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->AddAnglesInRad(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); // half of the pixel
 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
 387     image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
 388                                          image->GetLargestPossibleRegion().GetSize(), p);
 389
 390     return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
 391   }
 392   //--------------------------------------------------------------------
 393
 394
 395   //--------------------------------------------------------------------
 396   template<class ImageType>
 397   typename ImageType::Pointer
 398   CropImageAlongOneAxis(const ImageType * image,
 399                         int dim, double min, double max,
 400                         bool autoCrop, typename ImageType::PixelType BG)
 401   {
 402     // Compute region size
 403     typename ImageType::RegionType region;
 404     typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 405
 406     // Starting index
 407     typename ImageType::PointType p = image->GetOrigin(); // not at pixel center !
 408     if (min > p[dim]) p[dim] = min; // Check if not outside the image
 409     typename ImageType::IndexType start;
 410     image->TransformPhysicalPointToIndex(p, start);
 411
 412     // Size of the region
 413     // -1 because last point is size -1
 414     double m = image->GetOrigin()[dim] + (size[dim]-1)*image->GetSpacing()[dim];
 415     if (max > m) p[dim] = m; // Check if not outside the image
 416     else p[dim] = max;
 417
 418     typename ImageType::IndexType end;
 419     image->TransformPhysicalPointToIndex(p, end);
 420     size[dim] = abs(end[dim]-start[dim])+1;// +1 because we want to include the point.
 421
 422     // Set region
 423     region.SetIndex(start);
 424     region.SetSize(size);
 425
 426     // Perform Crop
 427     typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 428     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 429     cropFilter->SetInput(image);
 430     cropFilter->SetRegionOfInterest(region);
 431     cropFilter->Update();
 432     typename ImageType::Pointer result = cropFilter->GetOutput();
 433
 434     // Auto Crop
 435     if (autoCrop) {
 436       result = AutoCrop<ImageType>(result, BG);
 437     }
 438     return result;
 439   }
 440   //--------------------------------------------------------------------
 441
 442
 443   //--------------------------------------------------------------------
 444   template<class ImageType>
 445   void
 446   ComputeCentroids(const ImageType * image,
 447                    typename ImageType::PixelType BG,
 448                    std::vector<typename ImageType::PointType> & centroids)
 449   {
 450     typedef long LabelType;
 451     static const unsigned int Dim = ImageType::ImageDimension;
 452     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 453     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 454     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 455     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 456     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 457     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 458     imageToLabelFilter->SetBackgroundValue(BG);
 459     imageToLabelFilter->SetInput(image);
 460     statFilter->SetInput(imageToLabelFilter->GetOutput());
 461     statFilter->Update();
 462     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 463
 464     centroids.clear();
 465     typename ImageType::PointType dummy;
 466     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG
 467     //DS FIXME (not useful ! to change ..)
 468     for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
 469       int label = labelMap->GetLabels()[i];
 470       centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
 471     }
 472   }
 473   //--------------------------------------------------------------------
 474
 475
 476   //--------------------------------------------------------------------
 477   template<class ImageType, class LabelType>
 478   typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
 479   ComputeLabelMap(const ImageType * image,
 480                   typename ImageType::PixelType BG,
 481                   bool computePerimeterFlag)
 482   {
 483     static const unsigned int Dim = ImageType::ImageDimension;
 484     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 485     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 486     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 487     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 488     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 489     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 490     imageToLabelFilter->SetBackgroundValue(BG);
 491     imageToLabelFilter->SetInput(image);
 492     statFilter->SetInput(imageToLabelFilter->GetOutput());
 493     statFilter->SetComputePerimeter(computePerimeterFlag);
 494     statFilter->Update();
 495     return statFilter->GetOutput();
 496   }
 497   //--------------------------------------------------------------------
 498
 499
 500   //--------------------------------------------------------------------
 501   template<class ImageType>
 502   void
 503   ComputeCentroids2(const ImageType * image,
 504                    typename ImageType::PixelType BG,
 505                    std::vector<typename ImageType::PointType> & centroids)
 506   {
 507     typedef long LabelType;
 508     static const unsigned int Dim = ImageType::ImageDimension;
 509     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 510     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 511     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 512     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 513     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 514     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 515     imageToLabelFilter->SetBackgroundValue(BG);
 516     imageToLabelFilter->SetInput(image);
 517     statFilter->SetInput(imageToLabelFilter->GetOutput());
 518     statFilter->Update();
 519     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 520
 521     centroids.clear();
 522     typename ImageType::PointType dummy;
 523     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 524     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 525       centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 526     }
 527
 528     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 529       DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
 530       DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
 531       DD(labelMap->GetLabelObject(i)->GetRoundness ());
 532
 533       // search for the point on the boundary alog PA
 534
 535     }
 536
 537   }
 538   //--------------------------------------------------------------------
 539
 540
 541   //--------------------------------------------------------------------
 542   template<class ImageType>
 543   void
 544   PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
 545                                         const ImageType * image,
 546                                         const int slice,
 547                                         PointType3D & p3D)
 548   {
 549     IndexType3D index3D;
 550     index3D[0] = index3D[1] = 0;
 551     index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
 552     image->TransformIndexToPhysicalPoint(index3D, p3D);
 553     p3D[0] = p2D[0];
 554     p3D[1] = p2D[1];
 555     //  p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 556     //    + image->GetOrigin()[2];
 557   }
 558   //--------------------------------------------------------------------
 559
 560
 561   //--------------------------------------------------------------------
 562   template<class ImageType>
 563   void
 564   PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
 565                                             const ImageType * image,
 566                                             VectorPoint3DType & list)
 567   {
 568     typename MapPoint2DType::const_iterator iter = map.begin();
 569     while (iter != map.end()) {
 570       PointType3D p;
 571       Convert2DTo3D(iter->second, image, iter->first, p);
 572       list.push_back(p);
 573       ++iter;
 574     }
 575   }
 576   //--------------------------------------------------------------------
 577
 578
 579   //--------------------------------------------------------------------
 580   template<class ImageType>
 581   void
 582   PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D,
 583                                                 int slice,
 584                                                 const ImageType * image,
 585                                                 VectorPoint3DType & list)
 586   {
 587     for(uint i=0; i<p2D.size(); i++) {
 588       PointType3D p;
 589       Convert2DTo3D(p2D[i], image, slice, p);
 590       list.push_back(p);
 591     }
 592   }
 593   //--------------------------------------------------------------------
 594
 595
 596   //--------------------------------------------------------------------
 597   template<class ImageType>
 598   void
 599   WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 600                        std::string filename)
 601   {
 602     std::ofstream os;
 603     openFileForWriting(os, filename);
 604     os << "LANDMARKS1" << std::endl;
 605     for(uint i=0; i<points.size(); i++) {
 606       const typename ImageType::PointType & p = points[i];
 607       // Write it in the file
 608       os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 609     }
 610     os.close();
 611   }
 612   //--------------------------------------------------------------------
 613
 614
 615   //--------------------------------------------------------------------
 616   template<class ImageType>
 617   typename ImageType::Pointer
 618   Dilate(const ImageType * image, double radiusInMM,
 619          typename ImageType::PixelType BG,
 620          typename ImageType::PixelType FG,
 621          bool extendSupport)
 622   {
 623     typename ImageType::SizeType r;
 624     for(uint i=0; i<ImageType::ImageDimension; i++)
 625       r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 626     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 627   }
 628   //--------------------------------------------------------------------
 629
 630
 631   //--------------------------------------------------------------------
 632   template<class ImageType>
 633   typename ImageType::Pointer
 634   Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
 635          typename ImageType::PixelType BG,
 636          typename ImageType::PixelType FG,
 637          bool extendSupport)
 638   {
 639     typename ImageType::SizeType r;
 640     for(uint i=0; i<ImageType::ImageDimension; i++)
 641       r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 642     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 643   }
 644   //--------------------------------------------------------------------
 645
 646
 647   //--------------------------------------------------------------------
 648   template<class ImageType>
 649   typename ImageType::Pointer
 650   Dilate(const ImageType * image, typename ImageType::SizeType radius,
 651          typename ImageType::PixelType BG,
 652          typename ImageType::PixelType FG,
 653          bool extendSupport)
 654   {
 655     // Create kernel for dilatation
 656     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 657                                               ImageType::ImageDimension> KernelType;
 658     KernelType structuringElement;
 659     structuringElement.SetRadius(radius);
 660     structuringElement.CreateStructuringElement();
 661
 662     typename ImageType::Pointer output;
 663     if (extendSupport) {
 664       typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 665       typename PadFilterType::Pointer padFilter = PadFilterType::New();
 666       padFilter->SetInput(image);
 667       typename ImageType::SizeType lower;
 668       typename ImageType::SizeType upper;
 669       for(uint i=0; i<3; i++) {
 670         lower[i] = upper[i] = 2*(radius[i]+1);
 671       }
 672       padFilter->SetPadLowerBound(lower);
 673       padFilter->SetPadUpperBound(upper);
 674       padFilter->Update();
 675       output = padFilter->GetOutput();
 676     }
 677
 678     // Dilate  filter
 679     typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 680     typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 681     dilateFilter->SetBackgroundValue(BG);
 682     dilateFilter->SetForegroundValue(FG);
 683     dilateFilter->SetBoundaryToForeground(false);
 684     dilateFilter->SetKernel(structuringElement);
 685     if (extendSupport) dilateFilter->SetInput(output);
 686     else dilateFilter->SetInput(image);
 687     dilateFilter->Update();
 688     return dilateFilter->GetOutput();
 689   }
 690   //--------------------------------------------------------------------
 691
 692
 693   //--------------------------------------------------------------------
 694   template<class ImageType>
 695   typename ImageType::Pointer
 696   Opening(const ImageType * image, typename ImageType::SizeType radius,
 697          typename ImageType::PixelType BG,
 698          typename ImageType::PixelType FG)
 699   {
 700     // Kernel
 701     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 702                                               ImageType::ImageDimension> KernelType;
 703     KernelType structuringElement;
 704     structuringElement.SetRadius(radius);
 705     structuringElement.CreateStructuringElement();
 706
 707     // Filter
 708     typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
 709     typename OpeningFilterType::Pointer open = OpeningFilterType::New();
 710     open->SetInput(image);
 711     open->SetBackgroundValue(BG);
 712     open->SetForegroundValue(FG);
 713     open->SetKernel(structuringElement);
 714     open->Update();
 715     return open->GetOutput();
 716   }
 717   //--------------------------------------------------------------------
 718
 719
 720
 721   //--------------------------------------------------------------------
 722   template<class ValueType, class VectorType>
 723   void ConvertOption(std::string optionName, uint given,
 724                      ValueType * values, VectorType & p,
 725                      uint dim, bool required)
 726   {
 727     if (required && (given == 0)) {
 728       clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 729                           << dim << " values.");
 730     }
 731     if (given == 1) {
 732       for(uint i=0; i<dim; i++) p[i] = values[0];
 733       return;
 734     }
 735     if (given == dim) {
 736       for(uint i=0; i<dim; i++) p[i] = values[i];
 737       return;
 738     }
 739     if (given == 0) return;
 740     clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 741                         << dim << " values.");
 742   }
 743   //--------------------------------------------------------------------
 744
 745
 746   //--------------------------------------------------------------------
 747   /*
 748     http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
 749     Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
 750     (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
 751     This will equal zero if the point C is on the line formed by
 752     points A and B, and will have a different sign depending on the
 753     side. Which side this is depends on the orientation of your (x,y)
 754     coordinates, but you can plug test values for A,B and C into this
 755     formula to determine whether negative values are to the left or to
 756     the right.
 757     => to accelerate, start with formula, when change sign -> stop and fill
 758
 759     offsetToKeep = is used to determine which side of the line we
 760     keep. The point along the mainDirection but 'offsetToKeep' mm away
 761     is kept.
 762
 763   */
 764   template<class ImageType>
 765   void
 766   SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
 767                                               std::vector<typename ImageType::PointType> & lA,
 768                                               std::vector<typename ImageType::PointType> & lB,
 769                                               typename ImageType::PixelType BG,
 770                                               int mainDirection,
 771                                               double offsetToKeep)
 772   {
 773     assert((mainDirection==0) || (mainDirection==1));
 774     typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
 775     SliceIteratorType siter = SliceIteratorType(input, input->GetLargestPossibleRegion());
 776     siter.SetFirstDirection(0);
 777     siter.SetSecondDirection(1);
 778     siter.GoToBegin();
 779     uint i=0;
 780     typename ImageType::PointType A;
 781     typename ImageType::PointType B;
 782     typename ImageType::PointType C;
 783     assert(lA.size() == lB.size());
 784     while ((i<lA.size()) && (!siter.IsAtEnd())) {
 785       // Check that the current slice correspond to the current point
 786       input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 787       if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
 788       }
 789       else {
 790         // Define A,B,C points
 791         A = lA[i];
 792         B = lB[i];
 793         C = A;
 794         // Check that the line is not a point (A=B)
 795         bool p = (A[0] == B[0]) && (A[1] == B[1]);
 796
 797         if (!p) {
 798           C[mainDirection] += offsetToKeep; // I know I must keep this point
 799           double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 800           bool isPositive = s<0;
 801           while (!siter.IsAtEndOfSlice()) {
 802             while (!siter.IsAtEndOfLine()) {
 803               // Very slow, I know ... but image should be very small
 804               input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 805               double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 806               if (s == 0) siter.Set(BG); // on the line, we decide to remove
 807               if (isPositive) {
 808                 if (s > 0) siter.Set(BG);
 809               }
 810               else {
 811                 if (s < 0) siter.Set(BG);
 812               }
 813               ++siter;
 814             }
 815             siter.NextLine();
 816           } // end loop slice
 817         }
 818
 819         ++i;
 820       } // End of current slice
 821       siter.NextSlice();
 822     }
 823   }
 824   //--------------------------------------------------------------------
 825
 826
 827   //--------------------------------------------------------------------
 828   template<class ImageType>
 829   void
 830   AndNot(ImageType * input,
 831          const ImageType * object,
 832          typename ImageType::PixelType BG)
 833   {
 834     typename ImageType::Pointer o;
 835     bool resized=false;
 836     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 837       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 838       resized = true;
 839     }
 840
 841     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 842     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 843     boolFilter->InPlaceOn();
 844     boolFilter->SetInput1(input);
 845     if (resized) boolFilter->SetInput2(o);
 846     else boolFilter->SetInput2(object);
 847     boolFilter->SetBackgroundValue1(BG);
 848     boolFilter->SetBackgroundValue2(BG);
 849     boolFilter->SetOperationType(BoolFilterType::AndNot);
 850     boolFilter->Update();
 851   }
 852   //--------------------------------------------------------------------
 853
 854
 855   //--------------------------------------------------------------------
 856   template<class ImageType>
 857   void
 858   And(ImageType * input,
 859       const ImageType * object,
 860       typename ImageType::PixelType BG)
 861   {
 862     typename ImageType::Pointer o;
 863     bool resized=false;
 864     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 865       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 866       resized = true;
 867     }
 868
 869     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 870     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 871     boolFilter->InPlaceOn();
 872     boolFilter->SetInput1(input);
 873     if (resized) boolFilter->SetInput2(o);
 874     else boolFilter->SetInput2(object);
 875     boolFilter->SetBackgroundValue1(BG);
 876     boolFilter->SetBackgroundValue2(BG);
 877     boolFilter->SetOperationType(BoolFilterType::And);
 878     boolFilter->Update();
 879   }
 880   //--------------------------------------------------------------------
 881
 882
 883   //--------------------------------------------------------------------
 884   template<class ImageType>
 885   void
 886   Or(ImageType * input,
 887      const ImageType * object,
 888      typename ImageType::PixelType BG)
 889   {
 890     typename ImageType::Pointer o;
 891     bool resized=false;
 892     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 893       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 894       resized = true;
 895     }
 896
 897     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 898     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 899     boolFilter->InPlaceOn();
 900     boolFilter->SetInput1(input);
 901     if (resized) boolFilter->SetInput2(o);
 902     else boolFilter->SetInput2(object);
 903     boolFilter->SetBackgroundValue1(BG);
 904     boolFilter->SetBackgroundValue2(BG);
 905     boolFilter->SetOperationType(BoolFilterType::Or);
 906     boolFilter->Update();
 907   }
 908   //--------------------------------------------------------------------
 909
 910
 911   //--------------------------------------------------------------------
 912   template<class ImageType>
 913   typename ImageType::Pointer
 914   Binarize(const ImageType * input,
 915            typename ImageType::PixelType lower,
 916            typename ImageType::PixelType upper,
 917            typename ImageType::PixelType BG,
 918            typename ImageType::PixelType FG)
 919   {
 920     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
 921     typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
 922     binarizeFilter->SetInput(input);
 923     binarizeFilter->InPlaceOff();
 924     binarizeFilter->SetLowerThreshold(lower);
 925     binarizeFilter->SetUpperThreshold(upper);
 926     binarizeFilter->SetInsideValue(FG);
 927     binarizeFilter->SetOutsideValue(BG);
 928     binarizeFilter->Update();
 929     return binarizeFilter->GetOutput();
 930   }
 931   //--------------------------------------------------------------------
 932
 933
 934   //--------------------------------------------------------------------
 935   template<class ImageType>
 936   void
 937   GetMinMaxPointPosition(const ImageType * input,
 938                          typename ImageType::PointType & min,
 939                          typename ImageType::PointType & max)
 940   {
 941     typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
 942     input->TransformIndexToPhysicalPoint(index, min);
 943     index = index+input->GetLargestPossibleRegion().GetSize();
 944     input->TransformIndexToPhysicalPoint(index, max);
 945   }
 946   //--------------------------------------------------------------------
 947
 948
 949   //--------------------------------------------------------------------
 950   template<class ImageType>
 951   typename ImageType::PointType
 952   FindExtremaPointInAGivenLine(const ImageType * input,
 953                                int dimension,
 954                                bool inverse,
 955                                typename ImageType::PointType p,
 956                                typename ImageType::PixelType BG,
 957                                double distanceMax)
 958   {
 959     // Which direction ?  Increasing or decreasing.
 960     int d=1;
 961     if (inverse) d=-1;
 962
 963     // Transform to pixel index
 964     typename ImageType::IndexType index;
 965     input->TransformPhysicalPointToIndex(p, index);
 966
 967     // Loop while inside the mask;
 968     while (input->GetPixel(index) != BG) {
 969       index[dimension] += d;
 970     }
 971
 972     // Transform back to Physical Units
 973     typename ImageType::PointType result;
 974     input->TransformIndexToPhysicalPoint(index, result);
 975
 976     // Check that is is not too far away
 977     double distance = p.EuclideanDistanceTo(result);
 978     if (distance > distanceMax) {
 979       result = p; // Get back to initial value
 980     }
 981
 982     return result;
 983   }
 984   //--------------------------------------------------------------------
 985
 986
 987   //--------------------------------------------------------------------
 988   template<class PointType>
 989   bool
 990   IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
 991   {
 992     // Look at the position of point 'like' according to the AB line
 993     double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
 994     bool negative = s<0;
 995
 996     // Look the C position
 997     s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 998
 999     if (negative && (s<=0)) return true;
1000     if (!negative && (s>=0)) return true;
1001     return false;
1002   }
1003   //--------------------------------------------------------------------
1004
1005
1006   //--------------------------------------------------------------------
1007   /* Consider an input object, for each slice, find the extrema
1008      position according to a given direction and build a line segment
1009      passing throught this point in a given direction.  Output is a
1010      vector of line (from point A to B), for each slice;
1011    */
1012   template<class ImageType>
1013   void
1014   SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
1015                                                          typename ImageType::PixelType BG,
1016                                                          int sliceDimension,
1017                                                          int extremaDirection,
1018                                                          bool extremaOppositeFlag,
1019                                                          int lineDirection,
1020                                                          double margin,
1021                                                          std::vector<typename ImageType::PointType> & A,
1022                                                          std::vector<typename ImageType::PointType> & B)
1023   {
1024     // Type of a slice
1025     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1026
1027     // Build the list of slices
1028     std::vector<typename SliceType::Pointer> slices;
1029     clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
1030
1031     // Build the list of 2D points
1032     std::map<int, typename SliceType::PointType> position2D;
1033     for(uint i=0; i<slices.size(); i++) {
1034       typename SliceType::PointType p;
1035       bool found =
1036         clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
1037                                                             extremaDirection, extremaOppositeFlag, p);
1038       if (found) {
1039         position2D[i] = p;
1040       }
1041     }
1042
1043     // Convert 2D points in slice into 3D points
1044     clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
1045
1046     // Create additional point just right to the previous ones, on the
1047     // given lineDirection, in order to create a horizontal/vertical line.
1048     for(uint i=0; i<A.size(); i++) {
1049       typename ImageType::PointType p = A[i];
1050       p[lineDirection] += 10;
1051       B.push_back(p);
1052       // Margins ?
1053       A[i][extremaDirection] += margin;
1054       B[i][extremaDirection] += margin;
1055     }
1056
1057   }
1058   //--------------------------------------------------------------------
1059
1060
1061   //--------------------------------------------------------------------
1062   template<class ImageType>
1063   typename ImageType::Pointer
1064   SliceBySliceKeepMainCCL(const ImageType * input,
1065                           typename ImageType::PixelType BG,
1066                           typename ImageType::PixelType FG)  {
1067
1068     // Extract slices
1069     const int d = ImageType::ImageDimension-1;
1070     typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
1071     std::vector<typename SliceType::Pointer> slices;
1072     clitk::ExtractSlices<ImageType>(input, d, slices);
1073
1074     // Labelize and keep the main one
1075     std::vector<typename SliceType::Pointer> o;
1076     for(uint i=0; i<slices.size(); i++) {
1077       o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
1078       o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
1079     }
1080
1081     // Join slices
1082     typename ImageType::Pointer output;
1083     output = clitk::JoinSlices<ImageType>(o, input, d);
1084     return output;
1085   }
1086   //--------------------------------------------------------------------
1087
1088
1089   //--------------------------------------------------------------------
1090   template<class ImageType>
1091   typename ImageType::Pointer
1092   Clone(const ImageType * input) {
1093     typedef itk::ImageDuplicator<ImageType> DuplicatorType;
1094     typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
1095     duplicator->SetInputImage(input);
1096     duplicator->Update();
1097     return duplicator->GetOutput();
1098   }
1099   //--------------------------------------------------------------------
1100
1101
1102   //--------------------------------------------------------------------
1103   /* Consider an input object, start at A, for each slice (dim1):
1104      - compute the intersection between the AB line and the current slice
1105      - remove what is at lower or greater according to dim2 of this point
1106      - stop at B
1107   */
1108   template<class ImageType>
1109   typename ImageType::Pointer
1110   SliceBySliceSetBackgroundFromSingleLine(const ImageType * input,
1111                                           typename ImageType::PixelType BG,
1112                                           typename ImageType::PointType & A,
1113                                           typename ImageType::PointType & B,
1114                                           int dim1, int dim2, bool removeLowerPartFlag)
1115
1116   {
1117     // Extract slices
1118     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1119     typedef typename SliceType::Pointer SlicePointer;
1120     std::vector<SlicePointer> slices;
1121     clitk::ExtractSlices<ImageType>(input, dim1, slices);
1122
1123     // Start at slice that contains A, and stop at B
1124     typename ImageType::IndexType Ap;
1125     typename ImageType::IndexType Bp;
1126     input->TransformPhysicalPointToIndex(A, Ap);
1127     input->TransformPhysicalPointToIndex(B, Bp);
1128
1129     // Determine slice largest region
1130     typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1131     typename SliceType::SizeType size = region.GetSize();
1132     typename SliceType::IndexType index = region.GetIndex();
1133
1134     // Line slope
1135     double a = (Bp[dim2]-Ap[dim2])/(Bp[dim1]-Ap[dim1]);
1136     double b = Ap[dim2];
1137
1138     // Loop from slice A to slice B
1139     for(uint i=0; i<(Bp[dim1]-Ap[dim1]); i++) {
1140       // Compute intersection between line AB and current slice for the dim2
1141       double p = a*i+b;
1142       // Change region (lower than dim2)
1143       if (removeLowerPartFlag) {
1144         size[dim2] = p-Ap[dim2];
1145       }
1146       else {
1147         size[dim2] = slices[0]->GetLargestPossibleRegion().GetSize()[dim2]-p;
1148         index[dim2] = p;
1149       }
1150       region.SetSize(size);
1151       region.SetIndex(index);
1152       // Fill region with BG (simple region iterator)
1153       FillRegionWithValue<SliceType>(slices[i+Ap[dim1]], BG, region);
1154       /*
1155       typedef itk::ImageRegionIterator<SliceType> IteratorType;
1156       IteratorType iter(slices[i+Ap[dim1]], region);
1157       iter.GoToBegin();
1158       while (!iter.IsAtEnd()) {
1159         iter.Set(BG);
1160         ++iter;
1161       }
1162       */
1163       // Loop
1164     }
1165
1166     // Merge slices
1167     typename ImageType::Pointer output;
1168     output = clitk::JoinSlices<ImageType>(slices, input, dim1);
1169     return output;
1170   }
1171   //--------------------------------------------------------------------
1172
1173   //--------------------------------------------------------------------
1174   /* Consider an input object, slice by slice, use the point A and set
1175      pixel to BG according to their position relatively to A
1176   */
1177   template<class ImageType>
1178   typename ImageType::Pointer
1179   SliceBySliceSetBackgroundFromPoints(const ImageType * input,
1180                                       typename ImageType::PixelType BG,
1181                                       int sliceDim,
1182                                       std::vector<typename ImageType::PointType> & A,
1183                                       bool removeGreaterThanXFlag,
1184                                       bool removeGreaterThanYFlag)
1185
1186   {
1187     // Extract slices
1188     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1189     typedef typename SliceType::Pointer SlicePointer;
1190     std::vector<SlicePointer> slices;
1191     clitk::ExtractSlices<ImageType>(input, sliceDim, slices);
1192
1193     // Start at slice that contains A
1194     typename ImageType::IndexType Ap;
1195
1196     // Determine slice largest region
1197     typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1198     typename SliceType::SizeType size = region.GetSize();
1199     typename SliceType::IndexType index = region.GetIndex();
1200
1201     // Loop from slice A to slice B
1202     for(uint i=0; i<A.size(); i++) {
1203       input->TransformPhysicalPointToIndex(A[i], Ap);
1204       uint sliceIndex = Ap[2] - input->GetLargestPossibleRegion().GetIndex()[2];
1205       if ((sliceIndex < 0) || (sliceIndex >= slices.size())) {
1206         continue; // do not consider this slice
1207       }
1208
1209       // Compute region for BG
1210       if (removeGreaterThanXFlag) {
1211         index[0] = Ap[0];
1212         size[0] = region.GetSize()[0]-(index[0]-region.GetIndex()[0]);
1213       }
1214       else {
1215         index[0] = region.GetIndex()[0];
1216         size[0] = Ap[0] - index[0];
1217       }
1218
1219       if (removeGreaterThanYFlag) {
1220         index[1] = Ap[1];
1221         size[1] = region.GetSize()[1]-(index[1]-region.GetIndex()[1]);
1222       }
1223       else {
1224         index[1] = region.GetIndex()[1];
1225         size[1] = Ap[1] - index[1];
1226       }
1227
1228       // Set region
1229       region.SetSize(size);
1230       region.SetIndex(index);
1231
1232       // Fill region with BG (simple region iterator)
1233       FillRegionWithValue<SliceType>(slices[sliceIndex], BG, region);
1234       // Loop
1235     }
1236
1237     // Merge slices
1238     typename ImageType::Pointer output;
1239     output = clitk::JoinSlices<ImageType>(slices, input, sliceDim);
1240     return output;
1241   }
1242   //--------------------------------------------------------------------
1243
1244
1245   //--------------------------------------------------------------------
1246   template<class ImageType>
1247   void
1248   FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region)
1249   {
1250     typedef itk::ImageRegionIterator<ImageType> IteratorType;
1251     IteratorType iter(input, region);
1252     iter.GoToBegin();
1253     while (!iter.IsAtEnd()) {
1254       iter.Set(value);
1255       ++iter;
1256     }
1257   }
1258   //--------------------------------------------------------------------
1259
1260
1261   //--------------------------------------------------------------------
1262   template<class ImageType>
1263   void
1264   GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min,
1265                     typename ImageType::PointType & max)
1266   {
1267     typedef typename ImageType::PointType PointType;
1268     typedef typename ImageType::IndexType IndexType;
1269     IndexType min_i, max_i;
1270     min_i = input->GetLargestPossibleRegion().GetIndex();
1271     for(uint i=0; i<ImageType::ImageDimension; i++)
1272       max_i[i] = input->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
1273     input->TransformIndexToPhysicalPoint(min_i, min);
1274     input->TransformIndexToPhysicalPoint(max_i, max);
1275   }
1276   //--------------------------------------------------------------------
1277
1278
1279   //--------------------------------------------------------------------
1280   template<class ImageType>
1281   typename itk::Image<float, ImageType::ImageDimension>::Pointer
1282   DistanceMap(const ImageType * input, typename ImageType::PixelType BG)//,
1283   //              typename itk::Image<float, ImageType::ImageDimension>::Pointer dmap)
1284   {
1285     typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
1286     typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, FloatImageType> DistanceMapFilterType;
1287     typename DistanceMapFilterType::Pointer filter = DistanceMapFilterType::New();
1288     filter->SetInput(input);
1289     filter->SetUseImageSpacing(true);
1290     filter->SquaredDistanceOff();
1291     filter->SetBackgroundValue(BG);
1292     filter->Update();
1293     return filter->GetOutput();
1294   }
1295   //--------------------------------------------------------------------
1296
1297
1298   //--------------------------------------------------------------------
1299   template<class ImageType>
1300   void
1301   SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1,
1302                                                                           const ImageType * S2,
1303                                                                           typename ImageType::PixelType BG,
1304                                                                           int sliceDimension,
1305                                                                           std::vector<typename ImageType::PointType> & A,
1306                                                                           std::vector<typename ImageType::PointType> & B)
1307   {
1308     // Extract slices
1309     typedef typename itk::Image<typename ImageType::PixelType, 2> SliceType;
1310     typedef typename SliceType::Pointer SlicePointer;
1311     std::vector<SlicePointer> slices_s1;
1312     std::vector<SlicePointer> slices_s2;
1313     clitk::ExtractSlices<ImageType>(S1, sliceDimension, slices_s1);
1314     clitk::ExtractSlices<ImageType>(S2, sliceDimension, slices_s2);
1315
1316     assert(slices_s1.size() == slices_s2.size());
1317
1318     // Prepare dmap
1319     typedef itk::Image<float,2> FloatImageType;
1320     typedef itk::SignedMaurerDistanceMapImageFilter<SliceType, FloatImageType> DistanceMapFilterType;
1321     std::vector<typename FloatImageType::Pointer> dmaps1;
1322     std::vector<typename FloatImageType::Pointer> dmaps2;
1323     typename FloatImageType::Pointer dmap;
1324
1325     // loop on slices
1326     for(uint i=0; i<slices_s1.size(); i++) {
1327       // Compute dmap for S1 *TO PUT IN FONCTION*
1328       dmap = clitk::DistanceMap<SliceType>(slices_s1[i], BG);
1329       dmaps1.push_back(dmap);
1330       //writeImage<FloatImageType>(dmap, "dmap1.mha");
1331       // Compute dmap for S2
1332       dmap = clitk::DistanceMap<SliceType>(slices_s2[i], BG);
1333       dmaps2.push_back(dmap);
1334       //writeImage<FloatImageType>(dmap, "dmap2.mha");
1335
1336       // Look in S2 for the point the closest to S1
1337       typename SliceType::PointType p = ComputeClosestPoint<SliceType>(slices_s1[i], dmaps2[i], BG);
1338       typename ImageType::PointType p3D;
1339       clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S1, i, p3D);
1340       A.push_back(p3D);
1341
1342       // Look in S2 for the point the closest to S1
1343       p = ComputeClosestPoint<SliceType>(slices_s2[i], dmaps1[i], BG);
1344       clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S2, i, p3D);
1345       B.push_back(p3D);
1346
1347     }
1348
1349     // Debug dmap
1350     /*
1351       typedef itk::Image<float,3> FT;
1352       FT::Pointer f = FT::New();
1353       typename FT::Pointer d1 = clitk::JoinSlices<FT>(dmaps1, S1, 2);
1354       typename FT::Pointer d2 = clitk::JoinSlices<FT>(dmaps2, S2, 2);
1355       writeImage<FT>(d1, "d1.mha");
1356       writeImage<FT>(d2, "d2.mha");
1357     */
1358   }
1359   //--------------------------------------------------------------------
1360
1361
1362   //--------------------------------------------------------------------
1363   template<class ImageType>
1364   typename ImageType::PointType
1365   ComputeClosestPoint(const ImageType * input,
1366                       const itk::Image<float, ImageType::ImageDimension> * dmap,
1367                       typename ImageType::PixelType & BG)
1368   {
1369     // Loop dmap + S2, if FG, get min
1370     typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
1371     typedef itk::ImageRegionConstIteratorWithIndex<ImageType> ImageIteratorType;
1372     typedef itk::ImageRegionConstIterator<FloatImageType> DMapIteratorType;
1373     ImageIteratorType iter1(input, input->GetLargestPossibleRegion());
1374     DMapIteratorType iter2(dmap, dmap->GetLargestPossibleRegion());
1375
1376     iter1.GoToBegin();
1377     iter2.GoToBegin();
1378     double dmin = 100000.0;
1379     typename ImageType::IndexType indexmin;
1380     indexmin.Fill(0);
1381     while (!iter1.IsAtEnd()) {
1382       if (iter1.Get() != BG) {
1383         double d = iter2.Get();
1384         if (d<dmin) {
1385           indexmin = iter1.GetIndex();
1386           dmin = d;
1387         }
1388       }
1389       ++iter1;
1390       ++iter2;
1391     }
1392
1393     // Convert in Point
1394     typename ImageType::PointType p;
1395     input->TransformIndexToPhysicalPoint(indexmin, p);
1396     return p;
1397   }
1398   //--------------------------------------------------------------------
1399
1400
1401   //--------------------------------------------------------------------
1402   template<class ImageType>
1403   typename ImageType::Pointer
1404   RemoveNegativeIndexFromRegion(ImageType * input) {
1405     typedef itk::ChangeInformationImageFilter< ImageType > InfoFilterType;
1406     typename InfoFilterType::Pointer indexChangeFilter = InfoFilterType::New();
1407     indexChangeFilter->ChangeRegionOn();
1408     // The next line is commented because not exist in itk 3
1409     // typename InfoFilterType::OutputImageOffsetValueType indexShift[3];
1410     long indexShift[3];
1411     typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
1412     for(uint i=0;i<ImageType::ImageDimension; i++)
1413       indexShift[i] = (index[i]<0 ? -index[i]:0);
1414     typename ImageType::PointType origin;
1415     for(uint i=0;i<ImageType::ImageDimension; i++)
1416     origin[i] = input->GetOrigin()[i] - indexShift[i]*input->GetSpacing()[i];
1417     indexChangeFilter->SetOutputOffset( indexShift );
1418     indexChangeFilter->SetInput(input);
1419     indexChangeFilter->SetOutputOrigin(origin);
1420     indexChangeFilter->ChangeOriginOn();
1421     indexChangeFilter->Update();
1422     return indexChangeFilter->GetOutput();
1423   }
1424   //--------------------------------------------------------------------
1425
1426
1427 } // end of namespace
1428