itk/clitkSegmentationUtils.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ======================================================================-====*/
  18
  19 // clitk
  20 #include "clitkSetBackgroundImageFilter.h"
  21 #include "clitkSliceBySliceRelativePositionFilter.h"
  22 #include "clitkCropLikeImageFilter.h"
  23 #include "clitkMemoryUsage.h"
  24
  25 // itk
  26 #include <itkConnectedComponentImageFilter.h>
  27 #include <itkRelabelComponentImageFilter.h>
  28 #include <itkBinaryThresholdImageFilter.h>
  29 #include <itkPasteImageFilter.h>
  30 #include <itkStatisticsLabelMapFilter.h>
  31 #include <itkBinaryBallStructuringElement.h>
  32 #include <itkBinaryDilateImageFilter.h>
  33 #include <itkConstantPadImageFilter.h>
  34 #include <itkImageSliceIteratorWithIndex.h>
  35 #include <itkBinaryMorphologicalOpeningImageFilter.h>
  36 #include <itkImageDuplicator.h>
  37 #include <itkSignedMaurerDistanceMapImageFilter.h>
  38
  39 namespace clitk {
  40
  41   //--------------------------------------------------------------------
  42   template<class ImageType>
  43   void ComputeBBFromImageRegion(const ImageType * image,
  44                                 typename ImageType::RegionType region,
  45                                 typename itk::BoundingBox<unsigned long,
  46                                 ImageType::ImageDimension>::Pointer bb) {
  47     typedef typename ImageType::IndexType IndexType;
  48     IndexType firstIndex;
  49     IndexType lastIndex;
  50     for(unsigned int i=0; i<image->GetImageDimension(); i++) {
  51       firstIndex[i] = region.GetIndex()[i];
  52       lastIndex[i] = firstIndex[i]+region.GetSize()[i];
  53     }
  54
  55     typedef itk::BoundingBox<unsigned long,
  56                              ImageType::ImageDimension> BBType;
  57     typedef typename BBType::PointType PointType;
  58     PointType lastPoint;
  59     PointType firstPoint;
  60     image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
  61     image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
  62
  63     bb->SetMaximum(lastPoint);
  64     bb->SetMinimum(firstPoint);
  65   }
  66   //--------------------------------------------------------------------
  67
  68
  69   //--------------------------------------------------------------------
  70   template<int Dimension>
  71   void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  72                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  73                              typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
  74
  75     typedef itk::BoundingBox<unsigned long, Dimension> BBType;
  76     typedef typename BBType::PointType PointType;
  77     PointType lastPoint;
  78     PointType firstPoint;
  79
  80     for(unsigned int i=0; i<Dimension; i++) {
  81       firstPoint[i] = std::max(bbi1->GetMinimum()[i],
  82                                bbi2->GetMinimum()[i]);
  83       lastPoint[i] = std::min(bbi1->GetMaximum()[i],
  84                               bbi2->GetMaximum()[i]);
  85     }
  86
  87     bbo->SetMaximum(lastPoint);
  88     bbo->SetMinimum(firstPoint);
  89   }
  90   //--------------------------------------------------------------------
  91
  92
  93   //--------------------------------------------------------------------
  94   template<class ImageType>
  95   void ComputeRegionFromBB(const ImageType * image,
  96                            const typename itk::BoundingBox<unsigned long,
  97                                                            ImageType::ImageDimension>::Pointer bb,
  98                            typename ImageType::RegionType & region) {
  99     // Types
 100     typedef typename ImageType::IndexType  IndexType;
 101     typedef typename ImageType::PointType  PointType;
 102     typedef typename ImageType::RegionType RegionType;
 103     typedef typename ImageType::SizeType   SizeType;
 104
 105     // Region starting point
 106     IndexType regionStart;
 107     PointType start = bb->GetMinimum();
 108     image->TransformPhysicalPointToIndex(start, regionStart);
 109
 110     // Region size
 111     SizeType regionSize;
 112     PointType maxs = bb->GetMaximum();
 113     PointType mins = bb->GetMinimum();
 114     for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 115       regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
 116     }
 117
 118     // Create region
 119     region.SetIndex(regionStart);
 120     region.SetSize(regionSize);
 121   }
 122   //--------------------------------------------------------------------
 123
 124   //--------------------------------------------------------------------
 125   template<class ImageType, class TMaskImageType>
 126   typename ImageType::Pointer
 127   SetBackground(const ImageType * input,
 128                 const TMaskImageType * mask,
 129                 typename TMaskImageType::PixelType maskBG,
 130                 typename ImageType::PixelType outValue,
 131                 bool inPlace) {
 132     typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
 133       SetBackgroundImageFilterType;
 134     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
 135       = SetBackgroundImageFilterType::New();
 136     //  if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
 137     setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
 138     setBackgroundFilter->SetInput(input);
 139     setBackgroundFilter->SetInput2(mask);
 140     setBackgroundFilter->SetMaskValue(maskBG);
 141     setBackgroundFilter->SetOutsideValue(outValue);
 142     setBackgroundFilter->Update();
 143     return setBackgroundFilter->GetOutput();
 144   }
 145   //--------------------------------------------------------------------
 146
 147
 148   //--------------------------------------------------------------------
 149   template<class ImageType>
 150   int GetNumberOfConnectedComponentLabels(const ImageType * input,
 151                                           typename ImageType::PixelType BG,
 152                                           bool isFullyConnected) {
 153     // Connected Component label
 154     typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
 155     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 156     connectFilter->SetInput(input);
 157     connectFilter->SetBackgroundValue(BG);
 158     connectFilter->SetFullyConnected(isFullyConnected);
 159     connectFilter->Update();
 160
 161     // Return result
 162     return connectFilter->GetObjectCount();
 163   }
 164   //--------------------------------------------------------------------
 165
 166   //--------------------------------------------------------------------
 167   /*
 168     Warning : in this cas, we consider outputType like inputType, not
 169     InternalImageType. Be sure it fits.
 170   */
 171   template<class ImageType>
 172   typename ImageType::Pointer
 173   Labelize(const ImageType * input,
 174            typename ImageType::PixelType BG,
 175            bool isFullyConnected,
 176            int minimalComponentSize) {
 177     // InternalImageType for storing large number of component
 178     typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 179
 180     // Connected Component label
 181     typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 182     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 183     //  connectFilter->ReleaseDataFlagOn();
 184     connectFilter->SetInput(input);
 185     connectFilter->SetBackgroundValue(BG);
 186     connectFilter->SetFullyConnected(isFullyConnected);
 187
 188     // Sort by size and remove too small area.
 189     typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 190     typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 191     //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 192     relabelFilter->SetInput(connectFilter->GetOutput());
 193     relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 194     relabelFilter->Update();
 195
 196     // Return result
 197     typename ImageType::Pointer output = relabelFilter->GetOutput();
 198     return output;
 199   }
 200   //--------------------------------------------------------------------
 201
 202
 203   //--------------------------------------------------------------------
 204   /*
 205     Warning : in this cas, we consider outputType like inputType, not
 206     InternalImageType. Be sure it fits.
 207   */
 208   template<class ImageType>
 209   typename ImageType::Pointer
 210   LabelizeAndCountNumberOfObjects(const ImageType * input,
 211                                   typename ImageType::PixelType BG,
 212                                   bool isFullyConnected,
 213                                   int minimalComponentSize,
 214                                   int & nb) {
 215     // InternalImageType for storing large number of component
 216     typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 217
 218     // Connected Component label
 219     typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 220     typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 221     //  connectFilter->ReleaseDataFlagOn();
 222     connectFilter->SetInput(input);
 223     connectFilter->SetBackgroundValue(BG);
 224     connectFilter->SetFullyConnected(isFullyConnected);
 225
 226     // Sort by size and remove too small area.
 227     typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 228     typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 229     //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 230     relabelFilter->SetInput(connectFilter->GetOutput());
 231     relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 232     relabelFilter->Update();
 233
 234     nb = relabelFilter->GetNumberOfObjects();
 235     // DD(relabelFilter->GetOriginalNumberOfObjects());
 236     // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
 237
 238     // Return result
 239     typename ImageType::Pointer output = relabelFilter->GetOutput();
 240     return output;
 241   }
 242   //--------------------------------------------------------------------
 243
 244
 245
 246   //--------------------------------------------------------------------
 247   template<class ImageType>
 248   typename ImageType::Pointer
 249   RemoveLabels(const ImageType * input,
 250                typename ImageType::PixelType BG,
 251                std::vector<typename ImageType::PixelType> & labelsToRemove) {
 252     assert(labelsToRemove.size() != 0);
 253     typename ImageType::Pointer working_image;// = input;
 254     for (unsigned int i=0; i <labelsToRemove.size(); i++) {
 255       typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
 256       typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 257       setBackgroundFilter->SetInput(input);
 258       setBackgroundFilter->SetInput2(input);
 259       setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
 260       setBackgroundFilter->SetOutsideValue(BG);
 261       setBackgroundFilter->Update();
 262       working_image = setBackgroundFilter->GetOutput();
 263     }
 264     return working_image;
 265   }
 266   //--------------------------------------------------------------------
 267
 268
 269   //--------------------------------------------------------------------
 270   template<class ImageType>
 271   typename ImageType::Pointer
 272   KeepLabels(const ImageType * input,
 273              typename ImageType::PixelType BG,
 274              typename ImageType::PixelType FG,
 275              typename ImageType::PixelType firstKeep,
 276              typename ImageType::PixelType lastKeep,
 277              bool useLastKeep) {
 278     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
 279     typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 280     binarizeFilter->SetInput(input);
 281     binarizeFilter->SetLowerThreshold(firstKeep);
 282     if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 283     binarizeFilter->SetInsideValue(FG);
 284     binarizeFilter->SetOutsideValue(BG);
 285     binarizeFilter->Update();
 286     return binarizeFilter->GetOutput();
 287   }
 288   //--------------------------------------------------------------------
 289
 290
 291   //--------------------------------------------------------------------
 292   template<class ImageType>
 293   typename ImageType::Pointer
 294   LabelizeAndSelectLabels(const ImageType * input,
 295                           typename ImageType::PixelType BG,
 296                           typename ImageType::PixelType FG,
 297                           bool isFullyConnected,
 298                           int minimalComponentSize,
 299                           LabelizeParameters<typename ImageType::PixelType> * param)
 300   {
 301     typename ImageType::Pointer working_image;
 302     working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
 303     if (param->GetLabelsToRemove().size() != 0)
 304       working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
 305     working_image = KeepLabels<ImageType>(working_image,
 306                                           BG, FG,
 307                                           param->GetFirstKeep(),
 308                                           param->GetLastKeep(),
 309                                           param->GetUseLastKeep());
 310     return working_image;
 311   }
 312   //--------------------------------------------------------------------
 313
 314
 315   //--------------------------------------------------------------------
 316   template<class ImageType>
 317   typename ImageType::Pointer
 318   ResizeImageLike(const ImageType * input,
 319                   const itk::ImageBase<ImageType::ImageDimension> * like,
 320                   typename ImageType::PixelType backgroundValue)
 321   {
 322     typedef CropLikeImageFilter<ImageType> CropFilterType;
 323     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 324     cropFilter->SetInput(input);
 325     cropFilter->SetCropLikeImage(like);
 326     cropFilter->SetBackgroundValue(backgroundValue);
 327     cropFilter->Update();
 328     return cropFilter->GetOutput();
 329   }
 330   //--------------------------------------------------------------------
 331
 332
 333   //--------------------------------------------------------------------
 334   template<class MaskImageType>
 335   typename MaskImageType::Pointer
 336   SliceBySliceRelativePosition(const MaskImageType * input,
 337                                const MaskImageType * object,
 338                                int direction,
 339                                double threshold,
 340                                std::string orientation,
 341                                bool uniqueConnectedComponent,
 342                                double spacing,
 343                                bool autocropFlag,
 344                                bool singleObjectCCL)
 345   {
 346     typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 347     typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 348     sliceRelPosFilter->VerboseStepFlagOff();
 349     sliceRelPosFilter->WriteStepFlagOff();
 350     sliceRelPosFilter->SetInput(input);
 351     sliceRelPosFilter->SetInputObject(object);
 352     sliceRelPosFilter->SetDirection(direction);
 353     sliceRelPosFilter->SetFuzzyThreshold(threshold);
 354     sliceRelPosFilter->AddOrientationTypeString(orientation);
 355     sliceRelPosFilter->SetIntermediateSpacingFlag((spacing != -1));
 356     sliceRelPosFilter->SetIntermediateSpacing(spacing);
 357     sliceRelPosFilter->SetUniqueConnectedComponentBySliceFlag(uniqueConnectedComponent);
 358     sliceRelPosFilter->ObjectCCLSelectionFlagOff();
 359     sliceRelPosFilter->SetUseTheLargestObjectCCLFlag(singleObjectCCL);
 360     //    sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 361     sliceRelPosFilter->SetAutoCropFlag(autocropFlag);
 362     sliceRelPosFilter->IgnoreEmptySliceObjectFlagOn();
 363     sliceRelPosFilter->Update();
 364     return sliceRelPosFilter->GetOutput();
 365   }
 366   //--------------------------------------------------------------------
 367
 368
 369   //--------------------------------------------------------------------
 370   template<class ImageType>
 371   bool
 372   FindExtremaPointInAGivenDirection(const ImageType * input,
 373                                     typename ImageType::PixelType bg,
 374                                     int direction, bool opposite,
 375                                     typename ImageType::PointType & point)
 376   {
 377     typename ImageType::PointType dummy;
 378     return FindExtremaPointInAGivenDirection(input, bg, direction,
 379                                              opposite, dummy, 0, point);
 380   }
 381   //--------------------------------------------------------------------
 382
 383
 384   //--------------------------------------------------------------------
 385   template<class ImageType>
 386   bool
 387   FindExtremaPointInAGivenDirection(const ImageType * input,
 388                                     typename ImageType::PixelType bg,
 389                                     int direction, bool opposite,
 390                                     typename ImageType::PointType refpoint,
 391                                     double distanceMax,
 392                                     typename ImageType::PointType & point)
 393   {
 394     /*
 395       loop over input pixels, store the index in the fg that is max
 396       according to the given direction.
 397     */
 398     typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
 399     IteratorType iter(input, input->GetLargestPossibleRegion());
 400     iter.GoToBegin();
 401     typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
 402     if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
 403     bool found=false;
 404     while (!iter.IsAtEnd()) {
 405       if (iter.Get() != bg) {
 406         bool test = iter.GetIndex()[direction] >  max[direction];
 407         if (opposite) test = !test;
 408         if (test) {
 409           typename ImageType::PointType p;
 410           input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
 411           if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
 412             max = iter.GetIndex();
 413             found = true;
 414           }
 415         }
 416       }
 417       ++iter;
 418     }
 419     if (!found) return false;
 420     input->TransformIndexToPhysicalPoint(max, point);
 421     return true;
 422   }
 423   //--------------------------------------------------------------------
 424
 425
 426   //--------------------------------------------------------------------
 427   template<class ImageType>
 428   typename ImageType::Pointer
 429   CropImageRemoveGreaterThan(const ImageType * image,
 430                  int dim, double min, bool autoCrop,
 431                  typename ImageType::PixelType BG)
 432   {
 433     return CropImageAlongOneAxis<ImageType>(image, dim,
 434                                             image->GetOrigin()[dim],
 435                                             min,
 436                                             autoCrop, BG);
 437   }
 438   //--------------------------------------------------------------------
 439
 440
 441   //--------------------------------------------------------------------
 442   template<class ImageType>
 443   typename ImageType::Pointer
 444   CropImageRemoveLowerThan(const ImageType * image,
 445                  int dim, double max, bool autoCrop,
 446                  typename ImageType::PixelType BG)
 447   {
 448     typename ImageType::PointType p;
 449     image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
 450                                          image->GetLargestPossibleRegion().GetSize(), p);
 451     return CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
 452   }
 453   //--------------------------------------------------------------------
 454
 455
 456   //--------------------------------------------------------------------
 457   template<class ImageType>
 458   typename ImageType::Pointer
 459   CropImageAlongOneAxis(const ImageType * image,
 460                         int dim, double min, double max,
 461                         bool autoCrop, typename ImageType::PixelType BG)
 462   {
 463     // Compute region size
 464     typename ImageType::RegionType region;
 465     typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 466     typename ImageType::PointType p = image->GetOrigin();
 467     p[dim] = min;
 468     typename ImageType::IndexType start;
 469     image->TransformPhysicalPointToIndex(p, start);
 470     p[dim] = max;
 471     typename ImageType::IndexType end;
 472     image->TransformPhysicalPointToIndex(p, end);
 473     size[dim] = abs(end[dim]-start[dim]);
 474     region.SetIndex(start);
 475     region.SetSize(size);
 476
 477     // Perform Crop
 478     typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 479     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 480     cropFilter->SetInput(image);
 481     cropFilter->SetRegionOfInterest(region);
 482     cropFilter->Update();
 483     typename ImageType::Pointer result = cropFilter->GetOutput();
 484
 485     // Auto Crop
 486     if (autoCrop) {
 487       result = AutoCrop<ImageType>(result, BG);
 488     }
 489     return result;
 490   }
 491   //--------------------------------------------------------------------
 492
 493
 494   //--------------------------------------------------------------------
 495   template<class ImageType>
 496   void
 497   ComputeCentroids(const ImageType * image,
 498                    typename ImageType::PixelType BG,
 499                    std::vector<typename ImageType::PointType> & centroids)
 500   {
 501     typedef long LabelType;
 502     static const unsigned int Dim = ImageType::ImageDimension;
 503     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 504     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 505     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 506     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 507     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 508     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 509     imageToLabelFilter->SetBackgroundValue(BG);
 510     imageToLabelFilter->SetInput(image);
 511     statFilter->SetInput(imageToLabelFilter->GetOutput());
 512     statFilter->Update();
 513     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 514
 515     centroids.clear();
 516     typename ImageType::PointType dummy;
 517     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point for BG
 518     //DS FIXME (not useful ! to change ..)
 519     for(uint i=0; i<labelMap->GetNumberOfLabelObjects(); i++) {
 520       int label = labelMap->GetLabels()[i];
 521       centroids.push_back(labelMap->GetLabelObject(label)->GetCentroid());
 522     }
 523   }
 524   //--------------------------------------------------------------------
 525
 526
 527   //--------------------------------------------------------------------
 528   template<class ImageType, class LabelType>
 529   typename itk::LabelMap< itk::ShapeLabelObject<LabelType, ImageType::ImageDimension> >::Pointer
 530   ComputeLabelMap(const ImageType * image,
 531                   typename ImageType::PixelType BG,
 532                   bool computePerimeterFlag)
 533   {
 534     static const unsigned int Dim = ImageType::ImageDimension;
 535     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 536     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 537     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 538     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 539     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 540     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 541     imageToLabelFilter->SetBackgroundValue(BG);
 542     imageToLabelFilter->SetInput(image);
 543     statFilter->SetInput(imageToLabelFilter->GetOutput());
 544     statFilter->SetComputePerimeter(computePerimeterFlag);
 545     statFilter->Update();
 546     return statFilter->GetOutput();
 547   }
 548   //--------------------------------------------------------------------
 549
 550
 551   //--------------------------------------------------------------------
 552   template<class ImageType>
 553   void
 554   ComputeCentroids2(const ImageType * image,
 555                    typename ImageType::PixelType BG,
 556                    std::vector<typename ImageType::PointType> & centroids)
 557   {
 558     typedef long LabelType;
 559     static const unsigned int Dim = ImageType::ImageDimension;
 560     typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 561     typedef itk::LabelMap< LabelObjectType > LabelMapType;
 562     typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 563     typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 564     typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 565     typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 566     imageToLabelFilter->SetBackgroundValue(BG);
 567     imageToLabelFilter->SetInput(image);
 568     statFilter->SetInput(imageToLabelFilter->GetOutput());
 569     statFilter->Update();
 570     typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 571
 572     centroids.clear();
 573     typename ImageType::PointType dummy;
 574     centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 575     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 576       centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 577     }
 578
 579     for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 580       DD(labelMap->GetLabelObject(i)->GetBinaryPrincipalAxes());
 581       DD(labelMap->GetLabelObject(i)->GetBinaryFlatness());
 582       DD(labelMap->GetLabelObject(i)->GetRoundness ());
 583
 584       // search for the point on the boundary alog PA
 585
 586     }
 587
 588   }
 589   //--------------------------------------------------------------------
 590
 591
 592   //--------------------------------------------------------------------
 593   template<class ImageType>
 594   void
 595   PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p2D,
 596                                         const ImageType * image,
 597                                         const int slice,
 598                                         PointType3D & p3D)
 599   {
 600     IndexType3D index3D;
 601     index3D[0] = index3D[1] = 0;
 602     index3D[2] = image->GetLargestPossibleRegion().GetIndex()[2]+slice;
 603     image->TransformIndexToPhysicalPoint(index3D, p3D);
 604     p3D[0] = p2D[0];
 605     p3D[1] = p2D[1];
 606     //  p3D[2] = p[2];//(image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 607     //    + image->GetOrigin()[2];
 608   }
 609   //--------------------------------------------------------------------
 610
 611
 612   //--------------------------------------------------------------------
 613   template<class ImageType>
 614   void
 615   PointsUtils<ImageType>::Convert2DMapTo3DList(const MapPoint2DType & map,
 616                                             const ImageType * image,
 617                                             VectorPoint3DType & list)
 618   {
 619     typename MapPoint2DType::const_iterator iter = map.begin();
 620     while (iter != map.end()) {
 621       PointType3D p;
 622       Convert2DTo3D(iter->second, image, iter->first, p);
 623       list.push_back(p);
 624       ++iter;
 625     }
 626   }
 627   //--------------------------------------------------------------------
 628
 629
 630   //--------------------------------------------------------------------
 631   template<class ImageType>
 632   void
 633   PointsUtils<ImageType>::Convert2DListTo3DList(const VectorPoint2DType & p2D,
 634                                                 int slice,
 635                                                 const ImageType * image,
 636                                                 VectorPoint3DType & list)
 637   {
 638     for(uint i=0; i<p2D.size(); i++) {
 639       PointType3D p;
 640       Convert2DTo3D(p2D[i], image, slice, p);
 641       list.push_back(p);
 642     }
 643   }
 644   //--------------------------------------------------------------------
 645
 646
 647   //--------------------------------------------------------------------
 648   template<class ImageType>
 649   void
 650   WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 651                        std::string filename)
 652   {
 653     std::ofstream os;
 654     openFileForWriting(os, filename);
 655     os << "LANDMARKS1" << std::endl;
 656     for(uint i=0; i<points.size(); i++) {
 657       const typename ImageType::PointType & p = points[i];
 658       // Write it in the file
 659       os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 660     }
 661     os.close();
 662   }
 663   //--------------------------------------------------------------------
 664
 665
 666   //--------------------------------------------------------------------
 667   template<class ImageType>
 668   typename ImageType::Pointer
 669   Dilate(const ImageType * image, double radiusInMM,
 670          typename ImageType::PixelType BG,
 671          typename ImageType::PixelType FG,
 672          bool extendSupport)
 673   {
 674     typename ImageType::SizeType r;
 675     for(uint i=0; i<ImageType::ImageDimension; i++)
 676       r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 677     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 678   }
 679   //--------------------------------------------------------------------
 680
 681
 682   //--------------------------------------------------------------------
 683   template<class ImageType>
 684   typename ImageType::Pointer
 685   Dilate(const ImageType * image, typename ImageType::PointType radiusInMM,
 686          typename ImageType::PixelType BG,
 687          typename ImageType::PixelType FG,
 688          bool extendSupport)
 689   {
 690     typename ImageType::SizeType r;
 691     for(uint i=0; i<ImageType::ImageDimension; i++)
 692       r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 693     return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 694   }
 695   //--------------------------------------------------------------------
 696
 697
 698   //--------------------------------------------------------------------
 699   template<class ImageType>
 700   typename ImageType::Pointer
 701   Dilate(const ImageType * image, typename ImageType::SizeType radius,
 702          typename ImageType::PixelType BG,
 703          typename ImageType::PixelType FG,
 704          bool extendSupport)
 705   {
 706     // Create kernel for dilatation
 707     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 708                                               ImageType::ImageDimension> KernelType;
 709     KernelType structuringElement;
 710     structuringElement.SetRadius(radius);
 711     structuringElement.CreateStructuringElement();
 712
 713     typename ImageType::Pointer output;
 714     if (extendSupport) {
 715       typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 716       typename PadFilterType::Pointer padFilter = PadFilterType::New();
 717       padFilter->SetInput(image);
 718       typename ImageType::SizeType lower;
 719       typename ImageType::SizeType upper;
 720       for(uint i=0; i<3; i++) {
 721         lower[i] = upper[i] = 2*(radius[i]+1);
 722       }
 723       padFilter->SetPadLowerBound(lower);
 724       padFilter->SetPadUpperBound(upper);
 725       padFilter->Update();
 726       output = padFilter->GetOutput();
 727     }
 728
 729     // Dilate  filter
 730     typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 731     typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 732     dilateFilter->SetBackgroundValue(BG);
 733     dilateFilter->SetForegroundValue(FG);
 734     dilateFilter->SetBoundaryToForeground(false);
 735     dilateFilter->SetKernel(structuringElement);
 736     if (extendSupport) dilateFilter->SetInput(output);
 737     else dilateFilter->SetInput(image);
 738     dilateFilter->Update();
 739     return dilateFilter->GetOutput();
 740   }
 741   //--------------------------------------------------------------------
 742
 743
 744   //--------------------------------------------------------------------
 745   template<class ImageType>
 746   typename ImageType::Pointer
 747   Opening(const ImageType * image, typename ImageType::SizeType radius,
 748          typename ImageType::PixelType BG,
 749          typename ImageType::PixelType FG)
 750   {
 751     // Kernel
 752     typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 753                                               ImageType::ImageDimension> KernelType;
 754     KernelType structuringElement;
 755     structuringElement.SetRadius(radius);
 756     structuringElement.CreateStructuringElement();
 757
 758     // Filter
 759     typedef itk::BinaryMorphologicalOpeningImageFilter<ImageType, ImageType , KernelType> OpeningFilterType;
 760     typename OpeningFilterType::Pointer open = OpeningFilterType::New();
 761     open->SetInput(image);
 762     open->SetBackgroundValue(BG);
 763     open->SetForegroundValue(FG);
 764     open->SetKernel(structuringElement);
 765     open->Update();
 766     return open->GetOutput();
 767   }
 768   //--------------------------------------------------------------------
 769
 770
 771
 772   //--------------------------------------------------------------------
 773   template<class ValueType, class VectorType>
 774   void ConvertOption(std::string optionName, uint given,
 775                      ValueType * values, VectorType & p,
 776                      uint dim, bool required)
 777   {
 778     if (required && (given == 0)) {
 779       clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 780                           << dim << " values.");
 781     }
 782     if (given == 1) {
 783       for(uint i=0; i<dim; i++) p[i] = values[0];
 784       return;
 785     }
 786     if (given == dim) {
 787       for(uint i=0; i<dim; i++) p[i] = values[i];
 788       return;
 789     }
 790     if (given == 0) return;
 791     clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 792                         << dim << " values.");
 793   }
 794   //--------------------------------------------------------------------
 795
 796
 797   //--------------------------------------------------------------------
 798   /*
 799     http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
 800     Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
 801     (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
 802     This will equal zero if the point C is on the line formed by
 803     points A and B, and will have a different sign depending on the
 804     side. Which side this is depends on the orientation of your (x,y)
 805     coordinates, but you can plug test values for A,B and C into this
 806     formula to determine whether negative values are to the left or to
 807     the right.
 808     => to accelerate, start with formula, when change sign -> stop and fill
 809
 810     offsetToKeep = is used to determine which side of the line we
 811     keep. The point along the mainDirection but 'offsetToKeep' mm away
 812     is kept.
 813
 814   */
 815   template<class ImageType>
 816   void
 817   SliceBySliceSetBackgroundFromLineSeparation(ImageType * input,
 818                                               std::vector<typename ImageType::PointType> & lA,
 819                                               std::vector<typename ImageType::PointType> & lB,
 820                                               typename ImageType::PixelType BG,
 821                                               int mainDirection,
 822                                               double offsetToKeep)
 823   {
 824     assert((mainDirection==0) || (mainDirection==1));
 825     typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
 826     SliceIteratorType siter = SliceIteratorType(input,
 827                                                 input->GetLargestPossibleRegion());
 828     siter.SetFirstDirection(0);
 829     siter.SetSecondDirection(1);
 830     siter.GoToBegin();
 831     uint i=0;
 832     typename ImageType::PointType A;
 833     typename ImageType::PointType B;
 834     typename ImageType::PointType C;
 835     assert(lA.size() == lB.size());
 836     while ((i<lA.size()) && (!siter.IsAtEnd())) {
 837       // Check that the current slice correspond to the current point
 838       input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 839       if ((fabs(C[2] - lA[i][2]))>0.01) { // is !equal with a tolerance of 0.01 mm
 840       }
 841       else {
 842         // Define A,B,C points
 843         A = lA[i];
 844         B = lB[i];
 845         C = A;
 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   //--------------------------------------------------------------------
 881   template<class ImageType>
 882   void
 883   AndNot(ImageType * input,
 884          const ImageType * object,
 885          typename ImageType::PixelType BG)
 886   {
 887     typename ImageType::Pointer o;
 888     bool resized=false;
 889     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 890       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 891       resized = true;
 892     }
 893
 894     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 895     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 896     boolFilter->InPlaceOn();
 897     boolFilter->SetInput1(input);
 898     if (resized) boolFilter->SetInput2(o);
 899     else boolFilter->SetInput2(object);
 900     boolFilter->SetBackgroundValue1(BG);
 901     boolFilter->SetBackgroundValue2(BG);
 902     boolFilter->SetOperationType(BoolFilterType::AndNot);
 903     boolFilter->Update();
 904   }
 905   //--------------------------------------------------------------------
 906
 907
 908   //--------------------------------------------------------------------
 909   template<class ImageType>
 910   void
 911   And(ImageType * input,
 912       const ImageType * object,
 913       typename ImageType::PixelType BG)
 914   {
 915     typename ImageType::Pointer o;
 916     bool resized=false;
 917     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 918       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 919       resized = true;
 920     }
 921
 922     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 923     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 924     boolFilter->InPlaceOn();
 925     boolFilter->SetInput1(input);
 926     if (resized) boolFilter->SetInput2(o);
 927     else boolFilter->SetInput2(object);
 928     boolFilter->SetBackgroundValue1(BG);
 929     boolFilter->SetBackgroundValue2(BG);
 930     boolFilter->SetOperationType(BoolFilterType::And);
 931     boolFilter->Update();
 932   }
 933   //--------------------------------------------------------------------
 934
 935
 936   //--------------------------------------------------------------------
 937   template<class ImageType>
 938   void
 939   Or(ImageType * input,
 940      const ImageType * object,
 941      typename ImageType::PixelType BG)
 942   {
 943     typename ImageType::Pointer o;
 944     bool resized=false;
 945     if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, object)) {
 946       o = clitk::ResizeImageLike<ImageType>(object, input, BG);
 947       resized = true;
 948     }
 949
 950     typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 951     typename BoolFilterType::Pointer boolFilter = BoolFilterType::New();
 952     boolFilter->InPlaceOn();
 953     boolFilter->SetInput1(input);
 954     if (resized) boolFilter->SetInput2(o);
 955     else boolFilter->SetInput2(object);
 956     boolFilter->SetBackgroundValue1(BG);
 957     boolFilter->SetBackgroundValue2(BG);
 958     boolFilter->SetOperationType(BoolFilterType::Or);
 959     boolFilter->Update();
 960   }
 961   //--------------------------------------------------------------------
 962
 963
 964   //--------------------------------------------------------------------
 965   template<class ImageType>
 966   typename ImageType::Pointer
 967   Binarize(const ImageType * input,
 968            typename ImageType::PixelType lower,
 969            typename ImageType::PixelType upper,
 970            typename ImageType::PixelType BG,
 971            typename ImageType::PixelType FG)
 972   {
 973     typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinaryThresholdFilterType;
 974     typename BinaryThresholdFilterType::Pointer binarizeFilter = BinaryThresholdFilterType::New();
 975     binarizeFilter->SetInput(input);
 976     binarizeFilter->InPlaceOff();
 977     binarizeFilter->SetLowerThreshold(lower);
 978     binarizeFilter->SetUpperThreshold(upper);
 979     binarizeFilter->SetInsideValue(FG);
 980     binarizeFilter->SetOutsideValue(BG);
 981     binarizeFilter->Update();
 982     return binarizeFilter->GetOutput();
 983   }
 984   //--------------------------------------------------------------------
 985
 986
 987   //--------------------------------------------------------------------
 988   template<class ImageType>
 989   void
 990   GetMinMaxPointPosition(const ImageType * input,
 991                          typename ImageType::PointType & min,
 992                          typename ImageType::PointType & max)
 993   {
 994     typename ImageType::IndexType index = input->GetLargestPossibleRegion().GetIndex();
 995     input->TransformIndexToPhysicalPoint(index, min);
 996     index = index+input->GetLargestPossibleRegion().GetSize();
 997     input->TransformIndexToPhysicalPoint(index, max);
 998   }
 999   //--------------------------------------------------------------------
1000
1001
1002   //--------------------------------------------------------------------
1003   template<class ImageType>
1004   typename ImageType::PointType
1005   FindExtremaPointInAGivenLine(const ImageType * input,
1006                                int dimension,
1007                                bool inverse,
1008                                typename ImageType::PointType p,
1009                                typename ImageType::PixelType BG,
1010                                double distanceMax)
1011   {
1012     // Which direction ?  Increasing or decreasing.
1013     int d=1;
1014     if (inverse) d=-1;
1015
1016     // Transform to pixel index
1017     typename ImageType::IndexType index;
1018     input->TransformPhysicalPointToIndex(p, index);
1019
1020     // Loop while inside the mask;
1021     while (input->GetPixel(index) != BG) {
1022       index[dimension] += d;
1023     }
1024
1025     // Transform back to Physical Units
1026     typename ImageType::PointType result;
1027     input->TransformIndexToPhysicalPoint(index, result);
1028
1029     // Check that is is not too far away
1030     double distance = p.EuclideanDistanceTo(result);
1031     if (distance > distanceMax) {
1032       result = p; // Get back to initial value
1033     }
1034
1035     return result;
1036   }
1037   //--------------------------------------------------------------------
1038
1039
1040   //--------------------------------------------------------------------
1041   template<class PointType>
1042   bool
1043   IsOnTheSameLineSide(PointType C, PointType A, PointType B, PointType like)
1044   {
1045     // Look at the position of point 'like' according to the AB line
1046     double s = (B[0] - A[0]) * (like[1] - A[1]) - (B[1] - A[1]) * (like[0] - A[0]);
1047     bool negative = s<0;
1048
1049     // Look the C position
1050     s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
1051
1052     if (negative && (s<=0)) return true;
1053     if (!negative && (s>=0)) return true;
1054     return false;
1055   }
1056   //--------------------------------------------------------------------
1057
1058
1059   //--------------------------------------------------------------------
1060   /* Consider an input object, for each slice, find the extrema
1061      position according to a given direction and build a line segment
1062      passing throught this point in a given direction.  Output is a
1063      vector of line (from point A to B), for each slice;
1064    */
1065   template<class ImageType>
1066   void
1067   SliceBySliceBuildLineSegmentAccordingToExtremaPosition(const ImageType * input,
1068                                                          typename ImageType::PixelType BG,
1069                                                          int sliceDimension,
1070                                                          int extremaDirection,
1071                                                          bool extremaOppositeFlag,
1072                                                          int lineDirection,
1073                                                          double margin,
1074                                                          std::vector<typename ImageType::PointType> & A,
1075                                                          std::vector<typename ImageType::PointType> & B)
1076   {
1077     // Type of a slice
1078     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1079
1080     // Build the list of slices
1081     std::vector<typename SliceType::Pointer> slices;
1082     clitk::ExtractSlices<ImageType>(input, sliceDimension, slices);
1083
1084     // Build the list of 2D points
1085     std::map<int, typename SliceType::PointType> position2D;
1086     for(uint i=0; i<slices.size(); i++) {
1087       typename SliceType::PointType p;
1088       bool found =
1089         clitk::FindExtremaPointInAGivenDirection<SliceType>(slices[i], BG,
1090                                                             extremaDirection, extremaOppositeFlag, p);
1091       if (found) {
1092         position2D[i] = p;
1093       }
1094     }
1095
1096     // Convert 2D points in slice into 3D points
1097     clitk::PointsUtils<ImageType>::Convert2DMapTo3DList(position2D, input, A);
1098
1099     // Create additional point just right to the previous ones, on the
1100     // given lineDirection, in order to create a horizontal/vertical line.
1101     for(uint i=0; i<A.size(); i++) {
1102       typename ImageType::PointType p = A[i];
1103       p[lineDirection] += 10;
1104       B.push_back(p);
1105       // Margins ?
