+++ /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://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.
-
- 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 clitkCoeffsToDVF_h
-#define clitkCoeffsToDVF_h
-
-#include "itkImageFileReader.h"
-#include "itkImageIOBase.h"
-
-#include "clitkBSplineDeformableTransform.h"
-#include "clitkResampleBSplineDeformableTransformImageFilter.h"
-#if ITK_VERSION_MAJOR >= 4
-#include "itkTransformToDisplacementFieldSource.h"
-#else
-#include "itkTransformToDeformationFieldSource.h"
-#endif
-#include "itkBSplineDeformableTransform.h"
-
-namespace clitk
-{
- //-------------------------------------------------------------------
- // Initialize transform from coefficient images
- //-------------------------------------------------------------------
- template <class TransformType>
- void
- SetInitialTransformParameters(typename TransformType::Pointer transform, const typename TransformType::CoefficientImageType::Pointer coefficientImage, typename TransformType::CoefficientImageType::SpacingType outputSpacing)
- {
- unsigned int dim = TransformType::CoefficientImageType::ImageDimension;
- transform->SetSplineOrder(3);
- transform->SetGridRegion( coefficientImage->GetLargestPossibleRegion() );
- transform->SetGridOrigin( coefficientImage->GetOrigin() );
- transform->SetGridSpacing( coefficientImage->GetSpacing() );
- transform->SetGridDirection( coefficientImage->GetDirection() );
- typename TransformType::RegionType::SizeType samplingFactors;
- for (unsigned int i=0; i< dim; i++) {
- samplingFactors[i]= (int) ( coefficientImage->GetSpacing()[i]/ outputSpacing[i]);
- }
- transform->SetLUTSamplingFactors(samplingFactors);
-
- typedef typename TransformType::ParametersType ParametersType;
- const unsigned int numberOfParameters = transform->GetNumberOfParameters();
- ParametersType params(numberOfParameters);
- params.Fill( 0.0 );
-
- typedef itk::ImageRegionConstIterator<typename TransformType::CoefficientImageType> Iterator;
- Iterator it (coefficientImage, coefficientImage->GetLargestPossibleRegion() );
- it.GoToBegin();
- unsigned int k = 0;
- while (! it.IsAtEnd()) {
- for (unsigned int j = 0; j < dim; j++)
- params[k+j]=it.Get()[j];
-
- ++it;
- k += dim;
- }
-
- transform->SetParameters(params);
- transform->SetBulkTransform(NULL);
- }
-
- //-------------------------------------------------------------------
- // Convert Coefficient image to DVF
- //-------------------------------------------------------------------
- template<class DisplacementFieldType>
- typename DisplacementFieldType::Pointer
- BLUTCoeffsToDVF(std::string fileName, std::string likeFileName, bool verbose = false)
- {
- const unsigned int dim = DisplacementFieldType::ImageDimension;
- typedef clitk::BSplineDeformableTransform<double, DisplacementFieldType::ImageDimension, DisplacementFieldType::ImageDimension> TransformType;
- typedef typename TransformType::CoefficientImageType CoefficientImageType;
-
- typedef itk::ImageFileReader<CoefficientImageType> CoeffReaderType;
- typename CoeffReaderType::Pointer reader = CoeffReaderType::New();
- reader->SetFileName(fileName);
- reader->Update();
-
- #if ITK_VERSION_MAJOR >= 4
- typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
- #else
- typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
- #endif
-
- typedef itk::ImageIOBase ImageIOType;
- typename ImageIOType::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(likeFileName.c_str(), itk::ImageIOFactory::ReadMode);
- imageIO->SetFileName(likeFileName);
- imageIO->ReadImageInformation();
-
- typename ConvertorType::Pointer convertor= ConvertorType::New();
- typename ConvertorType::SizeType output_size;
- typename ConvertorType::SpacingType output_spacing;
- typename ConvertorType::OriginType output_origin;
- typename ConvertorType::DirectionType output_direction;
- for (unsigned int i = 0; i < dim; i++) {
- output_size[i] = imageIO->GetDimensions(i);
- output_spacing[i] = imageIO->GetSpacing(i);
- output_origin[i] = imageIO->GetOrigin(i);
- for (unsigned int j = 0; j < DisplacementFieldType::ImageDimension; j++)
- output_direction[i][j] = imageIO->GetDirection(i)[j];
- }
-
- typename CoefficientImageType::Pointer coeffs = reader->GetOutput();
- typename TransformType::Pointer transform = TransformType::New();
- SetInitialTransformParameters<TransformType>(transform, coeffs, output_spacing);
-
- if (verbose) {
- std::cout << "Interpolating coefficients with grid:" << std::endl;
- std::cout << output_size << output_spacing << std::endl;
- }
-
- convertor->SetNumberOfThreads(1);
- convertor->SetTransform(transform);
- convertor->SetOutputOrigin(output_origin);
- convertor->SetOutputSpacing(output_spacing);
- convertor->SetOutputSize(output_size);
- convertor->SetOutputDirection(output_direction);
- convertor->Update();
-
- return convertor->GetOutput();
- }
-}
-
-#endif
--- /dev/null
+
+#ifndef clitkConvertBLUTCoeffsToVFFilter_h
+#define clitkConvertBLUTCoeffsToVFFilter_h
+
+#include "clitkIO.h"
+#include "clitkCommon.h"
+#include "clitkImageCommon.h"
+#include "clitkBSplineDeformableTransform.h"
+#include "itkBSplineDeformableTransform.h"
+#if ITK_VERSION_MAJOR >= 4
+#include "itkTransformToDisplacementFieldSource.h"
+#else
+#include "itkTransformToDeformationFieldSource.h"
+#endif
+
+namespace clitk
+{
+ template <class TDVFType>
+ class ConvertBLUTCoeffsToVFFilter :
+ public itk::ImageSource<TDVFType>
+ {
+ public:
+
+ /** Standard class typedefs. */
+ typedef ConvertBLUTCoeffsToVFFilter Self;
+ typedef itk::ImageSource<TDVFType> Superclass;
+ typedef itk::SmartPointer<Self> Pointer;
+ typedef itk::SmartPointer<const Self> ConstPointer;
+
+ // ImageTypes
+ typedef itk::ImageIOBase LikeImageType;
+ typedef typename LikeImageType::Pointer LikeImagePointer;
+
+ typedef TDVFType OutputImageType;
+ typedef typename OutputImageType::Pointer OutputImagePointer;
+ typedef typename OutputImageType::ConstPointer OutputImageConstPointer;
+ typedef typename OutputImageType::RegionType OutputImageRegionType;
+ typedef typename OutputImageType::SizeType OutputImageSizeType;
+ typedef typename OutputImageType::PointType OutputImagePointType;
+ typedef typename OutputImageType::SpacingType OutputImageSpacingType;
+
+ typedef clitk::BSplineDeformableTransform<double, TDVFType::ImageDimension, TDVFType::ImageDimension> BLUTTransformType;
+ typedef typename BLUTTransformType::CoefficientImageType BLUTCoefficientImageType;
+ typedef itk::BSplineDeformableTransform<double, TDVFType::ImageDimension, TDVFType::ImageDimension> ITKTransformType;
+
+ typedef itk::Transform< double, TDVFType::ImageDimension, TDVFType::ImageDimension> GenericTransformType;
+
+#if ITK_VERSION_MAJOR >= 4
+ typedef itk::TransformToDisplacementFieldSource<OutputImageType, double> ConvertorType;
+#else
+ typedef itk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
+#endif
+
+ itkNewMacro(Self);
+
+ itkSetMacro(Verbose, bool);
+ itkSetMacro(InputFileName, std::string);
+ itkSetMacro(LikeFileName, std::string);
+ itkSetMacro(OutputOrigin, OutputImagePointType);
+ itkSetMacro(OutputSpacing, OutputImageSpacingType);
+ itkSetMacro(OutputSize, OutputImageSizeType);
+ itkSetMacro(TransformType, unsigned int);
+ itkSetMacro(MaskFileName, std::string);
+ itkSetMacro(BLUTSplineOrders, typename BLUTCoefficientImageType::SizeType);
+
+ /** DeformationFieldImageFilter produces a vector image. */
+ virtual void GenerateOutputInformation( void );
+
+ private:
+
+ ConvertBLUTCoeffsToVFFilter();
+ ~ConvertBLUTCoeffsToVFFilter() {};
+
+ virtual void GenerateData();
+
+ bool m_Verbose;
+ unsigned int m_TransformType;
+ typename BLUTTransformType::Pointer m_BLUTTransform;
+ typename ITKTransformType::Pointer m_ITKTransform;
+ typename GenericTransformType::Pointer m_GenericTransform;
+
+ std::string m_InputFileName, m_LikeFileName, m_MaskFileName;
+ OutputImageSizeType m_OutputSize;
+ OutputImageSpacingType m_OutputSpacing;
+ OutputImagePointType m_OutputOrigin;
+ typename BLUTCoefficientImageType::SizeType m_BLUTSplineOrders;
+ typename ConvertorType::Pointer m_Filter;
+ };
+}
+
+#include "clitkConvertBLUTCoeffsToVFFilter.txx"
+
+#endif // clitkConvertBLUTCoeffsToVFFilter_h
\ No newline at end of file
--- /dev/null
+
+#include "clitkConvertBLUTCoeffsToVFFilter.h"
+#include "clitkBSplineDeformableTransform.h"
+#include "clitkTransformToDeformationFieldSource.h"
+#include "clitkShapedBLUTSpatioTemporalDeformableTransform.h"
+#include "itkImageMaskSpatialObject.h"
+
+#include "clitkConvertBSplineDeformableTransformToVFGenericFilter.h"
+#include "clitkVectorImageToImageFilter.h"
+#if ITK_VERSION_MAJOR >= 4
+#include "itkTransformToDisplacementFieldSource.h"
+#else
+#include "itkTransformToDeformationFieldSource.h"
+#endif
+#include "itkBSplineDeformableTransform.h"
+
+namespace clitk
+{
+ template <class TDVFType>
+ ConvertBLUTCoeffsToVFFilter<TDVFType>::ConvertBLUTCoeffsToVFFilter()
+ {
+ m_Verbose = false;
+ m_TransformType = 0;
+ m_OutputOrigin.Fill(0);
+ m_OutputSpacing.Fill(1);
+ m_OutputSize.Fill(1);
+ m_BLUTSplineOrders.Fill(3);
+
+ m_Filter = ConvertorType::New();
+ m_BLUTTransform = BLUTTransformType::New();
+ m_ITKTransform = ITKTransformType::New();
+ }
+
+ template <class TDVFType>
+ void ConvertBLUTCoeffsToVFFilter<TDVFType>::GenerateOutputInformation()
+ {
+ if (m_Verbose)
+ std::cout << "ConvertBLUTCoeffsToVFFilter<TDVFType>::GenerateOutputInformation()" << std::endl;
+
+ Superclass::GenerateOutputInformation();
+ OutputImagePointer output = this->GetOutput();
+ if (!m_LikeFileName.empty())
+ {
+ typename LikeImageType::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(m_LikeFileName.c_str(), itk::ImageIOFactory::ReadMode);
+ imageIO->SetFileName(m_LikeFileName.c_str());
+ imageIO->ReadImageInformation();
+
+ typename ConvertorType::SizeType output_size;
+ typename ConvertorType::SpacingType output_spacing;
+ typename ConvertorType::OriginType output_origin;
+ typename ConvertorType::DirectionType output_direction;
+ for (unsigned int i = 0; i < OutputImageType::ImageDimension; i++) {
+ output_size[i] = imageIO->GetDimensions(i);
+ output_spacing[i] = imageIO->GetSpacing(i);
+ output_origin[i] = imageIO->GetOrigin(i);
+ //for (unsigned int j = 0; j < Dimension; j++)
+ // output_direction[i][j] = imageIO->GetDirection(i)[j];
+ }
+
+ if (m_Verbose)
+ std::cout << output_origin << output_size << output_spacing << std::endl;
+
+ output->SetOrigin(output_origin);
+ output->SetSpacing(output_spacing);
+ //output->SetDirection(output_direction);
+ OutputImageRegionType output_region;
+ output_region.SetSize(output_size);
+ output->SetRegions(output_region);
+ }
+ else
+ {
+ if (m_Verbose)
+ std::cout << m_OutputOrigin << m_OutputSize << m_OutputSpacing << std::endl;
+
+ output->SetOrigin(m_OutputOrigin);
+ output->SetSpacing(m_OutputSpacing);
+ OutputImageRegionType output_region;
+ output_region.SetSize(m_OutputSize);
+ output->SetRegions(output_region);
+ }
+
+ }
+
+ template <class TDVFType>
+ void ConvertBLUTCoeffsToVFFilter<TDVFType>::GenerateData()
+ {
+ // Read the input
+ typedef itk::ImageFileReader<BLUTCoefficientImageType> InputReaderType;
+ typename InputReaderType::Pointer reader = InputReaderType::New();
+ reader->SetFileName(m_InputFileName.c_str());
+ reader->Update();
+ typename BLUTCoefficientImageType::Pointer input = reader->GetOutput();
+ OutputImagePointer output = this->GetOutput();
+
+ if (m_TransformType != 0 ) { // using BLUT
+ // Spline orders: Default is cubic splines
+ if (m_Verbose) {
+ std::cout << "Using clitk::BLUT." << std::endl;
+ std::cout << "Setting spline orders and sampling factors." << std::endl;
+ }
+
+ m_BLUTTransform->SetSplineOrders(m_BLUTSplineOrders);
+
+ typename BLUTCoefficientImageType::SizeType samplingFactors;
+ for (unsigned int i=0; i< OutputImageType::ImageDimension; i++)
+ {
+ samplingFactors[i]= (int) ( input->GetSpacing()[i]/ output->GetSpacing()[i]);
+ if (m_Verbose) std::cout<<"Setting sampling factor "<<i<<" to "<<samplingFactors[i]<<"..."<<std::endl;
+ }
+ m_BLUTTransform->SetLUTSamplingFactors(samplingFactors);
+ m_BLUTTransform->SetCoefficientImage(input);
+
+ // Mask
+ typedef itk::ImageMaskSpatialObject<BLUTCoefficientImageType::ImageDimension > MaskType;
+ typename MaskType::Pointer spatialObjectMask=NULL;
+ if (!m_MaskFileName.empty())
+ {
+ typedef itk::Image< unsigned char, BLUTCoefficientImageType::ImageDimension > ImageMaskType;
+ typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
+ typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
+ maskReader->SetFileName(m_MaskFileName.c_str());
+
+ 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 <<"Mask was read..." <<std::endl;
+
+ // Set the image to the spatialObject
+ spatialObjectMask = MaskType::New();
+ spatialObjectMask->SetImage( maskReader->GetOutput() );
+ m_BLUTTransform->SetMask(spatialObjectMask);
+ }
+
+ m_GenericTransform = m_BLUTTransform;
+ }
+ else { // using ITK transform
+ if (m_Verbose) {
+ std::cout << "Using itk::BSpline" << std::endl;
+ std::cout << "Extracting components from input coefficient image and creating one coefficient image per-component" << std::endl;
+ }
+
+ typedef clitk::VectorImageToImageFilter<BLUTCoefficientImageType, typename ITKTransformType::ImageType> FilterType;
+ typename FilterType::Pointer component_filter[BLUTCoefficientImageType::ImageDimension];
+
+ typename ITKTransformType::ImagePointer coefficient_images[BLUTCoefficientImageType::ImageDimension];
+ for (unsigned int i=0; i < BLUTCoefficientImageType::ImageDimension; i++) {
+ component_filter[i] = FilterType::New();
+ component_filter[i]->SetInput(input);
+ component_filter[i]->SetComponentIndex(i);
+ component_filter[i]->Update();
+ coefficient_images[i] = component_filter[i]->GetOutput();
+ }
+ m_ITKTransform->SetCoefficientImage(coefficient_images);
+
+ m_GenericTransform = m_ITKTransform;
+ }
+
+ m_Filter->SetOutputOrigin(output->GetOrigin());
+ m_Filter->SetOutputSpacing(output->GetSpacing());
+ m_Filter->SetOutputSize(output->GetLargestPossibleRegion().GetSize());
+ m_Filter->SetTransform(m_GenericTransform);
+
+ m_Filter->Update();
+
+ SetNthOutput(0, m_Filter->GetOutput());
+ }
+
+
+}
\ No newline at end of file
section "IO"
-option "input" i "Input coefficient image filename" string yes
+option "input" i "Input BLUT-coefficient image filename" string yes
option "output" o "Output image filename" string yes
section "Transform"
-option "order" - "Spline order" int multiple no
-option "mask" - "Mask image filename" string no
-option "shape" - "Transform shape: 0=egg, 1=diamond" int no default="0"
+option "type" t "Type (0: itk bspline; 1: BLUT)" int no default="0"
+option "order" - "1: Spline order" int multiple no
+option "mask" - "1: Mask image filename" string no
+option "shape" - "1: Transform shape: 0=egg, 1=diamond" int no default="0"
*
===================================================*/
+// clitk include
+#include "clitkBSplineDeformableTransform.h"
+#include "clitkTransformToDeformationFieldSource.h"
+#include "clitkShapedBLUTSpatioTemporalDeformableTransform.h"
+#include "clitkConvertBLUTCoeffsToVFFilter.h"
#include "clitkConvertBSplineDeformableTransformToVFGenericFilter.h"
template<>
void
ConvertBSplineDeformableTransformToVFGenericFilter::UpdateWithDim<3>(std::string PixelType, int Components)
- {
+{
// Components
if (Components !=3)
- {
- std::cerr<<"Number of components is "<<Components<<"! Only 3 components is supported."<<std::endl;
- return;
- }
+ {
+ std::cerr<<"Number of components is "<<Components<<"! Only 3 components is supported."<<std::endl;
+ return;
+ }
if (PixelType != "double")
- {
- std::cerr<<"PixelType is "<<PixelType<<"! Only double coefficient images are supported."<<std::endl;
- std::cerr<<"Reading image as double..."<<std::endl;
- }
-
+ {
+
std::cerr<<"PixelType is "<<PixelType<<"! Only double coefficient images are supported."<<std::endl;
+ std::cerr<<"Reading image as double..."<<std::endl;
+ }
+
// ImageTypes
const unsigned int Dimension=3;
typedef itk::Vector<double, Dimension> InputPixelType;
typedef itk::Vector<float, Dimension> OutputPixelType;
typedef itk::Image<InputPixelType, Dimension> InputImageType;
typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
-
- // Read the input
- typedef itk::ImageFileReader<InputImageType> InputReaderType;
- InputReaderType::Pointer reader = InputReaderType::New();
- reader->SetFileName( m_InputFileName);
- reader->Update();
- InputImageType::Pointer input= reader->GetOutput();
-
- // -----------------------------------------------
- // Filter
- // -----------------------------------------------
-#if ITK_VERSION_MAJOR >= 4
- typedef itk::TransformToDisplacementFieldSource<OutputImageType, double> ConvertorType;
-#else
- typedef itk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
-#endif
- ConvertorType::Pointer filter= ConvertorType::New();
-
- //Output image info
- if (m_ArgsInfo.like_given)
- {
- typedef itk::ImageFileReader<OutputImageType> ReaderType;
- ReaderType::Pointer reader2=ReaderType::New();
- reader2->SetFileName(m_ArgsInfo.like_arg);
- reader2->Update();
-
- OutputImageType::Pointer image=reader2->GetOutput();
- filter->SetOutputParametersFromImage(image);
- }
- else
- {
- unsigned int i=0;
- if(m_ArgsInfo.origin_given)
- {
- OutputImageType::PointType origin;
- for(i=0;i<Dimension;i++)
- origin[i]=m_ArgsInfo.origin_arg[i];
- filter->SetOutputOrigin(origin);
- }
- if (m_ArgsInfo.spacing_given)
- {
- OutputImageType::SpacingType spacing;
- for(i=0;i<Dimension;i++)
- spacing[i]=m_ArgsInfo.spacing_arg[i];
- filter->SetOutputSpacing(spacing);
- }
- if (m_ArgsInfo.spacing_given)
- {
- OutputImageType::SizeType size;
- for(i=0;i<Dimension;i++)
- size[i]=m_ArgsInfo.size_arg[i];
- filter->SetOutputSize(size);
- }
+ typedef ConvertBLUTCoeffsToVFFilter<OutputImageType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetInputFileName(m_InputFileName);
+ filter->SetTransformType(m_ArgsInfo.type_arg);
+ filter->SetVerbose(m_ArgsInfo.verbose_flag);
+
+ if (m_ArgsInfo.like_given) {
+ filter->SetLikeFileName(m_ArgsInfo.like_arg);
+ }
+ else {
+ typename FilterType::OutputImagePointType origin;
+ typename FilterType::OutputImageSpacingType spacing;
+ typename FilterType::OutputImageSizeType size;
+ for (unsigned int i = 0; i < Dimension; i++) {
+ origin[i] = m_ArgsInfo.origin_arg[i];
+ spacing[i] = m_ArgsInfo.spacing_arg[i];
+ size[i] = m_ArgsInfo.size_arg[i];
}
-
- if (m_Verbose)
- {
- std::cout<< "Setting output origin to "<<filter->GetOutputOrigin()<<"..."<<std::endl;
- std::cout<< "Setting output spacing to "<<filter->GetOutputSpacing()<<"..."<<std::endl;
- std::cout<< "Setting output size to "<<filter->GetOutputSize()<<"..."<<std::endl;
+ filter->SetOutputOrigin(origin);
+ filter->SetOutputSpacing(spacing);
+ filter->SetOutputSize(size);
+ }
+
+ if (m_ArgsInfo.order_given) {
+ typename FilterType::OutputImageSizeType order;
+ for (unsigned int i = 0; i < Dimension; i++) {
+ order[i] = m_ArgsInfo.order_arg[i];
}
-
- // -----------------------------------------------
- // Transform
- // -----------------------------------------------
- typedef clitk::BSplineDeformableTransform< double, Dimension, Dimension> TransformType;
- TransformType::Pointer transform=TransformType::New();
-
- // Spline orders: Default is cubic splines
- InputImageType::RegionType::SizeType splineOrders ;
- splineOrders.Fill(3);
- if (m_ArgsInfo.order_given)
- for(unsigned int i=0; i<Dimension;i++)
- splineOrders[i]=m_ArgsInfo.order_arg[i];
- if (m_Verbose) std::cout<<"Setting the spline orders to "<<splineOrders<<"..."<<std::endl;
-
- // Mask
- typedef itk::ImageMaskSpatialObject< Dimension > MaskType;
- MaskType::Pointer spatialObjectMask=NULL;
+ filter->SetBLUTSplineOrders(order);
+ }
+
if (m_ArgsInfo.mask_given)
- {
- typedef itk::Image< unsigned char, Dimension > ImageMaskType;
- typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
- MaskReaderType::Pointer maskReader = MaskReaderType::New();
- maskReader->SetFileName(m_ArgsInfo.mask_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 <<"Mask was read..." <<std::endl;
-
- // Set the image to the spatialObject
- spatialObjectMask = MaskType::New();
- spatialObjectMask->SetImage( maskReader->GetOutput() );
- }
-
-
- // Samplingfactors
- InputImageType::SizeType samplingFactors;
- for (unsigned int i=0; i< Dimension; i++)
- {
- samplingFactors[i]= (int) ( input->GetSpacing()[i]/ filter->GetOutputSpacing()[i]);
- if (m_Verbose) std::cout<<"Setting sampling factor "<<i<<" to "<<samplingFactors[i]<<"..."<<std::endl;
- }
-
-
- // Set
- transform->SetSplineOrders(splineOrders);
- transform->SetMask(spatialObjectMask);
- transform->SetLUTSamplingFactors(samplingFactors);
- transform->SetCoefficientImage(input);
- filter->SetTransform(transform);
-
-
- // -----------------------------------------------
- // Update
- // -----------------------------------------------
- if (m_Verbose)std::cout<< "Converting the BSpline transform..."<<std::endl;
- try
- {
- filter->Update();
- }
- catch (itk::ExceptionObject)
- {
- std::cerr<<"Error: Exception thrown during execution convertion filter!"<<std::endl;
- }
-
+ filter->SetMaskFileName(m_ArgsInfo.mask_arg);
+
+ filter->Update();
+
OutputImageType::Pointer output=filter->GetOutput();
-
// -----------------------------------------------
// Output
// -----------------------------------------------
}
-
+/*
//-------------------------------------------------------------------
// Update with the number of dimensions
//-------------------------------------------------------------------
template<>
- void
- ConvertBSplineDeformableTransformToVFGenericFilter::UpdateWithDim<4>(std::string PixelType, int Components)
- {
+void
+ConvertBSplineDeformableTransformToVFGenericFilter::UpdateWithDim<4>(std::string PixelType, int Components)
+{
// Components
if (Components !=3)
- {
- std::cerr<<"Number of components is "<<Components<<"! Only 3 components is supported."<<std::endl;
- return;
- }
+ {
+ std::cerr<<"Number of components is "<<Components<<"! Only 3 components is supported."<<std::endl;
+ return;
+ }
if (PixelType != "double")
- {
- std::cerr<<"PixelType is "<<PixelType<<"! Only double coefficient images are supported."<<std::endl;
- std::cerr<<"Reading image as double..."<<std::endl;
- }
-
+ {
+
std::cerr<<"PixelType is "<<PixelType<<"! Only double coefficient images are supported."<<std::endl;
+ std::cerr<<"Reading image as double..."<<std::endl;
+ }
+
// ImageTypes
const unsigned int Dimension=4;
const unsigned int SpaceDimension=3;
typedef itk::Vector<float, SpaceDimension> OutputPixelType;
typedef itk::Image<InputPixelType, Dimension> InputImageType;
typedef itk::Image<OutputPixelType, Dimension> OutputImageType;
-
+
// Read the input
typedef itk::ImageFileReader<InputImageType> InputReaderType;
InputReaderType::Pointer reader = InputReaderType::New();
//Output image info
if (m_ArgsInfo.like_given)
- {
- typedef itk::ImageFileReader<OutputImageType> ReaderType;
- ReaderType::Pointer reader2=ReaderType::New();
- reader2->SetFileName(m_ArgsInfo.like_arg);
- reader2->Update();
-
- OutputImageType::Pointer image=reader2->GetOutput();
- filter->SetOutputParametersFromImage(image);
- }
+ {
+ typedef itk::ImageFileReader<OutputImageType> ReaderType;
+ ReaderType::Pointer reader2=ReaderType::New();
+ reader2->SetFileName(m_ArgsInfo.like_arg);
+ reader2->Update();
+
+ OutputImageType::Pointer image=reader2->GetOutput();
+ filter->SetOutputParametersFromImage(image);
+ }
else
- {
- unsigned int i=0;
- if(m_ArgsInfo.origin_given)
- {
- OutputImageType::PointType origin;
- for(i=0;i<Dimension;i++)
- origin[i]=m_ArgsInfo.origin_arg[i];
- filter->SetOutputOrigin(origin);
- }
- if (m_ArgsInfo.spacing_given)
- {
- OutputImageType::SpacingType spacing;
- for(i=0;i<Dimension;i++)
- spacing[i]=m_ArgsInfo.spacing_arg[i];
- filter->SetOutputSpacing(spacing);
- }
- if (m_ArgsInfo.spacing_given)
- {
- OutputImageType::SizeType size;
- for(i=0;i<Dimension;i++)
- size[i]=m_ArgsInfo.size_arg[i];
- filter->SetOutputSize(size);
- }
- }
+ {
+ unsigned int i=0;
+ if (m_ArgsInfo.origin_given)
+ {
+ OutputImageType::PointType origin;
+ for (i=0;i<Dimension;i++)
+ origin[i]=m_ArgsInfo.origin_arg[i];
+ filter->SetOutputOrigin(origin);
+ }
+ if (m_ArgsInfo.spacing_given)
+ {
+ OutputImageType::SpacingType spacing;
+ for (i=0;i<Dimension;i++)
+ spacing[i]=m_ArgsInfo.spacing_arg[i];
+ filter->SetOutputSpacing(spacing);
+ }
+ if (m_ArgsInfo.spacing_given)
+ {
+ OutputImageType::SizeType size;
+ for (i=0;i<Dimension;i++)
+ size[i]=m_ArgsInfo.size_arg[i];
+ filter->SetOutputSize(size);
+ }
+ }
//Output image info
if (m_Verbose)
- {
- std::cout<< "Setting output origin to "<<filter->GetOutputOrigin()<<"..."<<std::endl;
- std::cout<< "Setting output spacing to "<<filter->GetOutputSpacing()<<"..."<<std::endl;
- std::cout<< "Setting output size to "<<filter->GetOutputSize()<<"..."<<std::endl;
- }
+ {
+ std::cout<< "Setting output origin to "<<filter->GetOutputOrigin()<<"..."<<std::endl;
+ std::cout<< "Setting output spacing to "<<filter->GetOutputSpacing()<<"..."<<std::endl;
+ std::cout<< "Setting output size to "<<filter->GetOutputSize()<<"..."<<std::endl;
+ }
// -----------------------------------------------
// Transform
// -----------------------------------------------
- typedef clitk::ShapedBLUTSpatioTemporalDeformableTransform< double, Dimension, Dimension > TransformType;
+ typedef clitk::ShapedBLUTSpatioTemporalDeformableTransform< double, Dimension, Dimension > TransformType;
TransformType::Pointer transform=TransformType::New();
transform->SetTransformShape(m_ArgsInfo.shape_arg);
InputImageType::RegionType::SizeType splineOrders ;
splineOrders.Fill(3);
if (m_ArgsInfo.order_given)
- for(unsigned int i=0; i<Dimension;i++)
- splineOrders[i]=m_ArgsInfo.order_arg[i];
+ for (unsigned int i=0; i<Dimension;i++)
+ splineOrders[i]=m_ArgsInfo.order_arg[i];
if (m_Verbose) std::cout<<"Setting the spline orders to "<<splineOrders<<"..."<<std::endl;
// Mask
typedef itk::ImageMaskSpatialObject< Dimension > MaskType;
MaskType::Pointer spatialObjectMask=NULL;
if (m_ArgsInfo.mask_given)
- {
- typedef itk::Image< unsigned char, Dimension > ImageMaskType;
- typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
- MaskReaderType::Pointer maskReader = MaskReaderType::New();
- maskReader->SetFileName(m_ArgsInfo.mask_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 <<"Mask was read..." <<std::endl;
-
- // Set the image to the spatialObject
- spatialObjectMask = MaskType::New();
- spatialObjectMask->SetImage( maskReader->GetOutput() );
- }
+ {
+ typedef itk::Image< unsigned char, Dimension > ImageMaskType;
+ typedef itk::ImageFileReader< ImageMaskType > MaskReaderType;
+ MaskReaderType::Pointer maskReader = MaskReaderType::New();
+ maskReader->SetFileName(m_ArgsInfo.mask_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 <<"Mask was read..." <<std::endl;
+
+ // Set the image to the spatialObject
+ spatialObjectMask = MaskType::New();
+ spatialObjectMask->SetImage( maskReader->GetOutput() );
+ }
// Samplingfactors
- InputImageType::SizeType samplingFactors;
+ InputImageType::SizeType samplingFactors;
for (unsigned int i=0; i< Dimension; i++)
- {
- samplingFactors[i]= (int) ( input->GetSpacing()[i]/ filter->GetOutputSpacing()[i]);
- if (m_Verbose) std::cout<<"Setting sampling factor "<<i<<" to "<<samplingFactors[i]<<"..."<<std::endl;
- }
- if( !(m_ArgsInfo.shape_arg%2) )samplingFactors[Dimension-1]=5;
+ {
+ samplingFactors[i]= (int) ( input->GetSpacing()[i]/ filter->GetOutputSpacing()[i]);
+ if (m_Verbose) std::cout<<"Setting sampling factor "<<i<<" to "<<samplingFactors[i]<<"..."<<std::endl;
+ }
+ if ( !(m_ArgsInfo.shape_arg%2) )samplingFactors[Dimension-1]=5;
// Set
transform->SetSplineOrders(splineOrders);
// -----------------------------------------------
if (m_Verbose)std::cout<< "Converting the BSpline transform..."<<std::endl;
try
- {
- filter->Update();
- }
+ {
+ filter->Update();
+ }
catch (itk::ExceptionObject)
- {
- std::cerr<<"Error: Exception thrown during execution convertion filter!"<<std::endl;
- }
+ {
+ std::cerr<<"Error: Exception thrown during execution convertion filter!"<<std::endl;
+ }
OutputImageType::Pointer output=filter->GetOutput();
writer->SetInput(output);
writer->Update();
- }
-
-
-
+}
+*/
//-----------------------------------------------------------
// Update
//-----------------------------------------------------------
// Call UpdateWithDim
//if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
- else if (Dimension==4) UpdateWithDim<4>(PixelType, Components);
+ //else if (Dimension==4) UpdateWithDim<4>(PixelType, Components);
else
{
std::cout<<"Error, Only for 3 Dimensions!!!"<<std::endl ;
// clitk include
-#include "clitkIO.h"
#include "clitkCommon.h"
-#include "clitkImageCommon.h"
#include "clitkConvertBSplineDeformableTransformToVF_ggo.h"
-#include "clitkBSplineDeformableTransform.h"
-#include "clitkShapedBLUTSpatioTemporalDeformableTransform.h"
-#include "clitkTransformToDeformationFieldSource.h"
//itk include
#include "itkLightObject.h"
-#include "itkImageMaskSpatialObject.h"
-#if ITK_VERSION_MAJOR >= 4
- #include "itkTransformToDisplacementFieldSource.h"
-#else
- #include "itkTransformToDeformationFieldSource.h"
-#endif
namespace clitk
# registration
if [ "$method" == "blutdir" ]; then
- registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in $init_coeff_in
- registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out $init_coeff_out
+ registration_blutdir $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in $coeff_in
+ registration_blutdir $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out $coeff_out
elif [ "$method" == "elastix" ]; then
registration_elastix $reference_in $target_in $mask_ref_in $mask_targ_in $vf_in $result_in $params $log_in
registration_elastix $reference_out $target_out $mask_ref_out $mask_targ_out $vf_out $result_out $params $log_out
create_mhd_4D_pattern.sh $vf_dir/vf_inside_${ref_phase_nb}_
create_mhd_4D_pattern.sh $vf_dir/vf_outside_${ref_phase_nb}_
+ # create 4D coeffs
+ create_mhd_4D_pattern.sh $vf_dir/coeff_inside_${ref_phase_nb}_ _0
+ create_mhd_4D_pattern.sh $vf_dir/coeff_outside_${ref_phase_nb}_ _0
+
# create 4D result image
create_mhd_4D_pattern.sh $output_dir/result_inside_${ref_phase_nb}_
create_mhd_4D_pattern.sh $output_dir/result_outside_${ref_phase_nb}_
echo "Calculating midp_$phase_nb.mhd..."
vf_midp_in=$midp_dir/vf_inside_midp_$phase_nb.mhd
vf_midp_out=$midp_dir/vf_outside_midp_$phase_nb.mhd
+ coeff_midp_in=$midp_dir/coeff_inside_midp_$phase_nb.mhd
+ coeff_midp_out=$midp_dir/coeff_outside_midp_$phase_nb.mhd
# average the vf's from reference phase to phase
- clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
+ # clitkAverageTemporalDimension -i $vf_dir/vf_inside_${ref_phase_nb}_4D.mhd -o $vf_midp_in
+ clitkAverageTemporalDimension -i $vf_dir/coeff_inside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_in
abort_on_error midp $? clean_up_midp
- clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
+ # clitkAverageTemporalDimension -i $vf_dir/vf_outside_${ref_phase_nb}_4D.mhd -o $vf_midp_out
+ clitkAverageTemporalDimension -i $vf_dir/coeff_outside_${ref_phase_nb}_4D_0.mhd -o $coeff_midp_out
abort_on_error midp $? clean_up_midp
- # invert the vf (why?)
- clitkInvertVF -i $vf_midp_in -o $vf_midp_in
+ # invert the vf
+ # clitkInvertVF -i $vf_midp_in -o $vf_midp_in
+ clitkInvertVF -i $coeff_midp_in -o $vf_midp_in --type 1 --like $ref_phase_file
abort_on_error midp $? clean_up_midp
- clitkInvertVF -i $vf_midp_out -o $vf_midp_out
+ # clitkInvertVF -i $vf_midp_out -o $vf_midp_out
+ clitkInvertVF -i $coeff_midp_out -o $vf_midp_out --type 1 --like $ref_phase_file
abort_on_error midp $? clean_up_midp
# combine in and out VF's
TARGET_LINK_LIBRARIES(clitkCatImage clitkCommon ${ITK_LIBRARIES})
SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCatImage)
- WRAP_GGO(clitkCoeffsToDVF_GGO_C clitkCoeffsToDVF.ggo)
- ADD_EXECUTABLE(clitkCoeffsToDVF clitkCoeffsToDVF.cxx ${clitkCoeffsToDVF_GGO_C})
- TARGET_LINK_LIBRARIES(clitkCoeffsToDVF clitkCommon ${ITK_LIBRARIES})
- SET(TOOLS_INSTALL ${TOOLS_INSTALL} clitkCoeffsToDVF)
-
IF(CLITK_EXPERIMENTAL)
WRAP_GGO(clitkBinaryImageToMesh_GGO_C clitkBinaryImageToMesh.ggo)
ADD_EXECUTABLE(clitkBinaryImageToMesh clitkBinaryImageToMesh.cxx ${clitkBinaryImageToMesh_GGO_C})
+++ /dev/null
-#include "clitkCoeffsToDVF_ggo.h"
-#include "clitkCoeffsToDVF.h"
-#include "itkImage.h"
-#include "itkImageFileWriter.h"
-#include "itkImageIOFactory.h"
-#include <string>
-
-template <class DisplacementFieldType>
-void
-Write(typename DisplacementFieldType::Pointer dvf, std::string fileName)
-{
- typedef itk::ImageFileWriter<DisplacementFieldType> ImageWriterType;
- typename ImageWriterType::Pointer writer = ImageWriterType::New();
- writer->SetFileName(fileName);
- writer->SetInput(dvf);
- writer->Update();
-}
-
-int main(int argc, char** argv)
-{
- GGO(clitkCoeffsToDVF, args_info);
- CLITK_INIT;
-
- itk::ImageIOBase::Pointer image_io = itk::ImageIOFactory::CreateImageIO(args_info.input_arg, itk::ImageIOFactory::ReadMode);
- image_io->SetFileName(args_info.input_arg);
- image_io->ReadImageInformation();
-
- unsigned int ndim = image_io->GetNumberOfDimensions();
- switch (ndim) {
- case 2:
- {
- unsigned const dim = 2;
- typedef itk::Vector<double, dim> PixelType;
- typedef itk::Image<PixelType, dim> DVFType;
- DVFType::Pointer dvf = clitk::BLUTCoeffsToDVF<DVFType>(args_info.input_arg, args_info.like_arg);
- Write<DVFType>(dvf, args_info.output_arg);
- }
- break;
-
- case 3:
- {
- unsigned const dim = 3;
- typedef itk::Vector<double, dim> PixelType;
- typedef itk::Image<PixelType, dim> DVFType;
- DVFType::Pointer dvf = clitk::BLUTCoeffsToDVF<DVFType>(args_info.input_arg, args_info.like_arg);
- Write<DVFType>(dvf, args_info.output_arg);
- }
- break;
-
- default:
- std::cerr << "Unsupported image dimension (either 2 or 3)" << std::endl;
- return -1;
- }
-
- return 0;
-}
\ No newline at end of file
+++ /dev/null
-#File clitkComposeVF.ggo
-#Author: Rômulo Pinho
-#Date : Wed 24 January 2012
-
-package "clitk"
-version "Convert a BLUT-coefficient image to a vector field."
-
-option "config" - "Config file" string no
-option "input" i "Input1 VF filename" string yes
-option "output" o "Output VF filename" string yes
-option "like" l "Image to read output parameters from" string yes
-
#define __clitkComposeVFGenericFilter_txx
#include "clitkComposeVFGenericFilter.h"
-#include "clitkCoeffsToDVF.h"
+#include "clitkConvertBLUTCoeffsToVFFilter.h"
namespace clitk
{
//Define the image type
if (m_Type == 1) {
- input1 = BLUTCoeffsToDVF<ImageType>(m_InputName1, m_LikeImage, m_Verbose);
- input2 = BLUTCoeffsToDVF<ImageType>(m_InputName2, m_LikeImage, m_Verbose);
+ typedef ConvertBLUTCoeffsToVFFilter<ImageType> VFFilterType;
+ typename VFFilterType::Pointer vf_filter = VFFilterType::New();
+ vf_filter->SetInputFileName(m_InputName1);
+ vf_filter->SetLikeFileName(m_LikeImage);
+ vf_filter->SetVerbose(m_Verbose);
+ vf_filter->Update();
+ input1 = vf_filter->GetOutput();
+
+ vf_filter->SetInputFileName(m_InputName2);
+ vf_filter->Update();
+ input2 = vf_filter->GetOutput();
}
else {
//Read the input1
#define clitkInvertVFGenericFilter_txx
#include "itkVectorResampleImageFilter.h"
-#include "clitkCoeffsToDVF.h"
+#include "clitkConvertBLUTCoeffsToVFFilter.h"
/* =================================================
* @file clitkInvertVFGenericFilter.txx
typedef clitk::InvertVFFilter<InputImageType,OutputImageType> FilterType;
typename FilterType::Pointer filter =FilterType::New();
if (m_ArgsInfo.like_given) {
- filter->SetInput(BLUTCoeffsToDVF<OutputImageType>(m_InputFileName, m_ArgsInfo.like_arg));
+ typedef ConvertBLUTCoeffsToVFFilter<InputImageType> VFFilterType;
+ typename VFFilterType::Pointer vf_filter = VFFilterType::New();
+ vf_filter->SetInputFileName(m_InputFileName);
+ vf_filter->SetLikeFileName(m_ArgsInfo.like_arg);
+ vf_filter->SetVerbose(m_Verbose);
+ vf_filter->Update();
+ filter->SetInput(vf_filter->GetOutput());
}
filter->SetVerbose(m_Verbose);
===================================================*/
#include "itkVectorResampleImageFilter.h"
-#include "clitkCoeffsToDVF.h"
+#include "clitkConvertBLUTCoeffsToVFFilter.h"
namespace clitk
{
typename DeformationFieldType::Pointer deformationField;
if (m_ArgsInfo.coeff_given) {
- deformationField = BLUTCoeffsToDVF<DeformationFieldType>(m_ArgsInfo.coeff_arg, m_InputFileName, m_Verbose);
+ typedef ConvertBLUTCoeffsToVFFilter<DeformationFieldType> FilterType;
+ typename FilterType::Pointer filter = FilterType::New();
+ filter->SetInputFileName(m_ArgsInfo.coeff_arg);
+ filter->SetLikeFileName(m_InputFileName);
+ filter->SetVerbose(m_Verbose);
+ filter->Update();
+ deformationField = filter->GetOutput();
}
else {
//Read the deformation field
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff