registration->SetInitialTransformParametersOfNextLevel(*newParameters);
         }
@@ -332,8 +338,8 @@ namespace clitk
       //============================================================================
       typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension >   MaskType;
       typedef itk::Image< unsigned char, InputImageType::ImageDimension >   ImageLabelType;
-      typename MaskType::Pointer        fixedMask = NULL;
-      typename ImageLabelType::Pointer  labels = NULL;
+      typename MaskType::Pointer        fixedMask = ITK_NULLPTR;
+      typename ImageLabelType::Pointer  labels = ITK_NULLPTR;
       if (m_ArgsInfo.referenceMask_given)
       {
         fixedMask = MaskType::New();
@@ -368,11 +374,12 @@ namespace clitk
         fixedMask->SetImage(labels);
 
         // Find the bounding box of the "inside" label
-        typedef itk::LabelGeometryImageFilter<ImageLabelType> GeometryImageFilterType;
-        typename GeometryImageFilterType::Pointer geometryImageFilter=GeometryImageFilterType::New();
-        geometryImageFilter->SetInput(labels);
-        geometryImageFilter->Update();
-        typename GeometryImageFilterType::BoundingBoxType boundingBox = geometryImageFilter->GetBoundingBox(1);
+        typedef itk::LabelStatisticsImageFilter<ImageLabelType, ImageLabelType> StatisticsImageFilterType;
+        typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
+        statisticsImageFilter->SetInput(labels);
+        statisticsImageFilter->SetLabelInput(labels);
+        statisticsImageFilter->Update();
+        typename StatisticsImageFilterType::BoundingBoxType boundingBox = statisticsImageFilter->GetBoundingBox(1);
 
         // Limit the transform region to the mask
         for (unsigned int i=0; i<InputImageType::ImageDimension; i++)
@@ -387,9 +394,7 @@ namespace clitk
         // Crop the fixedImage to the bounding box to facilitate multi-resolution
         typedef itk::ExtractImageFilter<FixedImageType,FixedImageType> ExtractImageFilterType;
         typename ExtractImageFilterType::Pointer extractImageFilter=ExtractImageFilterType::New();
-#if ITK_VERSION_MAJOR == 4
         extractImageFilter->SetDirectionCollapseToSubmatrix();
-#endif
         extractImageFilter->SetInput(fixedImage);
         extractImageFilter->SetExtractionRegion(transformRegion);
         extractImageFilter->Update();
@@ -408,7 +413,7 @@ namespace clitk
       }
 
       typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension >   MaskType;
-      typename MaskType::Pointer  movingMask=NULL;
+      typename MaskType::Pointer  movingMask=ITK_NULLPTR;
       if (m_ArgsInfo.targetMask_given)
       {
         movingMask= MaskType::New();
@@ -481,7 +486,7 @@ namespace clitk
       // Rigid or Affine Transform
       //=======================================================
       typedef itk::AffineTransform <double,3> RigidTransformType;
-      RigidTransformType::Pointer rigidTransform=NULL;
+      RigidTransformType::Pointer rigidTransform=ITK_NULLPTR;
       if (m_ArgsInfo.initMatrix_given)
       {
         if(m_Verbose) std::cout<<"Reading the prior transform matrix "<< m_ArgsInfo.initMatrix_arg<<"..."<<std::endl;
@@ -618,7 +623,7 @@ namespace clitk
         sTransform->SetGridRegion( transform->GetTransforms()[0]->GetGridRegion() );
         sTransform->SetParameters( transform->GetTransforms()[0]->GetParameters() );
         regTransform = sTransform;
-        transform = NULL; // free memory
+        transform = ITK_NULLPTR; // free memory
       }
 
       //=======================================================
@@ -643,16 +648,14 @@ namespace clitk
       typedef itk::ImageToImageMetric< FixedImageType, MovingImageType >  MetricType;
       typename  MetricType::Pointer metric=genericMetric->GetMetricPointer();
       if (movingMask) metric->SetMovingImageMask(movingMask);
-
-#if defined(ITK_USE_OPTIMIZED_REGISTRATION_METHODS) || ITK_VERSION_MAJOR >= 4
       if (threadsGiven) {
+#if ITK_VERSION_MAJOR <= 4
         metric->SetNumberOfThreads( threads );
-        if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
-      }
 #else
-      if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
+        metric->SetNumberOfWorkUnits( threads );
 #endif
-
+        if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
+      }
 
       //=======================================================
       // Optimizer
@@ -676,7 +679,11 @@ namespace clitk
       registration->SetInterpolator(  interpolator  );
       registration->SetTransform (regTransform );
       if(threadsGiven) {
+#if ITK_VERSION_MAJOR <= 4
         registration->SetNumberOfThreads(threads);
+#else
+        registration->SetNumberOfWorkUnits(threads);
+#endif
         if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
       }
       registration->SetFixedImage(  croppedFixedImage   );
@@ -733,11 +740,7 @@ namespace clitk
 
       try
       {
-#if ITK_VERSION_MAJOR < 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR <= 2)
-        registration->StartRegistration();
-#else
         registration->Update();
-#endif
       }
       catch( itk::ExceptionObject & err )
       {
@@ -792,19 +795,27 @@ namespace clitk
       //=======================================================
       typedef itk::Vector< float, SpaceDimension >  DisplacementType;
       typedef itk::Image< DisplacementType, InputImageType::ImageDimension >  DisplacementFieldType;
-#if ITK_VERSION_MAJOR >= 4
+#if (ITK_VERSION_MAJOR == 4) && (ITK_VERSION_MINOR < 6)
       typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
 #else
-      typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
+      typedef itk::TransformToDisplacementFieldFilter<DisplacementFieldType, double> ConvertorType;
 #endif
       typename ConvertorType::Pointer filter= ConvertorType::New();
+#if ITK_VERSION_MAJOR <= 4
       filter->SetNumberOfThreads(1);
+#else
+      filter->SetNumberOfWorkUnits(1);
+#endif
       if(m_ArgsInfo.itkbspline_flag)
-        sTransform->SetBulkTransform(NULL);
+        sTransform->SetBulkTransform(ITK_NULLPTR);
       else
-        transform->SetBulkTransform(NULL);
+        transform->SetBulkTransform(ITK_NULLPTR);
       filter->SetTransform(regTransform);
+#if ITK_VERSION_MAJOR > 4 || (ITK_VERSION_MAJOR == 4 && ITK_VERSION_MINOR >= 6)
+      filter->SetReferenceImage(fixedImage);
+#else
       filter->SetOutputParametersFromImage(fixedImage);
+#endif
       filter->Update();
       typename DisplacementFieldType::Pointer field = filter->GetOutput();