tools/clitkComposeVFGenericFilter.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ===========================================================================**/
  18 #ifndef __clitkComposeVFGenericFilter_txx
  19 #define __clitkComposeVFGenericFilter_txx
  20 #include "clitkComposeVFGenericFilter.h"
  21
  22 #include "clitkBSplineDeformableTransform.h"
  23 #include "clitkBSplineDeformableTransformInitializer.h"
  24 #if ITK_VERSION_MAJOR >= 4
  25 #include "itkTransformToDisplacementFieldSource.h"
  26 #else
  27 #include "itkTransformToDeformationFieldSource.h"
  28 #endif
  29
  30 namespace clitk
  31 {
  32
  33   template<unsigned int Dimension>
  34   void ComposeVFGenericFilter::UpdateWithDim(std::string PixelType)
  35   {
  36     if (PixelType=="double")
  37       {
  38         UpdateWithDimAndPixelType<Dimension, double>();
  39       }
  40     else
  41       {
  42         UpdateWithDimAndPixelType<Dimension, float>();
  43       }
  44   }
  45
  46   template<class DisplacementFieldType>
  47   typename DisplacementFieldType::Pointer ComposeVFGenericFilter::CoeffsToDVF(std::string fileName, std::string likeFileName)
  48   {
  49     typedef clitk::BSplineDeformableTransform<double, DisplacementFieldType::ImageDimension, DisplacementFieldType::ImageDimension> TransformType;
  50     typedef typename TransformType::CoefficientImageType CoefficientImageType;
  51
  52     typedef itk::ImageFileReader<CoefficientImageType> CoeffReaderType;
  53     typename CoeffReaderType::Pointer reader = CoeffReaderType::New();
  54     reader->SetFileName(fileName);
  55     reader->Update();
  56
  57     typename TransformType::Pointer transform = TransformType::New();
  58     transform->SetCoefficientImage(reader->GetOutput());
  59
  60 #if ITK_VERSION_MAJOR >= 4
  61         typedef itk::TransformToDisplacementFieldSource<DisplacementFieldType, double> ConvertorType;
  62 #else
  63         typedef itk::TransformToDeformationFieldSource<DisplacementFieldType, double> ConvertorType;
  64 #endif
  65
  66     typedef itk::ImageIOBase ImageIOType;
  67     typename ImageIOType::Pointer imageIO = itk::ImageIOFactory::CreateImageIO(likeFileName.c_str(), itk::ImageIOFactory::ReadMode);
  68     imageIO->SetFileName(likeFileName);
  69     imageIO->ReadImageInformation();
  70
  71     typename ConvertorType::Pointer convertor= ConvertorType::New();
  72     typename ConvertorType::SizeType output_size;
  73     typename ConvertorType::SpacingType output_spacing;
  74     typename ConvertorType::OriginType output_origin;
  75     typename ConvertorType::DirectionType output_direction;
  76     for (unsigned int i = 0; i < DisplacementFieldType::ImageDimension; i++) {
  77       output_size[i] = imageIO->GetDimensions(i);
  78       output_spacing[i] = imageIO->GetSpacing(i);
  79       output_origin[i] = imageIO->GetOrigin(i);
  80       for (unsigned int j = 0; j < DisplacementFieldType::ImageDimension; j++)
  81         output_direction[i][j] = imageIO->GetDirection(i)[j];
  82     }
  83
  84     if (m_Verbose) {
  85       std::cout << "Interpolating coefficients with grid:" << std::endl;
  86       std::cout << output_size << output_spacing << std::endl;
  87     }
  88
  89     convertor->SetNumberOfThreads(1);
  90     convertor->SetTransform(transform);
  91     convertor->SetOutputOrigin(output_origin);
  92     convertor->SetOutputSpacing(output_spacing);
  93     convertor->SetOutputSize(output_size);
  94     convertor->SetOutputDirection(output_direction);
  95     convertor->Update();
  96
  97     return convertor->GetOutput();
  98   }
  99
 100   template<unsigned int Dimension, class PixelType>
 101   void ComposeVFGenericFilter::UpdateWithDimAndPixelType()
 102   {
 103     typedef itk::Vector<PixelType, Dimension> DisplacementType;
 104     typedef itk::Image<DisplacementType, Dimension> ImageType;
 105     typename ImageType::Pointer input1, input2;
 106
 107     //Define the image type
 108     if (m_Type == 1) {
 109       input1 = this->CoeffsToDVF<ImageType>(m_InputName1, m_LikeImage);
 110       input2 = this->CoeffsToDVF<ImageType>(m_InputName2, m_LikeImage);
 111     }
 112     else {
 113       //Read the input1
 114       typedef itk::ImageFileReader<ImageType> ImageReaderType;
 115       typename  ImageReaderType::Pointer reader1= ImageReaderType::New();
 116       reader1->SetFileName(m_InputName1);
 117       reader1->Update();
 118       input1 =reader1->GetOutput();
 119
 120       //Read the input2
 121       typename  ImageReaderType::Pointer reader2= ImageReaderType::New();
 122       reader2->SetFileName(m_InputName2);
 123       reader2->Update();
 124       input2=reader2->GetOutput();
 125     }
 126
 127       //Create the ComposeVFFilter
 128       typedef clitk::ComposeVFFilter<ImageType,ImageType> FilterType;
 129       typename FilterType::Pointer filter =FilterType::New();
 130       filter->SetInput1(input1);
 131       filter->SetInput2(input2);
 132       filter->SetVerbose(m_Verbose);
 133       filter->Update();
 134
 135       //Write the output
 136       typedef itk::ImageFileWriter<ImageType> WriterType;
 137       typename WriterType::Pointer writer = WriterType::New();
 138       writer->SetFileName(m_OutputName);
 139       writer->SetInput(filter->GetOutput());
 140       writer->Update();
 141
 142   }
 143 }
 144
 145 #endif