itk/clitkDecomposeThroughErosionImageFilter.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 clitkDecomposeThroughErosionImageFilter_txx
  19 #define clitkDecomposeThroughErosionImageFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkDecomposeThroughErosionImageFilter.txx
  23  * @author
  24  * @date
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30
  31 namespace clitk
  32 {
  33
  34   //-------------------------------------------------------------------
  35   // Update with the number of dimensions
  36   //-------------------------------------------------------------------
  37   template<class InputImageType, class OutputImageType>
  38   DecomposeThroughErosionImageFilter<InputImageType, OutputImageType>::DecomposeThroughErosionImageFilter()
  39   {
  40    m_Verbose=false;
  41    m_Lower =1;
  42    m_Upper=1;
  43    m_Inside=1;
  44    m_Outside=0;
  45    m_ErosionPaddingValue=static_cast<OutputPixelType>(-1);
  46    for (unsigned int i=0; i<InputImageDimension; i++)
  47      m_Radius[i]=1;
  48    m_NumberOfNewLabels=1;
  49    m_FullyConnected=true;
  50    m_MinimumObjectSize=10;
  51    m_MinimumNumberOfIterations=1;
  52   }
  53
  54
  55   //-------------------------------------------------------------------
  56   // Update with the number of dimensions and the pixeltype
  57   //-------------------------------------------------------------------
  58   template<class InputImageType, class  OutputImageType>
  59   void
  60   DecomposeThroughErosionImageFilter<InputImageType, OutputImageType>::GenerateData()
  61   {
  62
  63     //---------------------------------
  64     // Typedefs
  65     //---------------------------------
  66
  67     // Internal type
  68     typedef itk::Image<InternalPixelType, InputImageDimension> InternalImageType;
  69
  70     // Filters used
  71     typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinaryThresholdImageFilter;
  72     typedef itk::BinaryBallStructuringElement<InputPixelType,InputImageDimension > KernelType;
  73     typedef itk::BinaryErodeImageFilter<InternalImageType, InternalImageType , KernelType> BinaryErodeImageFilterType;
  74     typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> BinaryThresholdImageFilterType;
  75     typedef itk::StatisticsImageFilter<InternalImageType> StatisticsImageFilterType;
  76     typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
  77     typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelImageFilterType;
  78     typedef clitk::SetBackgroundImageFilter<InternalImageType, InternalImageType, InternalImageType> SetBackgroundImageFilterType;
  79
  80     //---------------------------------
  81     // Binarize input
  82     //---------------------------------
  83     typename  InputBinaryThresholdImageFilter::Pointer inputBinarizer=InputBinaryThresholdImageFilter::New();
  84     inputBinarizer->SetInput(this->GetInput());
  85     inputBinarizer->SetLowerThreshold(m_Lower);
  86     inputBinarizer->SetUpperThreshold(m_Upper);
  87     inputBinarizer ->SetInsideValue(m_Inside);
  88     inputBinarizer ->SetOutsideValue(m_Outside);
  89     if(m_Verbose) std::cout<<"Binarizing the input..."<<std::endl;
  90     inputBinarizer->Update();
  91
  92     //---------------------------------
  93     // Label the input
  94     //---------------------------------
  95     typename ConnectFilterType::Pointer inputConnectFilter=ConnectFilterType::New();
  96     inputConnectFilter->SetInput(inputBinarizer->GetOutput());
  97     inputConnectFilter->SetBackgroundValue(0);
  98     inputConnectFilter->SetFullyConnected(m_FullyConnected);
  99     if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
 100     //   inputConnectFilter->Update();
 101
 102     //---------------------------------
 103     // Count the initial labels
 104     //---------------------------------
 105     typename StatisticsImageFilterType::Pointer inputStatisticsImageFilter=StatisticsImageFilterType::New();
 106     inputStatisticsImageFilter->SetInput(inputConnectFilter->GetOutput());
 107     if(m_Verbose) std::cout<<"Counting the initial labels..."<<std::endl;
 108     inputStatisticsImageFilter->Update();
 109     unsigned int initialNumberOfLabels= inputStatisticsImageFilter->GetMaximum();
 110     if(m_Verbose) std::cout<<"The input contained "<<initialNumberOfLabels<<" disctictive label(s)..."<<std::endl;
 111     if(m_Verbose) std::cout<<"Performing erosions till at least "<<initialNumberOfLabels+m_NumberOfNewLabels<<" distinctive labels are counted..."<<std::endl;
 112
 113     //---------------------------------
 114     // Structuring element
 115     //---------------------------------
 116     KernelType structuringElement;
 117     structuringElement.SetRadius(m_Radius);
 118     structuringElement.CreateStructuringElement();
 119
 120     //---------------------------------
 121     // Repeat while not decomposed
 122     //---------------------------------
 123     typename InternalImageType::Pointer current=inputBinarizer->GetOutput();
 124     typename InternalImageType::Pointer output=inputBinarizer->GetOutput();
 125     unsigned int iteration=0;
 126     unsigned int max =initialNumberOfLabels;
 127
 128     while (  (iteration < m_MinimumNumberOfIterations) || ( (max< initialNumberOfLabels + m_NumberOfNewLabels ) && (iteration<100 ) ) )
 129       {
 130
 131
 132         if(m_Verbose) std::cout<<"Eroding image (iteration "<<iteration<<")..."<<std::endl;
 133
 134         //---------------------------------
 135         // Erode
 136         //---------------------------------
 137         typename BinaryErodeImageFilterType::Pointer erosionFilter=BinaryErodeImageFilterType::New();
 138         erosionFilter->SetInput (current);
 139         erosionFilter->SetForegroundValue (1);
 140         erosionFilter->SetBackgroundValue (-1);
 141         erosionFilter->SetBoundaryToForeground(false);
 142         erosionFilter->SetKernel(structuringElement);
 143         erosionFilter->Update();
 144         current=erosionFilter->GetOutput();
 145
 146         //---------------------------------
 147         // Binarize (remove -1)
 148         //---------------------------------
 149         typename  BinaryThresholdImageFilterType::Pointer binarizer=BinaryThresholdImageFilterType::New();
 150         binarizer->SetInput(erosionFilter->GetOutput());
 151         binarizer->SetLowerThreshold(1);
 152         binarizer->SetUpperThreshold(1);
 153         binarizer ->SetInsideValue(1);
 154         binarizer ->SetOutsideValue(0);
 155         if(m_Verbose) std::cout<<"Binarizing the eroded image..."<<std::endl;
 156         //binarizer->Update();
 157
 158
 159         //---------------------------------
 160         // ReLabel the connected components
 161         //---------------------------------
 162         typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 163         connectFilter->SetInput(binarizer->GetOutput());
 164         connectFilter->SetBackgroundValue(0);
 165         connectFilter->SetFullyConnected(m_FullyConnected);
 166         if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
 167         //connectFilter->Update();
 168
 169         //---------------------------------
 170         // Sort
 171         //---------------------------------
 172         typename RelabelImageFilterType::Pointer relabelFilter=RelabelImageFilterType::New();
 173         relabelFilter->SetInput(connectFilter->GetOutput());
 174         relabelFilter->SetMinimumObjectSize(m_MinimumObjectSize);
 175         //relabelFilter->Update();
 176
 177
 178         //---------------------------------
 179         // Count the labels
 180         //---------------------------------
 181         typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
 182         statisticsImageFilter->SetInput(relabelFilter->GetOutput());
 183         statisticsImageFilter->Update();
 184         max= statisticsImageFilter->GetMaximum();
 185         if(m_Verbose) std::cout<<"Counted "<<max<<" label (s) larger then "<<m_MinimumObjectSize<<" voxels..."<<std::endl;
 186         output=statisticsImageFilter->GetOutput();
 187
 188         // Next iteration
 189         iteration++;
 190       }
 191
 192
 193     //---------------------------------
 194     // Binarize current (remove -1)
 195     //---------------------------------
 196     typename  BinaryThresholdImageFilterType::Pointer binarizer=BinaryThresholdImageFilterType::New();
 197     binarizer->SetInput(current);
 198     binarizer->SetLowerThreshold(1);
 199     binarizer->SetUpperThreshold(1);
 200     binarizer ->SetInsideValue(1);
 201     binarizer ->SetOutsideValue(0);
 202     if(m_Verbose) std::cout<<"Binarizing the eroded image..."<<std::endl;
 203     //binarizer->Update();
 204
 205     //---------------------------------
 206     // ReLabel the connected components
 207     //---------------------------------
 208     typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 209     connectFilter->SetInput(binarizer->GetOutput());
 210     connectFilter->SetBackgroundValue(0);
 211     connectFilter->SetFullyConnected(m_FullyConnected);
 212     if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
 213     connectFilter->Update();
 214
 215     //---------------------------------
 216     // Sort
 217     //---------------------------------
 218     typename RelabelImageFilterType::Pointer relabelFilter=RelabelImageFilterType::New();
 219     relabelFilter->SetInput(connectFilter->GetOutput());
 220     //relabelFilter->SetMinimumObjectSize(m_MinimumObjectSize); // Preserve all intensities
 221     //relabelFilter->Update();
 222
 223     //---------------------------------
 224     // Set -1 to padding value
 225     //---------------------------------
 226     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter =SetBackgroundImageFilterType::New();
 227     setBackgroundFilter->SetInput(relabelFilter->GetOutput());
 228     setBackgroundFilter->SetInput2(current);
 229     setBackgroundFilter->SetMaskValue(-1);
 230     setBackgroundFilter->SetOutsideValue(m_ErosionPaddingValue);
 231     if(m_Verbose) std::cout<<"Setting the eroded region to "<<m_ErosionPaddingValue<<"..."<<std::endl;
 232
 233     //---------------------------------
 234     // Cast
 235     //---------------------------------
 236     typedef itk::CastImageFilter<InternalImageType, OutputImageType> CastImageFilterType;
 237     typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
 238     caster->SetInput(setBackgroundFilter->GetOutput());
 239     caster->Update();
 240
 241     //---------------------------------
 242     // SetOutput
 243     //---------------------------------
 244     this->SetNthOutput(0, caster->GetOutput());
 245   }
 246
 247
 248 }//end clitk
 249
 250 #endif //#define clitkDecomposeThroughErosionImageFilter_txx