Merge branch 'master' into extentSimon

[clitk.git] / registration / clitkBLUTDIRGenericFilter.cxx

diff --git a/registration/clitkBLUTDIRGenericFilter.cxx b/registration/clitkBLUTDIRGenericFilter.cxx
index ca10c2d04d4fc4adc52e035d160b66843808a663..9f7b84f456f36496f1be156400a0c43441dd2983 100644 (file)
--- a/registration/clitkBLUTDIRGenericFilter.cxx
+++ b/registration/clitkBLUTDIRGenericFilter.cxx
@@ -29,6 +29,16 @@ It is distributed under dual licence
 
 #include "clitkBLUTDIRGenericFilter.h"
 #include "clitkBLUTDIRCommandIterationUpdateDVF.h"
+#include "itkCenteredTransformInitializer.h"
+#if ITK_VERSION_MAJOR >= 4
+#  if ITK_VERSION_MINOR < 6
+#    include "itkTransformToDisplacementFieldSource.h"
+#  else
+#    include "itkTransformToDisplacementFieldFilter.h"
+#  endif
+#else
+#  include "itkTransformToDeformationFieldSource.h"
+#endif
 
 namespace clitk
 {
@@ -386,9 +396,7 @@ 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();
@@ -495,6 +503,20 @@ namespace clitk
         itk::Vector<double,3> finalTranslation = clitk::GetTranslationPartMatrix3D(rigidTransformMatrix);
         rigidTransform->SetTranslation(finalTranslation);
       }
+      else if (m_ArgsInfo.centre_flag)
+      {
+        if(m_Verbose) std::cout<<"No itinial matrix given and \"centre\" flag switched on. Centering all images..."<<std::endl;
+        
+        rigidTransform=RigidTransformType::New();
+        
+        typedef itk::CenteredTransformInitializer<RigidTransformType, FixedImageType, MovingImageType > TransformInitializerType;
+        typename TransformInitializerType::Pointer initializer = TransformInitializerType::New();
+        initializer->SetTransform( rigidTransform );
+        initializer->SetFixedImage( fixedImage );
+        initializer->SetMovingImage( movingImage );        
+        initializer->GeometryOn();
+        initializer->InitializeTransform();
+      }
 
 
       //=======================================================
@@ -628,16 +650,10 @@ 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) {
         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;
-#endif
-
 
       //=======================================================
       // Optimizer
@@ -718,7 +734,7 @@ namespace clitk
 
       try
       {
-        registration->StartRegistration();
+        registration->Update();
       }
       catch( itk::ExceptionObject & err )
       {
@@ -774,9 +790,11 @@ namespace clitk
       typedef itk::Vector< float, SpaceDimension >  DisplacementType;
       typedef itk::Image< DisplacementType, InputImageType::ImageDimension >  DisplacementFieldType;
 #if ITK_VERSION_MAJOR >= 4
+#  if ITK_VERSION_MINOR < 6
       typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
-#else
-      typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
+#  else
+      typedef itk::TransformToDisplacementFieldFilter<DisplacementFieldType, double> ConvertorType;
+#  endif
 #endif
       typename ConvertorType::Pointer filter= ConvertorType::New();
       filter->SetNumberOfThreads(1);
@@ -785,7 +803,11 @@ namespace clitk
       else
         transform->SetBulkTransform(NULL);
       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();