tools/clitkNormalizeImageFilterGenericFilter.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 clitkNormalizeImageFilterGenericFilter_txx
  19 #define clitkNormalizeImageFilterGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkNormalizeImageFilterGenericFilter.txx
  23  * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
  24  * @date   29 june 2009
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30 // itk include
  31 #include "itkLabelStatisticsImageFilter.h"
  32 #include "itkMaskImageFilter.h"
  33 #include "itkMaskNegatedImageFilter.h"
  34 #include <clitkCommon.h>
  35
  36 namespace clitk
  37 {
  38
  39     //--------------------------------------------------------------------
  40     template<class args_info_type>
  41     NormalizeImageFilterGenericFilter<args_info_type>::NormalizeImageFilterGenericFilter():
  42         ImageToImageGenericFilter<Self>("NormalizeImageFilter")
  43     {
  44         InitializeImageType<2>();
  45         InitializeImageType<3>();
  46     }
  47     //--------------------------------------------------------------------
  48
  49
  50     //--------------------------------------------------------------------
  51     template<class args_info_type>
  52     template<unsigned int Dim>
  53     void NormalizeImageFilterGenericFilter<args_info_type>::InitializeImageType()
  54     {
  55         ADD_DEFAULT_IMAGE_TYPES(Dim);
  56     }
  57     //--------------------------------------------------------------------
  58
  59
  60     //--------------------------------------------------------------------
  61     template<class args_info_type>
  62     void NormalizeImageFilterGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
  63     {
  64         mArgsInfo=a;
  65         this->SetIOVerbose(mArgsInfo.verbose_flag);
  66         if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  67
  68         if (mArgsInfo.input_given) {
  69             this->SetInputFilename(mArgsInfo.input_arg);
  70         }
  71         if (mArgsInfo.output_given) {
  72             this->SetOutputFilename(mArgsInfo.output_arg);
  73         }
  74         if (mArgsInfo.mask_given) {
  75             this->AddInputFilename(mArgsInfo.mask_arg);
  76         }
  77     }
  78     //--------------------------------------------------------------------
  79
  80     //--------------------------------------------------------------------
  81     // Update with the number of dimensions and the pixeltype
  82     //--------------------------------------------------------------------
  83     template<class args_info_type>
  84     template<class InputImageType>
  85     void
  86     NormalizeImageFilterGenericFilter<args_info_type>::UpdateWithInputImageType()
  87     {
  88
  89         // Main filter
  90         typedef typename InputImageType::PixelType InputPixelType;
  91         typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
  92         typedef itk::Image<unsigned char, OutputImageType::ImageDimension> MaskImageType;
  93
  94         // Reading input
  95         typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  96
  97         typename MaskImageType::Pointer mask = ITK_NULLPTR;
  98         if(mArgsInfo.mask_given) {
  99             mask = this->template GetInput<MaskImageType>(1);
 100         }
 101         else {
 102             mask = MaskImageType::New();
 103             mask->SetRegions(input->GetLargestPossibleRegion());
 104             mask->SetOrigin(input->GetOrigin());
 105             mask->SetSpacing(input->GetSpacing());
 106             mask->Allocate();
 107             mask->FillBuffer(1);
 108         }
 109
 110         // Create output image
 111         typename OutputImageType::Pointer outputImage = OutputImageType::New();
 112         outputImage->SetRegions(input->GetLargestPossibleRegion());
 113         outputImage->SetOrigin(input->GetOrigin());
 114         outputImage->SetSpacing(input->GetSpacing());
 115         outputImage->Allocate();
 116         outputImage->FillBuffer(0.0);
 117         // Set output iterator
 118         typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
 119         IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
 120
 121         // Filter
 122         // Set iterator
 123         typedef itk::ImageRegionIterator<InputImageType> IteratorType;
 124         IteratorType it(input, input->GetLargestPossibleRegion());
 125
 126         // Set mask iterator
 127         typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
 128         IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
 129
 130         typedef itk::LabelStatisticsImageFilter< InputImageType, MaskImageType > LabelStatisticsImageFilterType;
 131         typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
 132         labelStatisticsImageFilter->SetLabelInput( mask );
 133         labelStatisticsImageFilter->SetInput(input);
 134         labelStatisticsImageFilter->Update();
 135
 136         //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
 137
 138         float minImg = labelStatisticsImageFilter->GetMinimum(1);
 139         //std::cout << "minImg= " << minImg << std::endl;
 140         float maxImg = labelStatisticsImageFilter->GetMaximum(1);
 141         //std::cout << "maxImg= " << maxImg << std::endl;
 142
 143         it.GoToBegin();
 144         ito.GoToBegin();
 145         itm.GoToBegin();
 146
 147         double total = 0.0;
 148         while (!ito.IsAtEnd()) {
 149           if(itm.Get() == 1) {
 150             ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
 151             total += ito.Get();
 152           }
 153           ++it;
 154           ++ito;
 155           ++itm;
 156         }
 157
 158         // Normalisation wrt total ?
 159         if (mArgsInfo.total_normalisation_flag) {
 160           ito.GoToBegin();
 161           itm.GoToBegin();
 162           while (!ito.IsAtEnd()) {
 163             if(itm.Get() == 1) {
 164               ito.Set(ito.Get()/total);
 165             }
 166             ++ito;
 167             ++itm;
 168           }
 169         }
 170         //
 171         //
 172         // Write/Save results
 173         this->template SetNextOutput<OutputImageType>(outputImage);
 174     }
 175     //--------------------------------------------------------------------
 176
 177
 178 }//end clitk
 179
 180 #endif //#define clitkNormalizeImageFilterGenericFilter_txx