*
===================================================*/
+// 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 "clitkConvertBSplineDeformableTransformToVFGenericFilter.h"
+#include "clitkVectorImageToImageFilter.h"
+#if ITK_VERSION_MAJOR >= 4
+#include "itkTransformToDisplacementFieldSource.h"
+#else
+#include "itkTransformToDeformationFieldSource.h"
+#endif
+#include "itkBSplineDeformableTransform.h"
namespace clitk
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();
//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);*/
+
+ 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);
- }
- }
+ {
+ 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_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::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;
-
+ 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++)
{
- 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[i]= (int) ( input->GetSpacing()[i]/ filter->GetOutputSpacing()[i]);
+ if (m_Verbose) std::cout<<"Setting sampling factor "<<i<<" to "<<samplingFactors[i]<<"..."<<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;
- }
-
-
- // Set
- transform->SetSplineOrders(splineOrders);
- transform->SetMask(spatialObjectMask);
- transform->SetLUTSamplingFactors(samplingFactors);
- transform->SetCoefficientImage(input);
+ 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);
// -----------------------------------------------
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();
}
-
+/*
//-------------------------------------------------------------------
// 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 ;
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff