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->SetUseASingleObjectConnectedComponentBySliceFlag(singleObjectCCL);
 358     //    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 359     sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
 360     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 361     sliceRelPosFilter->Update();
 362     return sliceRelPosFilter->GetOutput();
 363   }
 364   //--------------------------------------------------------------------
 365
 366   //--------------------------------------------------------------------
 367   template<class ImageType>
 368   bool
 369   FindExtremaPointInAGivenDirection(const ImageType * input,
 370                                     typename ImageType::PixelType bg,
 371                                     int direction, bool opposite,
 372                                     typename ImageType::PointType & point)
 373   {
 374     typename ImageType::PointType dummy;
 375     return FindExtremaPointInAGivenDirection(input, bg, direction,
 376                                              opposite, dummy, 0, point);
 377   }
 378   //--------------------------------------------------------------------
 379
 380   //--------------------------------------------------------------------
 381   template<class ImageType>
 382   bool
 383   FindExtremaPointInAGivenDirection(const ImageType * input,
 384                                     typename ImageType::PixelType bg,
 385                                     int direction, bool opposite,
 386                                     typename ImageType::PointType refpoint,
 387                                     double distanceMax,
 388                                     typename ImageType::PointType & point)
 389   {
 390     /*
 391       loop over input pixels, store the index in the fg that is max
 392       according to the given direction.
 393     */
 394     typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
 395     IteratorType iter(input, input->GetLargestPossibleRegion());
 396     iter.GoToBegin();
 397     typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
 398     if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
 399     bool found=false;
 400     while (!iter.IsAtEnd()) {
 401       if (iter.Get() != bg) {
 402         bool test = iter.GetIndex()[direction] >  max[direction];
 403         if (opposite) test = !test;
 404         if (test) {
 405           typename ImageType::PointType p;
 406           input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
 407           if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
 408             max = iter.GetIndex();
 409             found = true;
 410           }
 411         }
 412       }
 413       ++iter;
 414     }
 415     if (!found) return false;
 416     input->TransformIndexToPhysicalPoint(max, point);
 417     return true;
 418   }
 419   //--------------------------------------------------------------------
 420
 421
 422   //--------------------------------------------------------------------
 423   template<class ImageType>
 424   typename ImageType::Pointer
 425   CropImageRemoveGreaterThan(const ImageType * image,
 426                  int dim, double min, bool autoCrop,
 427                  typename ImageType::PixelType BG)
 428   {
 429     return CropImageAlongOneAxis<ImageType>(image, dim,
 430                                             image->GetOrigin()[dim],
 431                                             min,
 432                                             autoCrop, BG);
 433   }
 434   //--------------------------------------------------------------------
 435
 436
 437   //--------------------------------------------------------------------
 438   template<class ImageType>
 439   typename ImageType::Pointer
 440   CropImageRemoveLowerThan(const ImageType * image,
 441                  int dim, double max, bool autoCrop,
 442                  typename ImageType::PixelType BG)
 443   {
 444     typename ImageType::PointType p;
 445     image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
 446                                          image->GetLargestPossibleRegion().GetSize(), p);
 447     return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
 448   }
 449   //--------------------------------------------------------------------
 450
 451
 452   //--------------------------------------------------------------------
 453   template<class ImageType>
 454   typename ImageType::Pointer
 455   CropImageAlongOneAxis(const ImageType * image,
 456                         int dim, double min, double max,
 457                         bool autoCrop, typename ImageType::PixelType BG)
 458   {
 459     // Compute region size
 460     typename ImageType::RegionType region;
 461     typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 462     typename ImageType::PointType p = image->GetOrigin();
 463     p[dim] = min;
 464     typename ImageType::IndexType start;
 465     image->TransformPhysicalPointToIndex(p, start);
 466     p[dim] = max;
 467     typename ImageType::IndexType end;
 468     image->TransformPhysicalPointToIndex(p, end);
 469     size[dim] = abs(end[dim]-start[dim]);
 470     region.SetIndex(start);
 471     region.SetSize(size);
 472
 473     // Perform Crop
 474     typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 475     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 476     cropFilter->SetInput(image);
 477     cropFilter->SetRegionOfInterest(region);
 478     cropFilter->Update();
 479     typename ImageType::Pointer result = cropFilter->GetOutput();
 480
 481     // Auto Crop
 482     if (autoCrop) {
 483       result = AutoCrop<ImageType>(result, BG);
 484     }
 485     return result;
 486   }
 487   //--------------------------------------------------------------------
 488
 489
 490   //--------------------------------------------------------------------
 491   template<class ImageType>
 492   void
 493   ComputeCentroids(const ImageType * image,
 494                    typename ImageType::PixelType BG,
 495                    std::vector<typename ImageType::PointType> & centroids)
 496   {
 497     typedef long LabelType;
 498     static const unsigned int Dim = ImageType::ImageDimension;
 499     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 500     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 501     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 502     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 503     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 504     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 505     imageToLabelFilter->SetBackgroundValue(BG);
 506     imageToLabelFilter->SetInput(image);
 507     statFilter->SetInput(imageToLabelFilter->GetOutput());
 508     statFilter->Update();
 509     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 510
 511     centroids.clear();
 512     typename ImageType::PointType dummy;
 513     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG
 514     //DS FIXME (not useful ! to change ..)
 515     for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
 516       int label = labelMap->GetLabels()[i];
 517       centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
 518     }
 519   }
 520   //--------------------------------------------------------------------
 521
 522
 523   //--------------------------------------------------------------------
 524   template<class ImageType, class LabelType>
 525   typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
 526   ComputeLabelMap(const ImageType * image,
 527                   typename ImageType::PixelType BG,
 528                   bool computePerimeterFlag)
 529   {
 530     static const unsigned int Dim = ImageType::ImageDimension;
 531     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 532     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 533     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 534     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 535     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 536     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 537     imageToLabelFilter->SetBackgroundValue(BG);
 538     imageToLabelFilter->SetInput(image);
 539     statFilter->SetInput(imageToLabelFilter->GetOutput());
 540     statFilter->SetComputePerimeter(computePerimeterFlag);
 541     statFilter->Update();
 542     return statFilter->GetOutput();
 543   }
 544   //--------------------------------------------------------------------
 545
 546
 547   //--------------------------------------------------------------------
 548   template<class ImageType>
 549   void
 550   ComputeCentroids2(const ImageType * image,
 551                    typename ImageType::PixelType BG,
 552                    std::vector<typename ImageType::PointType> & centroids)
 553   {
 554     typedef long LabelType;
 555     static const unsigned int Dim = ImageType::ImageDimension;
 556     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 557     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 558     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 559     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 560     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 561     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 562     imageToLabelFilter->SetBackgroundValue(BG);
 563     imageToLabelFilter->SetInput(image);
 564     statFilter->SetInput(imageToLabelFilter->GetOutput());
 565     statFilter->Update();
 566     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 567
 568     centroids.clear();
 569     typename ImageType::PointType dummy;
 570     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 571     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 572       centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 573     }
 574
 575     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 576       DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
 577       DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
 578       DD(labelMap->GetLabelObject(i)->GetRoundness ());
 579
 580       // search for the point on the boundary alog PA
 581
 582     }
 583
 584   }
 585   //--------------------------------------------------------------------
 586
 587
 588   //--------------------------------------------------------------------
 589   template<class ImageType>
 590   void
 591   PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
 592                                         const ImageType * image,
 593                                         const int slice,
 594                                         PointType3D & p3D)
 595   {
 596     IndexType3D index3D;
 597     index3D[0] = index3D[1] = 0;
 598     index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
 599     image->TransformIndexToPhysicalPoint(index3D, p3D);
 600     p3D[0] = p2D[0];
 601     p3D[1] = p2D[1];
 602     //  p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 603     //    + image->GetOrigin()[2];
 604   }
 605   //--------------------------------------------------------------------
 606
 607
 608   //--------------------------------------------------------------------
 609   template<class ImageType>
 610   void
 611   PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
 612                                             const ImageType * image,
 613                                             VectorPoint3DType & list)
 614   {
 615     typename MapPoint2DType::const_iterator iter = map.begin();
 616     while (iter != map.end()) {
 617       PointType3D p;
 618       Convert2DTo3D(iter->second, image, iter->first, p);
 619       list.push_back(p);
 620       ++iter;
 621     }
 622   }
 623   //--------------------------------------------------------------------
 624
 625
 626   //--------------------------------------------------------------------
 627   template<class ImageType>
 628   void
 629   PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D,
 630                                                 int slice,
 631                                                 const ImageType * image,
 632                                                 VectorPoint3DType & list)
 633   {
 634     for(uint i=0; i<p2D.size(); i++) {
 635       PointType3D p;
 636       Convert2DTo3D(p2D[i], image, slice, p);
 637       list.push_back(p);
 638     }
 639   }
 640   //--------------------------------------------------------------------
 641
 642
 643   //--------------------------------------------------------------------
 644   template<class ImageType>
 645   void
 646   WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 647                        std::string filename)
 648   {
 649     std::ofstream os;
 650     openFileForWriting(os, filename);
 651     os << "LANDMARKS1" << std::endl;
 652     for(uint i=0; i<points.size(); i++) {
 653       const typename ImageType::PointType & p = points[i];
 654       // Write it in the file
 655       os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 656     }
 657     os.close();
 658   }
 659   //--------------------------------------------------------------------
 660
 661
 662   //--------------------------------------------------------------------
 663   template<class ImageType>
 664   typename ImageType::Pointer
 665   Dilate(const ImageType * image, double radiusInMM,
 666          typename ImageType::PixelType BG,
 667          typename ImageType::PixelType FG,
 668          bool extendSupport)
 669   {
 670     typename ImageType::SizeType r;
 671     for(uint i=0; i<ImageType::ImageDimension; i++)
 672       r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 673     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 674   }
 675   //--------------------------------------------------------------------
 676
 677
 678   //--------------------------------------------------------------------
 679   template<class ImageType>
 680   typename ImageType::Pointer
 681   Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
 682          typename ImageType::PixelType BG,
 683          typename ImageType::PixelType FG,
 684          bool extendSupport)
 685   {
 686     typename ImageType::SizeType r;
 687     for(uint i=0; i<ImageType::ImageDimension; i++)
 688       r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 689     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 690   }
 691   //--------------------------------------------------------------------
 692
 693
 694   //--------------------------------------------------------------------
 695   template<class ImageType>
 696   typename ImageType::Pointer
 697   Dilate(const ImageType * image, typename ImageType::SizeType radius,
 698          typename ImageType::PixelType BG,
 699          typename ImageType::PixelType FG,
 700          bool extendSupport)
 701   {
 702     // Create kernel for dilatation
 703     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 704                                               ImageType::ImageDimension> KernelType;
 705     KernelType structuringElement;
 706     structuringElement.SetRadius(radius);
 707     structuringElement.CreateStructuringElement();
 708
 709     typename ImageType::Pointer output;
 710     if (extendSupport) {
 711       typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 712       typename PadFilterType::Pointer padFilter = PadFilterType::New();
 713       padFilter->SetInput(image);
 714       typename ImageType::SizeType lower;
 715       typename ImageType::SizeType upper;
 716       for(uint i=0; i<3; i++) {
 717         lower[i] = upper[i] = 2*(radius[i]+1);
 718       }
 719       padFilter->SetPadLowerBound(lower);
 720       padFilter->SetPadUpperBound(upper);
 721       padFilter->Update();
 722       output = padFilter->GetOutput();
 723     }
 724
 725     // Dilate  filter
 726     typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 727     typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 728     dilateFilter->SetBackgroundValue(BG);
 729     dilateFilter->SetForegroundValue(FG);
 730     dilateFilter->SetBoundaryToForeground(false);
 731     dilateFilter->SetKernel(structuringElement);
 732     dilateFilter->SetInput(output);
 733     dilateFilter->Update();
 734     return dilateFilter->GetOutput();
 735   }
 736   //--------------------------------------------------------------------
 737
 738
 739   //--------------------------------------------------------------------
 740   template<class ImageType>
 741   typename ImageType::Pointer
 742   Opening(const ImageType * image, typename ImageType::SizeType radius,
 743          typename ImageType::PixelType BG,
 744          typename ImageType::PixelType FG)
 745   {
 746     // Kernel
 747     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 748                                               ImageType::ImageDimension> KernelType;
 749     KernelType structuringElement;
 750     structuringElement.SetRadius(radius);
 751     structuringElement.CreateStructuringElement();
 752
 753     // Filter
 754     typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
 755     typename OpeningFilterType::Pointer open = OpeningFilterType::New();
 756     open->SetInput(image);
 757     open->SetBackgroundValue(BG);
 758     open->SetForegroundValue(FG);
 759     open->SetKernel(structuringElement);
 760     open->Update();
 761     return open->GetOutput();
 762   }
 763   //--------------------------------------------------------------------
 764
 765
 766
 767   //--------------------------------------------------------------------
 768   template<class ValueType, class VectorType>
 769   void ConvertOption(std::string optionName, uint given,
 770                      ValueType * values, VectorType & p,
 771                      uint dim, bool required)
 772   {
 773     if (required && (given == 0)) {
 774       clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 775                           << dim << " values.");
 776     }
 777     if (given == 1) {
 778       for(uint i=0; i<dim; i++) p[i] = values[0];
 779       return;
 780     }
 781     if (given == dim) {
 782       for(uint i=0; i<dim; i++) p[i] = values[i];
 783       return;
 784     }
 785     if (given == 0) return;
 786     clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 787                         << dim << " values.");
 788   }
 789   //--------------------------------------------------------------------
 790
 791
 792   //--------------------------------------------------------------------
 793   /*
 794     http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
 795     Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
 796     (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
 797     This will equal zero if the point C is on the line formed by
 798     points A and B, and will have a different sign depending on the
 799     side. Which side this is depends on the orientation of your (x,y)
 800     coordinates, but you can plug test values for A,B and C into this
 801     formula to determine whether negative values are to the left or to
 802     the right.
 803     => to accelerate, start with formula, when change sign -> stop and fill
 804
 805     offsetToKeep = is used to determine which side of the line we
 806     keep. The point along the mainDirection but 'offsetToKeep' mm away
 807     is kept.
 808
 809   */
 810   template<class ImageType>
 811   void
 812   SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
 813                                               std::vector<typename ImageType::PointType> & lA,
 814                                               std::vector<typename ImageType::PointType> & lB,
 815                                               typename ImageType::PixelType BG,
 816                                               int mainDirection,
 817                                               double offsetToKeep)
 818   {
 819     typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
 820     SliceIteratorType siter = SliceIteratorType(input,
 821                                                 input->GetLargestPossibleRegion());
 822     siter.SetFirstDirection(0);
 823     siter.SetSecondDirection(1);
 824     siter.GoToBegin();
 825     uint i=0;
 826     typename ImageType::PointType A;
 827     typename ImageType::PointType B;
 828     typename ImageType::PointType C;
 829     assert(lA.size() == lB.size());
 830     while ((i<lA.size()) && (!siter.IsAtEnd())) {
 831       // Check that the current slice correspond to the current point
 832       input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 833       // DD(C);
 834       // DD(i);
 835       // DD(lA[i]);
 836       if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
 837       }
 838       else {
 839         // Define A,B,C points
 840         A = lA[i];
 841         B = lB[i];
 842         C = A;
 843         // DD(A);
 844         // DD(B);
 845         // DD(C);
 846
 847         // Check that the line is not a point (A=B)
 848         bool p = (A[0] == B[0]) && (A[1] == B[1]);
 849
 850         if (!p) {
 851           C[mainDirection] += offsetToKeep; // I know I must keep this point
 852           double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 853           bool isPositive = s<0;
 854           while (!siter.IsAtEndOfSlice()) {
 855             while (!siter.IsAtEndOfLine()) {
 856               // Very slow, I know ... but image should be very small
 857               input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 858               double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 859               if (s == 0) siter.Set(BG); // on the line, we decide to remove
 860               if (isPositive) {
 861                 if (s > 0) siter.Set(BG);
 862               }
 863               else {
 864                 if (s < 0) siter.Set(BG);
 865               }
 866               ++siter;
 867             }
 868             siter.NextLine();
 869           } // end loop slice
 870         }
 871
 872         ++i;
 873       } // End of current slice
 874       siter.NextSlice();
 875     }
 876   }
 877   //--------------------------------------------------------------------
 878
 879   //--------------------------------------------------------------------
 880   template<class ImageType>
 881   void
 882   AndNot(ImageType * input,
 883          const ImageType * object,
 884          typename ImageType::PixelType BG)
 885   {
 886     typename ImageType::Pointer o;
 887     bool resized=false;
 888     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 889       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 890       resized = true;
 891     }
 892
 893     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 894     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 895     boolFilter->InPlaceOn();
 896     boolFilter->SetInput1(input);
 897     if (resized) boolFilter->SetInput2(o);
 898     else boolFilter->SetInput2(object);
 899     boolFilter->SetBackgroundValue1(BG);
 900     boolFilter->SetBackgroundValue2(BG);
 901     boolFilter->SetOperationType(BoolFilterType::AndNot);
 902     boolFilter->Update();
 903   }
 904   //--------------------------------------------------------------------
 905
 906
 907   //--------------------------------------------------------------------
 908   template<class ImageType>
 909   typename ImageType::Pointer
 910   Binarize(const ImageType * input,
 911            typename ImageType::PixelType lower,
 912            typename ImageType::PixelType upper,
 913            typename ImageType::PixelType BG,
 914            typename ImageType::PixelType FG)
 915   {
 916     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
 917     typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
 918     binarizeFilter->SetInput(input);
 919     binarizeFilter->InPlaceOff();
 920     binarizeFilter->SetLowerThreshold(lower);
 921     binarizeFilter->SetUpperThreshold(upper);
 922     binarizeFilter->SetInsideValue(FG);
 923     binarizeFilter->SetOutsideValue(BG);
 924     binarizeFilter->Update();
 925     return binarizeFilter->GetOutput();
 926   }
 927   //--------------------------------------------------------------------
 928
 929
 930   //--------------------------------------------------------------------
 931   template<class ImageType>
 932   void
 933   GetMinMaxPointPosition(const ImageType * input,
 934                          typename ImageType::PointType & min,
 935                          typename ImageType::PointType & max)
 936   {
 937     typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
 938     input->TransformIndexToPhysicalPoint(index, min);
 939     index = index+input->GetLargestPossibleRegion().GetSize();
 940     input->TransformIndexToPhysicalPoint(index, max);
 941   }
 942   //--------------------------------------------------------------------
 943
 944
 945   //--------------------------------------------------------------------
 946   template<class ImageType>
 947   typename ImageType::PointType
 948   FindExtremaPointInAGivenLine(const ImageType * input,
 949                                int dimension,
 950                                bool inverse,
 951                                typename ImageType::PointType p,
 952                                typename ImageType::PixelType BG,
 953                                double distanceMax)
 954   {
 955     // Which direction ?  Increasing or decreasing.
 956     int d=1;
 957     if (inverse) d=-1;
 958
 959     // Transform to pixel index
 960     typename ImageType::IndexType index;
 961     input->TransformPhysicalPointToIndex(p, index);
 962
 963     // Loop while inside the mask;
 964     while (input->GetPixel(index) != BG) {
 965       index[dimension] += d;
 966     }
 967
 968     // Transform back to Physical Units
 969     typename ImageType::PointType result;
 970     input->TransformIndexToPhysicalPoint(index, result);
 971
 972     // Check that is is not too far away
 973     double distance = p.EuclideanDistanceTo(result);
 974     if (distance > distanceMax) {
 975       result = p; // Get back to initial value
 976     }
 977
 978     return result;
 979   }
 980   //--------------------------------------------------------------------
 981
 982
 983   //--------------------------------------------------------------------
 984   template<class PointType>
 985   bool
 986   IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
 987   {
 988     // Look at the position of point 'like' according to the AB line
 989     double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
 990     bool negative = s<0;
 991
 992     // Look the C position
 993     s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 994
 995     if (negative && (s<=0)) return true;
 996     if (!negative && (s>=0)) return true;
 997     return false;
 998   }
 999   //--------------------------------------------------------------------
1000
1001
1002   //--------------------------------------------------------------------
1003   /* Consider an input object, for each slice, find the extrema
1004      position according to a given direction and build a line segment
1005      passing throught this point in a given direction.  Output is a
1006      vector of line (from point A to B), for each slice;
1007    */
1008   template<class ImageType>
1009   void
1010   SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
1011                                                          typename ImageType::PixelType BG,
1012                                                          int sliceDimension,
1013                                                          int extremaDirection,
1014                                                          bool extremaOppositeFlag,
1015                                                          int lineDirection,
1016                                                          double margin,
1017                                                          std::vector<typename ImageType::PointType> & A,
1018                                                          std::vector<typename ImageType::PointType> & B)
1019   {
1020     // Type of a slice
1021     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1022
1023     // Build the list of slices
1024     std::vector<typename SliceType::Pointer> slices;
1025     clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
1026
1027     // Build the list of 2D points
1028     std::map<int, typename SliceType::PointType> position2D;
1029     for(uint i=0; i<slices.size(); i++) {
1030       typename SliceType::PointType p;
1031       bool found =
1032         clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
1033                                                             extremaDirection, extremaOppositeFlag, p);
1034       if (found) {
1035         position2D[i] = p;
1036       }
1037     }
1038
1039     // Convert 2D points in slice into 3D points
1040     clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
1041
1042     // Create additional point just right to the previous ones, on the
1043     // given lineDirection, in order to create a horizontal/vertical line.
1044     for(uint i=0; i<A.size(); i++) {
1045       typename ImageType::PointType p = A[i];
1046       p[lineDirection] += 10;
1047       B.push_back(p);
1048       // Margins ?
1049       A[i][1] += margin;
1050       B[i][1] += margin;
1051     }
1052
1053   }
1054   //--------------------------------------------------------------------
1055
1056
1057   //--------------------------------------------------------------------
1058   template<class ImageType>
1059   typename ImageType::Pointer
1060   SliceBySliceKeepMainCCL(const ImageType * input,
1061                           typename ImageType::PixelType BG,
1062                           typename ImageType::PixelType FG)  {
1063
1064     // Extract slices
1065     const int d = ImageType::ImageDimension-1;
1066     typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
1067     std::vector<typename SliceType::Pointer> slices;
1068     clitk::ExtractSlices<ImageType>(input, d, slices);
1069
1070     // Labelize and keep the main one
1071     std::vector<typename SliceType::Pointer> o;
1072     for(uint i=0; i<slices.size(); i++) {
1073       o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
1074       o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
1075     }
1076
1077     // Join slices
1078     typename ImageType::Pointer output;
1079     output = clitk::JoinSlices<ImageType>(o, input, d);
1080     return output;
1081   }
1082   //--------------------------------------------------------------------
1083
1084
1085   //--------------------------------------------------------------------
1086   template<class ImageType>
1087   typename ImageType::Pointer
1088   Clone(const ImageType * input) {
1089     typedef itk::ImageDuplicator<ImageType> DuplicatorType;
1090     typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
1091     duplicator->SetInputImage(input);
1092     duplicator->Update();
1093     return duplicator->GetOutput();
1094   }
1095   //--------------------------------------------------------------------
1096
1097
1098 } // end of namespace
1099