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 /*
  31   According to
  32   http://answerpot.com/showthread.php?357451-Itk::SmartPointer%20-%20problem%20making%20code%20const-correct
  33   it is better to take raw pointer as argument instead of SmartPointer.
  34 */
  35
  36 namespace clitk {
  37
  38   //--------------------------------------------------------------------
  39   template<class ImageType>
  40   void ComputeBBFromImageRegion(const ImageType * image,
  41                                 typename ImageType::RegionType region,
  42                                 typename itk::BoundingBox<unsigned long,
  43                                                           ImageType::ImageDimension>::Pointer bb);
  44
  45   //--------------------------------------------------------------------
  46   template<int Dimension>
  47   void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  48                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  49                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2);
  50
  51   //--------------------------------------------------------------------
  52   template<class ImageType>
  53   void ComputeRegionFromBB(const ImageType * image,
  54                            const typename itk::BoundingBox<unsigned long,
  55                                                            ImageType::ImageDimension>::Pointer bb,
  56                            typename ImageType::RegionType & region);
  57   //--------------------------------------------------------------------
  58   template<class TInternalImageType, class TMaskInternalImageType>
  59   typename TInternalImageType::Pointer
  60   SetBackground(const TInternalImageType * input,
  61                 const TMaskInternalImageType * mask,
  62                 typename TMaskInternalImageType::PixelType maskBG,
  63                 typename TInternalImageType::PixelType outValue,
  64                 bool inPlace);
  65   //--------------------------------------------------------------------
  66
  67
  68   //--------------------------------------------------------------------
  69   template<class ImageType>
  70   int GetNumberOfConnectedComponentLabels(const ImageType * input,
  71                                           typename ImageType::PixelType BG,
  72                                           bool isFullyConnected);
  73   //--------------------------------------------------------------------
  74
  75
  76   //--------------------------------------------------------------------
  77   template<class TImageType>
  78   typename TImageType::Pointer
  79   Labelize(const TImageType * input, typename TImageType::PixelType BG,
  80            bool isFullyConnected, int minimalComponentSize);
  81   template<class TImageType>
  82   typename TImageType::Pointer
  83   LabelizeAndCountNumberOfObjects(const TImageType * input,
  84                                   typename TImageType::PixelType BG,
  85                                   bool isFullyConnected,
  86                                   int minimalComponentSize,
  87                                   int & nb);
  88   //--------------------------------------------------------------------
  89
  90
  91   //--------------------------------------------------------------------
  92   template<class ImageType>
  93   typename ImageType::Pointer
  94   RemoveLabels(const ImageType * 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(const ImageType * 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->SetBackgroundValue(BG);
 109     autoCropFilter->Update();
 110     return autoCropFilter->GetOutput();
 111   }
 112   //--------------------------------------------------------------------
 113
 114
 115   //--------------------------------------------------------------------
 116   template<class TImageType>
 117   typename TImageType::Pointer
 118   KeepLabels(const TImageType * 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(const TImageType * 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   ResizeImageLike(const ImageType * input,
 141                   const itk::ImageBase<ImageType::ImageDimension> * like,
 142                   typename ImageType::PixelType BG);
 143
 144
 145   //--------------------------------------------------------------------
 146   template<class MaskImageType>
 147   typename MaskImageType::Pointer
 148   SliceBySliceRelativePosition(const MaskImageType * input,
 149                                const MaskImageType * object,
 150                                int direction,
 151                                double threshold,
 152                                std::string orientation,
 153                                bool uniqueConnectedComponent=false,
 154                                double spacing=-1,
 155                                bool notflag=false);
 156
 157   //--------------------------------------------------------------------
 158   // In a binary image, search for the point belonging to the FG that
 159   // is the most exterma in the direction 'direction' (or in the
 160   // opposite if notFlag is given).
 161   template<class ImageType>
 162   bool
 163   FindExtremaPointInAGivenDirection(const ImageType * input,
 164                                     typename ImageType::PixelType bg,
 165                                     int direction, bool opposite,
 166                                     typename ImageType::PointType & p);
 167
 168   //--------------------------------------------------------------------
 169
 170   //--------------------------------------------------------------------
 171   // Same as above but check that the found point is not more than
 172   // 'distanceMax' away from 'refPoint'
 173   template<class ImageType>
 174   bool
 175   FindExtremaPointInAGivenDirection(const ImageType * input,
 176                                     typename ImageType::PixelType bg,
 177                                     int direction, bool opposite,
 178                                     typename ImageType::PointType refPoint,
 179                                     double distanceMax,
 180                                     typename ImageType::PointType & p);
 181
 182   //--------------------------------------------------------------------
 183
 184   //--------------------------------------------------------------------
 185   template<class ImageType>
 186   typename ImageType::Pointer
 187   CropImageAlongOneAxis(const ImageType * image,
 188                         int dim, double min, double max,
 189                         bool autoCrop = false,
 190                         typename ImageType::PixelType BG=0);
 191   template<class ImageType>
 192   typename ImageType::Pointer
 193   CropImageAbove(const ImageType * image,
 194                  int dim, double min, bool autoCrop = false,
 195                  typename ImageType::PixelType BG=0);
 196   template<class ImageType>
 197   typename ImageType::Pointer
 198   CropImageBelow(const ImageType * image,
 199                  int dim, double max,bool autoCrop = false,
 200                  typename ImageType::PixelType BG=0);
 201   //--------------------------------------------------------------------
 202
 203
 204   //--------------------------------------------------------------------
 205   template<class ImageType>
 206   void
 207   ComputeCentroids(const ImageType * image,
 208                    typename ImageType::PixelType BG,
 209                    std::vector<typename ImageType::PointType> & centroids);
 210   //--------------------------------------------------------------------
 211
 212
 213   //--------------------------------------------------------------------
 214   template<class ImageType>
 215   void
 216   ExtractSlices(const ImageType * image, int dim,
 217                 std::vector< typename itk::Image<typename ImageType::PixelType,
 218                                                  ImageType::ImageDimension-1>::Pointer > & slices);
 219   //--------------------------------------------------------------------
 220
 221
 222   //--------------------------------------------------------------------
 223   template<class ImageType>
 224   typename ImageType::Pointer
 225   JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
 226                                              ImageType::ImageDimension-1>::Pointer > & slices,
 227              const ImageType * input, 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::IndexType IndexType3D;
 238     typedef typename ImageType::PixelType PixelType;
 239     typedef typename ImageType::Pointer ImagePointer;
 240     typedef typename ImageType::ConstPointer ImageConstPointer;
 241     typedef itk::Image<PixelType, 2> SliceType;
 242     typedef typename SliceType::PointType PointType2D;
 243     typedef typename SliceType::IndexType IndexType2D;
 244
 245     typedef std::map<int, PointType2D> MapPoint2DType;
 246     typedef std::vector<PointType3D> VectorPoint3DType;
 247   public:
 248     static void Convert2DTo3D(const PointType2D & p2D,
 249                               const ImageType * image,
 250                               const int slice,
 251                               PointType3D & p3D);
 252     static void Convert2DTo3DList(const MapPoint2DType & map,
 253                                   const ImageType * image,
 254                                   VectorPoint3DType & list);
 255   };
 256
 257   //--------------------------------------------------------------------
 258   template<class ImageType>
 259   void
 260   WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 261                        std::string filename);
 262   //--------------------------------------------------------------------
 263
 264
 265   //--------------------------------------------------------------------
 266   template<class ImageType>
 267   typename ImageType::Pointer
 268   Dilate(const ImageType * image, double radiusInMM,
 269          typename ImageType::PixelType BG,
 270          typename ImageType::PixelType FG,
 271          bool extendSupport);
 272   template<class ImageType>
 273   typename ImageType::Pointer
 274   Dilate(const ImageType * image, 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(const ImageType * image, typename ImageType::PointType radiusInMM,
 281          typename ImageType::PixelType BG,
 282          typename ImageType::PixelType FG,
 283          bool extendSupport);
 284   //--------------------------------------------------------------------
 285
 286   //--------------------------------------------------------------------
 287   template<class ValueType, class VectorType>
 288   void ConvertOption(std::string optionName, uint given,
 289                      ValueType * values, VectorType & p,
 290                      uint dim, bool required);
 291 #define ConvertOptionMacro(OPTIONNAME, VAR, DIM, REQUIRED)              \
 292   ConvertOption(#OPTIONNAME, OPTIONNAME##_given, OPTIONNAME##_arg, VAR, DIM, REQUIRED);
 293   //--------------------------------------------------------------------
 294
 295   //--------------------------------------------------------------------
 296   template<class ImageType>
 297   void
 298   SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
 299                                               std::vector<typename ImageType::PointType> & lA,
 300                                               std::vector<typename ImageType::PointType> & lB,
 301                                               typename ImageType::PixelType BG,
 302                                               int mainDirection,
 303                                               double offsetToKeep);
 304   //--------------------------------------------------------------------
 305
 306
 307   //--------------------------------------------------------------------
 308   template<class ImageType>
 309   void AndNot(ImageType * input,
 310               const ImageType * object,
 311               typename ImageType::PixelType BG=0);
 312   //--------------------------------------------------------------------
 313
 314
 315   //--------------------------------------------------------------------
 316   template<class ImageType>
 317   typename ImageType::Pointer
 318   Binarize(const ImageType * input,
 319            typename ImageType::PixelType lower,
 320            typename ImageType::PixelType upper,
 321            typename ImageType::PixelType BG=0,
 322            typename ImageType::PixelType FG=1);
 323   //--------------------------------------------------------------------
 324
 325
 326   //--------------------------------------------------------------------
 327   template<class ImageType>
 328   void
 329   GetMinMaxPointPosition(const ImageType * input,
 330                          typename ImageType::PointType & min,
 331                          typename ImageType::PointType & max);
 332   //--------------------------------------------------------------------
 333
 334   //--------------------------------------------------------------------
 335   template<class ImageType>
 336   typename ImageType::PointType
 337   FindExtremaPointInAGivenLine(const ImageType * input,
 338                                int dimension, bool inverse,
 339                                typename ImageType::PointType p,
 340                                typename ImageType::PixelType BG,
 341                                double distanceMax);
 342   //--------------------------------------------------------------------
 343
 344
 345   //--------------------------------------------------------------------
 346   template<class PointType>
 347   bool
 348   IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like);
 349   //--------------------------------------------------------------------
 350
 351 }
 352
 353 #include "clitkSegmentationUtils.txx"
 354
 355 #endif