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                 bool inPlace);
  59   //--------------------------------------------------------------------
  60
  61
  62   //--------------------------------------------------------------------
  63   template<class ImageType>
  64   int GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
  65                                           typename ImageType::PixelType BG,
  66                                           bool isFullyConnected);
  67   //--------------------------------------------------------------------
  68
  69
  70   //--------------------------------------------------------------------
  71   template<class TImageType>
  72   typename TImageType::Pointer
  73   Labelize(const TImageType * input,
  74            typename TImageType::PixelType BG,
  75            bool isFullyConnected,
  76            int minimalComponentSize);
  77   //--------------------------------------------------------------------
  78
  79
  80   //--------------------------------------------------------------------
  81   template<class ImageType>
  82   typename ImageType::Pointer
  83   RemoveLabels(typename ImageType::Pointer input,
  84                typename ImageType::PixelType BG,
  85                std::vector<typename ImageType::PixelType> & labelsToRemove);
  86   //--------------------------------------------------------------------
  87
  88
  89   //--------------------------------------------------------------------
  90   template<class ImageType>
  91   typename ImageType::Pointer
  92   AutoCrop(typename ImageType::Pointer input,
  93            typename ImageType::PixelType BG) {
  94     typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
  95     typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
  96     autoCropFilter->SetInput(input);
  97     autoCropFilter->SetBackgroundValue(BG);
  98     autoCropFilter->Update();
  99     return autoCropFilter->GetOutput();
 100   }
 101   //--------------------------------------------------------------------
 102
 103
 104   //--------------------------------------------------------------------
 105   template<class TImageType>
 106   typename TImageType::Pointer
 107   KeepLabels(const TImageType * input,
 108              typename TImageType::PixelType BG,
 109              typename TImageType::PixelType FG,
 110              typename TImageType::PixelType firstKeep,
 111              typename TImageType::PixelType lastKeep,
 112              bool useLastKeep);
 113   //--------------------------------------------------------------------
 114
 115
 116   //--------------------------------------------------------------------
 117   template<class TImageType>
 118   typename TImageType::Pointer
 119   LabelizeAndSelectLabels(typename TImageType::Pointer input,
 120                           typename TImageType::PixelType BG,
 121                           typename TImageType::PixelType FG,
 122                           bool isFullyConnected,
 123                           int minimalComponentSize,
 124                           LabelizeParameters<typename TImageType::PixelType> * param);
 125
 126   //--------------------------------------------------------------------
 127   template<class ImageType>
 128   typename ImageType::Pointer
 129   ResizeImageLike(typename ImageType::Pointer input,
 130                   typename ImageType::Pointer like,
 131                   typename ImageType::PixelType BG);
 132
 133
 134   //--------------------------------------------------------------------
 135   template<class MaskImageType>
 136   typename MaskImageType::Pointer
 137   SliceBySliceRelativePosition(const MaskImageType * input,
 138                                const MaskImageType * object,
 139                                int direction,
 140                                double threshold,
 141                                std::string orientation,
 142                                bool uniqueConnectedComponent=false,
 143                                double spacing=-1,
 144                                bool notflag=false);
 145
 146   //--------------------------------------------------------------------
 147   // In a binary image, search for the point belonging to the FG that
 148   // is the most exterma in the direction 'direction' (or in the
 149   // opposite if notFlag is given).
 150   template<class ImageType>
 151   bool
 152   FindExtremaPointInAGivenDirection(const ImageType * input,
 153                                     typename ImageType::PixelType bg,
 154                                     int direction, bool opposite,
 155                                     typename ImageType::PointType & p);
 156
 157   //--------------------------------------------------------------------
 158
 159   //--------------------------------------------------------------------
 160   // Same as above but check that the found point is not more than
 161   // 'distanceMax' away from 'refPoint'
 162   template<class ImageType>
 163   bool
 164   FindExtremaPointInAGivenDirection(const ImageType * input,
 165                                     typename ImageType::PixelType bg,
 166                                     int direction, bool opposite,
 167                                     typename ImageType::PointType refPoint,
 168                                     double distanceMax,
 169                                     typename ImageType::PointType & p);
 170
 171   //--------------------------------------------------------------------
 172
 173   //--------------------------------------------------------------------
 174   template<class ImageType>
 175   typename ImageType::Pointer
 176   CropImageAlongOneAxis(typename ImageType::Pointer image,
 177                         int dim, double min, double max,
 178                         bool autoCrop = false,
 179                         typename ImageType::PixelType BG=0);
 180   template<class ImageType>
 181   typename ImageType::Pointer
 182   CropImageAbove(typename ImageType::Pointer image,
 183                  int dim, double min,
 184                  bool autoCrop = false,
 185                  typename ImageType::PixelType BG=0);
 186   template<class ImageType>
 187   typename ImageType::Pointer
 188   CropImageBelow(typename ImageType::Pointer image,
 189                  int dim, double max,
 190                  bool autoCrop = false,
 191                  typename ImageType::PixelType BG=0);
 192   //--------------------------------------------------------------------
 193
 194
 195   //--------------------------------------------------------------------
 196   template<class ImageType>
 197   void
 198   ComputeCentroids(typename ImageType::Pointer image,
 199                    typename ImageType::PixelType BG,
 200                    std::vector<typename ImageType::PointType> & centroids);
 201   //--------------------------------------------------------------------
 202
 203
 204   //--------------------------------------------------------------------
 205   template<class ImageType>
 206   void
 207   ExtractSlices(typename ImageType::Pointer image,
 208                 int dim,
 209                 std::vector< typename itk::Image<typename ImageType::PixelType,
 210                 ImageType::ImageDimension-1>::Pointer > & slices);
 211   //--------------------------------------------------------------------
 212
 213
 214   //--------------------------------------------------------------------
 215   template<class ImageType>
 216   typename ImageType::Pointer
 217   JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
 218              ImageType::ImageDimension-1>::Pointer > & slices,
 219              typename ImageType::Pointer input,
 220              int dim);
 221   //--------------------------------------------------------------------
 222
 223
 224   //--------------------------------------------------------------------
 225   // Set of tools to manage 3D points and 2D points in slices
 226   template<class ImageType>
 227   class PointsUtils
 228   {
 229     typedef typename ImageType::PointType PointType3D;
 230     typedef typename ImageType::PixelType PixelType;
 231     typedef typename ImageType::Pointer ImagePointer;
 232     typedef typename ImageType::ConstPointer ImageConstPointer;
 233     typedef itk::Image<PixelType, 2> SliceType;
 234     typedef typename SliceType::PointType PointType2D;
 235
 236     typedef std::map<int, PointType2D> MapPoint2DType;
 237     typedef std::vector<PointType3D> VectorPoint3DType;
 238   public:
 239     static void Convert2DTo3D(const PointType2D & p2D,
 240                               ImagePointer image,
 241                               const int slice,
 242                               PointType3D & p3D);
 243     static void Convert2DTo3DList(const MapPoint2DType & map,
 244                                   ImagePointer image,
 245                                   VectorPoint3DType & list);
 246   };
 247
 248   //--------------------------------------------------------------------
 249   template<class ImageType>
 250   void
 251   WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 252                        std::string filename);
 253   //--------------------------------------------------------------------
 254
 255
 256   //--------------------------------------------------------------------
 257   template<class ImageType>
 258   typename ImageType::Pointer
 259   Dilate(typename ImageType::Pointer image,
 260               double radiusInMM,
 261               typename ImageType::PixelType BG,
 262               typename ImageType::PixelType FG,
 263               bool extendSupport);
 264   template<class ImageType>
 265   typename ImageType::Pointer
 266   Dilate(typename ImageType::Pointer image,
 267               typename ImageType::SizeType radius,
 268               typename ImageType::PixelType BG,
 269               typename ImageType::PixelType FG,
 270               bool extendSupport);
 271   template<class ImageType>
 272   typename ImageType::Pointer
 273   Dilate(typename ImageType::Pointer image,
 274               typename ImageType::PointType radiusInMM,
 275               typename ImageType::PixelType BG,
 276               typename ImageType::PixelType FG,
 277               bool extendSupport);
 278   //--------------------------------------------------------------------
 279
 280   //--------------------------------------------------------------------
 281   template<class ValueType, class VectorType>
 282   void ConvertOption(std::string optionName, uint given,
 283                      ValueType * values, VectorType & p,
 284                      uint dim, bool required);
 285 #define ConvertOptionMacro(OPTIONNAME, VAR, DIM, REQUIRED)         \
 286   ConvertOption(#OPTIONNAME, OPTIONNAME##_given, OPTIONNAME##_arg, VAR, DIM, REQUIRED);
 287
 288 }
 289
 290 #include "clitkSegmentationUtils.txx"
 291
 292 #endif