itk/clitkSegmentationUtils.h

   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 #ifndef CLITKSEGMENTATIONUTILS_H
  20 #define CLITKSEGMENTATIONUTILS_H
  21
  22 #include "clitkCommon.h"
  23 #include "clitkAutoCropFilter.h"
  24 #include "clitkLabelizeParameters.h"
  25 #include <itkBoundingBox.h>
  26
  27 namespace clitk {
  28
  29   //--------------------------------------------------------------------
  30   template<class ImageType>
  31   void ComputeBBFromImageRegion(typename ImageType::Pointer image,
  32                                 typename ImageType::RegionType region,
  33                                 typename itk::BoundingBox<unsigned long,
  34                                 ImageType::ImageDimension>::Pointer bb);
  35
  36   //--------------------------------------------------------------------
  37   template<int Dimension>
  38   void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  39                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  40                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2);
  41
  42   //--------------------------------------------------------------------
  43   template<class ImageType>
  44   void ComputeRegionFromBB(typename ImageType::Pointer image,
  45                            const typename itk::BoundingBox<unsigned long,
  46                            ImageType::ImageDimension>::Pointer bb,
  47                            typename ImageType::RegionType & region);
  48   //--------------------------------------------------------------------
  49   template<class TInternalImageType, class TMaskInternalImageType>
  50   typename TInternalImageType::Pointer
  51   SetBackground(typename TInternalImageType::ConstPointer input,
  52                 typename TMaskInternalImageType::ConstPointer mask,
  53                 typename TMaskInternalImageType::PixelType maskBG,
  54                 typename TInternalImageType::PixelType outValue);
  55   //--------------------------------------------------------------------
  56
  57
  58   //--------------------------------------------------------------------
  59   template<class TInternalImageType, class TMaskInternalImageType>
  60   typename TInternalImageType::Pointer
  61   SetBackground(typename TInternalImageType::Pointer input,
  62                 typename TMaskInternalImageType::Pointer mask,
  63                 typename TMaskInternalImageType::PixelType maskBG,
  64                 typename TInternalImageType::PixelType outValue) {
  65     return SetBackground<TInternalImageType, TMaskInternalImageType>
  66       (static_cast<typename TInternalImageType::ConstPointer>(input),
  67        static_cast<typename TMaskInternalImageType::ConstPointer>(mask),
  68        maskBG, outValue);
  69   }
  70   //--------------------------------------------------------------------
  71
  72
  73   //--------------------------------------------------------------------
  74   template<class ImageType>
  75   int GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
  76                                           typename ImageType::PixelType BG,
  77                                           bool isFullyConnected);
  78   //--------------------------------------------------------------------
  79
  80
  81   //--------------------------------------------------------------------
  82   template<class TImageType>
  83   typename TImageType::Pointer
  84   Labelize(typename TImageType::Pointer input,
  85            typename TImageType::PixelType BG,
  86            bool isFullyConnected,
  87            int minimalComponentSize);
  88   //--------------------------------------------------------------------
  89
  90
  91   //--------------------------------------------------------------------
  92   template<class ImageType>
  93   typename ImageType::Pointer
  94   RemoveLabels(typename ImageType::Pointer input,
  95                typename ImageType::PixelType BG,
  96                std::vector<typename ImageType::PixelType> & labelsToRemove);
  97   //--------------------------------------------------------------------
  98
  99
 100   //--------------------------------------------------------------------
 101   template<class ImageType>
 102     typename ImageType::Pointer
 103     AutoCrop(typename ImageType::Pointer input,
 104              typename ImageType::PixelType BG) {
 105       typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
 106       typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
 107       autoCropFilter->SetInput(input);
 108       autoCropFilter->Update();
 109       return autoCropFilter->GetOutput();
 110   }
 111
 112   //--------------------------------------------------------------------
 113
 114
 115   //--------------------------------------------------------------------
 116   template<class TImageType>
 117   typename TImageType::Pointer
 118   KeepLabels(typename TImageType::Pointer input,
 119              typename TImageType::PixelType BG,
 120              typename TImageType::PixelType FG,
 121              typename TImageType::PixelType firstKeep,
 122              typename TImageType::PixelType lastKeep,
 123              bool useLastKeep);
 124   //--------------------------------------------------------------------
 125
 126
 127   //--------------------------------------------------------------------
 128   template<class TImageType>
 129   typename TImageType::Pointer
 130   LabelizeAndSelectLabels(typename TImageType::Pointer input,
 131                           typename TImageType::PixelType BG,
 132                           typename TImageType::PixelType FG,
 133                           bool isFullyConnected,
 134                           int minimalComponentSize,
 135                           LabelizeParameters<typename TImageType::PixelType> * param);
 136
 137   //--------------------------------------------------------------------
 138   template<class ImageType>
 139   typename ImageType::Pointer
 140   EnlargeImageLike(typename ImageType::Pointer input,
 141                    typename ImageType::Pointer like,
 142                    typename ImageType::PixelType BG);
 143
 144 }
 145
 146 #include "clitkSegmentationUtils.txx"
 147
 148 #endif