/*=========================================================================
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 clitkInvertVFGenericFilter_txx
#define clitkInvertVFGenericFilter_txx
+#if ( ITK_VERSION_MAJOR < 5 )
+#include "itkVectorResampleImageFilter.h"
+#else
+#include "itkResampleImageFilter.h"
+#endif
+#include "clitkConvertBLUTCoeffsToVFFilter.h"
+
/* =================================================
* @file clitkInvertVFGenericFilter.txx
- * @author
- * @date
- *
- * @brief
- *
+ * @author
+ * @date
+ *
+ * @brief
+ *
===================================================*/
namespace clitk
{
- //-----------------------------------------------------------
- // Constructor
- //-----------------------------------------------------------
- template<class args_info_type>
- InvertVFGenericFilter<args_info_type>::InvertVFGenericFilter()
- {
- m_Verbose=false;
- m_InputFileName="";
+//-----------------------------------------------------------
+// Constructor
+//-----------------------------------------------------------
+template<class args_info_type>
+InvertVFGenericFilter<args_info_type>::InvertVFGenericFilter()
+{
+ m_Verbose=false;
+ m_InputFileName="";
+}
+
+
+//-----------------------------------------------------------
+// Update
+//-----------------------------------------------------------
+template<class args_info_type>
+void InvertVFGenericFilter<args_info_type>::Update()
+{
+ // Read the Dimension and PixelType
+ int Dimension;
+ std::string PixelType;
+ ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
+
+
+ // Call UpdateWithDim
+ if(Dimension==2) UpdateWithDim<2>(PixelType);
+ else if(Dimension==3) UpdateWithDim<3>(PixelType);
+ // else if (Dimension==4)UpdateWithDim<4>(PixelType);
+ else {
+ std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
+ return;
}
+}
+//-------------------------------------------------------------------
+// Update with the number of dimensions
+//-------------------------------------------------------------------
+template<class args_info_type>
+template<unsigned int Dimension>
+void
+InvertVFGenericFilter<args_info_type>::UpdateWithDim(std::string PixelType)
+{
+ if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
- //-----------------------------------------------------------
- // Update
- //-----------------------------------------------------------
- template<class args_info_type>
- void InvertVFGenericFilter<args_info_type>::Update()
- {
- // Read the Dimension and PixelType
- int Dimension;
- std::string PixelType;
- ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType);
+ // 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>();
+ // }
-
- // Call UpdateWithDim
- if(Dimension==2) UpdateWithDim<2>(PixelType);
- else if(Dimension==3) UpdateWithDim<3>(PixelType);
- // else if (Dimension==4)UpdateWithDim<4>(PixelType);
- else
- {
- std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<<std::endl ;
- return;
+ // 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, itk::Vector<float, Dimension> >();
+ // }
+}
+
+
+//-------------------------------------------------------------------
+// Update with the number of dimensions and the pixeltype
+//-------------------------------------------------------------------
+template<class args_info_type>
+template <unsigned int Dimension, class PixelType>
+void
+InvertVFGenericFilter<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
+ typename OutputImageType::Pointer output;
+ switch (m_ArgsInfo.type_arg) {
+
+ // clitk filter
+ case 0: {
+ // Create the InvertVFFilter
+ typedef clitk::InvertVFFilter<InputImageType,OutputImageType> FilterType;
+ typename FilterType::Pointer filter =FilterType::New();
+ if (m_ArgsInfo.like_given) {
+ typename FilterType::SpacingType spacing;
+ typename FilterType::SizeType size;
+ itk::ImageIOBase::Pointer header = readImageHeader(m_ArgsInfo.like_arg);
+ for(unsigned int i=0; i<InputImageType::ImageDimension; i++) {
+ size[i] = header->GetDimensions(i);
+ spacing[i] = header->GetSpacing(i);
}
+
+#if ( ITK_VERSION_MAJOR < 5 )
+ typedef itk::VectorResampleImageFilter<InputImageType, OutputImageType> ResampleFilterType;
+#else
+ typedef itk::ResampleImageFilter<InputImageType, OutputImageType> ResampleFilterType;
+#endif
+ typename ResampleFilterType::Pointer resampler = ResampleFilterType::New();
+ resampler->SetInput(input);
+ resampler->SetOutputOrigin(input->GetOrigin());
+ resampler->SetOutputDirection(input->GetDirection());
+ resampler->SetOutputSpacing(spacing);
+ resampler->SetSize(size);
+ resampler->Update();
+ spacing = resampler->GetOutput()->GetSpacing();
+ size = resampler->GetOutput()->GetLargestPossibleRegion().GetSize();
