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(const TInternalImageType * input,
  52                 const TMaskInternalImageType * mask,
  53                 typename TMaskInternalImageType::PixelType maskBG,
  54                 typename TInternalImageType::PixelType outValue);
  55   //--------------------------------------------------------------------
  56
  57
  58   //--------------------------------------------------------------------
  59   template<class ImageType>
  60   int GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
  61                                           typename ImageType::PixelType BG,
  62                                           bool isFullyConnected);
  63   //--------------------------------------------------------------------
  64
  65
  66   //--------------------------------------------------------------------
  67   template<class TImageType>
  68   typename TImageType::Pointer
  69   Labelize(typename TImageType::Pointer input,
  70            typename TImageType::PixelType BG,
  71            bool isFullyConnected,
  72            int minimalComponentSize);
  73   //--------------------------------------------------------------------
  74
  75
  76   //--------------------------------------------------------------------
  77   template<class ImageType>
  78   typename ImageType::Pointer
  79   RemoveLabels(typename ImageType::Pointer input,
  80                typename ImageType::PixelType BG,
  81                std::vector<typename ImageType::PixelType> & labelsToRemove);
  82   //--------------------------------------------------------------------
  83
  84
  85   //--------------------------------------------------------------------
  86   template<class ImageType>
  87     typename ImageType::Pointer
  88     AutoCrop(typename ImageType::Pointer input,
  89              typename ImageType::PixelType BG) {
  90       typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
  91       typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
  92       autoCropFilter->SetInput(input);
  93       autoCropFilter->Update();
  94       return autoCropFilter->GetOutput();
  95   }
  96
  97   //--------------------------------------------------------------------
  98
  99
 100   //--------------------------------------------------------------------
 101   template<class TImageType>
 102   typename TImageType::Pointer
 103   KeepLabels(typename TImageType::Pointer input,
 104              typename TImageType::PixelType BG,
 105              typename TImageType::PixelType FG,
 106              typename TImageType::PixelType firstKeep,
 107              typename TImageType::PixelType lastKeep,
 108              bool useLastKeep);
 109   //--------------------------------------------------------------------
 110
 111
 112   //--------------------------------------------------------------------
 113   template<class TImageType>
 114   typename TImageType::Pointer
 115   LabelizeAndSelectLabels(typename TImageType::Pointer input,
 116                           typename TImageType::PixelType BG,
 117                           typename TImageType::PixelType FG,
 118                           bool isFullyConnected,
 119                           int minimalComponentSize,
 120                           LabelizeParameters<typename TImageType::PixelType> * param);
 121
 122   //--------------------------------------------------------------------
 123   template<class ImageType>
 124   typename ImageType::Pointer
 125   EnlargeImageLike(typename ImageType::Pointer input,
 126                    typename ImageType::Pointer like,
 127                    typename ImageType::PixelType BG);
 128
 129 }
 130
 131 #include "clitkSegmentationUtils.txx"
 132
 133 #endif