+++ /dev/null
-/*=========================================================================
- 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 clitkBLUTDIRGenericFilter_txx
-#define clitkBLUTDIRGenericFilter_txx
-
-/* =================================================
- * @file clitkBLUTDIRGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
-
-#include "clitkBLUTDIRGenericFilter.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;
- };
-
-
- //==============================================================================
- //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::BSplineDeformableTransform<double, ImageDimension, ImageDimension> TransformType;
- typedef clitk::BSplineDeformableTransformInitializer<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)
- {
- 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_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
- //==============================================================================
- template<unsigned int Dimension>
- void BLUTDIRGenericFilter::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
- BLUTDIRGenericFilter::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;
- 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();
- 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 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);
- }
-
-
- //=======================================================
- // B-LUT FFD Transform
- //=======================================================
- typedef clitk::BSplineDeformableTransform<TCoordRep,ImageDimension, SpaceDimension > TransformType;
- typename TransformType::Pointer transform= TransformType::New();
- if (fixedMask) transform->SetMask( fixedMask );
- if (rigidTransform) transform->SetBulkTransform( rigidTransform );
-
- //-------------------------------------------------------------------------
- // The transform initializer
- //-------------------------------------------------------------------------
- typedef clitk::BSplineDeformableTransformInitializer< 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;
- 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;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_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);
-
-#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_clitkBLUTDIR> 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 itk::MultiResolutionImageRegistrationMethod< 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
- 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 );
- }
-
-
- //=======================================================
- // 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 BSpline 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();
- }
-
-
-
- //=======================================================
- // Compute the DVF (only deformable transform)
- //=======================================================
- typedef itk::Vector< float, SpaceDimension > DisplacementType;
- typedef itk::Image< DisplacementType, ImageDimension > DeformationFieldType;
- typedef itk::TransformToDeformationFieldSource<DeformationFieldType, double> ConvertorType;
- typename ConvertorType::Pointer filter= ConvertorType::New();
- filter->SetNumberOfThreads(1);
- transform->SetBulkTransform(NULL);
- filter->SetTransform(transform);
- filter->SetOutputParametersFromImage(fixedImage);
- filter->Update();
- typename DeformationFieldType::Pointer field = filter->GetOutput();
-
-
- //=======================================================
- // 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::ResampleImageFilter< MovingImageType, FixedImageType > ResampleFilterType;
- typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
- if (rigidTransform) transform->SetBulkTransform(rigidTransform);
- resampler->SetTransform( transform );
- resampler->SetInput( movingImageReader->GetOutput() );
- 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
-
-#endif // #define clitkBLUTDIRGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff