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
  38 namespace clitk {
  39
  40   //--------------------------------------------------------------------
  41   template<class ImageType>
  42   void ComputeBBFromImageRegion(const ImageType * image,
  43                                 typename ImageType::RegionType region,
  44                                 typename itk::BoundingBox<unsigned long,
  45                                 ImageType::ImageDimension>::Pointer bb) {
  46     typedef typename ImageType::IndexType IndexType;
  47     IndexType firstIndex;
  48     IndexType lastIndex;
  49     for(unsigned int i=0; i<image->GetImageDimension(); i++) {
  50       firstIndex[i] = region.GetIndex()[i];
  51       lastIndex[i] = firstIndex[i]+region.GetSize()[i];
  52     }
  53
  54     typedef itk::BoundingBox<unsigned long,
  55                              ImageType::ImageDimension> BBType;
  56     typedef typename BBType::PointType PointType;
  57     PointType lastPoint;
  58     PointType firstPoint;
  59     image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
  60     image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
  61
  62     bb->SetMaximum(lastPoint);
  63     bb->SetMinimum(firstPoint);
  64   }
  65   //--------------------------------------------------------------------
  66
  67
  68   //--------------------------------------------------------------------
  69   template<int Dimension>
  70   void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  71                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  72                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
  73
  74     typedef itk::BoundingBox<unsigned long, Dimension> BBType;
  75     typedef typename BBType::PointType PointType;
  76     PointType lastPoint;
  77     PointType firstPoint;
  78
  79     for(unsigned int i=0; i<Dimension; i++) {
  80       firstPoint[i] = std::max(bbi1->GetMinimum()[i],
  81                                bbi2->GetMinimum()[i]);
  82       lastPoint[i] = std::min(bbi1->GetMaximum()[i],
  83                               bbi2->GetMaximum()[i]);
  84     }
  85
  86     bbo->SetMaximum(lastPoint);
  87     bbo->SetMinimum(firstPoint);
  88   }
  89   //--------------------------------------------------------------------
  90
  91
  92   //--------------------------------------------------------------------
  93   template<class ImageType>
  94   void ComputeRegionFromBB(const ImageType * image,
  95                            const typename itk::BoundingBox<unsigned long,
  96                                                            ImageType::ImageDimension>::Pointer bb,
  97                            typename ImageType::RegionType & region) {
  98     // Types
  99     typedef typename ImageType::IndexType  IndexType;
 100     typedef typename ImageType::PointType  PointType;
 101     typedef typename ImageType::RegionType RegionType;
 102     typedef typename ImageType::SizeType   SizeType;
 103
 104     // Region starting point
 105     IndexType regionStart;
 106     PointType start = bb->GetMinimum();
 107     image->TransformPhysicalPointToIndex(start, regionStart);
 108
 109     // Region size
 110     SizeType regionSize;
 111     PointType maxs = bb->GetMaximum();
 112     PointType mins = bb->GetMinimum();
 113     for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 114       regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
 115     }
 116
 117     // Create region
 118     region.SetIndex(regionStart);
 119     region.SetSize(regionSize);
 120   }
 121   //--------------------------------------------------------------------
 122
 123   //--------------------------------------------------------------------
 124   template<class ImageType, class TMaskImageType>
 125   typename ImageType::Pointer
 126   SetBackground(const ImageType * input,
 127                 const TMaskImageType * mask,
 128                 typename TMaskImageType::PixelType maskBG,
 129                 typename ImageType::PixelType outValue,
 130                 bool inPlace) {
 131     typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
 132       SetBackgroundImageFilterType;
 133     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
 134       = SetBackgroundImageFilterType::New();
 135     //  if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
 136     setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
 137     setBackgroundFilter->SetInput(input);
 138     setBackgroundFilter->SetInput2(mask);
 139     setBackgroundFilter->SetMaskValue(maskBG);
 140     setBackgroundFilter->SetOutsideValue(outValue);
 141     setBackgroundFilter->Update();
 142     return setBackgroundFilter->GetOutput();
 143   }
 144   //--------------------------------------------------------------------
 145
 146
 147   //--------------------------------------------------------------------
 148   template<class ImageType>
 149   int GetNumberOfConnectedComponentLabels(const ImageType * input,
 150                                           typename ImageType::PixelType BG,
 151                                           bool isFullyConnected) {
 152     // Connected Component label
 153     typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
 154     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 155     connectFilter->SetInput(input);
 156     connectFilter->SetBackgroundValue(BG);
 157     connectFilter->SetFullyConnected(isFullyConnected);
 158     connectFilter->Update();
 159
 160     // Return result
 161     return connectFilter->GetObjectCount();
 162   }
 163   //--------------------------------------------------------------------
 164
 165   //--------------------------------------------------------------------
 166   /*
 167     Warning : in this cas, we consider outputType like inputType, not
 168     InternalImageType. Be sure it fits.
 169   */
 170   template<class ImageType>
 171   typename ImageType::Pointer
 172   Labelize(const ImageType * input,
 173            typename ImageType::PixelType BG,
 174            bool isFullyConnected,
 175            int minimalComponentSize) {
 176     // InternalImageType for storing large number of component
 177     typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 178
 179     // Connected Component label
 180     typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 181     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 182     //  connectFilter->ReleaseDataFlagOn();
 183     connectFilter->SetInput(input);
 184     connectFilter->SetBackgroundValue(BG);
 185     connectFilter->SetFullyConnected(isFullyConnected);
 186
 187     // Sort by size and remove too small area.
 188     typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 189     typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 190     //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 191     relabelFilter->SetInput(connectFilter->GetOutput());
 192     relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 193     relabelFilter->Update();
 194
 195     // Return result
 196     typename ImageType::Pointer output = relabelFilter->GetOutput();
 197     return output;
 198   }
 199   //--------------------------------------------------------------------
 200
 201
 202   //--------------------------------------------------------------------
 203   /*
 204     Warning : in this cas, we consider outputType like inputType, not
 205     InternalImageType. Be sure it fits.
 206   */
 207   template<class ImageType>
 208   typename ImageType::Pointer
 209   LabelizeAndCountNumberOfObjects(const ImageType * input,
 210                                   typename ImageType::PixelType BG,
 211                                   bool isFullyConnected,
 212                                   int minimalComponentSize,
 213                                   int & nb) {
 214     // InternalImageType for storing large number of component
 215     typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 216
 217     // Connected Component label
 218     typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 219     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 220     //  connectFilter->ReleaseDataFlagOn();
 221     connectFilter->SetInput(input);
 222     connectFilter->SetBackgroundValue(BG);
 223     connectFilter->SetFullyConnected(isFullyConnected);
 224
 225     // Sort by size and remove too small area.
 226     typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 227     typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 228     //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 229     relabelFilter->SetInput(connectFilter->GetOutput());
 230     relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 231     relabelFilter->Update();
 232
 233     nb = relabelFilter->GetNumberOfObjects();
 234     // DD(relabelFilter->GetOriginalNumberOfObjects());
 235     // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
 236
 237     // Return result
 238     typename ImageType::Pointer output = relabelFilter->GetOutput();
 239     return output;
 240   }
 241   //--------------------------------------------------------------------
 242
 243
 244
 245   //--------------------------------------------------------------------
 246   template<class ImageType>
 247   typename ImageType::Pointer
 248   RemoveLabels(const ImageType * input,
 249                typename ImageType::PixelType BG,
 250                std::vector<typename ImageType::PixelType> & labelsToRemove) {
 251     assert(labelsToRemove.size() != 0);
 252     typename ImageType::Pointer working_image;// = input;
 253     for (unsigned int i=0; i <labelsToRemove.size(); i++) {
 254       typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
 255       typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 256       setBackgroundFilter->SetInput(input);
 257       setBackgroundFilter->SetInput2(input);
 258       setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
 259       setBackgroundFilter->SetOutsideValue(BG);
 260       setBackgroundFilter->Update();
 261       working_image = setBackgroundFilter->GetOutput();
 262     }
 263     return working_image;
 264   }
 265   //--------------------------------------------------------------------
 266
 267
 268   //--------------------------------------------------------------------
 269   template<class ImageType>
 270   typename ImageType::Pointer
 271   KeepLabels(const ImageType * input,
 272              typename ImageType::PixelType BG,
 273              typename ImageType::PixelType FG,
 274              typename ImageType::PixelType firstKeep,
 275              typename ImageType::PixelType lastKeep,
 276              bool useLastKeep) {
 277     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
 278     typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 279     binarizeFilter->SetInput(input);
 280     binarizeFilter->SetLowerThreshold(firstKeep);
 281     if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 282     binarizeFilter->SetInsideValue(FG);
 283     binarizeFilter->SetOutsideValue(BG);
 284     binarizeFilter->Update();
 285     return binarizeFilter->GetOutput();
 286   }
 287   //--------------------------------------------------------------------
 288
 289
 290   //--------------------------------------------------------------------
 291   template<class ImageType>
 292   typename ImageType::Pointer
 293   LabelizeAndSelectLabels(const ImageType * input,
 294                           typename ImageType::PixelType BG,
 295                           typename ImageType::PixelType FG,
 296                           bool isFullyConnected,
 297                           int minimalComponentSize,
 298                           LabelizeParameters<typename ImageType::PixelType> * param)
 299   {
 300     typename ImageType::Pointer working_image;
 301     working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
 302     if (param->GetLabelsToRemove().size() != 0)
 303       working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
 304     working_image = KeepLabels<ImageType>(working_image,
 305                                           BG, FG,
 306                                           param->GetFirstKeep(),
 307                                           param->GetLastKeep(),
 308                                           param->GetUseLastKeep());
 309     return working_image;
 310   }
 311   //--------------------------------------------------------------------
 312
 313
 314   //--------------------------------------------------------------------
 315   template<class ImageType>
 316   typename ImageType::Pointer
 317   ResizeImageLike(const ImageType * input,
 318                   const itk::ImageBase<ImageType::ImageDimension> * like,
 319                   typename ImageType::PixelType backgroundValue)
 320   {
 321     typedef CropLikeImageFilter<ImageType> CropFilterType;
 322     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 323     cropFilter->SetInput(input);
 324     cropFilter->SetCropLikeImage(like);
 325     cropFilter->SetBackgroundValue(backgroundValue);
 326     cropFilter->Update();
 327     return cropFilter->GetOutput();
 328   }
 329   //--------------------------------------------------------------------
 330
 331
 332   //--------------------------------------------------------------------
 333   template<class MaskImageType>
 334   typename MaskImageType::Pointer
 335   SliceBySliceRelativePosition(const MaskImageType * input,
 336                                const MaskImageType * object,
 337                                int direction,
 338                                double threshold,
 339                                std::string orientation,
 340                                bool uniqueConnectedComponent,
 341                                double spacing,
 342                                bool autocropFlag,
 343                                bool singleObjectCCL)
 344   {
 345     typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 346     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 347     sliceRelPosFilter->VerboseStepFlagOff();
 348     sliceRelPosFilter->WriteStepFlagOff();
 349     sliceRelPosFilter->SetInput(input);
 350     sliceRelPosFilter->SetInputObject(object);
 351     sliceRelPosFilter->SetDirection(direction);
 352     sliceRelPosFilter->SetFuzzyThreshold(threshold);
 353     sliceRelPosFilter->AddOrientationTypeString(orientation);
 354     sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
 355     sliceRelPosFilter->SetIntermediateSpacing(spacing);
 356     sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
 357     sliceRelPosFilter->CCLSelectionFlagOff();
 358     sliceRelPosFilter->SetUseASingleObjectConnectedComponentBySliceFlag(singleObjectCCL);
 359     //    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 360     sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
 361     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 362     sliceRelPosFilter->Update();
 363     return sliceRelPosFilter->GetOutput();
 364   }
 365   //--------------------------------------------------------------------
 366
 367   //--------------------------------------------------------------------
 368   template<class ImageType>
 369   bool
 370   FindExtremaPointInAGivenDirection(const ImageType * input,
 371                                     typename ImageType::PixelType bg,
 372                                     int direction, bool opposite,
 373                                     typename ImageType::PointType & point)
 374   {
 375     typename ImageType::PointType dummy;
 376     return FindExtremaPointInAGivenDirection(input, bg, direction,
 377                                              opposite, dummy, 0, point);
 378   }
 379   //--------------------------------------------------------------------
 380
 381   //--------------------------------------------------------------------
 382   template<class ImageType>
 383   bool
 384   FindExtremaPointInAGivenDirection(const ImageType * input,
 385                                     typename ImageType::PixelType bg,
 386                                     int direction, bool opposite,
 387                                     typename ImageType::PointType refpoint,
 388                                     double distanceMax,
 389                                     typename ImageType::PointType & point)
 390   {
 391     /*
 392       loop over input pixels, store the index in the fg that is max
 393       according to the given direction.
 394     */
 395     typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
 396     IteratorType iter(input, input->GetLargestPossibleRegion());
 397     iter.GoToBegin();
 398     typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
 399     if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
 400     bool found=false;
 401     while (!iter.IsAtEnd()) {
 402       if (iter.Get() != bg) {
 403         bool test = iter.GetIndex()[direction] >  max[direction];
 404         if (opposite) test = !test;
 405         if (test) {
 406           typename ImageType::PointType p;
 407           input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
 408           if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
 409             max = iter.GetIndex();
 410             found = true;
 411           }
 412         }
 413       }
 414       ++iter;
 415     }
 416     if (!found) return false;
 417     input->TransformIndexToPhysicalPoint(max, point);
 418     return true;
 419   }
 420   //--------------------------------------------------------------------
 421
 422
 423   //--------------------------------------------------------------------
 424   template<class ImageType>
 425   typename ImageType::Pointer
 426   CropImageRemoveGreaterThan(const ImageType * image,
 427                  int dim, double min, bool autoCrop,
 428                  typename ImageType::PixelType BG)
 429   {
 430     return CropImageAlongOneAxis<ImageType>(image, dim,
 431                                             image->GetOrigin()[dim],
 432                                             min,
 433                                             autoCrop, BG);
 434   }
 435   //--------------------------------------------------------------------
 436
 437
 438   //--------------------------------------------------------------------
 439   template<class ImageType>
 440   typename ImageType::Pointer
 441   CropImageRemoveLowerThan(const ImageType * image,
 442                  int dim, double max, bool autoCrop,
 443                  typename ImageType::PixelType BG)
 444   {
 445     typename ImageType::PointType p;
 446     image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
 447                                          image->GetLargestPossibleRegion().GetSize(), p);
 448     return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
 449   }
 450   //--------------------------------------------------------------------
 451
 452
 453   //--------------------------------------------------------------------
 454   template<class ImageType>
 455   typename ImageType::Pointer
 456   CropImageAlongOneAxis(const ImageType * image,
 457                         int dim, double min, double max,
 458                         bool autoCrop, typename ImageType::PixelType BG)
 459   {
 460     // Compute region size
 461     typename ImageType::RegionType region;
 462     typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 463     typename ImageType::PointType p = image->GetOrigin();
 464     p[dim] = min;
 465     typename ImageType::IndexType start;
 466     image->TransformPhysicalPointToIndex(p, start);
 467     p[dim] = max;
 468     typename ImageType::IndexType end;
 469     image->TransformPhysicalPointToIndex(p, end);
 470     size[dim] = abs(end[dim]-start[dim]);
 471     region.SetIndex(start);
 472     region.SetSize(size);
 473
 474     // Perform Crop
 475     typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 476     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 477     cropFilter->SetInput(image);
 478     cropFilter->SetRegionOfInterest(region);
 479     cropFilter->Update();
 480     typename ImageType::Pointer result = cropFilter->GetOutput();
 481
 482     // Auto Crop
 483     if (autoCrop) {
 484       result = AutoCrop<ImageType>(result, BG);
 485     }
 486     return result;
 487   }
 488   //--------------------------------------------------------------------
 489
 490
 491   //--------------------------------------------------------------------
 492   template<class ImageType>
 493   void
 494   ComputeCentroids(const ImageType * image,
 495                    typename ImageType::PixelType BG,
 496                    std::vector<typename ImageType::PointType> & centroids)
 497   {
 498     typedef long LabelType;
 499     static const unsigned int Dim = ImageType::ImageDimension;
 500     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 501     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 502     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 503     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 504     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 505     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 506     imageToLabelFilter->SetBackgroundValue(BG);
 507     imageToLabelFilter->SetInput(image);
 508     statFilter->SetInput(imageToLabelFilter->GetOutput());
 509     statFilter->Update();
 510     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 511
 512     centroids.clear();
 513     typename ImageType::PointType dummy;
 514     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG
 515     //DS FIXME (not useful ! to change ..)
 516     for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
 517       int label = labelMap->GetLabels()[i];
 518       centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
 519     }
 520   }
 521   //--------------------------------------------------------------------
 522
 523
 524   //--------------------------------------------------------------------
 525   template<class ImageType, class LabelType>
 526   typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
 527   ComputeLabelMap(const ImageType * image,
 528                   typename ImageType::PixelType BG,
 529                   bool computePerimeterFlag)
 530   {
 531     static const unsigned int Dim = ImageType::ImageDimension;
 532     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 533     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 534     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 535     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 536     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 537     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 538     imageToLabelFilter->SetBackgroundValue(BG);
 539     imageToLabelFilter->SetInput(image);
 540     statFilter->SetInput(imageToLabelFilter->GetOutput());
 541     statFilter->SetComputePerimeter(computePerimeterFlag);
 542     statFilter->Update();
 543     return statFilter->GetOutput();
 544   }
 545   //--------------------------------------------------------------------
 546
 547
 548   //--------------------------------------------------------------------
 549   template<class ImageType>
 550   void
 551   ComputeCentroids2(const ImageType * image,
 552                    typename ImageType::PixelType BG,
 553                    std::vector<typename ImageType::PointType> & centroids)
 554   {
 555     typedef long LabelType;
 556     static const unsigned int Dim = ImageType::ImageDimension;
 557     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 558     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 559     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 560     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 561     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 562     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 563     imageToLabelFilter->SetBackgroundValue(BG);
 564     imageToLabelFilter->SetInput(image);
 565     statFilter->SetInput(imageToLabelFilter->GetOutput());
 566     statFilter->Update();
 567     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 568
 569     centroids.clear();
 570     typename ImageType::PointType dummy;
 571     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 572     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 573       centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 574     }
 575
 576     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 577       DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
 578       DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
 579       DD(labelMap->GetLabelObject(i)->GetRoundness ());
 580
 581       // search for the point on the boundary alog PA
 582
 583     }
 584
 585   }
 586   //--------------------------------------------------------------------
 587
 588
 589   //--------------------------------------------------------------------
 590   template<class ImageType>
 591   void
 592   PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
 593                                         const ImageType * image,
 594                                         const int slice,
 595                                         PointType3D & p3D)
 596   {
 597     IndexType3D index3D;
 598     index3D[0] = index3D[1] = 0;
 599     index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
 600     image->TransformIndexToPhysicalPoint(index3D, p3D);
 601     p3D[0] = p2D[0];
 602     p3D[1] = p2D[1];
 603     //  p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 604     //    + image->GetOrigin()[2];
 605   }
 606   //--------------------------------------------------------------------
 607
 608
 609   //--------------------------------------------------------------------
 610   template<class ImageType>
 611   void
 612   PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
 613                                             const ImageType * image,
 614                                             VectorPoint3DType & list)
 615   {
 616     typename MapPoint2DType::const_iterator iter = map.begin();
 617     while (iter != map.end()) {
 618       PointType3D p;
 619       Convert2DTo3D(iter->second, image, iter->first, p);
 620       list.push_back(p);
 621       ++iter;
 622     }
 623   }
 624   //--------------------------------------------------------------------
 625
 626
 627   //--------------------------------------------------------------------
 628   template<class ImageType>
 629   void
 630   PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D,
 631                                                 int slice,
 632                                                 const ImageType * image,
 633                                                 VectorPoint3DType & list)
 634   {
 635     for(uint i=0; i<p2D.size(); i++) {
 636       PointType3D p;
 637       Convert2DTo3D(p2D[i], image, slice, p);
 638       list.push_back(p);
 639     }
 640   }
 641   //--------------------------------------------------------------------
 642
 643
 644   //--------------------------------------------------------------------
 645   template<class ImageType>
 646   void
 647   WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 648                        std::string filename)
 649   {
 650     std::ofstream os;
 651     openFileForWriting(os, filename);
 652     os << "LANDMARKS1" << std::endl;
 653     for(uint i=0; i<points.size(); i++) {
 654       const typename ImageType::PointType & p = points[i];
 655       // Write it in the file
 656       os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 657     }
 658     os.close();
 659   }
 660   //--------------------------------------------------------------------
 661
 662
 663   //--------------------------------------------------------------------
 664   template<class ImageType>
 665   typename ImageType::Pointer
 666   Dilate(const ImageType * image, double radiusInMM,
 667          typename ImageType::PixelType BG,
 668          typename ImageType::PixelType FG,
 669          bool extendSupport)
 670   {
 671     typename ImageType::SizeType r;
 672     for(uint i=0; i<ImageType::ImageDimension; i++)
 673       r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 674     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 675   }
 676   //--------------------------------------------------------------------
 677
 678
 679   //--------------------------------------------------------------------
 680   template<class ImageType>
 681   typename ImageType::Pointer
 682   Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
 683          typename ImageType::PixelType BG,
 684          typename ImageType::PixelType FG,
 685          bool extendSupport)
 686   {
 687     typename ImageType::SizeType r;
 688     for(uint i=0; i<ImageType::ImageDimension; i++)
 689       r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 690     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 691   }
 692   //--------------------------------------------------------------------
 693
 694
 695   //--------------------------------------------------------------------
 696   template<class ImageType>
 697   typename ImageType::Pointer
 698   Dilate(const ImageType * image, typename ImageType::SizeType radius,
 699          typename ImageType::PixelType BG,
 700          typename ImageType::PixelType FG,
 701          bool extendSupport)
 702   {
 703     // Create kernel for dilatation
 704     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 705                                               ImageType::ImageDimension> KernelType;
 706     KernelType structuringElement;
 707     structuringElement.SetRadius(radius);
 708     structuringElement.CreateStructuringElement();
 709
 710     typename ImageType::Pointer output;
 711     if (extendSupport) {
 712       typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 713       typename PadFilterType::Pointer padFilter = PadFilterType::New();
 714       padFilter->SetInput(image);
 715       typename ImageType::SizeType lower;
 716       typename ImageType::SizeType upper;
 717       for(uint i=0; i<3; i++) {
 718         lower[i] = upper[i] = 2*(radius[i]+1);
 719       }
 720       padFilter->SetPadLowerBound(lower);
 721       padFilter->SetPadUpperBound(upper);
 722       padFilter->Update();
 723       output = padFilter->GetOutput();
 724     }
 725
 726     // Dilate  filter
 727     typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 728     typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 729     dilateFilter->SetBackgroundValue(BG);
 730     dilateFilter->SetForegroundValue(FG);
 731     dilateFilter->SetBoundaryToForeground(false);
 732     dilateFilter->SetKernel(structuringElement);
 733     if (extendSupport) dilateFilter->SetInput(output);
 734     else dilateFilter->SetInput(image);
 735     dilateFilter->Update();
 736     return dilateFilter->GetOutput();
 737   }
 738   //--------------------------------------------------------------------
 739
 740
 741   //--------------------------------------------------------------------
 742   template<class ImageType>
 743   typename ImageType::Pointer
 744   Opening(const ImageType * image, typename ImageType::SizeType radius,
 745          typename ImageType::PixelType BG,
 746          typename ImageType::PixelType FG)
 747   {
 748     // Kernel
 749     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 750                                               ImageType::ImageDimension> KernelType;
 751     KernelType structuringElement;
 752     structuringElement.SetRadius(radius);
 753     structuringElement.CreateStructuringElement();
 754
 755     // Filter
 756     typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
 757     typename OpeningFilterType::Pointer open = OpeningFilterType::New();
 758     open->SetInput(image);
 759     open->SetBackgroundValue(BG);
 760     open->SetForegroundValue(FG);
 761     open->SetKernel(structuringElement);
 762     open->Update();
 763     return open->GetOutput();
 764   }
 765   //--------------------------------------------------------------------
 766
 767
 768
 769   //--------------------------------------------------------------------
 770   template<class ValueType, class VectorType>
 771   void ConvertOption(std::string optionName, uint given,
 772                      ValueType * values, VectorType & p,
 773                      uint dim, bool required)
 774   {
 775     if (required && (given == 0)) {
 776       clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 777                           << dim << " values.");
 778     }
 779     if (given == 1) {
 780       for(uint i=0; i<dim; i++) p[i] = values[0];
 781       return;
 782     }
 783     if (given == dim) {
 784       for(uint i=0; i<dim; i++) p[i] = values[i];
 785       return;
 786     }
 787     if (given == 0) return;
 788     clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 789                         << dim << " values.");
 790   }
 791   //--------------------------------------------------------------------
 792
 793
 794   //--------------------------------------------------------------------
 795   /*
 796     http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
 797     Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
 798     (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
 799     This will equal zero if the point C is on the line formed by
 800     points A and B, and will have a different sign depending on the
 801     side. Which side this is depends on the orientation of your (x,y)
 802     coordinates, but you can plug test values for A,B and C into this
 803     formula to determine whether negative values are to the left or to
 804     the right.
 805     => to accelerate, start with formula, when change sign -> stop and fill
 806
 807     offsetToKeep = is used to determine which side of the line we
 808     keep. The point along the mainDirection but 'offsetToKeep' mm away
 809     is kept.
