- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
+ ===========================================================================**/
#ifndef clitkAffineTransformGenericFilter_txx
#define clitkAffineTransformGenericFilter_txx
-/* =================================================
- * @file clitkAffineTransformGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
-
+#include <sstream>
+#include <istream>
+#include <iterator>
+#include <itkCenteredEuler3DTransform.h>
namespace clitk
{
-//-----------------------------------------------------------
-// Constructor
-//-----------------------------------------------------------
-template<class args_info_type>
-AffineTransformGenericFilter<args_info_type>::AffineTransformGenericFilter()
-{
- m_Verbose=false;
- m_InputFileName="";
-}
-
-
-//-----------------------------------------------------------
-// Update
-//-----------------------------------------------------------
-template<class args_info_type>
-void AffineTransformGenericFilter<args_info_type>::Update()
-{
- // Read the Dimension and PixelType
- int Dimension, Components;
- std::string PixelType;
- ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
-
-
- // Call UpdateWithDim
- if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
- else if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
- else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
- else {
- std::cout<<"Error, Only for 2, 3 or 4 Dimensions!!!"<<std::endl ;
- return;
+ //-----------------------------------------------------------
+ // Constructor
+ //-----------------------------------------------------------
+ template<class args_info_type>
+ AffineTransformGenericFilter<args_info_type>::AffineTransformGenericFilter()
+ {
+ m_Verbose=false;
+ m_InputFileName="";
}
-}
-
-//-------------------------------------------------------------------
-// Update with the number of dimensions
-//-------------------------------------------------------------------
-template<class args_info_type>
-template<unsigned int Dimension>
-void
-AffineTransformGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType, int Components)
-{
- if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
-
- if (Components==1) {
- if(PixelType == "short") {
- if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
- UpdateWithDimAndPixelType<Dimension, signed short>();
+ //-------------------------------------------------------------------
+
+
+ //-----------------------------------------------------------
+ // Update
+ //-----------------------------------------------------------
+ template<class args_info_type>
+ void AffineTransformGenericFilter<args_info_type>::Update()
+ {
+ // Read the Dimension and PixelType
+ int Dimension, Components;
+ std::string PixelType;
+ ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType, Components);
+
+ // Call UpdateWithDim
+ if(Dimension==2) UpdateWithDim<2>(PixelType, Components);
+ else
+ if(Dimension==3) UpdateWithDim<3>(PixelType, Components);
+ else if (Dimension==4)UpdateWithDim<4>(PixelType, Components);
+ else {
+ std::cout<<"Error, Only for 2, 3 or 4 Dimensions!!!"<<std::endl ;
+ return;
}
- // 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>();
+ }
+ //-------------------------------------------------------------------
+
+
+ //-------------------------------------------------------------------
+ // Update with the number of dimensions
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dimension>
+ void
+ AffineTransformGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType, int Components)
+ {
+ if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<<Components<<" component(s) of "<< PixelType<<"..."<<std::endl;
+
+ if (Components==1) {
+ 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>();
+ }
}
- // 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>();
+ else if (Components==3) {
+ if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
+ UpdateWithDimAndVectorType<Dimension, itk::Vector<float, Dimension> >();
}
- }
- else if (Components==3) {
- if (m_Verbose) std::cout << "Launching transform in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
- UpdateWithDimAndVectorType<Dimension, itk::Vector<float, Dimension> >();
+ else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
+
}
+ //-------------------------------------------------------------------
+
+
+ //-------------------------------------------------------------------
+ // Update with the number of dimensions and the pixeltype
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ template <unsigned int Dimension, class PixelType>
+ void
+ AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
+ {
- else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
+ // ImageTypes
+ typedef itk::Image<PixelType, Dimension> InputImageType;
+ typedef itk::Image<PixelType, Dimension> OutputImageType;
+
+ // Read the input
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ typename InputReaderType::Pointer reader = InputReaderType::New();
+ reader->SetFileName( m_InputFileName);
+ reader->Update();
+ typename InputImageType::Pointer input= reader->GetOutput();
+
+ //Filter
+ typedef itk::ResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
+ typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+
+ // Matrix
+ typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
+ if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+ return;
+ }
+ itk::Array<double> transformParameters(2 * Dimension);
+ transformParameters.Fill(0.0);
+ if (m_ArgsInfo.rotate_given)
+ {
+ if (Dimension == 2)
+ transformParameters[0] = m_ArgsInfo.rotate_arg[0];
+ else
+ for (unsigned int i = 0; i < 3; i++)
+ transformParameters[i] = m_ArgsInfo.rotate_arg[i];
+ }
+ if (m_ArgsInfo.translate_given)
+ {
+ int pos = 3;
+ if (Dimension == 2)
+ pos = 1;
+ for (unsigned int i = 0; i < Dimension && i < 3; i++)
+ transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
+ }
+ if (Dimension == 4)
+ {
+ matrix.SetIdentity();
+ itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
+ for (unsigned int i = 0; i < 3; ++i)
+ for (unsigned int j = 0; j < 3; ++j)
+ matrix[i][j] = tmp[i][j];
+ for (unsigned int i = 0; i < 3; ++i)
+ matrix[i][4] = tmp[i][3];
+ }
+ else
+ matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
+ }
+ else
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
+ }
+ else {
+ if (m_ArgsInfo.elastix_given) {
+ matrix = createMatrixFromElastixFile<Dimension,PixelType>(m_ArgsInfo.elastix_arg);
+ }
+ else
+ matrix.SetIdentity();
+ }
+ }
+ if (m_Verbose)
+ std::cout << "Using the following matrix:" << std::endl
+ << matrix << std::endl;
+ typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
+ typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
+
+ // Transform
+ typedef itk::AffineTransform<double, Dimension> AffineTransformType;
+ typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
+ affineTransform->SetMatrix(rotationMatrix);
+ affineTransform->SetTranslation(translationPart);
+
+ // Interp
+ typedef clitk::GenericInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
+ typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
+ genericInterpolator->SetArgsInfo(m_ArgsInfo);
+
+ // Properties
+ if (m_ArgsInfo.like_given) {
+ typename InputReaderType::Pointer likeReader=InputReaderType::New();
+ likeReader->SetFileName(m_ArgsInfo.like_arg);
+ likeReader->Update();
+ resampler->SetOutputParametersFromImage(likeReader->GetOutput());
+ } else if(m_ArgsInfo.transform_grid_flag) {
+ typename itk::Matrix<double, Dimension+1, Dimension+1> invMatrix( matrix.GetInverse() );
+ typename itk::Matrix<double, Dimension, Dimension> invRotMatrix( clitk::GetRotationalPartMatrix(invMatrix) );
+ typename itk::Vector<double,Dimension> invTrans = clitk::GetTranslationPartMatrix(invMatrix);
+
+ // Display warning
+ if (m_ArgsInfo.spacing_given)
+ std::cout << "Warning --spacing ignored (because --transform_grid_flag)" << std::endl;
+ if (m_ArgsInfo.origin_given)
+ std::cout << "Warning --origin ignored (because --transform_grid_flag)" << std::endl;
+
+ // Spacing is influenced by affine transform matrix and input direction
+ typename InputImageType::SpacingType outputSpacing;
+ outputSpacing = invRotMatrix *
+ input->GetDirection() *
+ input->GetSpacing();
+
+ // Origin is influenced by translation but not by input direction
+ typename InputImageType::PointType outputOrigin;
+ outputOrigin = invRotMatrix *
+ input->GetOrigin() +
+ invTrans;
+
+ // Size is influenced by affine transform matrix and input direction
+ // Size is converted to double, transformed and converted back to size type.
+ vnl_vector<double> vnlOutputSize(Dimension);
+ for(unsigned int i=0; i< Dimension; i++) {
+ vnlOutputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
+ }
+ vnlOutputSize = invRotMatrix *
+ input->GetDirection().GetVnlMatrix() *
+ vnlOutputSize;
+ typename OutputImageType::SizeType outputSize;
+ for(unsigned int i=0; i< Dimension; i++) {
+ // If the size is negative, we have a flip and we must modify
+ // the origin and the spacing accordingly.
+ if(vnlOutputSize[i]<0.) {
+ vnlOutputSize[i] *= -1.;
+ outputOrigin[i] = outputOrigin[i] + outputSpacing[i] * (vnlOutputSize[i]-1);
+ outputSpacing[i] *= -1.;
+ }
+ outputSize[i] = lrint(vnlOutputSize[i]);
+ }
+ resampler->SetSize( outputSize );
+ resampler->SetOutputSpacing( outputSpacing );
+ resampler->SetOutputOrigin( outputOrigin );
+ } else {
+ //Size
+ typename OutputImageType::SizeType outputSize;
+ if (m_ArgsInfo.size_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputSize[i]=m_ArgsInfo.size_arg[i];
+ } else outputSize=input->GetLargestPossibleRegion().GetSize();
+
+ //Spacing
+ typename OutputImageType::SpacingType outputSpacing;
+ if (m_ArgsInfo.spacing_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
+ } else outputSpacing=input->GetSpacing();
+
+ //Origin
+ typename OutputImageType::PointType outputOrigin;
+ if (m_ArgsInfo.origin_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputOrigin[i]=m_ArgsInfo.origin_arg[i];
+ } else outputOrigin=input->GetOrigin();
+
+ // Set
+ resampler->SetSize( outputSize );
+ resampler->SetOutputSpacing( outputSpacing );
+ resampler->SetOutputOrigin( outputOrigin );
-}
+ }
+ if (m_ArgsInfo.verbose_flag) {
+ std::cout << "Setting the output size to " << resampler->GetSize() << "..." << std::endl;
+ std::cout << "Setting the output spacing to " << resampler->GetOutputSpacing() << "..." << std::endl;
+ std::cout << "Setting the output origin to " << resampler->GetOutputOrigin() << "..." << std::endl;
+ }
-//-------------------------------------------------------------------
-// Update with the number of dimensions and the pixeltype
-//-------------------------------------------------------------------
-template<class args_info_type>
-template <unsigned int Dimension, class PixelType>
-void
-AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
-{
+ resampler->SetInput( input );
+ resampler->SetTransform( affineTransform );
+ resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
+ resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
- // ImageTypes
- typedef itk::Image<PixelType, Dimension> InputImageType;
- typedef itk::Image<PixelType, Dimension> OutputImageType;
+ try {
+ resampler->Update();
+ } catch(itk::ExceptionObject) {
+ std::cerr<<"Error resampling the image"<<std::endl;
+ }
- // Read the input
- typedef itk::ImageFileReader<InputImageType> InputReaderType;
- typename InputReaderType::Pointer reader = InputReaderType::New();
- reader->SetFileName( m_InputFileName);
- reader->Update();
- typename InputImageType::Pointer input= reader->GetOutput();
+ typename OutputImageType::Pointer output = resampler->GetOutput();
- //Filter
- typedef itk::ResampleImageFilter< InputImageType,OutputImageType > ResampleFilterType;
- typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+ // Output
+ typedef itk::ImageFileWriter<OutputImageType> WriterType;
+ typename WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(m_ArgsInfo.output_arg);
+ writer->SetInput(output);
+ writer->Update();
- // Matrix
- typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
- if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
- {
- if (m_ArgsInfo.matrix_given)
- {
- std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
- return;
- }
- itk::Array<double> transformParameters(2 * Dimension);
- transformParameters.Fill(0.0);
- if (m_ArgsInfo.rotate_given)
- {
- if (Dimension == 2)
- transformParameters[0] = m_ArgsInfo.rotate_arg[0];
- else
- for (unsigned int i = 0; i < 3; i++)
- transformParameters[i] = m_ArgsInfo.rotate_arg[i];
- }
- if (m_ArgsInfo.translate_given)
- {
- int pos = 3;
- if (Dimension == 2)
- pos = 1;
- for (unsigned int i = 0; i < Dimension && i < 3; i++)
- transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
- }
- if (Dimension == 4)
- {
- matrix.SetIdentity();
- itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
- for (unsigned int i = 0; i < 3; ++i)
- for (unsigned int j = 0; j < 3; ++j)
- matrix[i][j] = tmp[i][j];
- for (unsigned int i = 0; i < 3; ++i)
- matrix[i][4] = tmp[i][3];
- }
- else
- matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
}
- else
+ //-------------------------------------------------------------------
+
+
+ //-------------------------------------------------------------------
+ // Update with the number of dimensions and the pixeltype (components)
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dimension, class PixelType>
+ void AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndVectorType()
{
- if (m_ArgsInfo.matrix_given)
- {
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
- if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
- }
+ // ImageTypes
+ typedef itk::Image<PixelType, Dimension> InputImageType;
+ typedef itk::Image<PixelType, Dimension> OutputImageType;
+
+ // Read the input
+ typedef itk::ImageFileReader<InputImageType> InputReaderType;
+ typename InputReaderType::Pointer reader = InputReaderType::New();
+ reader->SetFileName( m_InputFileName);
+ reader->Update();
+ typename InputImageType::Pointer input= reader->GetOutput();
+
+ //Filter
+ typedef itk::VectorResampleImageFilter< InputImageType,OutputImageType, double > ResampleFilterType;
+ typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+
+ // Matrix
+ typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
+ if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
+ return;
+ }
+ itk::Array<double> transformParameters(2 * Dimension);
+ transformParameters.Fill(0.0);
+ if (m_ArgsInfo.rotate_given)
+ {
+ if (Dimension == 2)
+ transformParameters[0] = m_ArgsInfo.rotate_arg[0];
+ else
+ for (unsigned int i = 0; i < 3; i++)
+ transformParameters[i] = m_ArgsInfo.rotate_arg[i];
+ }
+ if (m_ArgsInfo.translate_given)
+ {
+ int pos = 3;
+ if (Dimension == 2)
+ pos = 1;
+ for (unsigned int i = 0; i < Dimension && i < 3; i++)
+ transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
+ }
+ if (Dimension == 4)
+ {
+ matrix.SetIdentity();
+ itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
+ for (unsigned int i = 0; i < 3; ++i)
+ for (unsigned int j = 0; j < 3; ++j)
+ matrix[i][j] = tmp[i][j];
+ for (unsigned int i = 0; i < 3; ++i)
+ matrix[i][4] = tmp[i][3];
+ }
+ else
+ matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
+ }
else
- matrix.SetIdentity();
- }
- if (m_Verbose)
- std::cout << "Using the following matrix:" << std::endl
- << matrix << std::endl;
- typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
- typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
-
- // Transform
- typedef itk::AffineTransform<double, Dimension> AffineTransformType;
- typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
- affineTransform->SetMatrix(rotationMatrix);
- affineTransform->SetTranslation(translationPart);
-
- // Interp
- typedef clitk::GenericInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
- typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
- genericInterpolator->SetArgsInfo(m_ArgsInfo);
-
- // Properties
- if (m_ArgsInfo.like_given) {
- typename InputReaderType::Pointer likeReader=InputReaderType::New();
- likeReader->SetFileName(m_ArgsInfo.like_arg);
- likeReader->Update();
- resampler->SetOutputParametersFromImage(likeReader->GetOutput());
- } else if(m_ArgsInfo.transform_grid_flag) {
- typename itk::Matrix<double, Dimension+1, Dimension+1> invMatrix( matrix.GetInverse() );
- typename itk::Matrix<double, Dimension, Dimension> invRotMatrix( clitk::GetRotationalPartMatrix(invMatrix) );
- typename itk::Vector<double,Dimension> invTrans = clitk::GetTranslationPartMatrix(invMatrix);
-
- // Display warning
- if (m_ArgsInfo.spacing_given)
- std::cout << "Warning --spacing ignored (because --transform_grid_flag)" << std::endl;
- if (m_ArgsInfo.origin_given)
- std::cout << "Warning --origin ignored (because --transform_grid_flag)" << std::endl;
-
- // Spacing is influenced by affine transform matrix and input direction
- typename InputImageType::SpacingType outputSpacing;
- outputSpacing = invRotMatrix *
- input->GetDirection() *
- input->GetSpacing();
-
- // Origin is influenced by translation but not by input direction
- typename InputImageType::PointType outputOrigin;
- outputOrigin = invRotMatrix *
- input->GetOrigin() +
- invTrans;
-
- // Size is influenced by affine transform matrix and input direction
- // Size is converted to double, transformed and converted back to size type.
- vnl_vector<double> vnlOutputSize(Dimension);
- for(unsigned int i=0; i< Dimension; i++) {
- vnlOutputSize[i] = input->GetLargestPossibleRegion().GetSize()[i];
- }
- vnlOutputSize = invRotMatrix *
- input->GetDirection().GetVnlMatrix() *
- vnlOutputSize;
- typename OutputImageType::SizeType outputSize;
- for(unsigned int i=0; i< Dimension; i++) {
- // If the size is negative, we have a flip and we must modify
- // the origin and the spacing accordingly.
- if(vnlOutputSize[i]<0.) {
- vnlOutputSize[i] *= -1.;
- outputOrigin[i] = outputOrigin[i] + outputSpacing[i] * (vnlOutputSize[i]-1);
- outputSpacing[i] *= -1.;
+ {
+ if (m_ArgsInfo.matrix_given)
+ {
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
+ }
+ else
+ matrix.SetIdentity();
}
- outputSize[i] = lrint(vnlOutputSize[i]);
- }
- resampler->SetSize( outputSize );
- resampler->SetOutputSpacing( outputSpacing );
- resampler->SetOutputOrigin( outputOrigin );
- } else {
- //Size
- typename OutputImageType::SizeType outputSize;
- if (m_ArgsInfo.size_given) {
- for(unsigned int i=0; i< Dimension; i++)
- outputSize[i]=m_ArgsInfo.size_arg[i];
- } else outputSize=input->GetLargestPossibleRegion().GetSize();
-
- //Spacing
- typename OutputImageType::SpacingType outputSpacing;
- if (m_ArgsInfo.spacing_given) {
- for(unsigned int i=0; i< Dimension; i++)
- outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
- } else outputSpacing=input->GetSpacing();
-
- //Origin
- typename OutputImageType::PointType outputOrigin;
- if (m_ArgsInfo.origin_given) {
- for(unsigned int i=0; i< Dimension; i++)
- outputOrigin[i]=m_ArgsInfo.origin_arg[i];
- } else outputOrigin=input->GetOrigin();
-
- // Set
- resampler->SetSize( outputSize );
- resampler->SetOutputSpacing( outputSpacing );
- resampler->SetOutputOrigin( outputOrigin );
+ if (m_Verbose)
+ std::cout << "Using the following matrix:" << std::endl
+ << matrix << std::endl;
+ typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
+ typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
+
+ // Transform
+ typedef itk::AffineTransform<double, Dimension> AffineTransformType;
+ typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
+ affineTransform->SetMatrix(rotationMatrix);
+ affineTransform->SetTranslation(translationPart);
+
+ // Interp
+ typedef clitk::GenericVectorInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
+ typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
+ genericInterpolator->SetArgsInfo(m_ArgsInfo);
+
+ // Properties
+ if (m_ArgsInfo.like_given) {
+ typename InputReaderType::Pointer likeReader=InputReaderType::New();
+ likeReader->SetFileName(m_ArgsInfo.like_arg);
+ likeReader->Update();
+ resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
+ resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
+ resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
+ } else {
+ //Size
+ typename OutputImageType::SizeType outputSize;
+ if (m_ArgsInfo.size_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputSize[i]=m_ArgsInfo.size_arg[i];
+ } else outputSize=input->GetLargestPossibleRegion().GetSize();
+ std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
+
+ //Spacing
+ typename OutputImageType::SpacingType outputSpacing;
+ if (m_ArgsInfo.spacing_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
+ } else outputSpacing=input->GetSpacing();
+ std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
+
+ //Origin
+ typename OutputImageType::PointType outputOrigin;
+ if (m_ArgsInfo.origin_given) {
+ for(unsigned int i=0; i< Dimension; i++)
+ outputOrigin[i]=m_ArgsInfo.origin_arg[i];
+ } else outputOrigin=input->GetOrigin();
+ std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
+
+ // Set
+ resampler->SetSize( outputSize );
+ resampler->SetOutputSpacing( outputSpacing );
+ resampler->SetOutputOrigin( outputOrigin );
- }
+ }
- if (m_ArgsInfo.verbose_flag) {
- std::cout << "Setting the output size to " << resampler->GetSize() << "..." << std::endl;
- std::cout << "Setting the output spacing to " << resampler->GetOutputSpacing() << "..." << std::endl;
- std::cout << "Setting the output origin to " << resampler->GetOutputOrigin() << "..." << std::endl;
- }
+ resampler->SetInput( input );
+ resampler->SetTransform( affineTransform );
+ resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
+ resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
- resampler->SetInput( input );
- resampler->SetTransform( affineTransform );
- resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
- resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
+ try {
+ resampler->Update();
+ } catch(itk::ExceptionObject) {
+ std::cerr<<"Error resampling the image"<<std::endl;
+ }
- try {
- resampler->Update();
- } catch(itk::ExceptionObject) {
- std::cerr<<"Error resampling the image"<<std::endl;
- }
+ typename OutputImageType::Pointer output = resampler->GetOutput();
- typename OutputImageType::Pointer output = resampler->GetOutput();
+ // Output
+ typedef itk::ImageFileWriter<OutputImageType> WriterType;
+ typename WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(m_ArgsInfo.output_arg);
+ writer->SetInput(output);
+ writer->Update();
- // Output
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
- typename WriterType::Pointer writer = WriterType::New();
- writer->SetFileName(m_ArgsInfo.output_arg);
- writer->SetInput(output);
- writer->Update();
+ }
+ //-------------------------------------------------------------------
+
+
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ template<unsigned int Dimension, class PixelType>
+ typename itk::Matrix<double, Dimension+1, Dimension+1>
+ AffineTransformGenericFilter<args_info_type>::createMatrixFromElastixFile(std::string filename)
+ {
+ if (Dimension != 3) {
+ FATAL("Only 3D yet" << std::endl);
+ }
+ typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
-}
+ // Open file
+ std::ifstream is;
+ clitk::openFileForReading(is, filename);
-//-------------------------------------------------------------------
-// Update with the number of dimensions and the pixeltype (components)
-//-------------------------------------------------------------------
-template<class args_info_type>
-template<unsigned int Dimension, class PixelType>
-void AffineTransformGenericFilter<args_info_type>::UpdateWithDimAndVectorType()
-{
- // ImageTypes
- typedef itk::Image<PixelType, Dimension> InputImageType;
- typedef itk::Image<PixelType, Dimension> OutputImageType;
-
- // Read the input
- typedef itk::ImageFileReader<InputImageType> InputReaderType;
- typename InputReaderType::Pointer reader = InputReaderType::New();
- reader->SetFileName( m_InputFileName);
- reader->Update();
- typename InputImageType::Pointer input= reader->GetOutput();
-
- //Filter
- typedef itk::VectorResampleImageFilter< InputImageType,OutputImageType, double > ResampleFilterType;
- typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
-
- // Matrix
- typename itk::Matrix<double, Dimension+1, Dimension+1> matrix;
- if (m_ArgsInfo.rotate_given || m_ArgsInfo.translate_given)
- {
- if (m_ArgsInfo.matrix_given)
- {
- std::cerr << "You must use either rotate/translate or matrix options" << std::cout;
- return;
+ // Check Transform
+ std::string s;
+ bool b = GetElastixValueFromTag(is, "Transform ", s);
+ if (!b) {
+ FATAL("Error must read 'Transform' in " << filename << std::endl);
}
- itk::Array<double> transformParameters(2 * Dimension);
- transformParameters.Fill(0.0);
- if (m_ArgsInfo.rotate_given)
- {
- if (Dimension == 2)
- transformParameters[0] = m_ArgsInfo.rotate_arg[0];
- else
- for (unsigned int i = 0; i < 3; i++)
- transformParameters[i] = m_ArgsInfo.rotate_arg[i];
+ if (s != "EulerTransform") {
+ FATAL("Sorry only 'EulerTransform'" << std::endl);
}
- if (m_ArgsInfo.translate_given)
- {
- int pos = 3;
- if (Dimension == 2)
- pos = 1;
- for (unsigned int i = 0; i < Dimension && i < 3; i++)
- transformParameters[pos++] = m_ArgsInfo.translate_arg[i];
+
+ // FIXME check
+ // (InitialTransformParametersFileName "NoInitialTransform")
+
+ // Get CenterOfRotationPoint
+ GetElastixValueFromTag(is, "CenterOfRotationPoint ", s); // space is needed
+ if (!b) {
+ FATAL("Error must read 'CenterOfRotationPoint' in " << filename << std::endl);
}
- if (Dimension == 4)
- {
- matrix.SetIdentity();
- itk::Matrix<double, 4, 4> tmp = GetForwardAffineMatrix3D(transformParameters);
- for (unsigned int i = 0; i < 3; ++i)
- for (unsigned int j = 0; j < 3; ++j)
- matrix[i][j] = tmp[i][j];
- for (unsigned int i = 0; i < 3; ++i)
- matrix[i][4] = tmp[i][3];
+ std::vector<std::string> cor;
+ GetValuesFromValue(s, cor);
+
+ // Get Transformparameters
+ GetElastixValueFromTag(is, "TransformParameters ", s); // space is needed
+ if (!b) {
+ FATAL("Error must read 'TransformParameters' in " << filename << std::endl);
}
- else
- matrix = GetForwardAffineMatrix<Dimension>(transformParameters);
- }
- else
- {
- if (m_ArgsInfo.matrix_given)
- {
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
- if (m_Verbose) std::cout << "Reading the matrix..." << std::endl;
+ std::vector<std::string> results;
+ GetValuesFromValue(s, results);
+
+ // construct a stream from the string
+ itk::CenteredEuler3DTransform<double>::Pointer mat = itk::CenteredEuler3DTransform<double>::New();
+ itk::CenteredEuler3DTransform<double>::ParametersType p;
+ p.SetSize(9);
+ for(uint i=0; i<3; i++)
+ p[i] = atof(results[i].c_str()); // Rotation
+ for(uint i=0; i<3; i++)
+ p[i+3] = atof(cor[i].c_str()); // Centre of rotation
+ for(uint i=0; i<3; i++)
+ p[i+6] = atof(results[i+3].c_str()); // Translation
+ mat->SetParameters(p);
+
+ if (m_Verbose) {
+ std::cout << "Rotation (deg) : " << rad2deg(p[0]) << " " << rad2deg(p[1]) << " " << rad2deg(p[2]) << std::endl;
+ std::cout << "Translation (phy) : " << p[3] << " " << p[4] << " " << p[5] << std::endl;
+ std::cout << "Center of rot (phy) : " << p[6] << " " << p[7] << " " << p[8] << std::endl;
}
- else
- matrix.SetIdentity();
- }
- if (m_Verbose)
- std::cout << "Using the following matrix:" << std::endl
- << matrix << std::endl;
- typename itk::Matrix<double, Dimension, Dimension> rotationMatrix = clitk::GetRotationalPartMatrix(matrix);
- typename itk::Vector<double, Dimension> translationPart = clitk::GetTranslationPartMatrix(matrix);
-
- // Transform
- typedef itk::AffineTransform<double, Dimension> AffineTransformType;
- typename AffineTransformType::Pointer affineTransform=AffineTransformType::New();
- affineTransform->SetMatrix(rotationMatrix);
- affineTransform->SetTranslation(translationPart);
-
- // Interp
- typedef clitk::GenericVectorInterpolator<args_info_type, InputImageType, double> GenericInterpolatorType;
- typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
- genericInterpolator->SetArgsInfo(m_ArgsInfo);
-
- // Properties
- if (m_ArgsInfo.like_given) {
- typename InputReaderType::Pointer likeReader=InputReaderType::New();
- likeReader->SetFileName(m_ArgsInfo.like_arg);
- likeReader->Update();
- resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
- resampler->SetOutputSpacing( likeReader->GetOutput()->GetSpacing() );
- resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
- } else {
- //Size
- typename OutputImageType::SizeType outputSize;
- if (m_ArgsInfo.size_given) {
- for(unsigned int i=0; i< Dimension; i++)
- outputSize[i]=m_ArgsInfo.size_arg[i];
- } else outputSize=input->GetLargestPossibleRegion().GetSize();
- std::cout<<"Setting the size to "<<outputSize<<"..."<<std::endl;
-
- //Spacing
- typename OutputImageType::SpacingType outputSpacing;
- if (m_ArgsInfo.spacing_given) {
- for(unsigned int i=0; i< Dimension; i++)
- outputSpacing[i]=m_ArgsInfo.spacing_arg[i];
- } else outputSpacing=input->GetSpacing();
- std::cout<<"Setting the spacing to "<<outputSpacing<<"..."<<std::endl;
-
- //Origin
- typename OutputImageType::PointType outputOrigin;
- if (m_ArgsInfo.origin_given) {
- for(unsigned int i=0; i< Dimension; i++)
- outputOrigin[i]=m_ArgsInfo.origin_arg[i];
- } else outputOrigin=input->GetOrigin();
- std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
-
- // Set
- resampler->SetSize( outputSize );
- resampler->SetOutputSpacing( outputSpacing );
- resampler->SetOutputOrigin( outputOrigin );
+ for(uint i=0; i<3; i++)
+ for(uint j=0; j<3; j++)
+ matrix[i][j] = mat->GetMatrix()[i][j];
+ // Offset is -Rc + t + c
+ matrix[0][3] = mat->GetOffset()[0];
+ matrix[1][3] = mat->GetOffset()[1];
+ matrix[2][3] = mat->GetOffset()[2];
+ matrix[3][3] = 1;
+
+ return matrix;
}
- resampler->SetInput( input );
- resampler->SetTransform( affineTransform );
- resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
- resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
-
- try {
- resampler->Update();
- } catch(itk::ExceptionObject) {
- std::cerr<<"Error resampling the image"<<std::endl;
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ bool
+ AffineTransformGenericFilter<args_info_type>::GetElastixValueFromTag(std::ifstream & is,
+ std::string tag,
+ std::string & value)
+ {
+ std::string line;
+ is.seekg (0, is.beg);
+ while(std::getline(is, line)) {
+ unsigned pos = line.find(tag);
+ if (pos<line.size()) {
+ value=line.substr(pos+tag.size(),line.size()-2);// remove last ')'
+ value.erase (std::remove (value.begin(), value.end(), '"'), value.end());
+ value.erase (std::remove (value.begin(), value.end(), ')'), value.end());
+ return true;
+ }
+ }
+ return false;
}
+ //-------------------------------------------------------------------
- typename OutputImageType::Pointer output = resampler->GetOutput();
-
- // Output
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
- typename WriterType::Pointer writer = WriterType::New();
- writer->SetFileName(m_ArgsInfo.output_arg);
- writer->SetInput(output);
- writer->Update();
-}
+ //-------------------------------------------------------------------
+ template<class args_info_type>
+ void
+ AffineTransformGenericFilter<args_info_type>::GetValuesFromValue(const std::string & s,
+ std::vector<std::string> & values)
+ {
+ std::stringstream strstr(s);
+ std::istream_iterator<std::string> it(strstr);
+ std::istream_iterator<std::string> end;
+ std::vector<std::string> results(it, end);
+ values.clear();
+ values.resize(results.size());
+ for(uint i=0; i<results.size(); i++) values[i] = results[i];
+ }
+ //-------------------------------------------------------------------
} //end clitk
git://git.creatis.insa-lyon.fr / clitk.git / commitdiff