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
+#include "itkVectorResampleImageFilter.h"
+#include "clitkBSplineDeformableTransform.h"
+#if ITK_VERSION_MAJOR >= 4
+#include "itkTransformToDisplacementFieldSource.h"
+#else
+#include "itkTransformToDeformationFieldSource.h"
+#endif
+
/* =================================================
* @file clitkInvertVFGenericFilter.txx
* @author
// }
}
+//-------------------------------------------------------------------
+// Convert Coefficient image to DVF
+//-------------------------------------------------------------------
+template<class args_info_type>
+template<class DisplacementFieldType>
+typename DisplacementFieldType::Pointer
+InvertVFGenericFilter<args_info_type>::CoeffsToDVF(std::string fileName, std::string likeFileName)
+{
+ typedef clitk::BSplineDeformableTransform<double, DisplacementFieldType::ImageDimension, DisplacementFieldType::ImageDimension> TransformType;
+ typedef typename TransformType::CoefficientImageType CoefficientImageType;
+
+ typedef itk::ImageFileReader<CoefficientImageType> CoeffReaderType;
+ typename CoeffReaderType::Pointer reader = CoeffReaderType::New();
+ reader->SetFileName(fileName);
+ reader->Update();
+
+ typename TransformType::Pointer transform = TransformType::New();
+ transform->SetCoefficientImage(reader->GetOutput());
+
+#if ITK_VERSION_MAJOR >= 4
+ typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
+#else
+ typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
+#endif
+
+ typedef itk::ImageIOBase ImageIOType;
+ typename ImageIOType::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(likeFileName.c_str(), itk::ImageIOFactory::ReadMode);
+ imageIO->SetFileName(likeFileName);
+ imageIO->ReadImageInformation();
+
+ typename ConvertorType::Pointer convertor= ConvertorType::New();
+ typename ConvertorType::SizeType output_size;
+ typename ConvertorType::SpacingType output_spacing;
+ typename ConvertorType::OriginType output_origin;
+ typename ConvertorType::DirectionType output_direction;
+ for (unsigned int i = 0; i < DisplacementFieldType::ImageDimension; i++) {
+ output_size[i] = imageIO->GetDimensions(i);
+ output_spacing[i] = imageIO->GetSpacing(i);
+ output_origin[i] = imageIO->GetOrigin(i);
+ for (unsigned int j = 0; j < DisplacementFieldType::ImageDimension; j++)
+ output_direction[i][j] = imageIO->GetDirection(i)[j];
+ }
+
+ if (m_Verbose) {
+ std::cout << "Interpolating coefficients with grid:" << std::endl;
+ std::cout << output_size << output_spacing << std::endl;
+ }
+
+ convertor->SetNumberOfThreads(1);
+ convertor->SetTransform(transform);
+ convertor->SetOutputOrigin(output_origin);
+ convertor->SetOutputSpacing(output_spacing);
+ convertor->SetOutputSize(output_size);
+ convertor->SetOutputDirection(output_direction);
+ convertor->Update();
+
+ return convertor->GetOutput();
+}
+
//-------------------------------------------------------------------
// Update with the number of dimensions and the pixeltype
typename InputReaderType::Pointer reader = InputReaderType::New();
reader->SetFileName( m_InputFileName);
reader->Update();
- typename InputImageType::Pointer input= reader->GetOutput();
+ typename InputImageType::Pointer input = reader->GetOutput();
// Filter
typename OutputImageType::Pointer output;
// Create the InvertVFFilter
typedef clitk::InvertVFFilter<InputImageType,OutputImageType> FilterType;
typename FilterType::Pointer filter =FilterType::New();
- filter->SetInput(input);
+ 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);
+ }
+
+ typedef itk::VectorResampleImageFilter<InputImageType, OutputImageType> ResampleFilterType;
+ 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) filter->SetNumberOfThreads(m_ArgsInfo.threads_arg);
if (m_ArgsInfo.pad_given) {
}
case 1: {
+ // Create the InvertVFFilter
+ typedef clitk::InvertVFFilter<InputImageType,OutputImageType> FilterType;
+ typename FilterType::Pointer filter =FilterType::New();
+ if (m_ArgsInfo.like_given) {
+ filter->SetInput(CoeffsToDVF<OutputImageType>(m_InputFileName, m_ArgsInfo.like_arg));
+ }
+
+ 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 2: {
// Create the InverseDeformationFieldFilter
+#if ITK_VERSION_MAJOR >= 4
+ typedef itk::InverseDisplacementFieldImageFilter<InputImageType,OutputImageType> FilterType;
+#else
typedef itk::InverseDeformationFieldImageFilter<InputImageType,OutputImageType> FilterType;
+#endif
typename FilterType::Pointer filter =FilterType::New();
filter->SetInput(input);
filter->SetOutputOrigin(input->GetOrigin());
break;
}
+
}
// Output
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff