itk/clitkSegmentationFunctions.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://oncora1.lyon.fnclcc.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
  19 // clitk
  20 #include "clitkSetBackgroundImageFilter.h"
  21
  22 // itk
  23 #include <itkConnectedComponentImageFilter.h>
  24 #include <itkRelabelComponentImageFilter.h>
  25 #include <itkBinaryThresholdImageFilter.h>
  26
  27 //--------------------------------------------------------------------
  28 template<class TImageType, class TMaskImageType>
  29 typename TImageType::Pointer
  30 clitk::SetBackground(typename TImageType::ConstPointer input,
  31                      typename TMaskImageType::ConstPointer mask,
  32                      typename TMaskImageType::PixelType maskBG,
  33                      typename TImageType::PixelType outValue) {
  34   typedef clitk::SetBackgroundImageFilter<TImageType, TMaskImageType, TImageType> SetBackgroundImageFilterType;
  35   typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
  36   setBackgroundFilter->SetInput(input);
  37   setBackgroundFilter->SetInput2(mask);
  38   setBackgroundFilter->SetMaskValue(maskBG);
  39   setBackgroundFilter->SetOutsideValue(outValue);
  40   setBackgroundFilter->Update();
  41   return setBackgroundFilter->GetOutput();
  42 }
  43 //--------------------------------------------------------------------
  44
  45
  46 //--------------------------------------------------------------------
  47 template<class TImageType>
  48 typename TImageType::Pointer
  49 clitk::Labelize(typename TImageType::Pointer input,
  50                 typename TImageType::PixelType BG,
  51                 bool isFullyConnected,
  52                 int minimalComponentSize) {
  53
  54   // Connected Component label
  55   typedef itk::ConnectedComponentImageFilter<TImageType, TImageType> ConnectFilterType;
  56   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
  57   connectFilter->SetInput(input);
  58   connectFilter->SetBackgroundValue(BG);
  59   connectFilter->SetFullyConnected(isFullyConnected);
  60
  61   // Sort by size and remove too small area.
  62   typedef itk::RelabelComponentImageFilter<TImageType, TImageType> RelabelFilterType;
  63   typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
  64   relabelFilter->InPlaceOn();
  65   relabelFilter->SetInput(connectFilter->GetOutput());
  66   relabelFilter->SetMinimumObjectSize(minimalComponentSize);
  67   relabelFilter->Update();
  68
  69   // Return result
  70   return relabelFilter->GetOutput();
  71 }
  72 //--------------------------------------------------------------------
  73
  74
  75 //--------------------------------------------------------------------
  76 template<class TImageType>
  77 typename TImageType::Pointer
  78 clitk::RemoveLabels(typename TImageType::Pointer input,
  79                     typename TImageType::PixelType BG,
  80                     std::vector<typename TImageType::PixelType> & labelsToRemove) {
  81   typename TImageType::Pointer working_image = input;
  82   for (unsigned int i=0; i <labelsToRemove.size(); i++) {
  83     typedef clitk::SetBackgroundImageFilter<TImageType, TImageType> SetBackgroundImageFilterType;
  84     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
  85     setBackgroundFilter->SetInput(input);
  86     setBackgroundFilter->SetInput2(input);
  87     setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
  88     setBackgroundFilter->SetOutsideValue(BG);
  89     setBackgroundFilter->Update();
  90     working_image = setBackgroundFilter->GetOutput();
  91   }
  92   return working_image;
  93 }
  94 //--------------------------------------------------------------------
  95
  96
  97 //--------------------------------------------------------------------
  98 template<class TImageType>
  99 typename TImageType::Pointer
 100 clitk::KeepLabels(typename TImageType::Pointer input,
 101                   typename TImageType::PixelType BG,
 102                   typename TImageType::PixelType FG,
 103                   typename TImageType::PixelType firstKeep,
 104                   typename TImageType::PixelType lastKeep,
 105                   bool useLastKeep) {
 106   typedef itk::BinaryThresholdImageFilter<TImageType, TImageType> BinarizeFilterType;
 107   typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 108   binarizeFilter->SetInput(input);
 109   binarizeFilter->SetLowerThreshold(firstKeep);
 110   if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 111   binarizeFilter->SetInsideValue(FG);
 112   binarizeFilter->SetOutsideValue(BG);
 113   binarizeFilter->Update();
 114   return binarizeFilter->GetOutput();
 115 }
 116 //--------------------------------------------------------------------
 117
 118
 119 //--------------------------------------------------------------------
 120 template<class TImageType>
 121 typename TImageType::Pointer
 122 clitk::LabelizeAndSelectLabels(typename TImageType::Pointer input,
 123                                typename TImageType::PixelType BG,
 124                                typename TImageType::PixelType FG,
 125                                bool isFullyConnected,
 126                                int minimalComponentSize,
 127                                LabelizeParameters<typename TImageType::PixelType> * param)
 128 {
 129   typename TImageType::Pointer working_image;
 130   working_image = Labelize<TImageType>(input, BG, isFullyConnected, minimalComponentSize);
 131   working_image = RemoveLabels<TImageType>(working_image, BG, param->GetLabelsToRemove());
 132   working_image = KeepLabels<TImageType>(working_image,
 133                                          BG, FG,
 134                                          param->GetFirstKeep(),
 135                                          param->GetLastKeep(),
 136                                          param->GetUseLastKeep());
 137   return working_image;
 138 }
 139 //--------------------------------------------------------------------