tools/clitkImageIntensityWindowingGenericFilter.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 clitkImageIntensityWindowingGenericFilter_txx
  19 #define clitkImageIntensityWindowingGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkImageIntensityWindowingGenericFilter.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 "itkIntensityWindowingImageFilter.h"
  32 #include "itkLabelStatisticsImageFilter.h"
  33 #include "itkMaskImageFilter.h"
  34 #include "itkMaskNegatedImageFilter.h"
  35 #include <clitkCommon.h>
  36
  37 namespace clitk
  38 {
  39
  40 //--------------------------------------------------------------------
  41 template<class args_info_type>
  42 ImageIntensityWindowingGenericFilter<args_info_type>::ImageIntensityWindowingGenericFilter():
  43   ImageToImageGenericFilter<Self>("ImageIntensityWindowing")
  44 {
  45   InitializeImageType<2>();
  46   InitializeImageType<3>();
  47 }
  48 //--------------------------------------------------------------------
  49
  50
  51 //--------------------------------------------------------------------
  52 template<class args_info_type>
  53 template<unsigned int Dim>
  54 void ImageIntensityWindowingGenericFilter<args_info_type>::InitializeImageType()
  55 {
  56   ADD_DEFAULT_IMAGE_TYPES(Dim);
  57 }
  58 //--------------------------------------------------------------------
  59
  60
  61 //--------------------------------------------------------------------
  62 template<class args_info_type>
  63 void ImageIntensityWindowingGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
  64 {
  65   mArgsInfo=a;
  66   this->SetIOVerbose(mArgsInfo.verbose_flag);
  67   if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  68
  69   if (mArgsInfo.input_given) {
  70     this->SetInputFilename(mArgsInfo.input_arg);
  71   }
  72   if (mArgsInfo.output_given) {
  73     this->SetOutputFilename(mArgsInfo.output_arg);
  74   }
  75   if (mArgsInfo.mask_given) {
  76     this->AddInputFilename(mArgsInfo.mask_arg);
  77   }
  78 }
  79 //--------------------------------------------------------------------
  80
  81 //--------------------------------------------------------------------
  82 // Update with the number of dimensions and the pixeltype
  83 //--------------------------------------------------------------------
  84 template<class args_info_type>
  85 template<class InputImageType>
  86 void
  87 ImageIntensityWindowingGenericFilter<args_info_type>::UpdateWithInputImageType()
  88 {
  89
  90   // Main filter
  91   typedef typename InputImageType::PixelType InputPixelType;
  92   typedef itk::Image<float, InputImageType::ImageDimension> OutputImageType;
  93   typedef itk::Image<unsigned char, InputImageType::ImageDimension> MaskImageType;
  94
  95   // Reading input
  96   typename OutputImageType::Pointer input = this->template GetInput<OutputImageType>(0);
  97
  98   typename MaskImageType::Pointer mask = ITK_NULLPTR;
  99   if(mArgsInfo.mask_given) {
 100    mask = this->template GetInput<MaskImageType>(1);
 101   }
 102   else {
 103    mask = MaskImageType::New();
 104    mask->SetRegions(input->GetLargestPossibleRegion());
 105    mask->SetOrigin(input->GetOrigin());
 106    mask->SetSpacing(input->GetSpacing());
 107    mask->Allocate();
 108    mask->FillBuffer(1);
 109   }
 110   // Set mask iterator
 111   typedef itk::ImageRegionIterator<MaskImageType> IteratorMaskType;
 112   IteratorMaskType itm(mask, mask->GetLargestPossibleRegion());
 113   //
 114   typedef itk::LabelStatisticsImageFilter< OutputImageType, MaskImageType > LabelStatisticsImageFilterType;
 115   typename LabelStatisticsImageFilterType::Pointer labelStatisticsImageFilter = LabelStatisticsImageFilterType::New();
 116   labelStatisticsImageFilter->SetLabelInput( mask );
 117   labelStatisticsImageFilter->SetInput(input);
 118   labelStatisticsImageFilter->Update();
 119   float maxImg = labelStatisticsImageFilter->GetMaximum(1);
 120   //std::cout << "maxImg: " << maxImg << std::endl;
 121   // Filter
 122   typedef itk::IntensityWindowingImageFilter <OutputImageType, OutputImageType> IntensityWindowingImageFilterType;
 123   typename IntensityWindowingImageFilterType::Pointer filter = IntensityWindowingImageFilterType::New();
 124   filter->SetInput(input);
 125   filter->SetWindowMinimum(0.0);
 126   filter->SetWindowMaximum(maxImg);
 127   filter->SetOutputMinimum(0.0);
 128   filter->SetOutputMaximum(1.0);
 129   filter->Update();
 130
 131   // Set iterator
 132   typedef itk::ImageRegionIterator<OutputImageType> IteratorType;
 133   IteratorType it(filter->GetOutput(), filter->GetOutput()->GetLargestPossibleRegion());
 134   //A little bit strange to do that but I think I need to do it.
 135   // Create output image
 136   typename OutputImageType::Pointer outputImage = OutputImageType::New();
 137   outputImage->SetRegions(filter->GetOutput()->GetLargestPossibleRegion());
 138   outputImage->SetOrigin(filter->GetOutput()->GetOrigin());
 139   outputImage->SetSpacing(filter->GetOutput()->GetSpacing());
 140   outputImage->Allocate();
 141   outputImage->FillBuffer(-100.0);
 142   // Set output iterator
 143   typedef itk::ImageRegionIterator<OutputImageType> IteratorOutputType;
 144   IteratorOutputType ito = IteratorOutputType(outputImage, outputImage->GetLargestPossibleRegion());
 145
 146   it.GoToBegin();
 147   ito.GoToBegin();
 148   itm.GoToBegin();
 149
 150   while (!ito.IsAtEnd()) {
 151       if(itm.Get() > 0) {
 152           ito.Set(it.Get());
 153       }
 154       ++it;
 155       ++ito;
 156       ++itm;
 157   }
 158
 159   // Write/Save results
 160   this->template SetNextOutput<OutputImageType>(outputImage);
 161 }
 162 //--------------------------------------------------------------------
 163
 164
 165 }//end clitk
 166
 167 #endif //#define clitkImageIntensityWindowingGenericFilter_txx