tools/clitkSplitImageGenericFilter.cxx

   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 /**
  19  -------------------------------------------------------------------
  20  * @file   clitkSplitImageGenericFilter.cxx
  21  * @author Joël Schaerer
  22  * @date   20 April 2009
  23
  24  * @brief
  25  -------------------------------------------------------------------*/
  26
  27 #include "clitkSplitImageGenericFilter.h"
  28 #include "itkChangeInformationImageFilter.h"
  29 #include <itkIntensityWindowingImageFilter.h>
  30 //--------------------------------------------------------------------
  31 clitk::SplitImageGenericFilter::SplitImageGenericFilter():
  32   clitk::ImageToImageGenericFilter<Self>("SplitImage")
  33 {
  34   mSplitDimension = 0;
  35   InitializeImageType<3>();
  36   InitializeImageType<4>();
  37 }
  38 //--------------------------------------------------------------------
  39
  40 //--------------------------------------------------------------------
  41 template<unsigned int Dim>
  42 void clitk::SplitImageGenericFilter::InitializeImageType()
  43 {
  44   ADD_DEFAULT_IMAGE_TYPES(Dim);
  45   ADD_VEC_IMAGE_TYPE(Dim, 3,float);
  46 }
  47 //--------------------------------------------------------------------
  48
  49 //--------------------------------------------------------------------
  50 template <class ImageType>
  51 typename clitk::SplitImageGenericFilter::PngConversion<ImageType>::OutputPngImagePointer
  52 clitk::SplitImageGenericFilter::PngConversion<ImageType>::Do(double window,
  53                                                              double level,
  54                                                              ImagePointer input)
  55 {
  56   static const unsigned int PixelDimension = itk::PixelTraits<typename ImageType::PixelType>::Dimension;
  57   return this->Do(window, level, input, static_cast< PixelDimType<PixelDimension> *>(ITK_NULLPTR) );
  58 }
  59 //--------------------------------------------------------------------
  60
  61 //--------------------------------------------------------------------
  62 template <class ImageType>
  63 template<unsigned int Dim>
  64 typename clitk::SplitImageGenericFilter::PngConversion<ImageType>::OutputPngImagePointer
  65 clitk::SplitImageGenericFilter::PngConversion<ImageType>::Do(double window,
  66                                                              double level,
  67                                                              ImagePointer input,
  68                                                              PixelDimType<Dim> *)
  69 {
  70   clitkExceptionMacro("Png conversion is not implemented for vector fields");
  71   return ITK_NULLPTR;
  72 }
  73 //--------------------------------------------------------------------
  74
  75 //--------------------------------------------------------------------
  76 template <class ImageType>
  77 typename clitk::SplitImageGenericFilter::PngConversion<ImageType>::OutputPngImagePointer
  78 clitk::SplitImageGenericFilter::PngConversion<ImageType>::Do(double window,
  79                                                              double level,
  80                                                              ImagePointer input,
  81                                                              PixelDimType<1> *)
  82 {
  83   typedef itk::IntensityWindowingImageFilter< ImageType, OutputPngImageType > CastFilterType;
  84   typename CastFilterType::Pointer cast = CastFilterType::New();
  85   cast->SetWindowLevel(window, level);
  86   cast->SetInput(input);
  87   cast->Update();
  88   return cast->GetOutput();
  89 }
  90 //--------------------------------------------------------------------
  91
  92 //--------------------------------------------------------------------
  93 template<class ImageType>
  94 void clitk::SplitImageGenericFilter::UpdateWithInputImageType()
  95 {
  96
  97   // Read input
  98   typedef typename ImageType::PixelType PixelType;
  99   typedef itk::Image<PixelType,ImageType::ImageDimension-1> OutputImageType;
 100   typename ImageType::Pointer input = this->GetInput<ImageType>(0);
 101   typedef itk::ExtractImageFilter<ImageType,OutputImageType> FilterType;
 102   typename FilterType::Pointer filter= FilterType::New();
 103
 104   filter->SetInput(input);
 105   typename ImageType::SizeType size=input->GetLargestPossibleRegion().GetSize();
 106   size[mSplitDimension]=0;
 107   typename ImageType::RegionType extracted_region;
 108   extracted_region.SetSize(size);
 109   filter->SetDirectionCollapseToIdentity();
 110   filter->SetExtractionRegion(extracted_region);
 111   filter->Update();
 112
 113   typedef itk::ChangeInformationImageFilter< OutputImageType > InformationFilterType;
 114
 115   typename ImageType::IndexType index=input->GetLargestPossibleRegion().GetIndex();
 116   std::string base_filename=GetOutputFilename();
 117   unsigned int number_of_output_images=input->GetLargestPossibleRegion().GetSize()[mSplitDimension];
 118   for (unsigned int i=0; i<number_of_output_images; i++) {
 119     std::ostringstream ss;
 120     ss << std::setfill('0') << std::setw((int)(log10(double(number_of_output_images))+1)) << i;
 121     index[mSplitDimension]=i;
 122     extracted_region.SetIndex(index);
 123     filter->SetExtractionRegion(extracted_region);
 124     filter->Update();
 125
 126     if (ImageType::ImageDimension == 4 && mSplitDimension == 3) //Copy the transformation matrix if the original image is a 4D image splitted along the time dimension
 127     {
 128       typename InformationFilterType::Pointer informationFilter = InformationFilterType::New();
 129       informationFilter->SetInput( filter->GetOutput() );
 130       typename OutputImageType::DirectionType directionOutput;
 131       for (unsigned j=0; j<3; ++j)
 132         for (unsigned k=0; k<3; ++k)
 133           directionOutput[j][k] = input->GetDirection()[j][k];
 134       informationFilter->SetOutputDirection( directionOutput );
 135       informationFilter->ChangeDirectionOn();
 136       informationFilter->UpdateOutputInformation();
 137
 138       if(this->m_Png){
 139         PngConversion<OutputImageType> png;
 140         SetOutputFilename(base_filename+"_"+ss.str()+".png");
 141         typename PngConversion<OutputImageType>::OutputPngImagePointer output;
 142         output = png.Do(this->m_Window, this->m_Level, informationFilter->GetOutput());
 143         this->template SetNextOutput<typename PngConversion<OutputImageType>::OutputPngImageType>(output);
 144       }
 145       else {
 146         SetOutputFilename(base_filename+"_"+ss.str()+".mhd");
 147         SetNextOutput<OutputImageType>(informationFilter->GetOutput());
 148       }
 149     }
 150     else
 151     {
 152       if(this->m_Png){
 153         PngConversion<OutputImageType> png;
 154         SetOutputFilename(base_filename+"_"+ss.str()+".png");
 155         typename PngConversion<OutputImageType>::OutputPngImagePointer output;
 156         output = png.Do(this->m_Window, this->m_Level, filter->GetOutput());
 157         this->template SetNextOutput<typename PngConversion<OutputImageType>::OutputPngImageType>(output);
 158       }
 159       else {
 160         SetOutputFilename(base_filename+"_"+ss.str()+".mhd");
 161         SetNextOutput<OutputImageType>(filter->GetOutput());
 162       }
 163     }
 164   }
 165 }
 166 //--------------------------------------------------------------------