+ filter->SetInput(resampler->GetOutput());
+ }
+ else
+ filter->SetInput(input);
+
+ filter->SetVerbose(m_Verbose);
+ if (m_ArgsInfo.threads_given) {
+#if ITK_VERSION_MAJOR <= 4
+ filter->SetNumberOfThreads(m_ArgsInfo.threads_arg);
+#else
+ filter->SetNumberOfWorkUnits(m_ArgsInfo.threads_arg);
+#endif
+ }
+ if (m_ArgsInfo.pad_given) {
+ PixelType pad;
+ if (m_ArgsInfo.pad_given != (pad.GetNumberOfComponents()) )
+ pad.Fill(m_ArgsInfo.pad_arg[0]);
+ else
+ for(unsigned int i=0; i<Dimension; i++)
+ pad[i]=m_ArgsInfo.pad_arg[i];
+ }
+ filter->SetThreadSafe(m_ArgsInfo.threadSafe_flag);
+ filter->Update();
+ output=filter->GetOutput();
+
+ break;
}
- //-------------------------------------------------------------------
- // Update with the number of dimensions
- //-------------------------------------------------------------------
- template<class args_info_type>
- template<unsigned int Dimension>
- void
- InvertVFGenericFilter<args_info_type>::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, itk::Vector<float, Dimension> >();
- // }
+ case 1: {
+ // Create the InvertVFFilter
+ typedef clitk::InvertVFFilter<InputImageType,OutputImageType> FilterType;
+ typename FilterType::Pointer filter =FilterType::New();
+ if (m_ArgsInfo.like_given) {
+ typedef ConvertBLUTCoeffsToVFFilter<InputImageType> VFFilterType;
+ typename VFFilterType::Pointer vf_filter = VFFilterType::New();
+ vf_filter->SetInputFileName(m_InputFileName);
+ vf_filter->SetLikeFileName(m_ArgsInfo.like_arg);
+ vf_filter->SetVerbose(m_Verbose);
+ vf_filter->Update();
+ filter->SetInput(vf_filter->GetOutput());
+ }
+
+ filter->SetVerbose(m_Verbose);
+ if (m_ArgsInfo.threads_given) {
+#if ITK_VERSION_MAJOR <= 4
+ filter->SetNumberOfThreads(m_ArgsInfo.threads_arg);
+#else
+ filter->SetNumberOfWorkUnits(m_ArgsInfo.threads_arg);
+#endif
+ }
+ if (m_ArgsInfo.pad_given) {
+ PixelType pad;
+ if (m_ArgsInfo.pad_given != (pad.GetNumberOfComponents()) )
+ pad.Fill(m_ArgsInfo.pad_arg[0]);
+ else
+ for(unsigned int i=0; i<Dimension; i++)
+ pad[i]=m_ArgsInfo.pad_arg[i];
+ }
+ filter->SetThreadSafe(m_ArgsInfo.threadSafe_flag);
+ filter->Update();
+ output=filter->GetOutput();
+
+ break;
}
+ case 2: {
+ // Create the InverseDeformationFieldFilter
+ typedef itk::InverseDisplacementFieldImageFilter<InputImageType,OutputImageType> FilterType;
+ typename FilterType::Pointer filter =FilterType::New();
+ filter->SetInput(input);
+ filter->SetOutputOrigin(input->GetOrigin());
+ filter->SetOutputSpacing(input->GetSpacing());
+ filter->SetSize(input->GetLargestPossibleRegion().GetSize());
+ filter->SetSubsamplingFactor(m_ArgsInfo.sampling_arg);
+ filter->Update();
+ output=filter->GetOutput();
- //-------------------------------------------------------------------
- // Update with the number of dimensions and the pixeltype
- //-------------------------------------------------------------------
- template<class args_info_type>
- template <unsigned int Dimension, class PixelType>
- void
- InvertVFGenericFilter<args_info_type>::UpdateWithDimAndPixelType()
- {
+ break;
+ }
- // 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
- typename OutputImageType::Pointer output;
- switch (m_ArgsInfo.type_arg)
- {
-
- // clitk filter
- case 0:
- {
- // Create the InvertVFFilter
- typedef clitk::InvertVFFilter<InputImageType,OutputImageType> FilterType;
- typename FilterType::Pointer filter =FilterType::New();
- filter->SetInput(input);
- filter->SetVerbose(m_Verbose);
- if (m_ArgsInfo.threads_given) filter->SetNumberOfThreads(m_ArgsInfo.threads_arg);
- if (m_ArgsInfo.pad_given)
- {
- PixelType pad;
- if (m_ArgsInfo.pad_given != (pad.GetNumberOfComponents()) )
- pad.Fill(m_ArgsInfo.pad_arg[0]);
- else
- for(unsigned int i=0; i<Dimension; i++)
- pad[i]=m_ArgsInfo.pad_arg[i];
- }
- filter->SetThreadSafe(m_ArgsInfo.threadSafe_flag);
- filter->Update();
- output=filter->GetOutput();
-
- break;
- }
-
- case 1:
- {
- // Create the InverseDeformationFieldFilter
- typedef itk::InverseDeformationFieldImageFilter<InputImageType,OutputImageType> FilterType;
- typename FilterType::Pointer filter =FilterType::New();
- filter->SetInput(input);
- filter->SetOutputOrigin(input->GetOrigin());
- filter->SetOutputSpacing(input->GetSpacing());
- filter->SetSize(input->GetLargestPossibleRegion().GetSize());
- filter->SetSubsamplingFactor(m_ArgsInfo.sampling_arg);
- filter->Update();
- output=filter->GetOutput();
-
- break;
- }
-
- }
-
- // 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();
+
+}
+
+
}//end clitk
-
+
#endif //#define clitkInvertVFGenericFilter_txx
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff