itk/clitkSegmentationUtils.txx

   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://www.centreleonberard.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 // clitk
  20 #include "clitkSetBackgroundImageFilter.h"
  21 #include "clitkSliceBySliceRelativePositionFilter.h"
  22 #include "clitkCropLikeImageFilter.h"
  23 #include "clitkMemoryUsage.h"
  24
  25 // itk
  26 #include <itkConnectedComponentImageFilter.h>
  27 #include <itkRelabelComponentImageFilter.h>
  28 #include <itkBinaryThresholdImageFilter.h>
  29 #include <itkPasteImageFilter.h>
  30 #include <itkStatisticsLabelMapFilter.h>
  31 #include <itkBinaryBallStructuringElement.h>
  32 #include <itkBinaryDilateImageFilter.h>
  33 #include <itkConstantPadImageFilter.h>
  34 #include <itkImageSliceIteratorWithIndex.h>
  35 #include <itkBinaryMorphologicalOpeningImageFilter.h>
  36 #include <itkImageDuplicator.h>
  37 #include <itkSignedMaurerDistanceMapImageFilter.h>
  38
  39 namespace clitk {
  40
  41   //--------------------------------------------------------------------
  42   template<class ImageType, class TMaskImageType>
  43   typename ImageType::Pointer
  44   SetBackground(const ImageType * input,
  45                 const TMaskImageType * mask,
  46                 typename TMaskImageType::PixelType maskBG,
  47                 typename ImageType::PixelType outValue,
  48                 bool inPlace) {
  49     typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
  50       SetBackgroundImageFilterType;
  51     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
  52       = SetBackgroundImageFilterType::New();
  53     //  if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
  54     setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
  55     setBackgroundFilter->SetInput(input);
  56     setBackgroundFilter->SetInput2(mask);
  57     setBackgroundFilter->SetMaskValue(maskBG);
  58     setBackgroundFilter->SetOutsideValue(outValue);
  59     setBackgroundFilter->Update();
  60     return setBackgroundFilter->GetOutput();
  61   }
  62   //--------------------------------------------------------------------
  63
  64
  65   //--------------------------------------------------------------------
  66   template<class ImageType>
  67   int GetNumberOfConnectedComponentLabels(const ImageType * input,
  68                                           typename ImageType::PixelType BG,
  69                                           bool isFullyConnected) {
  70     // Connected Component label
  71     typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
  72     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
  73     connectFilter->SetInput(input);
  74     connectFilter->SetBackgroundValue(BG);
  75     connectFilter->SetFullyConnected(isFullyConnected);
  76     connectFilter->Update();
  77
  78     // Return result
  79     return connectFilter->GetObjectCount();
  80   }
  81   //--------------------------------------------------------------------
  82
  83   //--------------------------------------------------------------------
  84   /*
  85     Warning : in this cas, we consider outputType like inputType, not
  86     InternalImageType. Be sure it fits.
  87   */
  88   template<class ImageType>
  89   typename ImageType::Pointer
  90   Labelize(const ImageType * input,
  91            typename ImageType::PixelType BG,
  92            bool isFullyConnected,
  93            int minimalComponentSize) {
  94     // InternalImageType for storing large number of component
  95     typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
  96
  97     // Connected Component label
  98     typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
  99     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 100     //  connectFilter->ReleaseDataFlagOn();
 101     connectFilter->SetInput(input);
 102     connectFilter->SetBackgroundValue(BG);
 103     connectFilter->SetFullyConnected(isFullyConnected);
 104
 105     // Sort by size and remove too small area.
 106     typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 107     typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 108     //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 109     relabelFilter->SetInput(connectFilter->GetOutput());
 110     relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 111     relabelFilter->Update();
 112
 113     // Return result
 114     typename ImageType::Pointer output = relabelFilter->GetOutput();
 115     return output;
 116   }
 117   //--------------------------------------------------------------------
 118
 119
 120   //--------------------------------------------------------------------
 121   /*
 122     Warning : in this cas, we consider outputType like inputType, not
 123     InternalImageType. Be sure it fits.
 124   */
 125   template<class ImageType>
 126   typename ImageType::Pointer
 127   LabelizeAndCountNumberOfObjects(const ImageType * input,
 128                                   typename ImageType::PixelType BG,
 129                                   bool isFullyConnected,
 130                                   int minimalComponentSize,
 131                                   int & nb) {
 132     // InternalImageType for storing large number of component
 133     typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 134
 135     // Connected Component label
 136     typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 137     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 138     //  connectFilter->ReleaseDataFlagOn();
 139     connectFilter->SetInput(input);
 140     connectFilter->SetBackgroundValue(BG);
 141     connectFilter->SetFullyConnected(isFullyConnected);
 142
 143     // Sort by size and remove too small area.
 144     typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 145     typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 146     //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 147     relabelFilter->SetInput(connectFilter->GetOutput());
 148     relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 149     relabelFilter->Update();
 150
 151     nb = relabelFilter->GetNumberOfObjects();
 152     // DD(relabelFilter->GetOriginalNumberOfObjects());
 153     // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
 154
 155     // Return result
 156     typename ImageType::Pointer output = relabelFilter->GetOutput();
 157     return output;
 158   }
 159   //--------------------------------------------------------------------
 160
 161
 162
 163   //--------------------------------------------------------------------
 164   template<class ImageType>
 165   typename ImageType::Pointer
 166   RemoveLabels(const ImageType * input,
 167                typename ImageType::PixelType BG,
 168                std::vector<typename ImageType::PixelType> & labelsToRemove) {
 169     assert(labelsToRemove.size() != 0);
 170     typename ImageType::Pointer working_image;// = input;
 171     for (unsigned int i=0; i <labelsToRemove.size(); i++) {
 172       typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
 173       typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 174       setBackgroundFilter->SetInput(input);
 175       setBackgroundFilter->SetInput2(input);
 176       setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
 177       setBackgroundFilter->SetOutsideValue(BG);
 178       setBackgroundFilter->Update();
 179       working_image = setBackgroundFilter->GetOutput();
 180     }
 181     return working_image;
 182   }
 183   //--------------------------------------------------------------------
 184
 185
 186   //--------------------------------------------------------------------
 187   template<class ImageType>
 188   typename ImageType::Pointer
 189   KeepLabels(const ImageType * input,
 190              typename ImageType::PixelType BG,
 191              typename ImageType::PixelType FG,
 192              typename ImageType::PixelType firstKeep,
 193              typename ImageType::PixelType lastKeep,
 194              bool useLastKeep) {
 195     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
 196     typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 197     binarizeFilter->SetInput(input);
 198     binarizeFilter->SetLowerThreshold(firstKeep);
 199     if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 200     binarizeFilter->SetInsideValue(FG);
 201     binarizeFilter->SetOutsideValue(BG);
 202     binarizeFilter->Update();
 203     return binarizeFilter->GetOutput();
 204   }
 205   //--------------------------------------------------------------------
 206
 207
 208   //--------------------------------------------------------------------
 209   template<class ImageType>
 210   typename ImageType::Pointer
 211   LabelizeAndSelectLabels(const ImageType * input,
 212                           typename ImageType::PixelType BG,
 213                           typename ImageType::PixelType FG,
 214                           bool isFullyConnected,
 215                           int minimalComponentSize,
 216                           LabelizeParameters<typename ImageType::PixelType> * param)
 217   {
 218     typename ImageType::Pointer working_image;
 219     working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
 220     if (param->GetLabelsToRemove().size() != 0)
 221       working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
 222     working_image = KeepLabels<ImageType>(working_image,
 223                                           BG, FG,
 224                                           param->GetFirstKeep(),
 225                                           param->GetLastKeep(),
 226                                           param->GetUseLastKeep());
 227     return working_image;
 228   }
 229   //--------------------------------------------------------------------
 230
 231
 232   //--------------------------------------------------------------------
 233   template<class MaskImageType>
 234   typename MaskImageType::Pointer
 235   SliceBySliceRelativePosition(const MaskImageType * input,
 236                                const MaskImageType * object,
 237                                int direction,
 238                                double threshold,
 239                                std::string orientation,
 240                                bool uniqueConnectedComponent,
 241                                double spacing,
 242                                bool autocropFlag,
 243                                bool singleObjectCCL)
 244   {
 245     typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 246     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 247     sliceRelPosFilter->VerboseStepFlagOff();
 248     sliceRelPosFilter->WriteStepFlagOff();
 249     sliceRelPosFilter->SetInput(input);
 250     sliceRelPosFilter->SetInputObject(object);
 251     sliceRelPosFilter->SetDirection(direction);
 252     sliceRelPosFilter->SetFuzzyThreshold(threshold);
 253     sliceRelPosFilter->AddOrientationTypeString(orientation);
 254     sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
 255     sliceRelPosFilter->SetIntermediateSpacing(spacing);
 256     sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
 257     sliceRelPosFilter->ObjectCCLSelectionFlagOff();
 258     sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
 259     //    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 260     sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
 261     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 262     sliceRelPosFilter->Update();
 263     return sliceRelPosFilter->GetOutput();
 264   }
 265   //--------------------------------------------------------------------
 266
 267
 268   //--------------------------------------------------------------------
 269   template<class MaskImageType>
 270   typename MaskImageType::Pointer
 271   SliceBySliceRelativePosition(const MaskImageType * input,
 272                                const MaskImageType * object,
 273                                int direction,
 274                                double threshold,
 275                                double angle,
 276                                bool inverseflag,
 277                                bool uniqueConnectedComponent,
 278                                double spacing,
 279                                bool autocropFlag,
 280                                bool singleObjectCCL)
 281   {
 282     typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 283     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 284     sliceRelPosFilter->VerboseStepFlagOff();
 285     sliceRelPosFilter->WriteStepFlagOff();
 286     sliceRelPosFilter->SetInput(input);
 287     sliceRelPosFilter->SetInputObject(object);
 288     sliceRelPosFilter->SetDirection(direction);
 289     sliceRelPosFilter->SetFuzzyThreshold(threshold);
 290     //    sliceRelPosFilter->AddOrientationTypeString(orientation);
 291     sliceRelPosFilter->AddAngles(angle, 0.0);
 292     sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
 293     sliceRelPosFilter->SetIntermediateSpacing(spacing);
 294     sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
 295     sliceRelPosFilter->ObjectCCLSelectionFlagOff();
 296     sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
 297     sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 298     sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
 299     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 300     sliceRelPosFilter->Update();
 301     return sliceRelPosFilter->GetOutput();
 302   }
 303   //--------------------------------------------------------------------
 304
 305
 306   //--------------------------------------------------------------------
 307   template<class ImageType>
 308   bool
 309   FindExtremaPointInAGivenDirection(const ImageType * input,
 310                                     typename ImageType::PixelType bg,
 311                                     int direction, bool opposite,
 312                                     typename ImageType::PointType & point)
 313   {
 314     typename ImageType::PointType dummy;
 315     return FindExtremaPointInAGivenDirection(input, bg, direction,
 316                                              opposite, dummy, 0, point);
 317   }
 318   //--------------------------------------------------------------------
 319
 320
 321   //--------------------------------------------------------------------
 322   template<class ImageType>
 323   bool
 324   FindExtremaPointInAGivenDirection(const ImageType * input,
 325                                     typename ImageType::PixelType bg,
 326                                     int direction, bool opposite,
 327                                     typename ImageType::PointType refpoint,
 328                                     double distanceMax,
 329                                     typename ImageType::PointType & point)
 330   {
 331     /*
 332       loop over input pixels, store the index in the fg that is max
 333       according to the given direction.
 334     */
 335     typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
 336     IteratorType iter(input, input->GetLargestPossibleRegion());
 337     iter.GoToBegin();
 338     typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
 339     if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
 340     bool found=false;
 341     while (!iter.IsAtEnd()) {
 342       if (iter.Get() != bg) {
 343         bool test = iter.GetIndex()[direction] >  max[direction];
 344         if (opposite) test = !test;
 345         if (test) {
 346           typename ImageType::PointType p;
 347           input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
 348           if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
 349             max = iter.GetIndex();
 350             found = true;
 351           }
 352         }
 353       }
 354       ++iter;
 355     }
 356     if (!found) return false;
 357     input->TransformIndexToPhysicalPoint(max, point);
 358     return true;
 359   }
 360   //--------------------------------------------------------------------
 361
 362
 363   //--------------------------------------------------------------------
 364   template<class ImageType>
 365   typename ImageType::Pointer
 366   CropImageRemoveGreaterThan(const ImageType * image,
 367                  int dim, double min, bool autoCrop,
 368                  typename ImageType::PixelType BG)
 369   {
 370     return CropImageAlongOneAxis<ImageType>(image, dim,
 371                                             image->GetOrigin()[dim],
 372                                             min,
 373                                             autoCrop, BG);
 374   }
 375   //--------------------------------------------------------------------
 376
 377
 378   //--------------------------------------------------------------------
 379   template<class ImageType>
 380   typename ImageType::Pointer
 381   CropImageRemoveLowerThan(const ImageType * image,
 382                  int dim, double max, bool autoCrop,
 383                  typename ImageType::PixelType BG)
 384   {
 385     typename ImageType::PointType p;
 386     image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
 387                                          image->GetLargestPossibleRegion().GetSize(), p);
 388     return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
 389   }
 390   //--------------------------------------------------------------------
 391
 392
 393   //--------------------------------------------------------------------
 394   template<class ImageType>
 395   typename ImageType::Pointer
 396   CropImageAlongOneAxis(const ImageType * image,
 397                         int dim, double min, double max,
 398                         bool autoCrop, typename ImageType::PixelType BG)
 399   {
 400     // Compute region size
 401     typename ImageType::RegionType region;
 402     typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 403     typename ImageType::PointType p = image->GetOrigin();
 404     if (min > p[dim]) p[dim] = min; // Check if not outside the image
 405     typename ImageType::IndexType start;
 406     image->TransformPhysicalPointToIndex(p, start);
 407     double m = image->GetOrigin()[dim] + size[dim]*image->GetSpacing()[dim];
 408     if (max > m) p[dim] = m; // Check if not outside the image
 409     else p[dim] = max;
 410     typename ImageType::IndexType end;
 411     image->TransformPhysicalPointToIndex(p, end);
 412     size[dim] = abs(end[dim]-start[dim]);
 413     region.SetIndex(start);
 414     region.SetSize(size);
 415
 416     // Perform Crop
 417     typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 418     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 419     cropFilter->SetInput(image);
 420     cropFilter->SetRegionOfInterest(region);
 421     cropFilter->Update();
 422     typename ImageType::Pointer result = cropFilter->GetOutput();
 423
 424     // Auto Crop
 425     if (autoCrop) {
 426       result = AutoCrop<ImageType>(result, BG);
 427     }
 428     return result;
 429   }
 430   //--------------------------------------------------------------------
 431
 432
 433   //--------------------------------------------------------------------
 434   template<class ImageType>
 435   void
 436   ComputeCentroids(const ImageType * image,
 437                    typename ImageType::PixelType BG,
 438                    std::vector<typename ImageType::PointType> & centroids)
 439   {
 440     typedef long LabelType;
 441     static const unsigned int Dim = ImageType::ImageDimension;
 442     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 443     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 444     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 445     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 446     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 447     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 448     imageToLabelFilter->SetBackgroundValue(BG);
 449     imageToLabelFilter->SetInput(image);
 450     statFilter->SetInput(imageToLabelFilter->GetOutput());
 451     statFilter->Update();
 452     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 453
 454     centroids.clear();
 455     typename ImageType::PointType dummy;
 456     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG
 457     //DS FIXME (not useful ! to change ..)
 458     for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
 459       int label = labelMap->GetLabels()[i];
 460       centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
 461     }
 462   }
 463   //--------------------------------------------------------------------
 464
 465
 466   //--------------------------------------------------------------------
 467   template<class ImageType, class LabelType>
 468   typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
 469   ComputeLabelMap(const ImageType * image,
 470                   typename ImageType::PixelType BG,
 471                   bool computePerimeterFlag)
 472   {
 473     static const unsigned int Dim = ImageType::ImageDimension;
 474     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 475     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 476     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 477     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 478     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 479     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 480     imageToLabelFilter->SetBackgroundValue(BG);
 481     imageToLabelFilter->SetInput(image);
 482     statFilter->SetInput(imageToLabelFilter->GetOutput());
 483     statFilter->SetComputePerimeter(computePerimeterFlag);
 484     statFilter->Update();
 485     return statFilter->GetOutput();
 486   }
 487   //--------------------------------------------------------------------
 488
 489
 490   //--------------------------------------------------------------------
 491   template<class ImageType>
 492   void
 493   ComputeCentroids2(const ImageType * image,
 494                    typename ImageType::PixelType BG,
 495                    std::vector<typename ImageType::PointType> & centroids)
 496   {
 497     typedef long LabelType;
 498     static const unsigned int Dim = ImageType::ImageDimension;
 499     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 500     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 501     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 502     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 503     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 504     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 505     imageToLabelFilter->SetBackgroundValue(BG);
 506     imageToLabelFilter->SetInput(image);
 507     statFilter->SetInput(imageToLabelFilter->GetOutput());
 508     statFilter->Update();
 509     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 510
 511     centroids.clear();
 512     typename ImageType::PointType dummy;
 513     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 514     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 515       centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 516     }
 517
 518     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 519       DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
 520       DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
 521       DD(labelMap->GetLabelObject(i)->GetRoundness ());
 522
 523       // search for the point on the boundary alog PA
 524
 525     }
 526
 527   }
 528   //--------------------------------------------------------------------
 529
 530
 531   //--------------------------------------------------------------------
 532   template<class ImageType>
 533   void
 534   PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
