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 // clitk
  23 #include "clitkCommon.h"
  24 #include "clitkAutoCropFilter.h"
  25 #include "clitkLabelizeParameters.h"
  26
  27 // itk
  28 #include <itkBoundingBox.h>
  29
  30 namespace clitk {
  31
  32   //--------------------------------------------------------------------
  33   template<class ImageType>
  34   void ComputeBBFromImageRegion(typename ImageType::Pointer image,
  35                                 typename ImageType::RegionType region,
  36                                 typename itk::BoundingBox<unsigned long,
  37                                                           ImageType::ImageDimension>::Pointer bb);
  38
  39   //--------------------------------------------------------------------
  40   template<int Dimension>
  41   void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  42                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  43                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2);
  44
  45   //--------------------------------------------------------------------
  46   template<class ImageType>
  47   void ComputeRegionFromBB(typename ImageType::Pointer image,
  48                            const typename itk::BoundingBox<unsigned long,
  49                            ImageType::ImageDimension>::Pointer bb,
  50                            typename ImageType::RegionType & region);
  51   //--------------------------------------------------------------------
  52   template<class TInternalImageType, class TMaskInternalImageType>
  53   typename TInternalImageType::Pointer
  54   SetBackground(const TInternalImageType * input,
  55                 const TMaskInternalImageType * mask,
  56                 typename TMaskInternalImageType::PixelType maskBG,
  57                 typename TInternalImageType::PixelType outValue);
  58   //--------------------------------------------------------------------
  59
  60
  61   //--------------------------------------------------------------------
  62   template<class ImageType>
  63   int GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
  64                                           typename ImageType::PixelType BG,
  65                                           bool isFullyConnected);
  66   //--------------------------------------------------------------------
  67
  68
  69   //--------------------------------------------------------------------
  70   template<class TImageType>
  71   typename TImageType::Pointer
  72   Labelize(const TImageType * input,
  73            typename TImageType::PixelType BG,
  74            bool isFullyConnected,
  75            int minimalComponentSize);
  76   //--------------------------------------------------------------------
  77
  78
  79   //--------------------------------------------------------------------
  80   template<class ImageType>
  81   typename ImageType::Pointer
  82   RemoveLabels(typename ImageType::Pointer input,
  83                typename ImageType::PixelType BG,
  84                std::vector<typename ImageType::PixelType> & labelsToRemove);
  85   //--------------------------------------------------------------------
  86
  87
  88   //--------------------------------------------------------------------
  89   template<class ImageType>
  90   typename ImageType::Pointer
  91   AutoCrop(typename ImageType::Pointer input,
  92            typename ImageType::PixelType BG) {
  93     typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
  94     typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
  95     autoCropFilter->SetInput(input);
  96     autoCropFilter->SetBackgroundValue(BG);
  97     autoCropFilter->Update();
  98     return autoCropFilter->GetOutput();
  99   }
 100   //--------------------------------------------------------------------
 101
 102
 103   //--------------------------------------------------------------------
 104   template<class TImageType>
 105   typename TImageType::Pointer
 106   KeepLabels(const TImageType * input,
 107              typename TImageType::PixelType BG,
 108              typename TImageType::PixelType FG,
 109              typename TImageType::PixelType firstKeep,
 110              typename TImageType::PixelType lastKeep,
 111              bool useLastKeep);
 112   //--------------------------------------------------------------------
 113
 114
 115   //--------------------------------------------------------------------
 116   template<class TImageType>
 117   typename TImageType::Pointer
 118   LabelizeAndSelectLabels(typename TImageType::Pointer input,
 119                           typename TImageType::PixelType BG,
 120                           typename TImageType::PixelType FG,
 121                           bool isFullyConnected,
 122                           int minimalComponentSize,
 123                           LabelizeParameters<typename TImageType::PixelType> * param);
 124
 125   //--------------------------------------------------------------------
 126   template<class ImageType>
 127   typename ImageType::Pointer
 128   ResizeImageLike(typename ImageType::Pointer input,
 129                   typename ImageType::Pointer like,
 130                   typename ImageType::PixelType BG);
 131
 132
 133   //--------------------------------------------------------------------
 134   template<class MaskImageType>
 135   typename MaskImageType::Pointer
 136   SliceBySliceRelativePosition(const MaskImageType * input,
 137                                const MaskImageType * object,
 138                                int direction,
 139                                double threshold,
 140                                std::string orientation,
 141                                bool uniqueConnectedComponent=false,
 142                                double spacing=-1,
 143                                bool notflag=false);
 144
 145   //--------------------------------------------------------------------
 146   // In a binary image, search for the point belonging to the FG that
 147   // is the most exterma in the direction 'direction' (or in the
 148   // opposite if notFlag is given). if 'point' and 'distanceMax' are
 149   // given, do not consider points that are away from 'point' more
 150   // than 'distanceMax'
 151   template<class SliceType>
 152   typename SliceType::PointType
 153   FindExtremaPointInAGivenDirection(const SliceType * input,
 154                                     typename SliceType::PixelType bg,
 155                                     int direction,
 156                                     bool notFlag,
 157                                     typename SliceType::PointType point,
 158                                     double distanceMax);
 159
 160   //--------------------------------------------------------------------
 161
 162   //--------------------------------------------------------------------
 163   template<class ImageType>
 164   typename ImageType::Pointer
 165   CropImageAlongOneAxis(typename ImageType::Pointer image,
 166                         int dim, double min, double max,
 167                         bool autoCrop = false,
 168                         typename ImageType::PixelType BG=0);
 169   //--------------------------------------------------------------------
 170 }
 171
 172 #include "clitkSegmentationUtils.txx"
 173
 174 #endif