===================================================*/
// clitk include
-#include "clitkIO.h"
-#include "clitkCommon.h"
-#include "clitkImageCommon.h"
-#include "clitkConvertBSplineDeformableTransformToVF_ggo.h"
#include "clitkBSplineDeformableTransform.h"
#include "clitkTransformToDeformationFieldSource.h"
#include "clitkShapedBLUTSpatioTemporalDeformableTransform.h"
-#include "itkImageMaskSpatialObject.h"
-
+#include "clitkConvertBLUTCoeffsToVFFilter.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
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();
-
+ typedef ConvertBLUTCoeffsToVFFilter<OutputImageType> FilterType;
+ FilterType::Pointer filter = FilterType::New();
+ filter->SetInputFileName(m_InputFileName);
+ filter->SetTransformType(m_ArgsInfo.type_arg);
+ filter->SetVerbose(m_ArgsInfo.verbose_flag);
- // -----------------------------------------------
- // 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);*/
-
- typedef itk::ImageIOBase ImageIOType;
- typename ImageIOType::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(m_ArgsInfo.like_arg, itk::ImageIOFactory::ReadMode);
- imageIO->SetFileName(m_ArgsInfo.like_arg);
- 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 < Dimension; 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];
- }
-
- filter->SetOutputOrigin(output_origin);
- filter->SetOutputSpacing(output_spacing);
- filter->SetOutputSize(output_size);
- filter->SetOutputDirection(output_direction);
- }
- 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);
- }
+ if (m_ArgsInfo.like_given) {
+ filter->SetLikeFileName(m_ArgsInfo.like_arg);
}
-
- 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;
+ else {
+ FilterType::OutputImagePointType origin;
+ FilterType::OutputImageSpacingType spacing;
+ 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];
+ }
+ filter->SetOutputOrigin(origin);
+ filter->SetOutputSpacing(spacing);
+ filter->SetOutputSize(size);
}
-
-
- // -----------------------------------------------
- // Transform
- // -----------------------------------------------
- typedef clitk::BSplineDeformableTransform< double, Dimension, Dimension> BLUTTransformType;
- BLUTTransformType::Pointer blut_transform=BLUTTransformType::New();
-
- typedef itk::BSplineDeformableTransform< double, Dimension, Dimension> ITKTransformType;
- ITKTransformType::Pointer itk_transform=ITKTransformType::New();
- typedef itk::Transform< double, Dimension, Dimension> GenericTransformType;
- typename GenericTransformType::Pointer transform;
-
- // 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() );
- blut_transform->SetMask(spatialObjectMask);
- }
-
- if (m_ArgsInfo.type_arg != 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;
- }
- 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;
-
- // 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.order_given) {
+ FilterType::OutputImageSizeType order;
+ for (unsigned int i = 0; i < Dimension; i++) {
+ order[i] = m_ArgsInfo.order_arg[i];
}
- blut_transform->SetSplineOrders(splineOrders);
- blut_transform->SetLUTSamplingFactors(samplingFactors);
- blut_transform->SetCoefficientImage(input);
-
- transform = blut_transform;
- }
- 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 double PixelType;
- typedef itk::Vector<PixelType, Dimension> CoefficientType;
- typedef itk::Image<CoefficientType, Dimension> CoefficientImageType;
- typedef clitk::VectorImageToImageFilter<CoefficientImageType, typename ITKTransformType::ImageType> FilterType;
- typename FilterType::Pointer component_filter[Dimension];
-
- typename ITKTransformType::ImagePointer coefficient_images[Dimension];
- for (unsigned int i=0; i < Dimension; 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();
- }
- itk_transform->SetCoefficientImage(coefficient_images);
- transform = itk_transform;
- }
-
- 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->SetBLUTSplineOrders(order);
}
-
+
+ if (m_ArgsInfo.mask_given)
+ filter->SetMaskFileName(m_ArgsInfo.mask_arg);
+
+ filter->Update();
+
OutputImageType::Pointer output=filter->GetOutput();
-
// -----------------------------------------------
// Output
// -----------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff