itk/clitkReconstructThroughDilationImageFilter.txx

   1 #ifndef clitkReconstructThroughDilationImageFilter_txx
   2 #define clitkReconstructThroughDilationImageFilter_txx
   3
   4 /* =================================================
   5  * @file   clitkReconstructThroughDilationImageFilter.txx
   6  * @author
   7  * @date
   8  *
   9  * @brief
  10  *
  11  ===================================================*/
  12
  13
  14 namespace clitk
  15 {
  16
  17   //-------------------------------------------------------------------
  18   // Update with the number of dimensions
  19   //-------------------------------------------------------------------
  20   template<class InputImageType, class OutputImageType>
  21   ReconstructThroughDilationImageFilter<InputImageType, OutputImageType>::ReconstructThroughDilationImageFilter()
  22   {
  23    m_Verbose=false;
  24    m_BackgroundValue=0;
  25    m_ForegroundValue=1;
  26    m_ErosionPaddingValue=static_cast<InputPixelType>(-1);
  27    for (unsigned int i=0; i<InputImageDimension; i++)
  28      m_Radius[i]=1;
  29    m_MaximumNumberOfLabels=10;
  30   }
  31
  32
  33   //-------------------------------------------------------------------
  34   // Update with the number of dimensions and the pixeltype
  35   //-------------------------------------------------------------------
  36   template<class InputImageType, class  OutputImageType>
  37   void
  38   ReconstructThroughDilationImageFilter<InputImageType, OutputImageType>::GenerateData()
  39   {
  40
  41     //---------------------------------
  42     // Typedefs
  43     //---------------------------------
  44
  45     // Internal type
  46     typedef itk::Image<InternalPixelType, InputImageDimension> InternalImageType;
  47
  48     // Filters used
  49     typedef itk::CastImageFilter<InputImageType, InternalImageType> InputCastImageFilterType;
  50     typedef itk::ThresholdImageFilter<InternalImageType> InputThresholdImageFilterType;
  51     typedef itk::StatisticsImageFilter<InternalImageType> StatisticsImageFilterType;
  52     typedef itk::BinaryBallStructuringElement<InternalPixelType,InputImageDimension > KernelType;
  53     typedef clitk::ConditionalBinaryDilateImageFilter<InternalImageType, InternalImageType , KernelType> ConditionalBinaryDilateImageFilterType;
  54     typedef itk::DifferenceImageFilter<InternalImageType, InternalImageType> DifferenceImageFilterType;
  55     typedef itk::CastImageFilter<InternalImageType, OutputImageType> OutputCastImageFilterType;
  56     typedef clitk::SetBackgroundImageFilter<InternalImageType, InternalImageType, InternalImageType> SetBackgroundImageFilterType;
  57
  58     //---------------------------------
  59     // Cast
  60     //---------------------------------
  61     typename InputCastImageFilterType::Pointer castImageFilter=InputCastImageFilterType::New();
  62     castImageFilter->SetInput(this->GetInput());
  63     castImageFilter->Update();
  64
  65     //---------------------------------
  66     // Threshold
  67     //---------------------------------
  68     typename InputThresholdImageFilterType::Pointer thresholdImageFilter=InputThresholdImageFilterType::New();
  69     thresholdImageFilter->SetInput(castImageFilter->GetOutput());
  70     thresholdImageFilter->ThresholdAbove(m_MaximumNumberOfLabels);
  71     thresholdImageFilter->SetOutsideValue(m_ForegroundValue);
  72     if(m_Verbose) std::cout<<"Thresholding the input to "<<m_MaximumNumberOfLabels<<" labels ..."<<std::endl;
  73     thresholdImageFilter->Update();
  74
  75     //---------------------------------
  76     // Set -1 to padding value
  77     //---------------------------------
  78     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter =SetBackgroundImageFilterType::New();
  79     setBackgroundFilter->SetInput(thresholdImageFilter->GetOutput());
  80     setBackgroundFilter->SetInput2(castImageFilter->GetOutput());
  81     setBackgroundFilter->SetMaskValue(m_ErosionPaddingValue);
  82     setBackgroundFilter->SetOutsideValue(-1);
  83     if(m_Verbose) std::cout<<"Setting the eroded region from "<<m_ErosionPaddingValue<<" to -1..."<<std::endl;
  84
  85
  86     //---------------------------------
  87     // Count the initial labels
  88     //---------------------------------
  89     typename StatisticsImageFilterType::Pointer inputStatisticsImageFilter=StatisticsImageFilterType::New();
  90     inputStatisticsImageFilter->SetInput(setBackgroundFilter->GetOutput());
  91     if(m_Verbose) std::cout<<"Counting the initial labels..."<<std::endl;
  92     inputStatisticsImageFilter->Update();
  93     unsigned int initialNumberOfLabels= inputStatisticsImageFilter->GetMaximum();
  94     if(m_Verbose) std::cout<<"The input contained "<<initialNumberOfLabels<<" disctictive label(s)..."<<std::endl;
  95     unsigned int numberOfConsideredLabels=std::min(initialNumberOfLabels, m_MaximumNumberOfLabels);
  96     if(m_Verbose) std::cout<<"Performing dilation the first "<<numberOfConsideredLabels<<" disctictive labels..."<<std::endl;
  97
  98     //---------------------------------
  99     // Dilate while change
 100     //---------------------------------
 101     typename itk::NumericTraits<InputPixelType>::AccumulateType difference=1;
 102     typename InternalImageType::Pointer labelImage=inputStatisticsImageFilter->GetOutput();
 103     typename InternalImageType::Pointer oldLabelImage=inputStatisticsImageFilter->GetOutput();
 104
 105     // element
 106     KernelType structuringElement;
 107     structuringElement.SetRadius(m_Radius);
 108     structuringElement.CreateStructuringElement();
 109
 110     while( difference)
 111       {
 112         // Dilate all labels once
 113         for ( int label=0; label<(int)numberOfConsideredLabels+1;label++)
 114           if ( m_BackgroundValue != label)
 115             {
 116               typename ConditionalBinaryDilateImageFilterType::Pointer dilateFilter=ConditionalBinaryDilateImageFilterType::New();
 117               dilateFilter->SetBoundaryToForeground(false);
 118               dilateFilter->SetKernel(structuringElement);
 119               dilateFilter->SetBackgroundValue (-1);
 120               dilateFilter->SetInput (labelImage);
 121               dilateFilter->SetForegroundValue (label);
 122               if(m_Verbose) std::cout<<"Dilating the label "<<label<<"..."<<std::endl;
 123               dilateFilter->Update();
 124               labelImage=dilateFilter->GetOutput();
 125             }
 126
 127         // Difference with previous labelImage
 128         typename DifferenceImageFilterType::Pointer differenceFilter=DifferenceImageFilterType::New();
 129         differenceFilter->SetValidInput(oldLabelImage);
 130         differenceFilter->SetTestInput(labelImage);
 131         differenceFilter->Update();
 132         difference =differenceFilter->GetTotalDifference();
 133         if(m_Verbose) std::cout<<"The change in this iteration was "<<difference<<"..."<<std::endl;
 134         oldLabelImage=labelImage;
 135       }
 136
 137     //---------------------------------
 138     // Set -1 to padding value
 139     //---------------------------------
 140     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter2 =SetBackgroundImageFilterType::New();
 141     setBackgroundFilter2->SetInput(labelImage);
 142     setBackgroundFilter2->SetInput2(labelImage);
 143     setBackgroundFilter2->SetMaskValue(-1);
 144     setBackgroundFilter2->SetOutsideValue(m_ErosionPaddingValue);
 145     if(m_Verbose) std::cout<<"Setting the eroded region to "<<m_ErosionPaddingValue<<"..."<<std::endl;
 146
 147     //---------------------------------
 148     // Cast
 149     //---------------------------------
 150     typename OutputCastImageFilterType::Pointer outputCastImageFilter=OutputCastImageFilterType::New();
 151     outputCastImageFilter->SetInput(setBackgroundFilter2->GetOutput());
 152     if(m_Verbose) std::cout<<"Casting the output..."<<std::endl;
 153     outputCastImageFilter->Update();
 154
 155     //---------------------------------
 156     // SetOutput
 157     //---------------------------------
 158     this->SetNthOutput(0, outputCastImageFilter->GetOutput());
 159
 160
 161   }
 162
 163
 164 }//end clitk
 165
 166 #endif //#define clitkReconstructThroughDilationImageFilter_txx