/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.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
- 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
- *
+ * @author
+ * @date
+ *
+ * @brief
+ *
===================================================*/
namespace clitk
{
- //-----------------------------------------------------------
- // Constructor
- //-----------------------------------------------------------
- template<class args_info_type>
-
AffineTransformGenericFilter<args_info_type>::AffineTransformGenericFilter()
- {
- m_Verbose=false;
- m_InputFileName="";
- }
+//-----------------------------------------------------------
+// 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;
- }
+//-----------------------------------------------------------
+// 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;
+ }
+}
+
+//-------------------------------------------------------------------
+// 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>();
+ }
}
- //-------------------------------------------------------------------
- // 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 (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;
-
+ 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()
- {
-
- // 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.matrix_given)
- {
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
- if (m_Verbose) std::cout<<"Reading the matrix..."<<std::endl;
- }
- else
- {
- matrix.SetIdentity();
- }
- if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
- if (m_Verbose) std::cout<<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
- {
- //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 );
+}
- }
- resampler->SetInput( input );
- resampler->SetTransform( affineTransform );
- resampler->SetInterpolator( genericInterpolator->GetInterpolatorPointer());
- resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
+//-------------------------------------------------------------------
+// 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()
+{
- try
- {
- resampler->Update();
- }
- catch(itk::ExceptionObject)
- {
- std::cerr<<"Error resampling the image"<<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.matrix_given) {
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ if (m_Verbose) std::cout<<"Reading the matrix..."<<std::endl;
+ } else {
+ matrix.SetIdentity();
+ }
+ if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
+ if (m_Verbose) std::cout<<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);
+
+ // 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 );
+
+ }
- typename OutputImageType::Pointer output = resampler->GetOutput();
+ 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;
+ }
- // Output
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
- typename WriterType::Pointer writer = WriterType::New();
- writer->SetFileName(m_ArgsInfo.output_arg);
- writer->SetInput(output);
- writer->Update();
+ 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;
}
- //-------------------------------------------------------------------
- // 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.matrix_given)
- matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
- else
- matrix.SetIdentity();
- if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
- if (m_Verbose) std::cout<<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 );
+ 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();
- 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;
- }
+//-------------------------------------------------------------------
+// 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.matrix_given)
+ matrix= clitk::ReadMatrix<Dimension>(m_ArgsInfo.matrix_arg);
+ else
+ matrix.SetIdentity();
+ if (m_Verbose) std::cout<<"Using the following matrix:"<<std::endl;
+ if (m_Verbose) std::cout<<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 );
- 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();
+ 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;
}
+ 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();
+
+}
+
} //end clitk
-
+
#endif //#define clitkAffineTransformGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff