/*=========================================================================
- Program: vv http://www.creatis.insa-lyon.fr/rio/vv
+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
+Authors belong to:
+- University of LYON http://www.universite-lyon.fr/
+- Léon Bérard cancer center http://www.centreleonberard.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.
+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
+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
-======================================================================-====*/
+- BSD See included LICENSE.txt file
+- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
+===========================================================================**/
#ifndef clitkBLUTDIRGenericFilter_cxx
#define clitkBLUTDIRGenericFilter_cxx
/* =================================================
* @file clitkBLUTDIRGenericFilter.cxx
- * @author
- * @date
- *
- * @brief
- *
+ * @author
+ * @date
+ *
+ * @brief
+ *
===================================================*/
#include "clitkBLUTDIRGenericFilter.h"
-
-
+#include "clitkBLUTDIRCommandIterationUpdateDVF.h"
+#include "itkCenteredTransformInitializer.h"
+
namespace clitk
{
+ //==============================================================================
+ // Creating an observer class that allows output at each iteration
+ //==============================================================================
+ class CommandIterationUpdate : public itk::Command
+ {
+ public:
+ typedef CommandIterationUpdate Self;
+ typedef itk::Command Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ itkNewMacro( Self );
+ protected:
+ CommandIterationUpdate() {};
+ public:
+ typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> OptimizerType;
+ typedef const OptimizerType * OptimizerPointer;
+
+ // Set the generic optimizer
+ void SetOptimizer(OptimizerPointer o){m_Optimizer=o;}
+
+ // 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;
+ }
+
+ m_Optimizer->OutputIterationInfo();
+ }
+
+ OptimizerPointer m_Optimizer;
+ };
- //-----------------------------------------------------------
- // Constructor
- //-----------------------------------------------------------
- BLUTDIRGenericFilter::BLUTDIRGenericFilter()
+ //===========================================================================//
+ //Constructor
+ //==========================================================================//
+ BLUTDIRGenericFilter::BLUTDIRGenericFilter():
+ ImageToImageGenericFilter<Self>("Register DIR")
{
+ InitializeImageType<2>();
+ InitializeImageType<3>();
m_Verbose=false;
- m_ReferenceFileName="";
}
+ //=========================================================================//
+ //SetArgsInfo
+ //==========================================================================//
+ void BLUTDIRGenericFilter::SetArgsInfo(const args_info_clitkBLUTDIR & a){
+ m_ArgsInfo=a;
+ if (m_ArgsInfo.reference_given) AddInputFilename(m_ArgsInfo.reference_arg);
- //-----------------------------------------------------------
- // Update
- //-----------------------------------------------------------
- void BLUTDIRGenericFilter::Update()
- {
- // Read the Dimension and PixelType
- int Dimension;
- std::string PixelType;
- ReadImageDimensionAndPixelType(m_ReferenceFileName, Dimension, PixelType);
+ if (m_ArgsInfo.target_given) {
+ AddInputFilename(m_ArgsInfo.target_arg);
+ }
+ if (m_ArgsInfo.output_given) SetOutputFilename(m_ArgsInfo.output_arg);
- // Call UpdateWithDim
- //if(Dimension==2) UpdateWithDim<2>(PixelType);
- //else
- if(Dimension==3) UpdateWithDim<3>(PixelType);
- // else if (Dimension==4)UpdateWithDim<4>(PixelType);
- else
+ if (m_ArgsInfo.verbose_given) m_Verbose=true;
+ }
+
+ //=========================================================================//
+ //===========================================================================//
+ template<unsigned int Dim>
+ void BLUTDIRGenericFilter::InitializeImageType()
+ {
+ ADD_DEFAULT_IMAGE_TYPES(3);
+ }
+ //--------------------------------------------------------------------
+
+ //==============================================================================
+ //Creating an observer class that allows us to change parameters at subsequent levels
+ //==============================================================================
+ template <typename TRegistration,class args_info_clitkBLUTDIR>
+ 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::MultipleBSplineDeformableTransform<double, ImageDimension, ImageDimension> TransformType;
+ typedef clitk::MultipleBSplineDeformableTransformInitializer<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 CommandIterationUpdate::Pointer CommandIterationUpdatePointer;
+
+ // Optimizer
+ typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
+ typedef typename GenericOptimizerType::Pointer GenericOptimizerPointer;
+
+ // Metric
+ typedef typename RegistrationType::FixedImageType InternalImageType;
+ typedef clitk::GenericMetric<args_info_clitkBLUTDIR, 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)
{
- std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
- return;
+ 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();
+ std::vector<typename CoefficientImageType::Pointer> currentCoefficientImages = m_Initializer->GetTransform()->GetCoefficientImages();
+ for (unsigned i = 0; i < currentCoefficientImages.size(); ++i)
+ {
+ caster->SetInputImage(currentCoefficientImages[i]);
+ caster->Update();
+ currentCoefficientImages[i] = 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());
+
+ // DS : if we want to skip the last pyramid level, force to only 1 iteration
+ DD(m_ArgsInfo.skipLastPyramidLevel_flag);
+ if ((currentLevel == numberOfLevels) && (m_ArgsInfo.skipLastPyramidLevel_flag)) {
+ DD(m_ArgsInfo.maxIt_arg);
+ std::cout << "I skip the last pyramid level : set max iteration to 0" << std::endl;
+ m_ArgsInfo.maxIt_arg = 0;
+ DD(m_ArgsInfo.maxIt_arg);
+ }
+
+ // 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(currentCoefficientImages, *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_clitkBLUTDIR a){m_ArgsInfo=a;}
+ args_info_clitkBLUTDIR 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 and pixeltype
+ //==============================================================================
+ template<class InputImageType>
+ void BLUTDIRGenericFilter::UpdateWithInputImageType()
+ {
+ if (m_Verbose) std::cout << "BLUTDIRGenericFilter::UpdateWithInputImageType()" << std::endl;
+
+ //=============================================================================
+ //Input
+ //=============================================================================
+ bool threadsGiven=m_ArgsInfo.threads_given;
+ int threads=m_ArgsInfo.threads_arg;
+ typedef typename InputImageType::PixelType PixelType;
+
+ typedef double TCoordRep;
+
+ typename InputImageType::Pointer fixedImage = this->template GetInput<InputImageType>(0);
+
+ typename InputImageType::Pointer inputFixedImage = this->template GetInput<InputImageType>(0);
+
+ // typedef input2
+ typename InputImageType::Pointer movingImage = this->template GetInput<InputImageType>(1);
+
+ typename InputImageType::Pointer inputMovingImage = this->template GetInput<InputImageType>(1);
+
+ typedef itk::Image< PixelType,InputImageType::ImageDimension > FixedImageType;
+ typedef itk::Image< PixelType, InputImageType::ImageDimension> MovingImageType;
+ const unsigned int SpaceDimension = InputImageType::ImageDimension;
+ //Whatever the pixel type, internally we work with an image represented in float
+ //Reading reference image
+ if (m_Verbose) std::cout<<"Reading images..."<<std::endl;
+ //=======================================================
+ //Input
+ //=======================================================
+ 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::IndexType metricRegionIndex=metricRegion.GetIndex();
+ typename FixedImageType::PointType metricRegionOrigin=fixedImage->GetOrigin();
+
+
+ //===========================================================================
+ // If given, we connect a mask to reference or target
+ //============================================================================
+ typedef itk::ImageMaskSpatialObject< InputImageType::ImageDimension > MaskType;
+ typedef itk::Image< unsigned char, InputImageType::ImageDimension > ImageLabelType;
+ typename MaskType::Pointer fixedMask = NULL;
+ typename ImageLabelType::Pointer labels = NULL;
+ if (m_ArgsInfo.referenceMask_given)
+ {
+ fixedMask = MaskType::New();
+ labels = ImageLabelType::New();
+ typedef itk::ImageFileReader< ImageLabelType > LabelReaderType;
+ typename LabelReaderType::Pointer labelReader = LabelReaderType::New();
+ labelReader->SetFileName(m_ArgsInfo.referenceMask_arg);
+ try
+ {
+ labelReader->Update();
+ }
+ catch( itk::ExceptionObject & err )
+ {
+ std::cerr << "ExceptionObject caught while reading mask or labels !" << std::endl;
+ std::cerr << err << std::endl;
+ return;
+ }
+ if (m_Verbose)std::cout <<"Reference image mask was read..." <<std::endl;
+
+ // Resample labels
+ typedef itk::ResampleImageFilter<ImageLabelType, ImageLabelType> ResamplerType;
+ typename ResamplerType::Pointer resampler = ResamplerType::New();
+ typedef itk::NearestNeighborInterpolateImageFunction<ImageLabelType, TCoordRep> InterpolatorType;
+ typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
+ resampler->SetOutputParametersFromImage(fixedImage);
+ resampler->SetInterpolator(interpolator);
+ resampler->SetInput(labelReader->GetOutput());
+ resampler->Update();
+ labels = resampler->GetOutput();
+
+ // Set the image to the spatialObject
+ 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);
+
+ // Limit the transform region to the mask
+ for (unsigned int i=0; i<InputImageType::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();
+#if ITK_VERSION_MAJOR == 4
+ extractImageFilter->SetDirectionCollapseToSubmatrix();
+#endif
+ extractImageFilter->SetInput(fixedImage);
+ extractImageFilter->SetExtractionRegion(transformRegion);
+ extractImageFilter->Update();
+ croppedFixedImage=extractImageFilter->GetOutput();
+
+ // Update the metric region
+ metricRegion = croppedFixedImage->GetLargestPossibleRegion();
+ metricRegionIndex=metricRegion.GetIndex();
+ 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< InputImageType::ImageDimension > MaskType;
+ typename MaskType::Pointer movingMask=NULL;
+ if (m_ArgsInfo.targetMask_given)
+ {
+ movingMask= MaskType::New();
+ typedef itk::Image< unsigned char, InputImageType::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 itk::RecursiveMultiResolutionPyramidImageFilter< FixedImageType, FixedImageType> FixedImagePyramidType;
+ typedef itk::RecursiveMultiResolutionPyramidImageFilter< 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 or Affine Transform
+ //=======================================================
+ typedef itk::AffineTransform <double,3> RigidTransformType;
+ RigidTransformType::Pointer rigidTransform=NULL;
+ if (m_ArgsInfo.initMatrix_given)
+ {
+ if(m_Verbose) std::cout<<"Reading the prior transform matrix "<< m_ArgsInfo.initMatrix_arg<<"..."<<std::endl;
+ rigidTransform=RigidTransformType::New();
+ itk::Matrix<double,4,4> rigidTransformMatrix=clitk::ReadMatrix3D(m_ArgsInfo.initMatrix_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);
+ }
+ else
+ {
+ if(m_Verbose) std::cout<<"No itinial matrix given. 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();
+ }
+
+
+ //=======================================================
+ // B-LUT FFD Transform
+ //=======================================================
+ typedef clitk::MultipleBSplineDeformableTransform<TCoordRep,InputImageType::ImageDimension, SpaceDimension > TransformType;
+ typename TransformType::Pointer transform = TransformType::New();
+ if (labels) transform->SetLabels(labels);
+ if (rigidTransform) transform->SetBulkTransform(rigidTransform);
+
+ //-------------------------------------------------------------------------
+ // The transform initializer
+ //-------------------------------------------------------------------------
+ typedef clitk::MultipleBSplineDeformableTransformInitializer< 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<InputImageType::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;
+ 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<InputImageType::ImageDimension;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);
+
+ //-------------------------------------------------------------------------
+ // DEBUG: use an itk BSpline instead of multilabel BLUTs
+ //-------------------------------------------------------------------------
+ typedef itk::Transform< TCoordRep, 3, 3 > RegistrationTransformType;
+ RegistrationTransformType::Pointer regTransform(transform);
+ typedef itk::BSplineDeformableTransform<TCoordRep,SpaceDimension, 3> SingleBSplineTransformType;
+ typename SingleBSplineTransformType::Pointer sTransform;
+ if(m_ArgsInfo.itkbspline_flag) {
+ if( transform->GetTransforms().size()>1)
+ itkExceptionMacro(<< "invalid --itkbspline option if there is more than 1 label")
+ sTransform = SingleBSplineTransformType::New();
+ sTransform->SetBulkTransform( transform->GetTransforms()[0]->GetBulkTransform() );
+ sTransform->SetGridSpacing( transform->GetTransforms()[0]->GetGridSpacing() );
+ sTransform->SetGridOrigin( transform->GetTransforms()[0]->GetGridOrigin() );
+ sTransform->SetGridRegion( transform->GetTransforms()[0]->GetGridRegion() );
+ sTransform->SetParameters( transform->GetTransforms()[0]->GetParameters() );
+ regTransform = sTransform;
+ transform = NULL; // free memory
+ }
+
+ //=======================================================
+ // Interpolator
+ //=======================================================
+ typedef clitk::GenericInterpolator<args_info_clitkBLUTDIR, 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_clitkBLUTDIR, 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);
+
+#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
+ //=======================================================
+ typedef clitk::GenericOptimizer<args_info_clitkBLUTDIR> GenericOptimizerType;
+ GenericOptimizerType::Pointer genericOptimizer = GenericOptimizerType::New();
+ genericOptimizer->SetArgsInfo(m_ArgsInfo);
+ genericOptimizer->SetMaximize(genericMetric->GetMaximize());
+ genericOptimizer->SetNumberOfParameters(regTransform->GetNumberOfParameters());
+ typedef itk::SingleValuedNonLinearOptimizer OptimizerType;
+ OptimizerType::Pointer optimizer = genericOptimizer->GetOptimizerPointer();
+
+
+ //=======================================================
+ // Registration
+ //=======================================================
+ typedef itk::MultiResolutionImageRegistrationMethod< FixedImageType, MovingImageType > RegistrationType;
+ typename RegistrationType::Pointer registration = RegistrationType::New();
+ registration->SetMetric( metric );
+ registration->SetOptimizer( optimizer );
+ registration->SetInterpolator( interpolator );
+ registration->SetTransform (regTransform );
+ if(threadsGiven) {
+ registration->SetNumberOfThreads(threads);
+ if (m_Verbose) std::cout<< "Using " << threads << " threads." << std::endl;
+ }
+ registration->SetFixedImage( croppedFixedImage );
+ registration->SetMovingImage( movingImage );
+ registration->SetFixedImageRegion( metricRegion );
+ registration->SetFixedImagePyramid( fixedImagePyramid );
+ registration->SetMovingImagePyramid( movingImagePyramid );
+ registration->SetInitialTransformParameters( regTransform->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
+ CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
+ observer->SetOptimizer(genericOptimizer);
+ optimizer->AddObserver( itk::IterationEvent(), observer );
+
+ // Output level info
+ typedef RegistrationInterfaceCommand<RegistrationType,args_info_clitkBLUTDIR> 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 );
+
+ if (m_ArgsInfo.coeff_given)
+ {
+ if(m_ArgsInfo.itkbspline_flag) {
+ itkExceptionMacro("--coeff and --itkbpline are incompatible");
+ }
+
+ std::cout << std::endl << "Output coefficient images every " << m_ArgsInfo.coeffEveryN_arg << " iterations." << std::endl;
+ typedef CommandIterationUpdateDVF<FixedImageType, OptimizerType, TransformType> DVFCommandType;
+ typename DVFCommandType::Pointer observerdvf = DVFCommandType::New();
+ observerdvf->SetFixedImage(fixedImage);
+ observerdvf->SetTransform(transform);
+ observerdvf->SetArgsInfo(m_ArgsInfo);
+ optimizer->AddObserver( itk::IterationEvent(), observerdvf );
+ }
+ }
+
+
+ //=======================================================
+ // 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();
+ regTransform->SetParameters( finalParameters );
+ if (m_Verbose)
+ {
+ std::cout<<"Stop condition description: "
+ <<registration->GetOptimizer()->GetStopConditionDescription()<<std::endl;
+ }
+
+
+ //=======================================================
+ // Get the BSpline coefficient images and write them
+ //=======================================================
+ if (m_ArgsInfo.coeff_given)
+ {
+ typedef typename TransformType::CoefficientImageType CoefficientImageType;
+ std::vector<typename CoefficientImageType::Pointer> coefficientImages = transform->GetCoefficientImages();
+ typedef itk::ImageFileWriter<CoefficientImageType> CoeffWriterType;
+ typename CoeffWriterType::Pointer coeffWriter = CoeffWriterType::New();
+ unsigned nLabels = transform->GetnLabels();
+
+ std::string fname(m_ArgsInfo.coeff_arg);
+ int dotpos = fname.length() - 1;
+ while (dotpos >= 0 && fname[dotpos] != '.')
+ dotpos--;
+
+ for (unsigned i = 0; i < nLabels; ++i)
+ {
+ std::ostringstream osfname;
+ osfname << fname.substr(0, dotpos) << '_' << i << fname.substr(dotpos);
+ coeffWriter->SetInput(coefficientImages[i]);
+ coeffWriter->SetFileName(osfname.str());
+ coeffWriter->Update();
+ }
+ }
+
+
+
+ //=======================================================
+ // Compute the DVF (only deformable transform)
+ //=======================================================
+ typedef itk::Vector< float, SpaceDimension > DisplacementType;
+ typedef itk::Image< DisplacementType, InputImageType::ImageDimension > DisplacementFieldType;
+#if ITK_VERSION_MAJOR >= 4
+ typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
+#else
+ typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
+#endif
+ typename ConvertorType::Pointer filter= ConvertorType::New();
+ filter->SetNumberOfThreads(1);
+ if(m_ArgsInfo.itkbspline_flag)
+ sTransform->SetBulkTransform(NULL);
+ else
+ transform->SetBulkTransform(NULL);
+ filter->SetTransform(regTransform);
+ filter->SetOutputParametersFromImage(fixedImage);
+ filter->Update();
+ typename DisplacementFieldType::Pointer field = filter->GetOutput();
+
+
+ //=======================================================
+ // Write the DVF
+ //=======================================================
+ typedef itk::ImageFileWriter< DisplacementFieldType > 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::ResampleImageFilter< MovingImageType, FixedImageType > ResampleFilterType;
+ typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+ if (rigidTransform) {
+ if(m_ArgsInfo.itkbspline_flag)
+ sTransform->SetBulkTransform(rigidTransform);
+ else
+ transform->SetBulkTransform(rigidTransform);
+ }
+ resampler->SetTransform( regTransform );
+ resampler->SetInput( movingImage);
+ resampler->SetOutputParametersFromImage(fixedImage);
+ resampler->Update();
+ typename FixedImageType::Pointer result=resampler->GetOutput();
+
+ // typedef itk::WarpImageFilter< MovingImageType, FixedImageType, DeformationFieldType > WarpFilterType;
+ // typename WarpFilterType::Pointer warp = WarpFilterType::New();
+
+ // warp->SetDeformationField( field );
+ // 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( result );
+
+ 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( result );
+
+ 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.initMatrix_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. );
+ if (rigidTransform ) 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
+ }
+}//end clitk
-#endif //#define clitkBLUTDIRGenericFilter_cxx
+#endif // #define clitkBLUTDIRGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff