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   template<class TImageType>
  78   typename TImageType::Pointer
  79   LabelizeAndCountNumberOfObjects(const TImageType * input,
  80                                   typename TImageType::PixelType BG,
  81                                   bool isFullyConnected,
  82                                   int minimalComponentSize,
  83                                   int & nb);
  84   //--------------------------------------------------------------------
  85
  86
  87   //--------------------------------------------------------------------
  88   template<class ImageType>
  89   typename ImageType::Pointer
  90   RemoveLabels(typename ImageType::Pointer input,
  91                typename ImageType::PixelType BG,
  92                std::vector<typename ImageType::PixelType> & labelsToRemove);
  93   //--------------------------------------------------------------------
  94
  95
  96   //--------------------------------------------------------------------
  97   template<class ImageType>
  98   typename ImageType::Pointer
  99   AutoCrop(typename ImageType::Pointer input,
 100            typename ImageType::PixelType BG) {
 101     typedef clitk::AutoCropFilter<ImageType> AutoCropFilterType;
 102     typename AutoCropFilterType::Pointer autoCropFilter = AutoCropFilterType::New();
 103     autoCropFilter->SetInput(input);
 104     autoCropFilter->SetBackgroundValue(BG);
 105     autoCropFilter->Update();
 106     return autoCropFilter->GetOutput();
 107   }
 108   //--------------------------------------------------------------------
 109
 110
 111   //--------------------------------------------------------------------
 112   template<class TImageType>
 113   typename TImageType::Pointer
 114   KeepLabels(const TImageType * input,
 115              typename TImageType::PixelType BG,
 116              typename TImageType::PixelType FG,
 117              typename TImageType::PixelType firstKeep,
 118              typename TImageType::PixelType lastKeep,
 119              bool useLastKeep);
 120   //--------------------------------------------------------------------
 121
 122
 123   //--------------------------------------------------------------------
 124   template<class TImageType>
 125   typename TImageType::Pointer
 126   LabelizeAndSelectLabels(typename TImageType::Pointer input,
 127                           typename TImageType::PixelType BG,
 128                           typename TImageType::PixelType FG,
 129                           bool isFullyConnected,
 130                           int minimalComponentSize,
 131                           LabelizeParameters<typename TImageType::PixelType> * param);
 132
 133   //--------------------------------------------------------------------
 134   template<class ImageType>
 135   typename ImageType::Pointer
 136   ResizeImageLike(typename ImageType::Pointer input,
 137                   typename ImageType::Pointer like,
 138                   typename ImageType::PixelType BG);
 139
 140
 141   //--------------------------------------------------------------------
 142   template<class MaskImageType>
 143   typename MaskImageType::Pointer
 144   SliceBySliceRelativePosition(const MaskImageType * input,
 145                                const MaskImageType * object,
 146                                int direction,
 147                                double threshold,
 148                                std::string orientation,
 149                                bool uniqueConnectedComponent=false,
 150                                double spacing=-1,
 151                                bool notflag=false);
 152
 153   //--------------------------------------------------------------------
 154   // In a binary image, search for the point belonging to the FG that
 155   // is the most exterma in the direction 'direction' (or in the
 156   // opposite if notFlag is given).
 157   template<class ImageType>
 158   bool
 159   FindExtremaPointInAGivenDirection(const ImageType * input,
 160                                     typename ImageType::PixelType bg,
 161                                     int direction, bool opposite,
 162                                     typename ImageType::PointType & p);
 163
 164   //--------------------------------------------------------------------
 165
 166   //--------------------------------------------------------------------
 167   // Same as above but check that the found point is not more than
 168   // 'distanceMax' away from 'refPoint'
 169   template<class ImageType>
 170   bool
 171   FindExtremaPointInAGivenDirection(const ImageType * input,
 172                                     typename ImageType::PixelType bg,
 173                                     int direction, bool opposite,
 174                                     typename ImageType::PointType refPoint,
 175                                     double distanceMax,
 176                                     typename ImageType::PointType & p);
 177
 178   //--------------------------------------------------------------------
 179
 180   //--------------------------------------------------------------------
 181   template<class ImageType>
 182   typename ImageType::Pointer
 183   CropImageAlongOneAxis(typename ImageType::Pointer image,
 184                         int dim, double min, double max,
 185                         bool autoCrop = false,
 186                         typename ImageType::PixelType BG=0);
 187   template<class ImageType>
 188   typename ImageType::Pointer
 189   CropImageAbove(typename ImageType::Pointer image,
 190                  int dim, double min,
 191                  bool autoCrop = false,
 192                  typename ImageType::PixelType BG=0);
 193   template<class ImageType>
 194   typename ImageType::Pointer
 195   CropImageBelow(typename ImageType::Pointer image,
 196                  int dim, double max,
 197                  bool autoCrop = false,
 198                  typename ImageType::PixelType BG=0);
 199   //--------------------------------------------------------------------
 200
 201
 202   //--------------------------------------------------------------------
 203   template<class ImageType>
 204   void
 205   ComputeCentroids(typename ImageType::Pointer image,
 206                    typename ImageType::PixelType BG,
 207                    std::vector<typename ImageType::PointType> & centroids);
 208   //--------------------------------------------------------------------
 209
 210
 211   //--------------------------------------------------------------------
 212   template<class ImageType>
 213   void
 214   ExtractSlices(typename ImageType::Pointer image,
 215                 int dim,
 216                 std::vector< typename itk::Image<typename ImageType::PixelType,
 217                 ImageType::ImageDimension-1>::Pointer > & slices);
 218   //--------------------------------------------------------------------
 219
 220
 221   //--------------------------------------------------------------------
 222   template<class ImageType>
 223   typename ImageType::Pointer
 224   JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
 225              ImageType::ImageDimension-1>::Pointer > & slices,
 226              typename ImageType::Pointer input,
 227              int dim);
 228   //--------------------------------------------------------------------
 229
 230
 231   //--------------------------------------------------------------------
 232   // Set of tools to manage 3D points and 2D points in slices
 233   template<class ImageType>
 234   class PointsUtils
 235   {
 236     typedef typename ImageType::PointType PointType3D;
 237     typedef typename ImageType::PixelType PixelType;
 238     typedef typename ImageType::Pointer ImagePointer;
 239     typedef typename ImageType::ConstPointer ImageConstPointer;
 240     typedef itk::Image<PixelType, 2> SliceType;
 241     typedef typename SliceType::PointType PointType2D;
 242
 243     typedef std::map<int, PointType2D> MapPoint2DType;
 244     typedef std::vector<PointType3D> VectorPoint3DType;
 245   public:
 246     static void Convert2DTo3D(const PointType2D & p2D,
 247                               ImagePointer image,
 248                               const int slice,
 249                               PointType3D & p3D);
 250     static void Convert2DTo3DList(const MapPoint2DType & map,
 251                                   ImagePointer image,
 252                                   VectorPoint3DType & list);
 253   };
 254
 255   //--------------------------------------------------------------------
 256   template<class ImageType>
 257   void
 258   WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 259                        std::string filename);
 260   //--------------------------------------------------------------------
 261
 262
 263   //--------------------------------------------------------------------
 264   template<class ImageType>
 265   typename ImageType::Pointer
 266   Dilate(typename ImageType::Pointer image,
 267               double radiusInMM,
 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::SizeType radius,
 275               typename ImageType::PixelType BG,
 276               typename ImageType::PixelType FG,
 277               bool extendSupport);
 278   template<class ImageType>
 279   typename ImageType::Pointer
 280   Dilate(typename ImageType::Pointer image,
 281               typename ImageType::PointType radiusInMM,
 282               typename ImageType::PixelType BG,
 283               typename ImageType::PixelType FG,
 284               bool extendSupport);
 285   //--------------------------------------------------------------------
 286
 287   //--------------------------------------------------------------------
 288   template<class ValueType, class VectorType>
 289   void ConvertOption(std::string optionName, uint given,
 290                      ValueType * values, VectorType & p,
 291                      uint dim, bool required);
 292 #define ConvertOptionMacro(OPTIONNAME, VAR, DIM, REQUIRED)         \
 293   ConvertOption(#OPTIONNAME, OPTIONNAME##_given, OPTIONNAME##_arg, VAR, DIM, REQUIRED);
 294   //--------------------------------------------------------------------
 295
 296   //--------------------------------------------------------------------
 297   template<class ImageType>
 298   void
 299   SliceBySliceSetBackgroundFromLineSeparation(typename ImageType::Pointer input,
 300                                               std::vector<typename ImageType::PointType> & lA,
 301                                               std::vector<typename ImageType::PointType> & lB,
 302                                               typename ImageType::PixelType BG,
 303                                               int mainDirection,
 304                                               double offsetToKeep);
 305
 306
 307 }
 308
 309 #include "clitkSegmentationUtils.txx"
 310
 311 #endif