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->SetDirection(input->GetDirection());
 107             mask->Allocate();
 108             mask->FillBuffer(1);
 109         }
 110
 111         // Create output image
 112         typename OutputImageType::Pointer outputImage = OutputImageType::New();
 113         outputImage->SetRegions(input->GetLargestPossibleRegion());
 114         outputImage->SetOrigin(input->GetOrigin());
 115         outputImage->SetSpacing(input->GetSpacing());
 116         outputImage->SetDirection(input->GetDirection());
 117         outputImage->Allocate();
 118         outputImage->FillBuffer(0.0);
 119         // Set output iterator
 120         typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
 121         IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
 122
 123         // Filter
 124         // Set iterator
 125         typedef itk::ImageRegionIterator<InputImageType> IteratorType;
 126         IteratorType it(input, input->GetLargestPossibleRegion());
 127
 128         // Set mask iterator
 129         typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
 130         IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
 131
 132         typedef itk::LabelStatisticsImageFilter< InputImageType, MaskImageType > LabelStatisticsImageFilterType;
 133         typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
 134         labelStatisticsImageFilter->SetLabelInput( mask );
 135         labelStatisticsImageFilter->SetInput(input);
 136         labelStatisticsImageFilter->Update();
 137
 138         //std::cout << "Number of labels: " << labelStatisticsImageFilter->GetNumberOfLabels() << std::endl;
 139
 140         float minImg = labelStatisticsImageFilter->GetMinimum(1);
 141         //std::cout << "minImg= " << minImg << std::endl;
 142         float maxImg = labelStatisticsImageFilter->GetMaximum(1);
 143         //std::cout << "maxImg= " << maxImg << std::endl;
 144
 145         it.GoToBegin();
 146         ito.GoToBegin();
 147         itm.GoToBegin();
 148
 149         double total = 0.0;
 150         while (!ito.IsAtEnd()) {
 151           if(itm.Get() == 1) {
 152             ito.Set(((float) it.Get() - minImg)/(maxImg-minImg));
 153             total += ito.Get();
 154           }
 155           ++it;
 156           ++ito;
 157           ++itm;
 158         }
 159
 160         // Normalisation wrt total ?
 161         if (mArgsInfo.total_normalisation_flag) {
 162           ito.GoToBegin();
 163           itm.GoToBegin();
 164           while (!ito.IsAtEnd()) {
 165             if(itm.Get() == 1) {
 166               ito.Set(ito.Get()/total);
 167             }
 168             ++ito;
 169             ++itm;
 170           }
 171         }
 172         //
 173         //
 174         // Write/Save results
 175         this->template SetNextOutput<OutputImageType>(outputImage);
 176     }
 177     //--------------------------------------------------------------------
 178
 179
 180 }//end clitk
 181
 182 #endif //#define clitkNormalizeImageFilterGenericFilter_txx