/*=========================================================================
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
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
/* =================================================
* @file clitkWarpImageGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
+ * @author
+ * @date
+ *
+ * @brief
+ *
===================================================*/
namespace clitk
{
- //-------------------------------------------------------------------
- // Update with the number of dimensions
- //-------------------------------------------------------------------
- template<unsigned int Dimension>
- void
- WarpImageGenericFilter::UpdateWithDim(std::string PixelType)
- {
- if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
-
- 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<unsigned int Dimension>
+void
+WarpImageGenericFilter::UpdateWithDim(std::string PixelType)
+{
+ if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
+
+ 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 and the pixeltype
- //-------------------------------------------------------------------
- template <unsigned int Dimension, class PixelType>
- void
- WarpImageGenericFilter::UpdateWithDimAndPixelType()
- {
-
- // ImageTypes
- typedef itk::Image<PixelType, Dimension> InputImageType;
- typedef itk::Image<PixelType, Dimension> OutputImageType;
- typedef itk::Vector<float, Dimension> DisplacementType;
- typedef itk::Image<DisplacementType, Dimension> DeformationFieldType;
-
-
- // 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();
-
- //Read the deformation field
- typedef itk::ImageFileReader<DeformationFieldType> DeformationFieldReaderType;
- typename DeformationFieldReaderType::Pointer deformationFieldReader= DeformationFieldReaderType::New();
- deformationFieldReader->SetFileName(m_ArgsInfo.vf_arg);
- deformationFieldReader->Update();
- typename DeformationFieldType::Pointer deformationField =deformationFieldReader->GetOutput();
-
- // Intensity interpolator
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//-------------------------------------------------------------------
+template <unsigned int Dimension, class PixelType>
+void
+WarpImageGenericFilter::UpdateWithDimAndPixelType()
+{
+
+ // ImageTypes
+ typedef itk::Image<PixelType, Dimension> InputImageType;
+ typedef itk::Image<PixelType, Dimension> OutputImageType;
+ typedef itk::Vector<float, Dimension> DisplacementType;
+ typedef itk::Image<DisplacementType, Dimension> DeformationFieldType;
+
+
+ // 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();
+
+ //Read the deformation field
+ typedef itk::ImageFileReader<DeformationFieldType> DeformationFieldReaderType;
+ typename DeformationFieldReaderType::Pointer deformationFieldReader= DeformationFieldReaderType::New();
+ deformationFieldReader->SetFileName(m_ArgsInfo.vf_arg);
+ deformationFieldReader->Update();
+ typename DeformationFieldType::Pointer deformationField =deformationFieldReader->GetOutput();
+
+ // Intensity interpolator
+ typedef clitk::GenericVectorInterpolator<args_info_clitkWarpImage, DeformationFieldType, double> GenericInterpolatorType;
+ typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
+ genericInterpolator->SetArgsInfo(m_ArgsInfo);
+
+
+ // -------------------------------------------
+ // Spacing like DVF
+ // -------------------------------------------
+ if (m_ArgsInfo.spacing_arg == 0) {
+ // Calculate the region
+ typename DeformationFieldType::SizeType newSize;
+ for (unsigned int i=0 ; i <Dimension; i++)
+ newSize[i]=(unsigned int) (input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i]/deformationField->GetSpacing()[i]);
+
+ // Get the interpolator
typedef clitk::GenericVectorInterpolator<args_info_clitkWarpImage, DeformationFieldType, double> GenericInterpolatorType;
typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
genericInterpolator->SetArgsInfo(m_ArgsInfo);
-
-
- // -------------------------------------------
- // Spacing like DVF
- // -------------------------------------------
- if (m_ArgsInfo.spacing_arg == 0)
- {
- // Calculate the region
- typename DeformationFieldType::SizeType newSize;
- for (unsigned int i=0 ; i <Dimension; i++)
- newSize[i]=(unsigned int) (input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i]/deformationField->GetSpacing()[i]);
-
- // Get the interpolator
- typedef clitk::GenericVectorInterpolator<args_info_clitkWarpImage, DeformationFieldType, double> GenericInterpolatorType;
- typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
- genericInterpolator->SetArgsInfo(m_ArgsInfo);
-
- // Resample to match the extent of the input
- typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
- resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
- resampler->SetInput(deformationField);
- resampler->SetOutputSpacing(deformationField->GetSpacing());
- resampler->SetSize(newSize);
- resampler->SetOutputOrigin(input->GetOrigin());
- resampler->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
-
- // Update
- if (m_Verbose) std::cout<< "Resampling the VF..." <<std::endl;
- try {
- resampler->Update();
- }
- catch( itk::ExceptionObject & excp ) {
- std::cerr << "Problem resampling the input vector field file" << std::endl;
- std::cerr << excp << std::endl;
- return;
- }
- deformationField= resampler->GetOutput();
-
- }
-
- // -------------------------------------------
- // Spacing like input
- // -------------------------------------------
- else
- {
- // Get size
- typename DeformationFieldType::SizeType newSize;
- for (unsigned int i=0 ; i <Dimension; i++)
- newSize[i]=input->GetLargestPossibleRegion().GetSize()[i];
-
- // Resample to match the extent of the input
- typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
- resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
- resampler->SetInput(deformationField);
- resampler->SetOutputSpacing(input->GetSpacing());
- resampler->SetSize(newSize);
- resampler->SetOutputOrigin(input->GetOrigin());
- resampler->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
-
- // Update
- if (m_Verbose) std::cout<< "Resampling the VF..." <<std::endl;
- try {
- resampler->Update();
- }
- catch( itk::ExceptionObject & excp ) {
- std::cerr << "Problem resampling the input vector field file" << std::endl;
- std::cerr << excp << std::endl;
- return;
- }
- deformationField= resampler->GetOutput();
- }
-
-
- // -------------------------------------------
- // Forward Warp
- // -------------------------------------------
- typename itk::ImageToImageFilter<InputImageType, InputImageType>::Pointer warpFilter;
- if (m_ArgsInfo.forward_flag)
- {
- //Forward warping: always linear
- typedef clitk::ForwardWarpImageFilter<InputImageType, InputImageType, DeformationFieldType> ForwardWarpFilterType;
- typename ForwardWarpFilterType::Pointer forwardWarpFilter= ForwardWarpFilterType::New();
- forwardWarpFilter->SetDeformationField( deformationField );
- forwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
- warpFilter=forwardWarpFilter;
- }
-
- // -------------------------------------------
- // Backward Warp
- // -------------------------------------------
- else
- {
- // Get the interpolator
- typedef clitk::GenericInterpolator<args_info_clitkWarpImage, InputImageType, double> GenericInterpolatorType;
- typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
- genericInterpolator->SetArgsInfo(m_ArgsInfo);
-
- //Backward mapping
- typedef itk::WarpImageFilter<InputImageType, InputImageType, DeformationFieldType> BackwardWarpFilterType;
- typename BackwardWarpFilterType::Pointer backwardWarpFilter= BackwardWarpFilterType::New();
- backwardWarpFilter->SetDeformationField( deformationField );
- backwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
- backwardWarpFilter->SetOutputSpacing( deformationField->GetSpacing() );
- backwardWarpFilter->SetOutputOrigin( input->GetOrigin() );
- backwardWarpFilter->SetOutputSize( deformationField->GetLargestPossibleRegion().GetSize() );
- typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
- resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
- backwardWarpFilter->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
- warpFilter=backwardWarpFilter;
- }
-
-
- // -------------------------------------------
+
+ // Resample to match the extent of the input
+ typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
+ resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
+ resampler->SetInput(deformationField);
+ resampler->SetOutputSpacing(deformationField->GetSpacing());
+ resampler->SetSize(newSize);
+ resampler->SetOutputOrigin(input->GetOrigin());
+ resampler->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
+
// Update
- // -------------------------------------------
- warpFilter->SetInput(input);
- if (m_Verbose) std::cout<< "Warping the input..." <<std::endl;
+ if (m_Verbose) std::cout<< "Resampling the VF..." <<std::endl;
try {
- warpFilter->Update();
+ resampler->Update();
+ } catch( itk::ExceptionObject & excp ) {
+ std::cerr << "Problem resampling the input vector field file" << std::endl;
+ std::cerr << excp << std::endl;
+ return;
}
- catch( itk::ExceptionObject & excp ) {
- std::cerr << "Problem warping the input image" << std::endl;
+ deformationField= resampler->GetOutput();
+
+ }
+
+ // -------------------------------------------
+ // Spacing like input
+ // -------------------------------------------
+ else {
+ // Get size
+ typename DeformationFieldType::SizeType newSize;
+ for (unsigned int i=0 ; i <Dimension; i++)
+ newSize[i]=input->GetLargestPossibleRegion().GetSize()[i];
+
+ // Resample to match the extent of the input
+ typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
+ resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
+ resampler->SetInput(deformationField);
+ resampler->SetOutputSpacing(input->GetSpacing());
+ resampler->SetSize(newSize);
+ resampler->SetOutputOrigin(input->GetOrigin());
+ resampler->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
+
+ // Update
+ if (m_Verbose) std::cout<< "Resampling the VF..." <<std::endl;
+ try {
+ resampler->Update();
+ } catch( itk::ExceptionObject & excp ) {
+ std::cerr << "Problem resampling the input vector field file" << std::endl;
std::cerr << excp << std::endl;
return;
- }
-
+ }
+ deformationField= resampler->GetOutput();
+ }
- // Output
- typedef itk::ImageFileWriter<OutputImageType> WriterType;
- typename WriterType::Pointer writer = WriterType::New();
- writer->SetFileName(m_ArgsInfo.output_arg);
- writer->SetInput(warpFilter->GetOutput());
- writer->Update();
+ // -------------------------------------------
+ // Forward Warp
+ // -------------------------------------------
+ typename itk::ImageToImageFilter<InputImageType, InputImageType>::Pointer warpFilter;
+ if (m_ArgsInfo.forward_flag) {
+ //Forward warping: always linear
+ typedef clitk::ForwardWarpImageFilter<InputImageType, InputImageType, DeformationFieldType> ForwardWarpFilterType;
+ typename ForwardWarpFilterType::Pointer forwardWarpFilter= ForwardWarpFilterType::New();
+ forwardWarpFilter->SetDeformationField( deformationField );
+ forwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
+ warpFilter=forwardWarpFilter;
}
+ // -------------------------------------------
+ // Backward Warp
+ // -------------------------------------------
+ else {
+ // Get the interpolator
+ typedef clitk::GenericInterpolator<args_info_clitkWarpImage, InputImageType, double> GenericInterpolatorType;
+ typename GenericInterpolatorType::Pointer genericInterpolator=GenericInterpolatorType::New();
+ genericInterpolator->SetArgsInfo(m_ArgsInfo);
+
+ //Backward mapping
+ typedef itk::WarpImageFilter<InputImageType, InputImageType, DeformationFieldType> BackwardWarpFilterType;
+ typename BackwardWarpFilterType::Pointer backwardWarpFilter= BackwardWarpFilterType::New();
+ backwardWarpFilter->SetDeformationField( deformationField );
+ backwardWarpFilter->SetEdgePaddingValue( static_cast<PixelType>(m_ArgsInfo.pad_arg) );
+ backwardWarpFilter->SetOutputSpacing( deformationField->GetSpacing() );
+ backwardWarpFilter->SetOutputOrigin( input->GetOrigin() );
+ backwardWarpFilter->SetOutputSize( deformationField->GetLargestPossibleRegion().GetSize() );
+ typename itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::Pointer
+ resampler =itk::VectorResampleImageFilter<DeformationFieldType, DeformationFieldType >::New();
+ backwardWarpFilter->SetInterpolator(genericInterpolator->GetInterpolatorPointer());
+ warpFilter=backwardWarpFilter;
+ }
+
+
+ // -------------------------------------------
+ // Update
+ // -------------------------------------------
+ warpFilter->SetInput(input);
+ if (m_Verbose) std::cout<< "Warping the input..." <<std::endl;
+ try {
+ warpFilter->Update();
+ } catch( itk::ExceptionObject & excp ) {
+ std::cerr << "Problem warping the input image" << std::endl;
+ std::cerr << excp << std::endl;
+ return;
+ }
+
+
+ // Output
+ typedef itk::ImageFileWriter<OutputImageType> WriterType;
+ typename WriterType::Pointer writer = WriterType::New();
+ writer->SetFileName(m_ArgsInfo.output_arg);
+ writer->SetInput(warpFilter->GetOutput());
+ writer->Update();
+
+}
+
}//end clitk
-
+
#endif //#define clitkWarpImageGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff