X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkDecomposeThroughErosionImageFilter.txx;fp=segmentation%2FclitkDecomposeThroughErosionImageFilter.txx;h=0000000000000000000000000000000000000000;hb=9427090c47a46eaa2c0a6ef876a4b0af404abfce;hp=6a7ffbc347bfc5ed35eddc5bb5001d012a8a2661;hpb=86c83f6c6ee7e1645f638f32d7ad4811122ec00b;p=clitk.git

diff --git a/segmentation/clitkDecomposeThroughErosionImageFilter.txx b/segmentation/clitkDecomposeThroughErosionImageFilter.txx
deleted file mode 100644
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--- a/segmentation/clitkDecomposeThroughErosionImageFilter.txx
+++ /dev/null
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-/*=========================================================================
-  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
-
-  Authors belong to: 
-  - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://www.centreleonberard.fr
-  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
-
-  This software is distributed WITHOUT ANY WARRANTY; without even
-  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
-  PURPOSE.  See the copyright notices for more information.
-
-  It is distributed under dual licence
-
-  - BSD        See included LICENSE.txt file
-  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-===========================================================================**/
-#ifndef clitkDecomposeThroughErosionImageFilter_txx
-#define clitkDecomposeThroughErosionImageFilter_txx
-
-/* =================================================
- * @file   clitkDecomposeThroughErosionImageFilter.txx
- * @author 
- * @date   
- * 
- * @brief 
- * 
- ===================================================*/
-
-
-namespace clitk
-{
-
-  //-------------------------------------------------------------------
-  // Update with the number of dimensions
-  //-------------------------------------------------------------------
-  template<class InputImageType, class OutputImageType>
-  DecomposeThroughErosionImageFilter<InputImageType, OutputImageType>::DecomposeThroughErosionImageFilter()
-  {
-   m_Verbose=false;
-   m_Lower =1;
-   m_Upper=1;
-   m_Inside=1;
-   m_Outside=0;
-   m_ErosionPaddingValue=static_cast<OutputPixelType>(-1);
-   for (unsigned int i=0; i<InputImageDimension; i++)
-     m_Radius[i]=1;
-   m_NumberOfNewLabels=1;
-   m_FullyConnected=true;
-   m_MinimumObjectSize=10;
-   m_MinimumNumberOfIterations=1;
-  }
-
-
-  //-------------------------------------------------------------------
-  // Update with the number of dimensions and the pixeltype
-  //-------------------------------------------------------------------
-  template<class InputImageType, class  OutputImageType> 
-  void 
-  DecomposeThroughErosionImageFilter<InputImageType, OutputImageType>::GenerateData()
-  {
-
-    //---------------------------------
-    // Typedefs 
-    //--------------------------------- 
-
-    // Internal type
-    typedef itk::Image<InternalPixelType, InputImageDimension> InternalImageType;
-
-    // Filters used
-    typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinaryThresholdImageFilter;
-    typedef itk::BinaryBallStructuringElement<InputPixelType,InputImageDimension > KernelType;
-    typedef itk::BinaryErodeImageFilter<InternalImageType, InternalImageType , KernelType> BinaryErodeImageFilterType;
-    typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> BinaryThresholdImageFilterType;
-    typedef itk::StatisticsImageFilter<InternalImageType> StatisticsImageFilterType;
-    typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
-    typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelImageFilterType;
-    typedef clitk::SetBackgroundImageFilter<InternalImageType, InternalImageType, InternalImageType> SetBackgroundImageFilterType;
-  
-    //---------------------------------
-    // Binarize input
-    //--------------------------------- 
-    typename  InputBinaryThresholdImageFilter::Pointer inputBinarizer=InputBinaryThresholdImageFilter::New();
-    inputBinarizer->SetInput(this->GetInput());
-    inputBinarizer->SetLowerThreshold(m_Lower);
-    inputBinarizer->SetUpperThreshold(m_Upper);
-    inputBinarizer ->SetInsideValue(m_Inside);
-    inputBinarizer ->SetOutsideValue(m_Outside);
-    if(m_Verbose) std::cout<<"Binarizing the input..."<<std::endl;
-    inputBinarizer->Update();
- 
-    //---------------------------------
-    // Label the input
-    //---------------------------------
-    typename ConnectFilterType::Pointer inputConnectFilter=ConnectFilterType::New();
-    inputConnectFilter->SetInput(inputBinarizer->GetOutput());
-    inputConnectFilter->SetBackgroundValue(0);
-    inputConnectFilter->SetFullyConnected(m_FullyConnected);
-    if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
-    //   inputConnectFilter->Update();
- 
-    //---------------------------------
-    // Count the initial labels
-    //---------------------------------
-    typename StatisticsImageFilterType::Pointer inputStatisticsImageFilter=StatisticsImageFilterType::New();
-    inputStatisticsImageFilter->SetInput(inputConnectFilter->GetOutput());
-    if(m_Verbose) std::cout<<"Counting the initial labels..."<<std::endl;
-    inputStatisticsImageFilter->Update();
-    unsigned int initialNumberOfLabels= inputStatisticsImageFilter->GetMaximum();
-    if(m_Verbose) std::cout<<"The input contained "<<initialNumberOfLabels<<" disctictive label(s)..."<<std::endl;
-    if(m_Verbose) std::cout<<"Performing erosions till at least "<<initialNumberOfLabels+m_NumberOfNewLabels<<" distinctive labels are counted..."<<std::endl;
- 
-    //---------------------------------
-    // Structuring element
-    //---------------------------------
-    KernelType structuringElement;
-    structuringElement.SetRadius(m_Radius);
-    structuringElement.CreateStructuringElement();
-
-    //---------------------------------
-    // Repeat while not decomposed
-    //---------------------------------
-    typename InternalImageType::Pointer current=inputBinarizer->GetOutput();
-    typename InternalImageType::Pointer output=inputBinarizer->GetOutput();
-    unsigned int iteration=0;
-    unsigned int max =initialNumberOfLabels;
-
-    while (  (iteration < m_MinimumNumberOfIterations) || ( (max< initialNumberOfLabels + m_NumberOfNewLabels ) && (iteration<100 ) ) )
-      {
-
-
-	if(m_Verbose) std::cout<<"Eroding image (iteration "<<iteration<<")..."<<std::endl;
-	
-	//---------------------------------
-	// Erode
-	//---------------------------------
-	typename BinaryErodeImageFilterType::Pointer erosionFilter=BinaryErodeImageFilterType::New();
-	erosionFilter->SetInput (current);
-	erosionFilter->SetForegroundValue (1);
-	erosionFilter->SetBackgroundValue (-1);
-	erosionFilter->SetBoundaryToForeground(false);
-	erosionFilter->SetKernel(structuringElement);
-	erosionFilter->Update();
-	current=erosionFilter->GetOutput();
-	
-	//---------------------------------
-	// Binarize (remove -1)
-	//--------------------------------- 
-	typename  BinaryThresholdImageFilterType::Pointer binarizer=BinaryThresholdImageFilterType::New();
-	binarizer->SetInput(erosionFilter->GetOutput());
-	binarizer->SetLowerThreshold(1);
-	binarizer->SetUpperThreshold(1);
-	binarizer ->SetInsideValue(1);
-	binarizer ->SetOutsideValue(0);
-	if(m_Verbose) std::cout<<"Binarizing the eroded image..."<<std::endl;
-	//binarizer->Update();
-
-	
-	//---------------------------------
-	// ReLabel the connected components
-	//---------------------------------
-	typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
-	connectFilter->SetInput(binarizer->GetOutput());
-	connectFilter->SetBackgroundValue(0);
-	connectFilter->SetFullyConnected(m_FullyConnected);
-	if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
-	//connectFilter->Update();
-		
-	//---------------------------------
-	// Sort
-	//---------------------------------
-	typename RelabelImageFilterType::Pointer relabelFilter=RelabelImageFilterType::New();
-	relabelFilter->SetInput(connectFilter->GetOutput());
-	relabelFilter->SetMinimumObjectSize(m_MinimumObjectSize);
-	//relabelFilter->Update();   
-	
-	
-	//---------------------------------
-	// Count the labels
-	//---------------------------------
-	typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
-	statisticsImageFilter->SetInput(relabelFilter->GetOutput());
-	statisticsImageFilter->Update();
-	max= statisticsImageFilter->GetMaximum();
-	if(m_Verbose) std::cout<<"Counted "<<max<<" label (s) larger then "<<m_MinimumObjectSize<<" voxels..."<<std::endl;
-	output=statisticsImageFilter->GetOutput();
-	
-	// Next iteration
-	iteration++;
-      }
-
-
-    //---------------------------------
-    // Binarize current (remove -1)
-    //--------------------------------- 
-    typename  BinaryThresholdImageFilterType::Pointer binarizer=BinaryThresholdImageFilterType::New();
-    binarizer->SetInput(current);
-    binarizer->SetLowerThreshold(1);
-    binarizer->SetUpperThreshold(1);
-    binarizer ->SetInsideValue(1);
-    binarizer ->SetOutsideValue(0);
-    if(m_Verbose) std::cout<<"Binarizing the eroded image..."<<std::endl;
-    //binarizer->Update();
-    
-    //---------------------------------
-    // ReLabel the connected components
-    //---------------------------------
-    typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
-    connectFilter->SetInput(binarizer->GetOutput());
-    connectFilter->SetBackgroundValue(0);
-    connectFilter->SetFullyConnected(m_FullyConnected);
-    if(m_Verbose) std::cout<<"Labelling the connected components..."<<std::endl;
-    connectFilter->Update();
-    
-    //---------------------------------
-    // Sort
-    //---------------------------------
-    typename RelabelImageFilterType::Pointer relabelFilter=RelabelImageFilterType::New();
-    relabelFilter->SetInput(connectFilter->GetOutput());
-    //relabelFilter->SetMinimumObjectSize(m_MinimumObjectSize); // Preserve all intensities
-    //relabelFilter->Update();   
-
-    //---------------------------------
-    // Set -1 to padding value
-    //---------------------------------
-    typename SetBackgroundImageFilterType::Pointer setBackgroundFilter =SetBackgroundImageFilterType::New();
-    setBackgroundFilter->SetInput(relabelFilter->GetOutput());
-    setBackgroundFilter->SetInput2(current);
-    setBackgroundFilter->SetMaskValue(-1);
-    setBackgroundFilter->SetOutsideValue(m_ErosionPaddingValue);
-    if(m_Verbose) std::cout<<"Setting the eroded region to "<<m_ErosionPaddingValue<<"..."<<std::endl;
-        
-    //---------------------------------
-    // Cast
-    //---------------------------------
-    typedef itk::CastImageFilter<InternalImageType, OutputImageType> CastImageFilterType;
-    typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
-    caster->SetInput(setBackgroundFilter->GetOutput());
-    caster->Update();
-    
-    //---------------------------------
-    // SetOutput
-    //---------------------------------
-    this->SetNthOutput(0, caster->GetOutput());
-  }
-
-
-}//end clitk
- 
-#endif //#define clitkDecomposeThroughErosionImageFilter_txx