 810
 811   */
 812   template<class ImageType>
 813   void
 814   SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
 815                                               std::vector<typename ImageType::PointType> & lA,
 816                                               std::vector<typename ImageType::PointType> & lB,
 817                                               typename ImageType::PixelType BG,
 818                                               int mainDirection,
 819                                               double offsetToKeep)
 820   {
 821     typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
 822     SliceIteratorType siter = SliceIteratorType(input,
 823                                                 input->GetLargestPossibleRegion());
 824     siter.SetFirstDirection(0);
 825     siter.SetSecondDirection(1);
 826     siter.GoToBegin();
 827     uint i=0;
 828     typename ImageType::PointType A;
 829     typename ImageType::PointType B;
 830     typename ImageType::PointType C;
 831     assert(lA.size() == lB.size());
 832     while ((i<lA.size()) && (!siter.IsAtEnd())) {
 833       // Check that the current slice correspond to the current point
 834       input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 835       if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
 836       }
 837       else {
 838         // Define A,B,C points
 839         A = lA[i];
 840         B = lB[i];
 841         C = A;
 842
 843         // Check that the line is not a point (A=B)
 844         bool p = (A[0] == B[0]) && (A[1] == B[1]);
 845
 846         if (!p) {
 847           C[mainDirection] += offsetToKeep; // I know I must keep this point
 848           double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 849           bool isPositive = s<0;
 850           while (!siter.IsAtEndOfSlice()) {
 851             while (!siter.IsAtEndOfLine()) {
 852               // Very slow, I know ... but image should be very small
 853               input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 854               double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 855               if (s == 0) siter.Set(BG); // on the line, we decide to remove
 856               if (isPositive) {
 857                 if (s > 0) siter.Set(BG);
 858               }
 859               else {
 860                 if (s < 0) siter.Set(BG);
 861               }
 862               ++siter;
 863             }
 864             siter.NextLine();
 865           } // end loop slice
 866         }
 867
 868         ++i;
 869       } // End of current slice
 870       siter.NextSlice();
 871     }
 872   }
 873   //--------------------------------------------------------------------
 874
 875
 876   //--------------------------------------------------------------------
 877   template<class ImageType>
 878   void
 879   AndNot(ImageType * input,
 880          const ImageType * object,
 881          typename ImageType::PixelType BG)
 882   {
 883     typename ImageType::Pointer o;
 884     bool resized=false;
 885     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 886       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 887       resized = true;
 888     }
 889
 890     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 891     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 892     boolFilter->InPlaceOn();
 893     boolFilter->SetInput1(input);
 894     if (resized) boolFilter->SetInput2(o);
 895     else boolFilter->SetInput2(object);
 896     boolFilter->SetBackgroundValue1(BG);
 897     boolFilter->SetBackgroundValue2(BG);
 898     boolFilter->SetOperationType(BoolFilterType::AndNot);
 899     boolFilter->Update();
 900   }
 901   //--------------------------------------------------------------------
 902
 903
 904   //--------------------------------------------------------------------
 905   template<class ImageType>
 906   void
 907   And(ImageType * input,
 908       const ImageType * object,
 909       typename ImageType::PixelType BG)
 910   {
 911     typename ImageType::Pointer o;
 912     bool resized=false;
 913     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 914       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 915       resized = true;
 916     }
 917
 918     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 919     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 920     boolFilter->InPlaceOn();
 921     boolFilter->SetInput1(input);
 922     if (resized) boolFilter->SetInput2(o);
 923     else boolFilter->SetInput2(object);
 924     boolFilter->SetBackgroundValue1(BG);
 925     boolFilter->SetBackgroundValue2(BG);
 926     boolFilter->SetOperationType(BoolFilterType::And);
 927     boolFilter->Update();
 928   }
 929   //--------------------------------------------------------------------
 930
 931
 932   //--------------------------------------------------------------------
 933   template<class ImageType>
 934   typename ImageType::Pointer
 935   Binarize(const ImageType * input,
 936            typename ImageType::PixelType lower,
 937            typename ImageType::PixelType upper,
 938            typename ImageType::PixelType BG,
 939            typename ImageType::PixelType FG)
 940   {
 941     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
 942     typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
 943     binarizeFilter->SetInput(input);
 944     binarizeFilter->InPlaceOff();
 945     binarizeFilter->SetLowerThreshold(lower);
 946     binarizeFilter->SetUpperThreshold(upper);
 947     binarizeFilter->SetInsideValue(FG);
 948     binarizeFilter->SetOutsideValue(BG);
 949     binarizeFilter->Update();
 950     return binarizeFilter->GetOutput();
 951   }
 952   //--------------------------------------------------------------------
 953
 954
 955   //--------------------------------------------------------------------
 956   template<class ImageType>
 957   void
 958   GetMinMaxPointPosition(const ImageType * input,
 959                          typename ImageType::PointType & min,
 960                          typename ImageType::PointType & max)
 961   {
 962     typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
 963     input->TransformIndexToPhysicalPoint(index, min);
 964     index = index+input->GetLargestPossibleRegion().GetSize();
 965     input->TransformIndexToPhysicalPoint(index, max);
 966   }
 967   //--------------------------------------------------------------------
 968
 969
 970   //--------------------------------------------------------------------
 971   template<class ImageType>
 972   typename ImageType::PointType
 973   FindExtremaPointInAGivenLine(const ImageType * input,
 974                                int dimension,
 975                                bool inverse,
 976                                typename ImageType::PointType p,
 977                                typename ImageType::PixelType BG,
 978                                double distanceMax)
 979   {
 980     // Which direction ?  Increasing or decreasing.
 981     int d=1;
 982     if (inverse) d=-1;
 983
 984     // Transform to pixel index
 985     typename ImageType::IndexType index;
 986     input->TransformPhysicalPointToIndex(p, index);
 987
 988     // Loop while inside the mask;
 989     while (input->GetPixel(index) != BG) {
 990       index[dimension] += d;
 991     }
 992
 993     // Transform back to Physical Units
 994     typename ImageType::PointType result;
 995     input->TransformIndexToPhysicalPoint(index, result);
 996
 997     // Check that is is not too far away
 998     double distance = p.EuclideanDistanceTo(result);
 999     if (distance > distanceMax) {
1000       result = p; // Get back to initial value
1001     }
1002
1003     return result;
1004   }
1005   //--------------------------------------------------------------------
1006
1007
1008   //--------------------------------------------------------------------
1009   template<class PointType>
1010   bool
1011   IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
1012   {
1013     // Look at the position of point 'like' according to the AB line
1014     double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
1015     bool negative = s<0;
1016
1017     // Look the C position
1018     s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
1019
1020     if (negative && (s<=0)) return true;
1021     if (!negative && (s>=0)) return true;
1022     return false;
1023   }
1024   //--------------------------------------------------------------------
1025
1026
1027   //--------------------------------------------------------------------
1028   /* Consider an input object, for each slice, find the extrema
1029      position according to a given direction and build a line segment
1030      passing throught this point in a given direction.  Output is a
1031      vector of line (from point A to B), for each slice;
1032    */
1033   template<class ImageType>
1034   void
1035   SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
1036                                                          typename ImageType::PixelType BG,
1037                                                          int sliceDimension,
1038                                                          int extremaDirection,
1039                                                          bool extremaOppositeFlag,
1040                                                          int lineDirection,
1041                                                          double margin,
1042                                                          std::vector<typename ImageType::PointType> & A,
1043                                                          std::vector<typename ImageType::PointType> & B)
1044   {
1045     // Type of a slice
1046     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1047
1048     // Build the list of slices
1049     std::vector<typename SliceType::Pointer> slices;
1050     clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
1051
1052     // Build the list of 2D points
1053     std::map<int, typename SliceType::PointType> position2D;
1054     for(uint i=0; i<slices.size(); i++) {
1055       typename SliceType::PointType p;
1056       bool found =
1057         clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
1058                                                             extremaDirection, extremaOppositeFlag, p);
1059       if (found) {
1060         position2D[i] = p;
1061       }
1062     }
1063
1064     // Convert 2D points in slice into 3D points
1065     clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
1066
1067     // Create additional point just right to the previous ones, on the
1068     // given lineDirection, in order to create a horizontal/vertical line.
1069     for(uint i=0; i<A.size(); i++) {
1070       typename ImageType::PointType p = A[i];
1071       p[lineDirection] += 10;
1072       B.push_back(p);
1073       // Margins ?
1074       A[i][extremaDirection] += margin;
1075       B[i][extremaDirection] += margin;
1076     }
1077
1078   }
1079   //--------------------------------------------------------------------
1080
1081
1082   //--------------------------------------------------------------------
1083   template<class ImageType>
1084   typename ImageType::Pointer
1085   SliceBySliceKeepMainCCL(const ImageType * input,
1086                           typename ImageType::PixelType BG,
1087                           typename ImageType::PixelType FG)  {
1088
1089     // Extract slices
1090     const int d = ImageType::ImageDimension-1;
1091     typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
1092     std::vector<typename SliceType::Pointer> slices;
1093     clitk::ExtractSlices<ImageType>(input, d, slices);
1094
1095     // Labelize and keep the main one
1096     std::vector<typename SliceType::Pointer> o;
1097     for(uint i=0; i<slices.size(); i++) {
1098       o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
1099       o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
1100     }
1101
1102     // Join slices
1103     typename ImageType::Pointer output;
1104     output = clitk::JoinSlices<ImageType>(o, input, d);
1105     return output;
1106   }
1107   //--------------------------------------------------------------------
1108
1109
1110   //--------------------------------------------------------------------
1111   template<class ImageType>
1112   typename ImageType::Pointer
1113   Clone(const ImageType * input) {
1114     typedef itk::ImageDuplicator<ImageType> DuplicatorType;
1115     typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
1116     duplicator->SetInputImage(input);
1117     duplicator->Update();
1118     return duplicator->GetOutput();
1119   }
1120   //--------------------------------------------------------------------
1121
1122
1123   //--------------------------------------------------------------------
1124   /* Consider an input object, start at A, for each slice (dim1):
1125      - compute the intersection between the AB line and the current slice
1126      - remove what is at lower or greater according to dim2 of this point
1127      - stop at B
1128   */
1129   template<class ImageType>
1130   typename ImageType::Pointer
1131   SliceBySliceSetBackgroundFromSingleLine(const ImageType * input,
1132                                           typename ImageType::PixelType BG,
1133                                           typename ImageType::PointType & A,
1134                                           typename ImageType::PointType & B,
1135                                           int dim1, int dim2, bool removeLowerPartFlag)
1136
1137   {
1138     // Extract slices
1139     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1140     typedef typename SliceType::Pointer SlicePointer;
1141     std::vector<SlicePointer> slices;
1142     clitk::ExtractSlices<ImageType>(input, dim1, slices);
1143
1144     // Start at slice that contains A, and stop at B
1145     typename ImageType::IndexType Ap;
1146     typename ImageType::IndexType Bp;
1147     input->TransformPhysicalPointToIndex(A, Ap);
1148     input->TransformPhysicalPointToIndex(B, Bp);
1149
1150     // Determine slice largest region
1151     typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1152     typename SliceType::SizeType size = region.GetSize();
1153     typename SliceType::IndexType index = region.GetIndex();
1154
1155     // Line slope
1156     double a = (Bp[dim2]-Ap[dim2])/(Bp[dim1]-Ap[dim1]);
1157     double b = Ap[dim2];
1158
1159     // Loop from slice A to slice B
1160     for(uint i=0; i<(Bp[dim1]-Ap[dim1]); i++) {
1161       // Compute intersection between line AB and current slice for the dim2
1162       double p = a*i+b;
1163       // Change region (lower than dim2)
1164       if (removeLowerPartFlag) {
1165         size[dim2] = p-Ap[dim2];
1166       }
1167       else {
1168         size[dim2] = slices[0]->GetLargestPossibleRegion().GetSize()[dim2]-p;
1169         index[dim2] = p;
1170       }
1171       region.SetSize(size);
1172       region.SetIndex(index);
1173       // Fill region with BG (simple region iterator)
1174       FillRegionWithValue<SliceType>(slices[i+Ap[dim1]], BG, region);
1175       /*
1176       typedef itk::ImageRegionIterator<SliceType> IteratorType;
1177       IteratorType iter(slices[i+Ap[dim1]], region);
1178       iter.GoToBegin();
1179       while (!iter.IsAtEnd()) {
1180         iter.Set(BG);
1181         ++iter;
1182       }
1183       */
1184       // Loop
1185     }
1186
1187     // Merge slices
1188     typename ImageType::Pointer output;
1189     output = clitk::JoinSlices<ImageType>(slices, input, dim1);
1190     return output;
1191   }
1192   //--------------------------------------------------------------------
1193
1194   //--------------------------------------------------------------------
1195   /* Consider an input object, slice by slice, use the point A and set
1196      pixel to BG according to their position relatively to A
1197   */
1198   template<class ImageType>
1199   typename ImageType::Pointer
1200   SliceBySliceSetBackgroundFromPoints(const ImageType * input,
1201                                       typename ImageType::PixelType BG,
1202                                       int sliceDim,
1203                                       std::vector<typename ImageType::PointType> & A,
1204                                       bool removeGreaterThanXFlag,
1205                                       bool removeGreaterThanYFlag)
1206
1207   {
1208     // Extract slices
1209     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1210     typedef typename SliceType::Pointer SlicePointer;
1211     std::vector<SlicePointer> slices;
1212     clitk::ExtractSlices<ImageType>(input, sliceDim, slices);
1213
1214     // Start at slice that contains A
1215     typename ImageType::IndexType Ap;
1216
1217     // Determine slice largest region
1218     typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1219     typename SliceType::SizeType size = region.GetSize();
1220     typename SliceType::IndexType index = region.GetIndex();
1221
1222     // Loop from slice A to slice B
1223     for(uint i=0; i<A.size(); i++) {
1224       input->TransformPhysicalPointToIndex(A[i], Ap);
1225       uint sliceIndex = Ap[2] - input->GetLargestPossibleRegion().GetIndex()[2];
1226       if ((sliceIndex < 0) || (sliceIndex >= slices.size())) {
1227         continue; // do not consider this slice
1228       }
1229
1230       // Compute region for BG
1231       if (removeGreaterThanXFlag) {
1232         index[0] = Ap[0];
1233         size[0] = region.GetSize()[0]-(index[0]-region.GetIndex()[0]);
1234       }
1235       else {
1236         index[0] = region.GetIndex()[0];
1237         size[0] = Ap[0] - index[0];
1238       }
1239
1240       if (removeGreaterThanYFlag) {
1241         index[1] = Ap[1];
1242         size[1] = region.GetSize()[1]-(index[1]-region.GetIndex()[1]);
1243       }
1244       else {
1245         index[1] = region.GetIndex()[1];
1246         size[1] = Ap[1] - index[1];
1247       }
1248
1249       // Set region
1250       region.SetSize(size);
1251       region.SetIndex(index);
1252
1253       // Fill region with BG (simple region iterator)
1254       FillRegionWithValue<SliceType>(slices[sliceIndex], BG, region);
1255       // Loop
1256     }
1257
1258     // Merge slices
1259     typename ImageType::Pointer output;
1260     output = clitk::JoinSlices<ImageType>(slices, input, sliceDim);
1261     return output;
1262   }
1263   //--------------------------------------------------------------------
1264
1265
1266   //--------------------------------------------------------------------
1267   template<class ImageType>
1268   void
1269   FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region)
1270   {
1271     typedef itk::ImageRegionIterator<ImageType> IteratorType;
1272     IteratorType iter(input, region);
1273     iter.GoToBegin();
1274     while (!iter.IsAtEnd()) {
1275       iter.Set(value);
1276       ++iter;
1277     }
1278   }
1279   //--------------------------------------------------------------------
1280
1281
1282   //--------------------------------------------------------------------
1283   template<class ImageType>
1284   void
1285   GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min,
1286                     typename ImageType::PointType & max)
1287   {
1288     typedef typename ImageType::PointType PointType;
1289     typedef typename ImageType::IndexType IndexType;
1290     IndexType min_i, max_i;
1291     min_i = input->GetLargestPossibleRegion().GetIndex();
1292     for(uint i=0; i<ImageType::ImageDimension; i++)
1293       max_i[i] = input->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
1294     input->TransformIndexToPhysicalPoint(min_i, min);
1295     input->TransformIndexToPhysicalPoint(max_i, max);
1296   }
1297   //--------------------------------------------------------------------
1298
1299 } // end of namespace
1300