+++ /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 clitkBSplineCoefficientsToValuesGenericFilter_txx
-#define clitkBSplineCoefficientsToValuesGenericFilter_txx
-#include <itkAffineTransform.h>
-
-/* =================================================
- * @file clitkBSplineCoefficientsToValuesGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
- ===================================================*/
-
-
-namespace clitk
-{
-
- //-------------------------------------------------------------------
- // Update with the number of dimensions
- //-------------------------------------------------------------------
- template<unsigned int Dimension>
- void
- BSplineCoefficientsToValuesGenericFilter::UpdateWithDim(std::string PixelType, unsigned 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 filter in "<< Dimension <<"D and 3D float (DVF)" << std::endl;
- UpdateWithDimAndVectorType<Dimension, itk::Vector<float, 3> >();
- }
-
- else std::cerr<<"Number of components is "<<Components<<", not supported!"<<std::endl;
-
- }
-
-
- //-------------------------------------------------------------------
- // Update with the number of dimensions and the pixeltype
- //-------------------------------------------------------------------
- template <unsigned int Dimension, class PixelType>
- void
- BSplineCoefficientsToValuesGenericFilter::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();
-
- // Properties
- if (m_ArgsInfo.like_given)
- {
- typename InputReaderType::Pointer likeReader=InputReaderType::New();
- likeReader->SetFileName(m_ArgsInfo.like_arg);
- likeReader->Update();
- resampler->SetOutputParametersFromImage(likeReader->GetOutput());
- if (m_Verbose)std::cout<<"Resampling output like "<<m_ArgsInfo.like_arg<<"..."<<std::endl;
- }
- 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();
- if (m_Verbose)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();
- if (m_Verbose)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();
- if (m_Verbose)std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
-
- // Set
- resampler->SetSize( outputSize );
- resampler->SetOutputSpacing( outputSpacing );
- resampler->SetOutputOrigin( outputOrigin );
-
- }
-
- // Interp : coeff
- typedef itk::BSplineResampleImageFunction<InputImageType, double> InterpolatorType;
- typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
- interpolator->SetSplineOrder(m_ArgsInfo.order_arg);
-
- // Set
- resampler->SetInterpolator( interpolator);
- resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
- resampler->SetInput( input );
-
- // Update
- 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();
- }
-
-
- //-------------------------------------------------------------------
- // Update with the number of dimensions and the Vectortype
- //-------------------------------------------------------------------
- template <unsigned int Dimension, class PixelType>
- void
- BSplineCoefficientsToValuesGenericFilter::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 > ResampleFilterType;
- typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
-
- // Properties
- if (m_ArgsInfo.like_given)
- {
- typename InputReaderType::Pointer likeReader=InputReaderType::New();
- likeReader->SetFileName(m_ArgsInfo.like_arg);
- likeReader->Update();
-
- // Set
- resampler->SetSize( likeReader->GetOutput()->GetLargestPossibleRegion().GetSize() );
- resampler->SetOutputSpacing(likeReader->GetOutput()->GetSpacing() );
- resampler->SetOutputOrigin( likeReader->GetOutput()->GetOrigin() );
- if (m_Verbose)std::cout<<"Resampling output like "<<m_ArgsInfo.like_arg<<"..."<<std::endl;
- }
- 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();
- if (m_Verbose)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();
- if (m_Verbose)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();
- if (m_Verbose)std::cout<<"Setting the origin to "<<outputOrigin<<"..."<<std::endl;
-
- // Set
- resampler->SetSize( outputSize );
- resampler->SetOutputSpacing( outputSpacing );
- resampler->SetOutputOrigin( outputOrigin );
-
- }
-
- // Interp : coeff
- typedef clitk::VectorBSplineResampleImageFunction<InputImageType, double> InterpolatorType;
- typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
- interpolator->SetSplineOrder(m_ArgsInfo.order_arg);
-
-
- // Set
- resampler->SetInterpolator( interpolator);
- resampler->SetDefaultPixelValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
- resampler->SetInput( input );
-
- // Update
- try
- {
- resampler->Update();
- }
- catch(itk::ExceptionObject)
- {
- std::cerr<<"Error resampling the image"<<std::endl;
- }
-
- typename OutputImageType::Pointer output = resampler->GetOutput();
- //writeImage<OutputImageType>(output, "/home/jef/tmp/output1.mhd", true);
-
-
- // Matrix Transform
- if(m_ArgsInfo.matrix_given)
- {
-#if ITK_VERSION_MAJOR >= 4
- typedef itk::TransformToDisplacementFieldSource<OutputImageType, double> ConvertorType;
-#else
- typedef itk::TransformToDeformationFieldSource<OutputImageType, double> ConvertorType;
-#endif
- typename ConvertorType::Pointer filter= ConvertorType::New();
- filter->SetOutputParametersFromImage(output);
-
- typedef itk::AffineTransform<double, Dimension> TransformType;
- typename TransformType::Pointer transform =TransformType::New();
- itk::Matrix<double, Dimension+1, Dimension+1> homMatrix= ReadMatrix<Dimension>( m_ArgsInfo.matrix_arg);
- itk::Matrix<double, Dimension, Dimension> matrix =GetRotationalPartMatrix( homMatrix);
- itk::Vector<double, Dimension> offset= GetTranslationPartMatrix( homMatrix);
- transform->SetMatrix(matrix);
- transform->SetOffset(offset);
- filter->SetTransform(transform);
- filter->Update();
- typename OutputImageType::Pointer output2=filter->GetOutput();
- //writeImage<OutputImageType>(output2, "/home/jef/tmp/output2.mhd", true);
-
- // Add
- typedef itk::AddImageFilter< OutputImageType, OutputImageType, OutputImageType > AddType;
- typename AddType::Pointer adder= AddType::New();
- adder->SetInput(output);
- adder->SetInput(1,output2);
- adder->Update();
- output=adder->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 clitkBSplineCoefficientsToValuesGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff