X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;ds=sidebyside;f=registration%2FclitkShapedBLUTSpatioTemporalDIRGenericFilter.txx;fp=registration%2FclitkShapedBLUTSpatioTemporalDIRGenericFilter.txx;h=16109367cd3ac613e7a62d89ae0378c39afb9a23;hb=657652a78c2e2717a6f77e027049173442ca29f0;hp=0000000000000000000000000000000000000000;hpb=8abe9edbdc63a33f8fbb1f321073b762e08be9aa;p=clitk.git

diff --git a/registration/clitkShapedBLUTSpatioTemporalDIRGenericFilter.txx b/registration/clitkShapedBLUTSpatioTemporalDIRGenericFilter.txx
new file mode 100755
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--- /dev/null
+++ b/registration/clitkShapedBLUTSpatioTemporalDIRGenericFilter.txx
@@ -0,0 +1,929 @@
+/*=========================================================================
+  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
+
+  Authors belong to: 
+  - University of LYON              http://www.universite-lyon.fr/
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
+  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
+
+  This software is distributed WITHOUT ANY WARRANTY; without even
+  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+  PURPOSE.  See the copyright notices for more information.
+
+  It is distributed under dual licence
+
+  - BSD        See included LICENSE.txt file
+  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+======================================================================-====*/
+#ifndef clitkShapedBLUTSpatioTemporalDIRGenericFilter_txx
+#define clitkShapedBLUTSpatioTemporalDIRGenericFilter_txx
+
+/* =================================================
+ * @file   clitkShapedBLUTSpatioTemporalDIRGenericFilter.txx
+ * @author 
+ * @date   
+ * 
+ * @brief 
+ * 
+ ===================================================*/
+
+#include "clitkShapedBLUTSpatioTemporalDIRGenericFilter.h"
+
+namespace clitk
+{
+
+  //==============================================================================
+  // Creating an observer class that allows output at each iteration
+  //==============================================================================
+  template <typename TRegistration, class args_info_clitkShapedBLUTSpatioTemporalDIR>
+  class CommandIterationUpdate : public itk::Command 
+  {
+  public:
+    typedef  CommandIterationUpdate   Self;
+    typedef  itk::Command             Superclass;
+    typedef  itk::SmartPointer<Self>  Pointer;
+    itkNewMacro( Self );
+
+    // Registration
+    typedef   TRegistration                              RegistrationType;
+    typedef   RegistrationType *                         RegistrationPointer;
+
+    // Transform
+    typedef typename RegistrationType::FixedImageType FixedImageType;
+    typedef typename FixedImageType::RegionType RegionType;
+    itkStaticConstMacro(ImageDimension, unsigned int,FixedImageType::ImageDimension); 
+    typedef clitk::ShapedBLUTSpatioTemporalDeformableTransform<double, ImageDimension, ImageDimension> TransformType;
+    typedef clitk::ShapedBLUTSpatioTemporalDeformableTransformInitializer<TransformType, FixedImageType> InitializerType;
+    typedef typename InitializerType::CoefficientImageType CoefficientImageType;
+    typedef itk::CastImageFilter<CoefficientImageType, CoefficientImageType> CastImageFilterType;
+    typedef typename TransformType::ParametersType ParametersType;
+    typedef typename InitializerType::Pointer InitializerPointer;
+
+  protected:
+    CommandIterationUpdate() { m_IterationCounter=0;}
+  public:
+    typedef   clitk::GenericOptimizer<args_info_clitkShapedBLUTSpatioTemporalDIR>     OptimizerType;
+    typedef   const OptimizerType   *           OptimizerPointer;
+  
+    // Execute
+    void Execute(itk::Object *caller, const itk::EventObject & event)
+    {
+      Execute( (const itk::Object *)caller, event);
+    }
+  
+    void Execute(const itk::Object * object, const itk::EventObject & event)
+    {  
+      if( !(itk::IterationEvent().CheckEvent( &event )) )
+	{
+	  return;
+	}
+      
+      // Output
+      m_Optimizer->OutputIterationInfo();
+      m_IterationCounter++;
+
+      // Write intermediate result
+      if (m_ArgsInfo.current_given && (m_IterationCounter> m_ArgsInfo.current_arg) )
+	{
+	  // Write && Reset
+	  writeImage<CoefficientImageType>(m_Initializer->GetTransform()->GetCoefficientImage(), m_ArgsInfo.coeff_arg, m_ArgsInfo.verbose_flag );
+	  m_IterationCounter=0;
+	}
+    }
+
+   // Members
+    void SetOptimizer(OptimizerPointer o){m_Optimizer=o;}
+    OptimizerPointer m_Optimizer;
+
+    void SetInitializer(InitializerPointer i){m_Initializer=i;}
+    InitializerPointer m_Initializer;
+    
+    void SetArgsInfo(args_info_clitkShapedBLUTSpatioTemporalDIR a){m_ArgsInfo=a;}
+    args_info_clitkShapedBLUTSpatioTemporalDIR m_ArgsInfo;
+
+    int m_IterationCounter;
+  };
+
+
+  //==============================================================================
+  //Creating an observer class that allows us to change parameters at subsequent levels
+  //==============================================================================
+  template <typename TRegistration, class args_info_clitkShapedBLUTSpatioTemporalDIR>
+  class RegistrationInterfaceCommand : public itk::Command 
+  {
+  public:
+    typedef RegistrationInterfaceCommand   Self;
+    typedef itk::Command             Superclass;
+    typedef itk::SmartPointer<Self>  Pointer;
+    itkNewMacro( Self );
+  protected:
+    RegistrationInterfaceCommand() {};
+  public:
+
+    // Registration
+    typedef   TRegistration                              RegistrationType;
+    typedef   RegistrationType *                         RegistrationPointer;
+
+    // Transform
+    typedef typename RegistrationType::FixedImageType FixedImageType;
+    typedef typename FixedImageType::RegionType RegionType;
+    itkStaticConstMacro(ImageDimension, unsigned int,FixedImageType::ImageDimension); 
+    typedef clitk::ShapedBLUTSpatioTemporalDeformableTransform<double, ImageDimension, ImageDimension> TransformType;
+    typedef clitk::ShapedBLUTSpatioTemporalDeformableTransformInitializer<TransformType, FixedImageType> InitializerType;
+    typedef typename InitializerType::CoefficientImageType CoefficientImageType;
+    typedef itk::CastImageFilter<CoefficientImageType, CoefficientImageType> CastImageFilterType;
+    typedef typename TransformType::ParametersType ParametersType;
+    typedef typename InitializerType::Pointer InitializerPointer;
+    typedef  typename  CommandIterationUpdate< TRegistration, args_info_clitkShapedBLUTSpatioTemporalDIR>::Pointer CommandIterationUpdatePointer;
+
+    // Optimizer
+    typedef clitk::GenericOptimizer<args_info_clitkShapedBLUTSpatioTemporalDIR> GenericOptimizerType;
+    typedef typename GenericOptimizerType::Pointer GenericOptimizerPointer;
+
+    // Metric
+    typedef typename RegistrationType::FixedImageType    InternalImageType;
+    typedef clitk::GenericMetric<args_info_clitkShapedBLUTSpatioTemporalDIR, InternalImageType, InternalImageType> GenericMetricType;
+    typedef typename GenericMetricType::Pointer GenericMetricPointer;
+
+    // Two arguments are passed to the Execute() method: the first
+    // is the pointer to the object which invoked the event and the 
+    // second is the event that was invoked.
+    void Execute(itk::Object * object, const itk::EventObject & event)
+    {
+      if( !(itk::IterationEvent().CheckEvent( &event )) )
+	{
+	  return;
+	}
+
+      // Get the levels
+      RegistrationPointer registration = dynamic_cast<RegistrationPointer>( object );
+      unsigned int numberOfLevels=registration->GetNumberOfLevels();
+      unsigned int currentLevel=registration->GetCurrentLevel()+1;
+
+      // Output the levels
+      std::cout<<std::endl;
+      std::cout<<"========================================"<<std::endl;
+      std::cout<<"Starting resolution level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
+      std::cout<<"========================================"<<std::endl;	
+      std::cout<<std::endl;
+
+      // Higher level?
+      if (currentLevel>1)
+	{
+	  // fixed image region pyramid
+	  typedef clitk::MultiResolutionPyramidRegionFilter<InternalImageType> FixedImageRegionPyramidType;
+	  typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
+	  fixedImageRegionPyramid->SetRegion(m_MetricRegion);
+	  fixedImageRegionPyramid->SetSchedule(registration->GetFixedImagePyramid()->GetSchedule());
+
+	  // Reinitialize the metric (!= number of samples)
+	  m_GenericMetric= GenericMetricType::New();
+	  m_GenericMetric->SetArgsInfo(m_ArgsInfo);
+	  m_GenericMetric->SetFixedImage(registration->GetFixedImagePyramid()->GetOutput(registration->GetCurrentLevel()));
+	  if (m_ArgsInfo.referenceMask_given)  m_GenericMetric->SetFixedImageMask(registration->GetMetric()->GetFixedImageMask());
+	  m_GenericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(registration->GetCurrentLevel()));
+	  typedef itk::ImageToImageMetric< InternalImageType, InternalImageType >  MetricType;
+	  typename  MetricType::Pointer metric=m_GenericMetric->GetMetricPointer();
+	  registration->SetMetric(metric);	
+
+	  // Get the current coefficient image and make a COPY
+	  typename itk::ImageDuplicator<CoefficientImageType>::Pointer caster=itk::ImageDuplicator<CoefficientImageType>::New();
+	  caster->SetInputImage(m_Initializer->GetTransform()->GetCoefficientImage());
+	  caster->Update();
+	  typename CoefficientImageType::Pointer currentCoefficientImage=caster->GetOutput();
+
+	  // Write the intermediate result?
+	  if (m_ArgsInfo.intermediate_given>=numberOfLevels)
+	    writeImage<CoefficientImageType>(currentCoefficientImage, m_ArgsInfo.intermediate_arg[currentLevel-2], m_ArgsInfo.verbose_flag);
+	  
+	  // Set the new transform properties
+	  m_Initializer->SetImage(registration->GetFixedImagePyramid()->GetOutput(currentLevel-1));
+	  if( m_Initializer->m_ControlPointSpacingIsGiven) 
+	    m_Initializer->SetControlPointSpacing(m_Initializer->m_ControlPointSpacingArray[registration->GetCurrentLevel()]);
+	  if( m_Initializer->m_NumberOfControlPointsIsGiven) 
+	    m_Initializer->SetNumberOfControlPointsInsideTheImage(m_Initializer->m_NumberOfControlPointsInsideTheImageArray[registration->GetCurrentLevel()]);
+  
+	  // Reinitialize the transform
+	  if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level "<<currentLevel<<" of "<<numberOfLevels<<"..."<<std::endl;
+	  m_Initializer->InitializeTransform();
+	  ParametersType* newParameters= new typename TransformType::ParametersType(m_Initializer->GetTransform()->GetNumberOfParameters());
+
+	  // Reinitialize an Optimizer (!= number of parameters)
+	  m_GenericOptimizer = GenericOptimizerType::New();
+	  m_GenericOptimizer->SetArgsInfo(m_ArgsInfo);
+	  m_GenericOptimizer->SetMaximize(m_Maximize);
+	  m_GenericOptimizer->SetNumberOfParameters(m_Initializer->GetTransform()->GetNumberOfParameters());
+	  typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
+	  OptimizerType::Pointer optimizer = m_GenericOptimizer->GetOptimizerPointer();
+	  optimizer->AddObserver( itk::IterationEvent(), m_CommandIterationUpdate);
+	  registration->SetOptimizer(optimizer);						  
+	  m_CommandIterationUpdate->SetOptimizer(m_GenericOptimizer);
+	  
+	  // Set the previous transform parameters to the registration
+	  // if(m_Initializer->m_Parameters!=NULL )delete m_Initializer->m_Parameters;
+	  m_Initializer->SetInitialParameters(currentCoefficientImage,*newParameters); 
+ 	  registration->SetInitialTransformParametersOfNextLevel(*newParameters);  
+	}
+    }
+
+    void Execute(const itk::Object * , const itk::EventObject & )
+    { return; }
+
+
+    // Members
+    void SetInitializer(InitializerPointer i){m_Initializer=i;}
+    InitializerPointer m_Initializer;
+
+    void SetArgsInfo(args_info_clitkShapedBLUTSpatioTemporalDIR a){m_ArgsInfo=a;}
+    args_info_clitkShapedBLUTSpatioTemporalDIR m_ArgsInfo;
+
+    void SetCommandIterationUpdate(CommandIterationUpdatePointer c){m_CommandIterationUpdate=c;};
+    CommandIterationUpdatePointer m_CommandIterationUpdate;
+
+    GenericOptimizerPointer m_GenericOptimizer;
+    void SetMaximize(bool b){m_Maximize=b;}
+    bool m_Maximize;
+
+    GenericMetricPointer m_GenericMetric;
+    void SetMetricRegion(RegionType i){m_MetricRegion=i;}
+    RegionType m_MetricRegion;
+    
+ 
+  };
+
+
+  //==============================================================================
+  // Update with the number of dimensions
+  //==============================================================================
+  template<unsigned int Dimension>
+  void 
+  ShapedBLUTSpatioTemporalDIRGenericFilter::UpdateWithDim(std::string PixelType)
+  {
+    if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
+
+    if(PixelType == "short"){  
+      if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
+      UpdateWithDimAndPixelType<Dimension, signed short>(); 
+    }
+    //    else if(PixelType == "unsigned_short"){  
+    //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
+    //       UpdateWithDimAndPixelType<Dimension, unsigned short>(); 
+    //     }
+    
+    //     else if (PixelType == "unsigned_char"){ 
+    //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
+    //       UpdateWithDimAndPixelType<Dimension, unsigned char>();
+    //     }
+    
+    //     else if (PixelType == "char"){ 
+    //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
+    //       UpdateWithDimAndPixelType<Dimension, signed char>();
+    //    }
+    else {
+      if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
+      UpdateWithDimAndPixelType<Dimension, float>();
+    }
+  }
+
+
+  //==============================================================================
+  // Update with the number of dimensions and pixeltype
+  //==============================================================================
+  template<unsigned int ImageDimension, class PixelType> 
+  void 
+  ShapedBLUTSpatioTemporalDIRGenericFilter::UpdateWithDimAndPixelType()
+  {
+
+
+    //=============================================================================
+    //Input
+    //=============================================================================
+    bool threadsGiven=m_ArgsInfo.threads_given;
+    int threads=m_ArgsInfo.threads_arg;
+    
+    typedef itk::Image< PixelType, ImageDimension >  FixedImageType;
+    typedef itk::Image< PixelType, ImageDimension >  MovingImageType;
+    const unsigned int SpaceDimension = ImageDimension-1;
+    typedef double TCoordRep;
+
+
+    //=======================================================
+    //Input
+    //=======================================================
+    typedef itk::ImageFileReader< FixedImageType  > FixedImageReaderType;
+    typedef itk::ImageFileReader< MovingImageType > MovingImageReaderType;
+
+    typename FixedImageReaderType::Pointer  fixedImageReader  = FixedImageReaderType::New();
+    typename MovingImageReaderType::Pointer movingImageReader = MovingImageReaderType::New();
+
+    fixedImageReader->SetFileName(  m_ArgsInfo.reference_arg );
+    movingImageReader->SetFileName( m_ArgsInfo.target_arg );
+    if (m_Verbose) std::cout<<"Reading images..."<<std::endl;
+    fixedImageReader->Update();
+    movingImageReader->Update();
+
+    typename FixedImageType::Pointer fixedImage = fixedImageReader->GetOutput();
+    typename MovingImageType::Pointer movingImage =movingImageReader->GetOutput();
+    typename FixedImageType::Pointer croppedFixedImage=fixedImage;
+
+
+    //=======================================================
+    // Regions
+    //=======================================================
+
+    // The original input region    
+    typename FixedImageType::RegionType fixedImageRegion = fixedImage->GetLargestPossibleRegion();
+
+    // The transform region with respect to the input region:
+    // where should the transform be DEFINED (depends on mask)
+    typename FixedImageType::RegionType transformRegion = fixedImage->GetLargestPossibleRegion();
+    typename FixedImageType::RegionType::SizeType transformRegionSize=transformRegion.GetSize();
+    typename FixedImageType::RegionType::IndexType transformRegionIndex=transformRegion.GetIndex();
+    typename FixedImageType::PointType transformRegionOrigin=fixedImage->GetOrigin();
+
+    // 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();
+
+    //===========================================================================
+    // If given, we connect a mask to reference or target
+    //============================================================================
+    typedef itk::ImageMaskSpatialObject<  ImageDimension >   MaskType;
+    typename MaskType::Pointer  fixedMask=NULL;
+    if (m_ArgsInfo.referenceMask_given)
+      {
+	fixedMask= MaskType::New();
+	typedef itk::Image< unsigned char, ImageDimension >   ImageMaskType;
+	typedef itk::ImageFileReader< ImageMaskType >    MaskReaderType;
+	typename MaskReaderType::Pointer  maskReader = MaskReaderType::New();
+	maskReader->SetFileName(m_ArgsInfo.referenceMask_arg);
+	try 
+	  { 
+	    maskReader->Update(); 
+	  } 
+	catch( itk::ExceptionObject & err ) 
+	  { 
+	    std::cerr << "ExceptionObject caught while reading mask !" << std::endl; 
+	    std::cerr << err << std::endl; 
+	    return;
+	  } 
+	if (m_Verbose)std::cout <<"Reference image mask was read..." <<std::endl;
+
+	// Set the image to the spatialObject
+	fixedMask->SetImage( maskReader->GetOutput() );
+
+	// Find the bounding box of the "inside" label
+	typedef itk::LabelStatisticsImageFilter<ImageMaskType, ImageMaskType> StatisticsImageFilterType;
+	typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
+	statisticsImageFilter->SetInput(maskReader->GetOutput());
+	statisticsImageFilter->SetLabelInput(maskReader->GetOutput());
+	statisticsImageFilter->Update();
+	typename StatisticsImageFilterType::BoundingBoxType boundingBox = statisticsImageFilter->GetBoundingBox(1);
+
+	// Limit the transform region to the mask
+	for (unsigned int i=0; i<ImageDimension; i++)
+	  {
+	    transformRegionIndex[i]=boundingBox[2*i];
+	    transformRegionSize[i]=boundingBox[2*i+1]-boundingBox[2*i]+1;
+	  }
+	transformRegion.SetSize(transformRegionSize);
+	transformRegion.SetIndex(transformRegionIndex);
+	fixedImage->TransformIndexToPhysicalPoint(transformRegion.GetIndex(), transformRegionOrigin);
+	
+	// Crop the fixedImage to the bounding box to facilitate multi-resolution 
+	typedef itk::ExtractImageFilter<FixedImageType,FixedImageType> ExtractImageFilterType; 
+	typename ExtractImageFilterType::Pointer extractImageFilter=ExtractImageFilterType::New();
+	extractImageFilter->SetInput(fixedImage);
+	extractImageFilter->SetExtractionRegion(transformRegion);
+	extractImageFilter->Update();
+	croppedFixedImage=extractImageFilter->GetOutput();
+
+	// Update the metric region	
+	metricRegion = croppedFixedImage->GetLargestPossibleRegion();
+	metricRegionIndex=metricRegion.GetIndex();
+	metricRegionSize=metricRegion.GetSize();
+	croppedFixedImage->TransformIndexToPhysicalPoint(metricRegionIndex, metricRegionOrigin);
+
+	// Set start index to zero (with respect to croppedFixedImage/transform region)
+	metricRegionIndex.Fill(0);
+	metricRegion.SetIndex(metricRegionIndex);
+	croppedFixedImage->SetRegions(metricRegion);
+	croppedFixedImage->SetOrigin(metricRegionOrigin);
+
+      }
+
+    typedef itk::ImageMaskSpatialObject<  ImageDimension >   MaskType;
+    typename MaskType::Pointer  movingMask=NULL;
+    if (m_ArgsInfo.targetMask_given)
+      {
+	movingMask= MaskType::New();
+	typedef itk::Image< unsigned char, ImageDimension >   ImageMaskType;
+	typedef itk::ImageFileReader< ImageMaskType >    MaskReaderType;
+	typename MaskReaderType::Pointer  maskReader = MaskReaderType::New();
+	maskReader->SetFileName(m_ArgsInfo.targetMask_arg);
+	try 
+	  { 
+	    maskReader->Update(); 
+	  } 
+	catch( itk::ExceptionObject & err ) 
+	  { 
+	    std::cerr << "ExceptionObject caught !" << std::endl; 
+	    std::cerr << err << std::endl; 
+	  } 
+	if (m_Verbose)std::cout <<"Target image mask was read..." <<std::endl;
+	
+	movingMask->SetImage( maskReader->GetOutput() );
+      }
+
+
+    //=======================================================
+    // Output Regions
+    //=======================================================
+
+    if (m_Verbose)
+      {
+	// Fixed image region
+	std::cout<<"The fixed image has its origin at "<<fixedImage->GetOrigin()<<std::endl 
+		 <<"The fixed image region starts at index "<<fixedImageRegion.GetIndex()<<std::endl
+		 <<"The fixed image region has size "<< fixedImageRegion.GetSize()<<std::endl;
+
+	// Transform region
+	std::cout<<"The transform has its origin at "<<transformRegionOrigin<<std::endl 
+		 <<"The transform region will start at index "<<transformRegion.GetIndex()<<std::endl
+		 <<"The transform region has size "<< transformRegion.GetSize()<<std::endl;
+
+	// Metric region
+	std::cout<<"The metric region has its origin at "<<metricRegionOrigin<<std::endl 
+		 <<"The metric region will start at index "<<metricRegion.GetIndex()<<std::endl
+		 <<"The metric region has size "<< metricRegion.GetSize()<<std::endl;
+	
+      }  
+
+
+    //=======================================================
+    // Pyramids (update them for transform initializer)
+    //=======================================================
+    typedef clitk::RecursiveSpatioTemporalMultiResolutionPyramidImageFilter< FixedImageType, FixedImageType>    FixedImagePyramidType;
+    typedef clitk::RecursiveSpatioTemporalMultiResolutionPyramidImageFilter< MovingImageType, MovingImageType>    MovingImagePyramidType;
+    typename FixedImagePyramidType::Pointer fixedImagePyramid = FixedImagePyramidType::New();
+    typename MovingImagePyramidType::Pointer movingImagePyramid = MovingImagePyramidType::New();
+    fixedImagePyramid->SetUseShrinkImageFilter(false);
+    fixedImagePyramid->SetInput(croppedFixedImage);
+    fixedImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
+    movingImagePyramid->SetUseShrinkImageFilter(false);    
+    movingImagePyramid->SetInput(movingImage);
+    movingImagePyramid->SetNumberOfLevels(m_ArgsInfo.levels_arg);
+    if (m_Verbose) std::cout<<"Creating the image pyramid..."<<std::endl;
+    fixedImagePyramid->Update();
+    movingImagePyramid->Update();
+    typedef clitk::MultiResolutionPyramidRegionFilter<FixedImageType> FixedImageRegionPyramidType;
+    typename FixedImageRegionPyramidType::Pointer fixedImageRegionPyramid=FixedImageRegionPyramidType::New();
+    fixedImageRegionPyramid->SetRegion(metricRegion);
+    fixedImageRegionPyramid->SetSchedule(fixedImagePyramid->GetSchedule());
+
+
+
+
+    //     //=======================================================
+    //     // Rigid Transform
+    //     //=======================================================
+    //     typedef itk::Euler3DTransform <double> RigidTransformType;
+    //     RigidTransformType::Pointer rigidTransform;
+    //     if (m_ArgsInfo.rigid_given)
+    //       {
+    // 	rigidTransform=RigidTransformType::New();
+    // 	itk::Matrix<double,4,4> rigidTransformMatrix=clitk::ReadMatrix3D(m_ArgsInfo.rigid_arg);
+    
+    // 	//Set the rotation
+    // 	itk::Matrix<double,3,3> finalRotation = clitk::GetRotationalPartMatrix3D(rigidTransformMatrix);
+    // 	rigidTransform->SetMatrix(finalRotation);
+    
+    // 	//Set the translation
+    // 	itk::Vector<double,3> finalTranslation = clitk::GetTranslationPartMatrix3D(rigidTransformMatrix);
+    // 	rigidTransform->SetTranslation(finalTranslation);
+    
+    //       }
+
+
+    //=======================================================
+    // ShapedBSplineSpatioTemporal Transform
+    //=======================================================
+    typedef  clitk::ShapedBLUTSpatioTemporalDeformableTransform<TCoordRep,ImageDimension, ImageDimension > TransformType;
+    typename TransformType::Pointer transform= TransformType::New();
+    transform->SetTransformShape(m_ArgsInfo.shape_arg);
+    if (fixedMask) transform->SetMask( fixedMask );
+    // if (rigidTransform) transform->SetBulkTransform( rigidTransform );	
+
+    //-------------------------------------------------------------------------
+    // The transform initializer
+    //-------------------------------------------------------------------------
+    typedef clitk::ShapedBLUTSpatioTemporalDeformableTransformInitializer< TransformType,FixedImageType> InitializerType;
+    typename InitializerType::Pointer initializer = InitializerType::New();
+    initializer->SetVerbose(m_Verbose);
+    initializer->SetImage(fixedImagePyramid->GetOutput(0));
+    initializer->SetTransform(transform);
+
+    //-------------------------------------------------------------------------
+    // Order
+    //-------------------------------------------------------------------------
+    typename FixedImageType::RegionType::SizeType splineOrders ;
+    splineOrders.Fill(3);
+    if (m_ArgsInfo.order_given)
+      for(unsigned int i=0; i<ImageDimension;i++) 
+	splineOrders[i]=m_ArgsInfo.order_arg[i];
+    if (m_Verbose) std::cout<<"Setting the spline orders  to "<<splineOrders<<"..."<<std::endl;
+    initializer->SetSplineOrders(splineOrders);
+
+    //-------------------------------------------------------------------------
+    // Levels
+    //-------------------------------------------------------------------------
+  
+    // Spacing
+    if (m_ArgsInfo.spacing_given)
+      {
+	initializer->m_ControlPointSpacingArray.resize(m_ArgsInfo.levels_arg);
+	initializer->SetControlPointSpacing(m_ArgsInfo.spacing_arg);
+	initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]=initializer->m_ControlPointSpacing;
+	if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1]
+				<<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;   
+	
+	for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
+	  {
+	    initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]=initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-i]*2;
+	    initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i][ImageDimension-1]=2;
+	    if (m_Verbose) std::cout<<"Using a control point spacing of "<<initializer->m_ControlPointSpacingArray[m_ArgsInfo.levels_arg-1-i]
+				    <<" at level "<<m_ArgsInfo.levels_arg-i<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;   
+	  }
+	  
+      }  
+    
+    // Control
+    if (m_ArgsInfo.control_given)
+      {
+	initializer->m_NumberOfControlPointsInsideTheImageArray.resize(m_ArgsInfo.levels_arg);
+	initializer->SetNumberOfControlPointsInsideTheImage(m_ArgsInfo.control_arg);
+	initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]=initializer->m_NumberOfControlPointsInsideTheImage;
+	if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1]<<"control points inside the image"
+				<<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;   
+	
+	for (int i=1; i<m_ArgsInfo.levels_arg; i++ )
+	  {
+	    for(unsigned int j=0;j<ImageDimension-1;j++)
+	      initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i][j]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i][j]/2.);
+	      //	    initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]=ceil ((double)initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-i]/2.);
+	    if (m_Verbose) std::cout<<"Using "<< initializer->m_NumberOfControlPointsInsideTheImageArray[m_ArgsInfo.levels_arg-1-i]<<"control points inside the image"
+				    <<" at level "<<m_ArgsInfo.levels_arg<<" of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;   
+	
+	  }
+      }  
+
+    // Inialize on the first level 
+    if (m_ArgsInfo.verbose_flag) std::cout<<"Initializing transform for level 1 of "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
+    if (m_ArgsInfo.spacing_given) initializer->SetControlPointSpacing(	initializer->m_ControlPointSpacingArray[0]);
+    if (m_ArgsInfo.control_given) initializer->SetNumberOfControlPointsInsideTheImage(initializer->m_NumberOfControlPointsInsideTheImageArray[0]);	
+    if (m_ArgsInfo.samplingFactor_given) initializer->SetSamplingFactors(m_ArgsInfo.samplingFactor_arg);	
+ 
+    // Initialize 
+    initializer->InitializeTransform();
+
+    //-------------------------------------------------------------------------
+    // Initial parameters (passed by reference)
+    //-------------------------------------------------------------------------
+    typedef typename TransformType::ParametersType     ParametersType;
+    const unsigned int numberOfParameters =    transform->GetNumberOfParameters();
+    ParametersType parameters(numberOfParameters);
+    parameters.Fill( 0.0 );
+    transform->SetParameters( parameters );
+    if (m_ArgsInfo.initCoeff_given) initializer->SetInitialParameters(m_ArgsInfo.initCoeff_arg, parameters);
+
+	    
+    //=======================================================
+    // Interpolator
+    //=======================================================
+    typedef clitk::GenericInterpolator<args_info_clitkShapedBLUTSpatioTemporalDIR, FixedImageType,TCoordRep > GenericInterpolatorType;
+    typename   GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
+    genericInterpolator->SetArgsInfo(m_ArgsInfo);
+    typedef itk::InterpolateImageFunction< FixedImageType, TCoordRep >  InterpolatorType;
+    typename  InterpolatorType::Pointer interpolator=genericInterpolator->GetInterpolatorPointer();
+
+
+    //=======================================================
+    // Metric
+    //=======================================================
+    typedef clitk::GenericMetric< args_info_clitkShapedBLUTSpatioTemporalDIR, FixedImageType,MovingImageType > GenericMetricType;
+    typename GenericMetricType::Pointer genericMetric=GenericMetricType::New();
+    genericMetric->SetArgsInfo(m_ArgsInfo);
+    genericMetric->SetFixedImage(fixedImagePyramid->GetOutput(0));
+    if (fixedMask) genericMetric->SetFixedImageMask(fixedMask);
+    genericMetric->SetFixedImageRegion(fixedImageRegionPyramid->GetOutput(0));
+    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 );
+#else
+    if (m_Verbose) std::cout<<"Not setting the number of threads (not compiled with USE_OPTIMIZED_REGISTRATION_METHODS)..."<<std::endl;
+#endif
+
+
+    //=======================================================
+    // Optimizer
+    //=======================================================
+    typedef clitk::GenericOptimizer<args_info_clitkShapedBLUTSpatioTemporalDIR> GenericOptimizerType;
+    GenericOptimizerType::Pointer genericOptimizer = GenericOptimizerType::New();
+    genericOptimizer->SetArgsInfo(m_ArgsInfo);
+    genericOptimizer->SetMaximize(genericMetric->GetMaximize());
+    genericOptimizer->SetNumberOfParameters(transform->GetNumberOfParameters());
+    typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
+    OptimizerType::Pointer optimizer = genericOptimizer->GetOptimizerPointer();
+
+
+    //=======================================================
+    // Registration
+    //=======================================================
+    typedef clitk::SpatioTemporalMultiResolutionImageRegistrationMethod<  FixedImageType, MovingImageType >    RegistrationType;
+    typename RegistrationType::Pointer   registration  = RegistrationType::New();
+    registration->SetMetric(        metric        );
+    registration->SetOptimizer(     optimizer     );
+    registration->SetInterpolator(  interpolator  );
+    registration->SetTransform (transform);
+    if(threadsGiven) registration->SetNumberOfThreads(threads);
+    registration->SetFixedImage(  croppedFixedImage   );
+    registration->SetMovingImage(  movingImage   );
+    registration->SetFixedImageRegion( metricRegion );
+    registration->SetFixedImagePyramid( fixedImagePyramid );
+    registration->SetMovingImagePyramid( movingImagePyramid );
+    registration->SetInitialTransformParameters( transform->GetParameters() );
+    registration->SetNumberOfLevels( m_ArgsInfo.levels_arg );
+    if (m_Verbose) std::cout<<"Setting the number of resolution levels to "<<m_ArgsInfo.levels_arg<<"..."<<std::endl;
+       
+  
+    //================================================================================================
+    // Observers
+    //================================================================================================
+    if (m_Verbose)
+      {
+	// Output iteration info
+	typedef	CommandIterationUpdate <RegistrationType,args_info_clitkShapedBLUTSpatioTemporalDIR> CommandIterationUpdateType;
+	typename CommandIterationUpdateType::Pointer observer = CommandIterationUpdateType::New();
+	observer->SetInitializer(initializer);
+	observer->SetArgsInfo(m_ArgsInfo);
+	observer->SetOptimizer(genericOptimizer);
+	optimizer->AddObserver( itk::IterationEvent(), observer );
+	
+	// Output level info
+	typedef RegistrationInterfaceCommand<RegistrationType,args_info_clitkShapedBLUTSpatioTemporalDIR> CommandType;
+	typename CommandType::Pointer command = CommandType::New();
+	command->SetInitializer(initializer);
+	command->SetArgsInfo(m_ArgsInfo);
+	command->SetCommandIterationUpdate(observer);
+	command->SetMaximize(genericMetric->GetMaximize());
+	command->SetMetricRegion(metricRegion);
+  	registration->AddObserver( itk::IterationEvent(), command );
+      }
+
+
+    //=======================================================
+    // Let's go
+    //=======================================================
+    if (m_Verbose) std::cout << std::endl << "Starting Registration" << std::endl;
+
+    try 
+      { 
+	registration->StartRegistration(); 
+      } 
+    catch( itk::ExceptionObject & err ) 
+      { 
+	std::cerr << "ExceptionObject caught while registering!" << std::endl; 
+	std::cerr << err << std::endl; 
+	return;
+      } 
+  
+
+    //=======================================================
+    // Get the result
+    //=======================================================
+    OptimizerType::ParametersType finalParameters =  registration->GetLastTransformParameters();
+    transform->SetParameters( finalParameters );
+    if (m_Verbose)
+      {
+	std::cout<<"Stop condition description: "
+		 <<registration->GetOptimizer()->GetStopConditionDescription()<<std::endl;
+      }
+
+ 
+    //=======================================================
+    // Get the BSplineSpatioTemporal coefficient images and write them
+    //=======================================================
+    if (m_ArgsInfo.coeff_given)
+      { 
+	typedef typename TransformType::CoefficientImageType CoefficientImageType;
+	typename CoefficientImageType::Pointer coefficientImage =transform->GetCoefficientImage();
+	typedef itk::ImageFileWriter<CoefficientImageType> CoeffWriterType;
+	typename CoeffWriterType::Pointer coeffWriter=CoeffWriterType::New();
+	coeffWriter->SetInput(coefficientImage);
+	coeffWriter->SetFileName(m_ArgsInfo.coeff_arg);
+	coeffWriter->Update();
+	
+      }
+    if (m_ArgsInfo.padCoeff_given)
+      { 
+	typedef  itk::Image<itk::Vector<TCoordRep, SpaceDimension>, ImageDimension> CoefficientImageType;
+	typename CoefficientImageType::Pointer coefficientImage =transform->GetPaddedCoefficientImage();
+	typedef itk::ImageFileWriter<CoefficientImageType> CoeffWriterType;
+	typename CoeffWriterType::Pointer coeffWriter=CoeffWriterType::New();
+	coeffWriter->SetInput(coefficientImage);
+	coeffWriter->SetFileName(m_ArgsInfo.padCoeff_arg);
+	coeffWriter->Update();
+      }    
+  
+
+    //=======================================================
+    // Generate the DVF (4D with 3 comps and 4D with 4 comps)
+    //=======================================================
+    typedef itk::Vector< float, SpaceDimension >  DisplacementType;
+    typedef itk::Vector< float, ImageDimension >  Displacement4DType;
+    typedef itk::Image< DisplacementType, ImageDimension >  DeformationFieldType;
+    typedef itk::Image< Displacement4DType, ImageDimension >  DeformationField4DType;
+  
+    typename DeformationFieldType::Pointer field = DeformationFieldType::New();
+    typename DeformationField4DType::Pointer field4D = DeformationField4DType::New();
+    field->SetRegions( fixedImageRegion );
+    field->SetOrigin( fixedImage->GetOrigin() );
+    field->SetSpacing( fixedImage->GetSpacing() );
+    field->SetDirection( fixedImage->GetDirection() );
+    field->Allocate();
+    field4D->SetRegions( fixedImageRegion );
+    field4D->SetOrigin( fixedImage->GetOrigin() );
+    field4D->SetSpacing( fixedImage->GetSpacing() );
+    field4D->SetDirection( fixedImage->GetDirection() );
+    field4D->Allocate();
+  
+    typedef itk::ImageRegionIteratorWithIndex< DeformationFieldType > FieldIterator;
+    typedef itk::ImageRegionIteratorWithIndex< DeformationField4DType > Field4DIterator;
+    FieldIterator fi( field, fixedImageRegion );
+    Field4DIterator fi4D( field4D, fixedImageRegion );
+    fi.GoToBegin();
+    fi4D.GoToBegin();
+  
+    typename TransformType::InputPointType  fixedPoint;
+    typename TransformType::OutputPointType movingPoint;
+    typename DeformationFieldType::IndexType index;
+  
+    DisplacementType displacement;
+    Displacement4DType displacement4D;
+    displacement4D[ImageDimension-1]=0;
+    while( ! fi.IsAtEnd() )
+      {
+	index = fi.GetIndex();
+	field->TransformIndexToPhysicalPoint( index, fixedPoint );
+	movingPoint = transform->TransformPoint( fixedPoint );
+	for (unsigned int i=0; i<SpaceDimension; i++)
+	  {
+	    displacement[i] = movingPoint[i] - fixedPoint[i];
+	    displacement4D[i] = movingPoint[i] - fixedPoint[i];
+	  }
+	fi.Set( displacement );
+	fi4D.Set(displacement4D);
+	++fi;
+	++fi4D;
+      }
+
+ 
+    //=======================================================
+    // Write the DVF
+    //=======================================================
+    typedef itk::ImageFileWriter< DeformationFieldType >  FieldWriterType;
+    typename FieldWriterType::Pointer fieldWriter = FieldWriterType::New();
+    fieldWriter->SetFileName( m_ArgsInfo.vf_arg );
+    fieldWriter->SetInput( field );
+    try
+      {
+	fieldWriter->Update();
+      }
+    catch( itk::ExceptionObject & excp )
+      {
+	std::cerr << "Exception thrown writing the DVF" << std::endl;
+	std::cerr << excp << std::endl;
+	return;
+      }
+  
+  
+    //=======================================================
+    // Resample the moving image
+    //=======================================================
+    typedef itk::WarpImageFilter< MovingImageType, FixedImageType, DeformationField4DType >    WarpFilterType;
+    typename WarpFilterType::Pointer warp = WarpFilterType::New();
+
+    warp->SetDeformationField( field4D );
+    warp->SetInput( movingImageReader->GetOutput() );
+    warp->SetOutputOrigin(  fixedImage->GetOrigin() );
+    warp->SetOutputSpacing( fixedImage->GetSpacing() );
+    warp->SetOutputDirection( fixedImage->GetDirection() );
+    warp->SetEdgePaddingValue( 0.0 );
+    warp->Update();
+ 
+
+    //=======================================================
+    // Write the warped image
+    //=======================================================
+    typedef itk::ImageFileWriter< FixedImageType >  WriterType;
+    typename WriterType::Pointer      writer =  WriterType::New();
+    writer->SetFileName( m_ArgsInfo.output_arg );
+    writer->SetInput( warp->GetOutput()    );
+
+    try
+      {
+	writer->Update();
+      }
+    catch( itk::ExceptionObject & err ) 
+      { 
+	std::cerr << "ExceptionObject caught !" << std::endl; 
+	std::cerr << err << std::endl; 
+	return;
+      } 
+ 
+
+    //=======================================================
+    // Calculate the difference after the deformable transform
+    //=======================================================
+    typedef clitk::DifferenceImageFilter<  FixedImageType, FixedImageType> DifferenceFilterType;
+    if (m_ArgsInfo.after_given)
+      {
+	typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
+	difference->SetValidInput( fixedImage );
+	difference->SetTestInput( warp->GetOutput() );
+      
+	try
+	  {
+	    difference->Update();
+	  }
+	catch( itk::ExceptionObject & err ) 
+	  { 
+	    std::cerr << "ExceptionObject caught calculating the difference !" << std::endl; 
+	    std::cerr << err << std::endl; 
+	    return;
+	  }
+      
+	typename WriterType::Pointer differenceWriter=WriterType::New();
+	differenceWriter->SetInput(difference->GetOutput());
+	differenceWriter->SetFileName(m_ArgsInfo.after_arg);
+	differenceWriter->Update(); 
+      
+      }
+
+
+    //=======================================================
+    // Calculate the difference before the deformable transform
+    //=======================================================
+    if( m_ArgsInfo.before_given )
+      {
+
+	typename FixedImageType::Pointer moving=FixedImageType::New();
+	if (m_ArgsInfo.rigid_given)
+	  {
+	    typedef itk::ResampleImageFilter<MovingImageType, FixedImageType> ResamplerType;
+	    typename ResamplerType::Pointer resampler=ResamplerType::New();
+	    resampler->SetInput(movingImage);
+	    resampler->SetOutputOrigin(fixedImage->GetOrigin());
+	    resampler->SetSize(fixedImage->GetLargestPossibleRegion().GetSize());
+	    resampler->SetOutputSpacing(fixedImage->GetSpacing());  
+	    resampler->SetDefaultPixelValue( 0. );
+	    //resampler->SetTransform(rigidTransform);
+	    resampler->Update();
+	    moving=resampler->GetOutput();
+	  }
+	else
+	  moving=movingImage;
+
+	typename DifferenceFilterType::Pointer difference = DifferenceFilterType::New();
+	difference->SetValidInput( fixedImage );
+	difference->SetTestInput( moving );
+    
+	try
+	  {
+	    difference->Update();
+	  }
+	catch( itk::ExceptionObject & err ) 
+	  { 
+	    std::cerr << "ExceptionObject caught calculating the difference !" << std::endl; 
+	    std::cerr << err << std::endl; 
+	    return;
+	  }
+
+	typename WriterType::Pointer differenceWriter=WriterType::New();
+	writer->SetFileName( m_ArgsInfo.before_arg  );
+	writer->SetInput( difference->GetOutput()  );
+	writer->Update( );
+      }
+
+    return;
+  
+  }
+}//end clitk
+
+#endif //#define clitkShapedBLUTSpatioTemporalDIRGenericFilter_txx