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