itk/clitkDecomposeThroughErosionImageFilter.txx

   1 #ifndef clitkDecomposeThroughErosionImageFilter_txx
   2 #define clitkDecomposeThroughErosionImageFilter_txx
   3
   4 /* =================================================
   5  * @file   clitkDecomposeThroughErosionImageFilter.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   DecomposeThroughErosionImageFilter<InputImageType, OutputImageType>::DecomposeThroughErosionImageFilter()
  22   {
  23    m_Verbose=false;
  24    m_Lower =1;
  25    m_Upper=1;
  26    m_Inside=1;
  27    m_Outside=0;
  28    m_ErosionPaddingValue=static_cast<OutputPixelType>(-1);
  29    for (unsigned int i=0; i<InputImageDimension; i++)
  30      m_Radius[i]=1;
  31    m_NumberOfNewLabels=1;
  32    m_FullyConnected=true;
  33    m_MinimumObjectSize=10;
  34    m_MinimumNumberOfIterations=1;
  35   }
  36
  37
  38   //-------------------------------------------------------------------
  39   // Update with the number of dimensions and the pixeltype
  40   //-------------------------------------------------------------------
  41   template<class InputImageType, class  OutputImageType>
  42   void
  43   DecomposeThroughErosionImageFilter<InputImageType, OutputImageType>::GenerateData()
  44   {
  45
  46     //---------------------------------
  47     // Typedefs
  48     //---------------------------------
  49
  50     // Internal type
  51     typedef itk::Image<InternalPixelType, InputImageDimension> InternalImageType;
  52
  53     // Filters used
  54     typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinaryThresholdImageFilter;
  55     typedef itk::BinaryBallStructuringElement<InputPixelType,InputImageDimension > KernelType;
  56     typedef itk::BinaryErodeImageFilter<InternalImageType, InternalImageType , KernelType> BinaryErodeImageFilterType;
  57     typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> BinaryThresholdImageFilterType;
  58     typedef itk::StatisticsImageFilter<InternalImageType> StatisticsImageFilterType;
  59     typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
  60     typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelImageFilterType;
  61     typedef clitk::SetBackgroundImageFilter<InternalImageType, InternalImageType, InternalImageType> SetBackgroundImageFilterType;
  62
  63     //---------------------------------
  64     // Binarize input
  65     //---------------------------------
  66     typename  InputBinaryThresholdImageFilter::Pointer inputBinarizer=InputBinaryThresholdImageFilter::New();
  67     inputBinarizer->SetInput(this->GetInput());
  68     inputBinarizer->SetLowerThreshold(m_Lower);
  69     inputBinarizer->SetUpperThreshold(m_Upper);
  70     inputBinarizer ->SetInsideValue(m_Inside);
  71     inputBinarizer ->SetOutsideValue(m_Outside);
  72     if(m_Verbose) std::cout<<"Binarizing the input..."<<std::endl;
  73     inputBinarizer->Update();
  74
  75     //---------------------------------
  76     // Label the input
  77     //---------------------------------
  78     typename ConnectFilterType::Pointer inputConnectFilter=ConnectFilterType::New();
  79     inputConnectFilter->SetInput(inputBinarizer->GetOutput());
  80     inputConnectFilter->SetBackgroundValue(0);
  81     inputConnectFilter->SetFullyConnected(m_FullyConnected);
  82     if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
  83     //   inputConnectFilter->Update();
  84
  85     //---------------------------------
  86     // Count the initial labels
  87     //---------------------------------
  88     typename StatisticsImageFilterType::Pointer inputStatisticsImageFilter=StatisticsImageFilterType::New();
  89     inputStatisticsImageFilter->SetInput(inputConnectFilter->GetOutput());
  90     if(m_Verbose) std::cout<<"Counting the initial labels..."<<std::endl;
  91     inputStatisticsImageFilter->Update();
  92     unsigned int initialNumberOfLabels= inputStatisticsImageFilter->GetMaximum();
  93     if(m_Verbose) std::cout<<"The input contained "<<initialNumberOfLabels<<" disctictive label(s)..."<<std::endl;
  94     if(m_Verbose) std::cout<<"Performing erosions till at least "<<initialNumberOfLabels+m_NumberOfNewLabels<<" distinctive labels are counted..."<<std::endl;
  95
  96     //---------------------------------
  97     // Structuring element
  98     //---------------------------------
  99     KernelType structuringElement;
 100     structuringElement.SetRadius(m_Radius);
 101     structuringElement.CreateStructuringElement();
 102
 103     //---------------------------------
 104     // Repeat while not decomposed
 105     //---------------------------------
 106     typename InternalImageType::Pointer current=inputBinarizer->GetOutput();
 107     typename InternalImageType::Pointer output=inputBinarizer->GetOutput();
 108     unsigned int iteration=0;
 109     unsigned int max =initialNumberOfLabels;
 110
 111     while (  (iteration < m_MinimumNumberOfIterations) || ( (max< initialNumberOfLabels + m_NumberOfNewLabels ) && (iteration<100 ) ) )
 112       {
 113
 114
 115         if(m_Verbose) std::cout<<"Eroding image (iteration "<<iteration<<")..."<<std::endl;
 116
 117         //---------------------------------
 118         // Erode
 119         //---------------------------------
 120         typename BinaryErodeImageFilterType::Pointer erosionFilter=BinaryErodeImageFilterType::New();
 121         erosionFilter->SetInput (current);
 122         erosionFilter->SetForegroundValue (1);
 123         erosionFilter->SetBackgroundValue (-1);
 124         erosionFilter->SetBoundaryToForeground(false);
 125         erosionFilter->SetKernel(structuringElement);
 126         erosionFilter->Update();
 127         current=erosionFilter->GetOutput();
 128
 129         //---------------------------------
 130         // Binarize (remove -1)
 131         //---------------------------------
 132         typename  BinaryThresholdImageFilterType::Pointer binarizer=BinaryThresholdImageFilterType::New();
 133         binarizer->SetInput(erosionFilter->GetOutput());
 134         binarizer->SetLowerThreshold(1);
 135         binarizer->SetUpperThreshold(1);
 136         binarizer ->SetInsideValue(1);
 137         binarizer ->SetOutsideValue(0);
 138         if(m_Verbose) std::cout<<"Binarizing the eroded image..."<<std::endl;
 139         //binarizer->Update();
 140
 141
 142         //---------------------------------
 143         // ReLabel the connected components
 144         //---------------------------------
 145         typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 146         connectFilter->SetInput(binarizer->GetOutput());
 147         connectFilter->SetBackgroundValue(0);
 148         connectFilter->SetFullyConnected(m_FullyConnected);
 149         if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
 150         //connectFilter->Update();
 151
 152         //---------------------------------
 153         // Sort
 154         //---------------------------------
 155         typename RelabelImageFilterType::Pointer relabelFilter=RelabelImageFilterType::New();
 156         relabelFilter->SetInput(connectFilter->GetOutput());
 157         relabelFilter->SetMinimumObjectSize(m_MinimumObjectSize);
 158         //relabelFilter->Update();
 159
 160
 161         //---------------------------------
 162         // Count the labels
 163         //---------------------------------
 164         typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
 165         statisticsImageFilter->SetInput(relabelFilter->GetOutput());
 166         statisticsImageFilter->Update();
 167         max= statisticsImageFilter->GetMaximum();
 168         if(m_Verbose) std::cout<<"Counted "<<max<<" label (s) larger then "<<m_MinimumObjectSize<<" voxels..."<<std::endl;
 169         output=statisticsImageFilter->GetOutput();
 170
 171         // Next iteration
 172         iteration++;
 173       }
 174
 175
 176     //---------------------------------
 177     // Binarize current (remove -1)
 178     //---------------------------------
 179     typename  BinaryThresholdImageFilterType::Pointer binarizer=BinaryThresholdImageFilterType::New();
 180     binarizer->SetInput(current);
 181     binarizer->SetLowerThreshold(1);
 182     binarizer->SetUpperThreshold(1);
 183     binarizer ->SetInsideValue(1);
 184     binarizer ->SetOutsideValue(0);
 185     if(m_Verbose) std::cout<<"Binarizing the eroded image..."<<std::endl;
 186     //binarizer->Update();
 187
 188     //---------------------------------
 189     // ReLabel the connected components
 190     //---------------------------------
 191     typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 192     connectFilter->SetInput(binarizer->GetOutput());
 193     connectFilter->SetBackgroundValue(0);
 194     connectFilter->SetFullyConnected(m_FullyConnected);
 195     if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
 196     connectFilter->Update();
 197
 198     //---------------------------------
 199     // Sort
 200     //---------------------------------
 201     typename RelabelImageFilterType::Pointer relabelFilter=RelabelImageFilterType::New();
 202     relabelFilter->SetInput(connectFilter->GetOutput());
 203     //relabelFilter->SetMinimumObjectSize(m_MinimumObjectSize); // Preserve all intensities
 204     //relabelFilter->Update();
 205
 206     //---------------------------------
 207     // Set -1 to padding value
 208     //---------------------------------
 209     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter =SetBackgroundImageFilterType::New();
 210     setBackgroundFilter->SetInput(relabelFilter->GetOutput());
 211     setBackgroundFilter->SetInput2(current);
 212     setBackgroundFilter->SetMaskValue(-1);
 213     setBackgroundFilter->SetOutsideValue(m_ErosionPaddingValue);
 214     if(m_Verbose) std::cout<<"Setting the eroded region to "<<m_ErosionPaddingValue<<"..."<<std::endl;
 215
 216     //---------------------------------
 217     // Cast
 218     //---------------------------------
 219     typedef itk::CastImageFilter<InternalImageType, OutputImageType> CastImageFilterType;
 220     typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
 221     caster->SetInput(setBackgroundFilter->GetOutput());
 222     caster->Update();
 223
 224     //---------------------------------
 225     // SetOutput
 226     //---------------------------------
 227     this->SetNthOutput(0, caster->GetOutput());
 228   }
 229
 230
 231 }//end clitk
 232
 233 #endif //#define clitkDecomposeThroughErosionImageFilter_txx