 535                                         const ImageType * image,
 536                                         const int slice,
 537                                         PointType3D & p3D)
 538   {
 539     IndexType3D index3D;
 540     index3D[0] = index3D[1] = 0;
 541     index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
 542     image->TransformIndexToPhysicalPoint(index3D, p3D);
 543     p3D[0] = p2D[0];
 544     p3D[1] = p2D[1];
 545     //  p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 546     //    + image->GetOrigin()[2];
 547   }
 548   //--------------------------------------------------------------------
 549
 550
 551   //--------------------------------------------------------------------
 552   template<class ImageType>
 553   void
 554   PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
 555                                             const ImageType * image,
 556                                             VectorPoint3DType & list)
 557   {
 558     typename MapPoint2DType::const_iterator iter = map.begin();
 559     while (iter != map.end()) {
 560       PointType3D p;
 561       Convert2DTo3D(iter->second, image, iter->first, p);
 562       list.push_back(p);
 563       ++iter;
 564     }
 565   }
 566   //--------------------------------------------------------------------
 567
 568
 569   //--------------------------------------------------------------------
 570   template<class ImageType>
 571   void
 572   PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D,
 573                                                 int slice,
 574                                                 const ImageType * image,
 575                                                 VectorPoint3DType & list)
 576   {
 577     for(uint i=0; i<p2D.size(); i++) {
 578       PointType3D p;
 579       Convert2DTo3D(p2D[i], image, slice, p);
 580       list.push_back(p);
 581     }
 582   }
 583   //--------------------------------------------------------------------
 584
 585
 586   //--------------------------------------------------------------------
 587   template<class ImageType>
 588   void
 589   WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 590                        std::string filename)
 591   {
 592     std::ofstream os;
 593     openFileForWriting(os, filename);
 594     os << "LANDMARKS1" << std::endl;
 595     for(uint i=0; i<points.size(); i++) {
 596       const typename ImageType::PointType & p = points[i];
 597       // Write it in the file
 598       os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 599     }
 600     os.close();
 601   }
 602   //--------------------------------------------------------------------
 603
 604
 605   //--------------------------------------------------------------------
 606   template<class ImageType>
 607   typename ImageType::Pointer
 608   Dilate(const ImageType * image, double radiusInMM,
 609          typename ImageType::PixelType BG,
 610          typename ImageType::PixelType FG,
 611          bool extendSupport)
 612   {
 613     typename ImageType::SizeType r;
 614     for(uint i=0; i<ImageType::ImageDimension; i++)
 615       r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 616     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 617   }
 618   //--------------------------------------------------------------------
 619
 620
 621   //--------------------------------------------------------------------
 622   template<class ImageType>
 623   typename ImageType::Pointer
 624   Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
 625          typename ImageType::PixelType BG,
 626          typename ImageType::PixelType FG,
 627          bool extendSupport)
 628   {
 629     typename ImageType::SizeType r;
 630     for(uint i=0; i<ImageType::ImageDimension; i++)
 631       r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 632     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 633   }
 634   //--------------------------------------------------------------------
 635
 636
 637   //--------------------------------------------------------------------
 638   template<class ImageType>
 639   typename ImageType::Pointer
 640   Dilate(const ImageType * image, typename ImageType::SizeType radius,
 641          typename ImageType::PixelType BG,
 642          typename ImageType::PixelType FG,
 643          bool extendSupport)
 644   {
 645     // Create kernel for dilatation
 646     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 647                                               ImageType::ImageDimension> KernelType;
 648     KernelType structuringElement;
 649     structuringElement.SetRadius(radius);
 650     structuringElement.CreateStructuringElement();
 651
 652     typename ImageType::Pointer output;
 653     if (extendSupport) {
 654       typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 655       typename PadFilterType::Pointer padFilter = PadFilterType::New();
 656       padFilter->SetInput(image);
 657       typename ImageType::SizeType lower;
 658       typename ImageType::SizeType upper;
 659       for(uint i=0; i<3; i++) {
 660         lower[i] = upper[i] = 2*(radius[i]+1);
 661       }
 662       padFilter->SetPadLowerBound(lower);
 663       padFilter->SetPadUpperBound(upper);
 664       padFilter->Update();
 665       output = padFilter->GetOutput();
 666     }
 667
 668     // Dilate  filter
 669     typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 670     typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 671     dilateFilter->SetBackgroundValue(BG);
 672     dilateFilter->SetForegroundValue(FG);
 673     dilateFilter->SetBoundaryToForeground(false);
 674     dilateFilter->SetKernel(structuringElement);
 675     if (extendSupport) dilateFilter->SetInput(output);
 676     else dilateFilter->SetInput(image);
 677     dilateFilter->Update();
 678     return dilateFilter->GetOutput();
 679   }
 680   //--------------------------------------------------------------------
 681
 682
 683   //--------------------------------------------------------------------
 684   template<class ImageType>
 685   typename ImageType::Pointer
 686   Opening(const ImageType * image, typename ImageType::SizeType radius,
 687          typename ImageType::PixelType BG,
 688          typename ImageType::PixelType FG)
 689   {
 690     // Kernel
 691     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 692                                               ImageType::ImageDimension> KernelType;
 693     KernelType structuringElement;
 694     structuringElement.SetRadius(radius);
 695     structuringElement.CreateStructuringElement();
 696
 697     // Filter
 698     typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
 699     typename OpeningFilterType::Pointer open = OpeningFilterType::New();
 700     open->SetInput(image);
 701     open->SetBackgroundValue(BG);
 702     open->SetForegroundValue(FG);
 703     open->SetKernel(structuringElement);
 704     open->Update();
 705     return open->GetOutput();
 706   }
 707   //--------------------------------------------------------------------
 708
 709
 710
 711   //--------------------------------------------------------------------
 712   template<class ValueType, class VectorType>
 713   void ConvertOption(std::string optionName, uint given,
 714                      ValueType * values, VectorType & p,
 715                      uint dim, bool required)
 716   {
 717     if (required && (given == 0)) {
 718       clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 719                           << dim << " values.");
 720     }
 721     if (given == 1) {
 722       for(uint i=0; i<dim; i++) p[i] = values[0];
 723       return;
 724     }
 725     if (given == dim) {
 726       for(uint i=0; i<dim; i++) p[i] = values[i];
 727       return;
 728     }
 729     if (given == 0) return;
 730     clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 731                         << dim << " values.");
 732   }
 733   //--------------------------------------------------------------------
 734
 735
 736   //--------------------------------------------------------------------
 737   /*
 738     http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
 739     Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
 740     (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
 741     This will equal zero if the point C is on the line formed by
 742     points A and B, and will have a different sign depending on the
 743     side. Which side this is depends on the orientation of your (x,y)
 744     coordinates, but you can plug test values for A,B and C into this
 745     formula to determine whether negative values are to the left or to
 746     the right.
 747     => to accelerate, start with formula, when change sign -> stop and fill
 748
 749     offsetToKeep = is used to determine which side of the line we
 750     keep. The point along the mainDirection but 'offsetToKeep' mm away
 751     is kept.
 752
 753   */
 754   template<class ImageType>
 755   void
 756   SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
 757                                               std::vector<typename ImageType::PointType> & lA,
 758                                               std::vector<typename ImageType::PointType> & lB,
 759                                               typename ImageType::PixelType BG,
 760                                               int mainDirection,
 761                                               double offsetToKeep)
 762   {
 763     assert((mainDirection==0) || (mainDirection==1));
 764     typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
 765     SliceIteratorType siter = SliceIteratorType(input,
 766                                                 input->GetLargestPossibleRegion());
 767     siter.SetFirstDirection(0);
 768     siter.SetSecondDirection(1);
 769     siter.GoToBegin();
 770     uint i=0;
 771     typename ImageType::PointType A;
 772     typename ImageType::PointType B;
 773     typename ImageType::PointType C;
 774     assert(lA.size() == lB.size());
 775     while ((i<lA.size()) && (!siter.IsAtEnd())) {
 776       // Check that the current slice correspond to the current point
 777       input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 778       if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
 779       }
 780       else {
 781         // Define A,B,C points
 782         A = lA[i];
 783         B = lB[i];
 784         C = A;
 785
 786         // Check that the line is not a point (A=B)
 787         bool p = (A[0] == B[0]) && (A[1] == B[1]);
 788
 789         if (!p) {
 790           C[mainDirection] += offsetToKeep; // I know I must keep this point
 791           double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 792           bool isPositive = s<0;
 793           while (!siter.IsAtEndOfSlice()) {
 794             while (!siter.IsAtEndOfLine()) {
 795               // Very slow, I know ... but image should be very small
 796               input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 797               double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 798               if (s == 0) siter.Set(BG); // on the line, we decide to remove
 799               if (isPositive) {
 800                 if (s > 0) siter.Set(BG);
 801               }
 802               else {
 803                 if (s < 0) siter.Set(BG);
 804               }
 805               ++siter;
 806             }
 807             siter.NextLine();
 808           } // end loop slice
 809         }
 810
 811         ++i;
 812       } // End of current slice
 813       siter.NextSlice();
 814     }
 815   }
 816   //--------------------------------------------------------------------
 817
 818
 819   //--------------------------------------------------------------------
 820   template<class ImageType>
 821   void
 822   AndNot(ImageType * input,
 823          const ImageType * object,
 824          typename ImageType::PixelType BG)
 825   {
 826     typename ImageType::Pointer o;
 827     bool resized=false;
 828     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 829       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 830       resized = true;
 831     }
 832
 833     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 834     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 835     boolFilter->InPlaceOn();
 836     boolFilter->SetInput1(input);
 837     if (resized) boolFilter->SetInput2(o);
 838     else boolFilter->SetInput2(object);
 839     boolFilter->SetBackgroundValue1(BG);
 840     boolFilter->SetBackgroundValue2(BG);
 841     boolFilter->SetOperationType(BoolFilterType::AndNot);
 842     boolFilter->Update();
 843   }
 844   //--------------------------------------------------------------------
 845
 846
 847   //--------------------------------------------------------------------
 848   template<class ImageType>
 849   void
 850   And(ImageType * input,
 851       const ImageType * object,
 852       typename ImageType::PixelType BG)
 853   {
 854     typename ImageType::Pointer o;
 855     bool resized=false;
 856     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 857       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 858       resized = true;
 859     }
 860
 861     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 862     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 863     boolFilter->InPlaceOn();
 864     boolFilter->SetInput1(input);
 865     if (resized) boolFilter->SetInput2(o);
 866     else boolFilter->SetInput2(object);
 867     boolFilter->SetBackgroundValue1(BG);
 868     boolFilter->SetBackgroundValue2(BG);
 869     boolFilter->SetOperationType(BoolFilterType::And);
 870     boolFilter->Update();
 871   }
 872   //--------------------------------------------------------------------
 873
 874
 875   //--------------------------------------------------------------------
 876   template<class ImageType>
 877   void
 878   Or(ImageType * input,
 879      const ImageType * object,
 880      typename ImageType::PixelType BG)
 881   {
 882     typename ImageType::Pointer o;
 883     bool resized=false;
 884     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 885       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 886       resized = true;
 887     }
 888
 889     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 890     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 891     boolFilter->InPlaceOn();
 892     boolFilter->SetInput1(input);
 893     if (resized) boolFilter->SetInput2(o);
 894     else boolFilter->SetInput2(object);
 895     boolFilter->SetBackgroundValue1(BG);
 896     boolFilter->SetBackgroundValue2(BG);
 897     boolFilter->SetOperationType(BoolFilterType::Or);
 898     boolFilter->Update();
 899   }
 900   //--------------------------------------------------------------------
 901
 902
 903   //--------------------------------------------------------------------
 904   template<class ImageType>
 905   typename ImageType::Pointer
 906   Binarize(const ImageType * input,
 907            typename ImageType::PixelType lower,
 908            typename ImageType::PixelType upper,
 909            typename ImageType::PixelType BG,
 910            typename ImageType::PixelType FG)
 911   {
 912     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
 913     typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
 914     binarizeFilter->SetInput(input);
 915     binarizeFilter->InPlaceOff();
 916     binarizeFilter->SetLowerThreshold(lower);
 917     binarizeFilter->SetUpperThreshold(upper);
 918     binarizeFilter->SetInsideValue(FG);
 919     binarizeFilter->SetOutsideValue(BG);
 920     binarizeFilter->Update();
 921     return binarizeFilter->GetOutput();
 922   }
 923   //--------------------------------------------------------------------
 924
 925
 926   //--------------------------------------------------------------------
 927   template<class ImageType>
 928   void
 929   GetMinMaxPointPosition(const ImageType * input,
 930                          typename ImageType::PointType & min,
 931                          typename ImageType::PointType & max)
 932   {
 933     typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
 934     input->TransformIndexToPhysicalPoint(index, min);
 935     index = index+input->GetLargestPossibleRegion().GetSize();
 936     input->TransformIndexToPhysicalPoint(index, max);
 937   }
 938   //--------------------------------------------------------------------
 939
 940
 941   //--------------------------------------------------------------------
 942   template<class ImageType>
 943   typename ImageType::PointType
 944   FindExtremaPointInAGivenLine(const ImageType * input,
 945                                int dimension,
 946                                bool inverse,
 947                                typename ImageType::PointType p,
 948                                typename ImageType::PixelType BG,
 949                                double distanceMax)
 950   {
 951     // Which direction ?  Increasing or decreasing.
 952     int d=1;
 953     if (inverse) d=-1;
 954
 955     // Transform to pixel index
 956     typename ImageType::IndexType index;
 957     input->TransformPhysicalPointToIndex(p, index);
 958
 959     // Loop while inside the mask;
 960     while (input->GetPixel(index) != BG) {
 961       index[dimension] += d;
 962     }
 963
 964     // Transform back to Physical Units
 965     typename ImageType::PointType result;
 966     input->TransformIndexToPhysicalPoint(index, result);
 967
 968     // Check that is is not too far away
 969     double distance = p.EuclideanDistanceTo(result);
 970     if (distance > distanceMax) {
 971       result = p; // Get back to initial value
 972     }
 973
 974     return result;
 975   }
 976   //--------------------------------------------------------------------
 977
 978
 979   //--------------------------------------------------------------------
 980   template<class PointType>
 981   bool
 982   IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
 983   {
 984     // Look at the position of point 'like' according to the AB line
 985     double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
 986     bool negative = s<0;
 987
 988     // Look the C position
 989     s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 990
 991     if (negative && (s<=0)) return true;
 992     if (!negative && (s>=0)) return true;
 993     return false;
 994   }
 995   //--------------------------------------------------------------------
 996
 997
 998   //--------------------------------------------------------------------
 999   /* Consider an input object, for each slice, find the extrema
1000      position according to a given direction and build a line segment
1001      passing throught this point in a given direction.  Output is a
1002      vector of line (from point A to B), for each slice;
1003    */
1004   template<class ImageType>
1005   void
1006   SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
1007                                                          typename ImageType::PixelType BG,
1008                                                          int sliceDimension,
1009                                                          int extremaDirection,
1010                                                          bool extremaOppositeFlag,
1011                                                          int lineDirection,
1012                                                          double margin,
1013                                                          std::vector<typename ImageType::PointType> & A,
1014                                                          std::vector<typename ImageType::PointType> & B)
1015   {
1016     // Type of a slice
1017     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1018
1019     // Build the list of slices
1020     std::vector<typename SliceType::Pointer> slices;
1021     clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
1022
1023     // Build the list of 2D points
1024     std::map<int, typename SliceType::PointType> position2D;
1025     for(uint i=0; i<slices.size(); i++) {
1026       typename SliceType::PointType p;
1027       bool found =
1028         clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
1029                                                             extremaDirection, extremaOppositeFlag, p);
1030       if (found) {
1031         position2D[i] = p;
1032       }
1033     }
1034
1035     // Convert 2D points in slice into 3D points
1036     clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
1037
1038     // Create additional point just right to the previous ones, on the
1039     // given lineDirection, in order to create a horizontal/vertical line.
1040     for(uint i=0; i<A.size(); i++) {
1041       typename ImageType::PointType p = A[i];
1042       p[lineDirection] += 10;
1043       B.push_back(p);
1044       // Margins ?
1045       A[i][extremaDirection] += margin;
1046       B[i][extremaDirection] += margin;
1047     }
1048
1049   }
1050   //--------------------------------------------------------------------
1051
1052
1053   //--------------------------------------------------------------------
1054   template<class ImageType>
1055   typename ImageType::Pointer
1056   SliceBySliceKeepMainCCL(const ImageType * input,
1057                           typename ImageType::PixelType BG,
1058                           typename ImageType::PixelType FG)  {
1059
1060     // Extract slices
1061     const int d = ImageType::ImageDimension-1;
1062     typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
1063     std::vector<typename SliceType::Pointer> slices;
1064     clitk::ExtractSlices<ImageType>(input, d, slices);
1065
1066     // Labelize and keep the main one
1067     std::vector<typename SliceType::Pointer> o;
1068     for(uint i=0; i<slices.size(); i++) {
1069       o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
1070       o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
1071     }
1072
1073     // Join slices
1074     typename ImageType::Pointer output;
1075     output = clitk::JoinSlices<ImageType>(o, input, d);
1076     return output;
1077   }
1078   //--------------------------------------------------------------------
1079
1080
1081   //--------------------------------------------------------------------
1082   template<class ImageType>
1083   typename ImageType::Pointer
1084   Clone(const ImageType * input) {
1085     typedef itk::ImageDuplicator<ImageType> DuplicatorType;
1086     typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
1087     duplicator->SetInputImage(input);
1088     duplicator->Update();
1089     return duplicator->GetOutput();
1090   }
1091   //--------------------------------------------------------------------
1092
1093
1094   //--------------------------------------------------------------------
1095   /* Consider an input object, start at A, for each slice (dim1):
1096      - compute the intersection between the AB line and the current slice
1097      - remove what is at lower or greater according to dim2 of this point
1098      - stop at B
1099   */
1100   template<class ImageType>
1101   typename ImageType::Pointer
1102   SliceBySliceSetBackgroundFromSingleLine(const ImageType * input,
1103                                           typename ImageType::PixelType BG,
1104                                           typename ImageType::PointType & A,
1105                                           typename ImageType::PointType & B,
1106                                           int dim1, int dim2, bool removeLowerPartFlag)
1107
1108   {
1109     // Extract slices
1110     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1111     typedef typename SliceType::Pointer SlicePointer;
1112     std::vector<SlicePointer> slices;
1113     clitk::ExtractSlices<ImageType>(input, dim1, slices);
1114
1115     // Start at slice that contains A, and stop at B
1116     typename ImageType::IndexType Ap;
1117     typename ImageType::IndexType Bp;
1118     input->TransformPhysicalPointToIndex(A, Ap);
1119     input->TransformPhysicalPointToIndex(B, Bp);
1120
1121     // Determine slice largest region
1122     typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1123     typename SliceType::SizeType size = region.GetSize();
1124     typename SliceType::IndexType index = region.GetIndex();
1125
1126     // Line slope
1127     double a = (Bp[dim2]-Ap[dim2])/(Bp[dim1]-Ap[dim1]);
1128     double b = Ap[dim2];
1129
1130     // Loop from slice A to slice B
1131     for(uint i=0; i<(Bp[dim1]-Ap[dim1]); i++) {
1132       // Compute intersection between line AB and current slice for the dim2
1133       double p = a*i+b;
1134       // Change region (lower than dim2)
1135       if (removeLowerPartFlag) {
1136         size[dim2] = p-Ap[dim2];
1137       }
1138       else {
1139         size[dim2] = slices[0]->GetLargestPossibleRegion().GetSize()[dim2]-p;
1140         index[dim2] = p;
1141       }
1142       region.SetSize(size);
1143       region.SetIndex(index);
1144       // Fill region with BG (simple region iterator)
1145       FillRegionWithValue<SliceType>(slices[i+Ap[dim1]], BG, region);
1146       /*
1147       typedef itk::ImageRegionIterator<SliceType> IteratorType;
1148       IteratorType iter(slices[i+Ap[dim1]], region);
1149       iter.GoToBegin();
1150       while (!iter.IsAtEnd()) {
1151         iter.Set(BG);
1152         ++iter;
1153       }
1154       */
1155       // Loop
1156     }
1157
1158     // Merge slices
1159     typename ImageType::Pointer output;
1160     output = clitk::JoinSlices<ImageType>(slices, input, dim1);
1161     return output;
1162   }
1163   //--------------------------------------------------------------------
1164
1165   //--------------------------------------------------------------------
1166   /* Consider an input object, slice by slice, use the point A and set
1167      pixel to BG according to their position relatively to A
1168   */
1169   template<class ImageType>
1170   typename ImageType::Pointer
1171   SliceBySliceSetBackgroundFromPoints(const ImageType * input,
1172                                       typename ImageType::PixelType BG,
1173                                       int sliceDim,
1174                                       std::vector<typename ImageType::PointType> & A,
1175                                       bool removeGreaterThanXFlag,
1176                                       bool removeGreaterThanYFlag)
1177
1178   {
1179     // Extract slices
1180     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1181     typedef typename SliceType::Pointer SlicePointer;
1182     std::vector<SlicePointer> slices;
1183     clitk::ExtractSlices<ImageType>(input, sliceDim, slices);
1184
1185     // Start at slice that contains A
1186     typename ImageType::IndexType Ap;
1187
1188     // Determine slice largest region
1189     typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1190     typename SliceType::SizeType size = region.GetSize();
1191     typename SliceType::IndexType index = region.GetIndex();
1192
1193     // Loop from slice A to slice B
1194     for(uint i=0; i<A.size(); i++) {
1195       input->TransformPhysicalPointToIndex(A[i], Ap);
1196       uint sliceIndex = Ap[2] - input->GetLargestPossibleRegion().GetIndex()[2];
1197       if ((sliceIndex < 0) || (sliceIndex >= slices.size())) {
1198         continue; // do not consider this slice
1199       }
1200
1201       // Compute region for BG
1202       if (removeGreaterThanXFlag) {
1203         index[0] = Ap[0];
1204         size[0] = region.GetSize()[0]-(index[0]-region.GetIndex()[0]);
1205       }
1206       else {
1207         index[0] = region.GetIndex()[0];
1208         size[0] = Ap[0] - index[0];
1209       }
1210
1211       if (removeGreaterThanYFlag) {
1212         index[1] = Ap[1];
1213         size[1] = region.GetSize()[1]-(index[1]-region.GetIndex()[1]);
1214       }
1215       else {
1216         index[1] = region.GetIndex()[1];
1217         size[1] = Ap[1] - index[1];
1218       }
1219
1220       // Set region
1221       region.SetSize(size);
1222       region.SetIndex(index);
1223
1224       // Fill region with BG (simple region iterator)
1225       FillRegionWithValue<SliceType>(slices[sliceIndex], BG, region);
1226       // Loop
1227     }
1228
1229     // Merge slices
1230     typename ImageType::Pointer output;
1231     output = clitk::JoinSlices<ImageType>(slices, input, sliceDim);
1232     return output;
1233   }
1234   //--------------------------------------------------------------------
1235
1236
1237   //--------------------------------------------------------------------
1238   template<class ImageType>
1239   void
1240   FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region)
1241   {
1242     typedef itk::ImageRegionIterator<ImageType> IteratorType;
1243     IteratorType iter(input, region);
1244     iter.GoToBegin();
1245     while (!iter.IsAtEnd()) {
1246       iter.Set(value);
1247       ++iter;
1248     }
1249   }
1250   //--------------------------------------------------------------------
1251
1252
1253   //--------------------------------------------------------------------
1254   template<class ImageType>
1255   void
1256   GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min,
1257                     typename ImageType::PointType & max)
1258   {
1259     typedef typename ImageType::PointType PointType;
1260     typedef typename ImageType::IndexType IndexType;
1261     IndexType min_i, max_i;
1262     min_i = input->GetLargestPossibleRegion().GetIndex();
1263     for(uint i=0; i<ImageType::ImageDimension; i++)
1264       max_i[i] = input->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
1265     input->TransformIndexToPhysicalPoint(min_i, min);
1266     input->TransformIndexToPhysicalPoint(max_i, max);
1267   }
1268   //--------------------------------------------------------------------
1269
1270
1271   //--------------------------------------------------------------------
1272   template<class ImageType>
1273   typename itk::Image<float, ImageType::ImageDimension>::Pointer
1274   DistanceMap(const ImageType * input, typename ImageType::PixelType BG)//,
1275   //              typename itk::Image<float, ImageType::ImageDimension>::Pointer dmap)
1276   {
1277     typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
1278     typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, FloatImageType> DistanceMapFilterType;
1279     typename DistanceMapFilterType::Pointer filter = DistanceMapFilterType::New();
1280     filter->SetInput(input);
1281     filter->SetUseImageSpacing(true);
1282     filter->SquaredDistanceOff();
1283     filter->SetBackgroundValue(BG);
1284     filter->Update();
1285     return filter->GetOutput();
1286   }
1287   //--------------------------------------------------------------------
1288
1289
1290   //--------------------------------------------------------------------
1291   template<class ImageType>
1292   void
1293   SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1,
1294                                                                           const ImageType * S2,
1295                                                                           typename ImageType::PixelType BG,
1296                                                                           int sliceDimension,
1297                                                                           std::vector<typename ImageType::PointType> & A,
1298                                                                           std::vector<typename ImageType::PointType> & B)
1299   {
1300     // Extract slices
1301     typedef typename itk::Image<typename ImageType::PixelType, 2> SliceType;
1302     typedef typename SliceType::Pointer SlicePointer;
1303     std::vector<SlicePointer> slices_s1;
1304     std::vector<SlicePointer> slices_s2;
1305     clitk::ExtractSlices<ImageType>(S1, sliceDimension, slices_s1);
1306     clitk::ExtractSlices<ImageType>(S2, sliceDimension, slices_s2);
1307
1308     assert(slices_s1.size() == slices_s2.size());
1309
1310     // Prepare dmap
1311     typedef itk::Image<float,2> FloatImageType;
1312     typedef itk::SignedMaurerDistanceMapImageFilter<SliceType, FloatImageType> DistanceMapFilterType;
1313     std::vector<typename FloatImageType::Pointer> dmaps1;
1314     std::vector<typename FloatImageType::Pointer> dmaps2;
1315     typename FloatImageType::Pointer dmap;
1316
1317     // loop on slices
1318     for(uint i=0; i<slices_s1.size(); i++) {
1319       // Compute dmap for S1 *TO PUT IN FONCTION*
1320       dmap = clitk::DistanceMap<SliceType>(slices_s1[i], BG);
1321       dmaps1.push_back(dmap);
1322       writeImage<FloatImageType>(dmap, "dmap1.mha");
1323       // Compute dmap for S2
1324       dmap = clitk::DistanceMap<SliceType>(slices_s2[i], BG);
1325       dmaps2.push_back(dmap);
1326       writeImage<FloatImageType>(dmap, "dmap2.mha");
1327
1328       // Look in S2 for the point the closest to S1
1329       typename SliceType::PointType p = ComputeClosestPoint<SliceType>(slices_s1[i], dmaps2[i], BG);
1330       typename ImageType::PointType p3D;
1331       clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S1, i, p3D);
1332       A.push_back(p3D);
1333
1334       // Look in S2 for the point the closest to S1
1335       p = ComputeClosestPoint<SliceType>(slices_s2[i], dmaps1[i], BG);
1336       clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S2, i, p3D);
1337       B.push_back(p3D);
1338
1339     }
1340
1341     // Debug dmap
1342     /*
1343       typedef itk::Image<float,3> FT;
1344       FT::Pointer f = FT::New();
1345       typename FT::Pointer d1 = clitk::JoinSlices<FT>(dmaps1, S1, 2);
1346       typename FT::Pointer d2 = clitk::JoinSlices<FT>(dmaps2, S2, 2);
1347       writeImage<FT>(d1, "d1.mha");
1348       writeImage<FT>(d2, "d2.mha");
1349     */
1350   }
1351   //--------------------------------------------------------------------
1352
1353
1354   //--------------------------------------------------------------------
1355   template<class ImageType>
1356   typename ImageType::PointType
1357   ComputeClosestPoint(const ImageType * input,
1358                       const itk::Image<float, ImageType::ImageDimension> * dmap,
1359                       typename ImageType::PixelType & BG)
1360   {
1361     // Loop dmap + S2, if FG, get min
1362     typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
1363     typedef itk::ImageRegionConstIteratorWithIndex<ImageType> ImageIteratorType;
1364     typedef itk::ImageRegionConstIterator<FloatImageType> DMapIteratorType;
1365     ImageIteratorType iter1(input, input->GetLargestPossibleRegion());
1366     DMapIteratorType iter2(dmap, dmap->GetLargestPossibleRegion());
1367
1368     iter1.GoToBegin();
1369     iter2.GoToBegin();
1370     double dmin = 100000.0;
1371     typename ImageType::IndexType indexmin;
1372     while (!iter1.IsAtEnd()) {
1373       if (iter1.Get() != BG) {
1374         double d = iter2.Get();
1375         if (d<dmin) {
1376           indexmin = iter1.GetIndex();
1377           dmin = d;
1378         }
1379       }
1380       ++iter1;
1381       ++iter2;
1382     }
1383
1384     // Convert in Point
1385     typename ImageType::PointType p;
1386     input->TransformIndexToPhysicalPoint(indexmin, p);
1387     return p;
1388   }
1389   //--------------------------------------------------------------------
1390
1391
1392
1393
1394 } // end of namespace
1395