X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=registration%2FclitkBLUTDIRGenericFilter.cxx;h=60cd30db0bc21024e3c187d642062be4b4bb88fe;hb=78bd7fb31b49e7b7557c062a691f622f6dec58a0;hp=ca10c2d04d4fc4adc52e035d160b66843808a663;hpb=7f7c290c75d4917446f8751856ae7d450f58a6f0;p=clitk.git

diff --git a/registration/clitkBLUTDIRGenericFilter.cxx b/registration/clitkBLUTDIRGenericFilter.cxx
index ca10c2d..60cd30d 100644
--- a/registration/clitkBLUTDIRGenericFilter.cxx
+++ b/registration/clitkBLUTDIRGenericFilter.cxx
@@ -29,6 +29,13 @@ 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
 {
@@ -367,11 +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++)
@@ -386,9 +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();
@@ -495,6 +501,20 @@ 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 +648,10 @@ 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 +732,7 @@ namespace clitk
 
       try
       {
-        registration->StartRegistration();
+        registration->Update();
       }
       catch( itk::ExceptionObject & err )
       {
@@ -773,10 +787,10 @@ 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);
@@ -785,7 +799,11 @@ 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();