X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=registration%2FclitkBLUTDIRGenericFilter.cxx;h=6c80fd911859199d28b36f618e2d01472c0d8eaa;hb=103778ec7e0d03e32d9ecfa1306312d32d72ad4c;hp=39c1d3d53b529d263947edeca5715f2bcc66326c;hpb=52ed5f9ca1bbe477fecfe703566993fed4e8895a;p=clitk.git

diff --git a/registration/clitkBLUTDIRGenericFilter.cxx b/registration/clitkBLUTDIRGenericFilter.cxx
index 39c1d3d..6c80fd9 100644
--- a/registration/clitkBLUTDIRGenericFilter.cxx
+++ b/registration/clitkBLUTDIRGenericFilter.cxx
@@ -29,6 +29,12 @@ It is distributed under dual licence
 
 #include "clitkBLUTDIRGenericFilter.h"
 #include "clitkBLUTDIRCommandIterationUpdateDVF.h"
+#include "itkCenteredTransformInitializer.h"
+#if (ITK_VERSION_MAJOR == 4) && (ITK_VERSION_MINOR < 6)
+# include "itkTransformToDisplacementFieldSource.h"
+#else
+# include "itkTransformToDisplacementFieldFilter.h"
+#endif
 
 namespace clitk
 {
@@ -322,7 +328,6 @@ namespace clitk
       // The metric region with respect to the extracted transform region:
       // where should the metric be CALCULATED (depends on transform)
       typename FixedImageType::RegionType metricRegion = fixedImage->GetLargestPossibleRegion();
-      typename FixedImageType::RegionType::SizeType metricRegionSize=metricRegion.GetSize();
       typename FixedImageType::RegionType::IndexType metricRegionIndex=metricRegion.GetIndex();
       typename FixedImageType::PointType metricRegionOrigin=fixedImage->GetOrigin();
 
@@ -387,6 +392,7 @@ 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();
+        extractImageFilter->SetDirectionCollapseToSubmatrix();
         extractImageFilter->SetInput(fixedImage);
         extractImageFilter->SetExtractionRegion(transformRegion);
         extractImageFilter->Update();
@@ -493,6 +499,20 @@ 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();
+      }
 
 
       //=======================================================
@@ -626,16 +646,10 @@ namespace clitk
       typedef itk::ImageToImageMetric< FixedImageType, MovingImageType >  MetricType;
       typename  MetricType::Pointer metric=genericMetric->GetMetricPointer();
       if (movingMask) metric->SetMovingImageMask(movingMask);
-
-#ifdef ITK_USE_OPTIMIZED_REGISTRATION_METHODS
       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
@@ -716,7 +730,7 @@ namespace clitk
 
       try
       {
-        registration->StartRegistration();
+        registration->Update();
       }
       catch( itk::ExceptionObject & err )
       {
@@ -771,10 +785,10 @@ 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();
       filter->SetNumberOfThreads(1);
@@ -783,7 +797,11 @@ 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();