1106       A[i][extremaDirection] += margin;
1107       B[i][extremaDirection] += margin;
1108     }
1109
1110   }
1111   //--------------------------------------------------------------------
1112
1113
1114   //--------------------------------------------------------------------
1115   template<class ImageType>
1116   typename ImageType::Pointer
1117   SliceBySliceKeepMainCCL(const ImageType * input,
1118                           typename ImageType::PixelType BG,
1119                           typename ImageType::PixelType FG)  {
1120
1121     // Extract slices
1122     const int d = ImageType::ImageDimension-1;
1123     typedef typename itk::Image<typename ImageType::PixelType, d> SliceType;
1124     std::vector<typename SliceType::Pointer> slices;
1125     clitk::ExtractSlices<ImageType>(input, d, slices);
1126
1127     // Labelize and keep the main one
1128     std::vector<typename SliceType::Pointer> o;
1129     for(uint i=0; i<slices.size(); i++) {
1130       o.push_back(clitk::Labelize<SliceType>(slices[i], BG, false, 1));
1131       o[i] = clitk::KeepLabels<SliceType>(o[i], BG, FG, 1, 1, true);
1132     }
1133
1134     // Join slices
1135     typename ImageType::Pointer output;
1136     output = clitk::JoinSlices<ImageType>(o, input, d);
1137     return output;
1138   }
1139   //--------------------------------------------------------------------
1140
1141
1142   //--------------------------------------------------------------------
1143   template<class ImageType>
1144   typename ImageType::Pointer
1145   Clone(const ImageType * input) {
1146     typedef itk::ImageDuplicator<ImageType> DuplicatorType;
1147     typename DuplicatorType::Pointer duplicator = DuplicatorType::New();
1148     duplicator->SetInputImage(input);
1149     duplicator->Update();
1150     return duplicator->GetOutput();
1151   }
1152   //--------------------------------------------------------------------
1153
1154
1155   //--------------------------------------------------------------------
1156   /* Consider an input object, start at A, for each slice (dim1):
1157      - compute the intersection between the AB line and the current slice
1158      - remove what is at lower or greater according to dim2 of this point
1159      - stop at B
1160   */
1161   template<class ImageType>
1162   typename ImageType::Pointer
1163   SliceBySliceSetBackgroundFromSingleLine(const ImageType * input,
1164                                           typename ImageType::PixelType BG,
1165                                           typename ImageType::PointType & A,
1166                                           typename ImageType::PointType & B,
1167                                           int dim1, int dim2, bool removeLowerPartFlag)
1168
1169   {
1170     // Extract slices
1171     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1172     typedef typename SliceType::Pointer SlicePointer;
1173     std::vector<SlicePointer> slices;
1174     clitk::ExtractSlices<ImageType>(input, dim1, slices);
1175
1176     // Start at slice that contains A, and stop at B
1177     typename ImageType::IndexType Ap;
1178     typename ImageType::IndexType Bp;
1179     input->TransformPhysicalPointToIndex(A, Ap);
1180     input->TransformPhysicalPointToIndex(B, Bp);
1181
1182     // Determine slice largest region
1183     typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1184     typename SliceType::SizeType size = region.GetSize();
1185     typename SliceType::IndexType index = region.GetIndex();
1186
1187     // Line slope
1188     double a = (Bp[dim2]-Ap[dim2])/(Bp[dim1]-Ap[dim1]);
1189     double b = Ap[dim2];
1190
1191     // Loop from slice A to slice B
1192     for(uint i=0; i<(Bp[dim1]-Ap[dim1]); i++) {
1193       // Compute intersection between line AB and current slice for the dim2
1194       double p = a*i+b;
1195       // Change region (lower than dim2)
1196       if (removeLowerPartFlag) {
1197         size[dim2] = p-Ap[dim2];
1198       }
1199       else {
1200         size[dim2] = slices[0]->GetLargestPossibleRegion().GetSize()[dim2]-p;
1201         index[dim2] = p;
1202       }
1203       region.SetSize(size);
1204       region.SetIndex(index);
1205       // Fill region with BG (simple region iterator)
1206       FillRegionWithValue<SliceType>(slices[i+Ap[dim1]], BG, region);
1207       /*
1208       typedef itk::ImageRegionIterator<SliceType> IteratorType;
1209       IteratorType iter(slices[i+Ap[dim1]], region);
1210       iter.GoToBegin();
1211       while (!iter.IsAtEnd()) {
1212         iter.Set(BG);
1213         ++iter;
1214       }
1215       */
1216       // Loop
1217     }
1218
1219     // Merge slices
1220     typename ImageType::Pointer output;
1221     output = clitk::JoinSlices<ImageType>(slices, input, dim1);
1222     return output;
1223   }
1224   //--------------------------------------------------------------------
1225
1226   //--------------------------------------------------------------------
1227   /* Consider an input object, slice by slice, use the point A and set
1228      pixel to BG according to their position relatively to A
1229   */
1230   template<class ImageType>
1231   typename ImageType::Pointer
1232   SliceBySliceSetBackgroundFromPoints(const ImageType * input,
1233                                       typename ImageType::PixelType BG,
1234                                       int sliceDim,
1235                                       std::vector<typename ImageType::PointType> & A,
1236                                       bool removeGreaterThanXFlag,
1237                                       bool removeGreaterThanYFlag)
1238
1239   {
1240     // Extract slices
1241     typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
1242     typedef typename SliceType::Pointer SlicePointer;
1243     std::vector<SlicePointer> slices;
1244     clitk::ExtractSlices<ImageType>(input, sliceDim, slices);
1245
1246     // Start at slice that contains A
1247     typename ImageType::IndexType Ap;
1248
1249     // Determine slice largest region
1250     typename SliceType::RegionType region = slices[0]->GetLargestPossibleRegion();
1251     typename SliceType::SizeType size = region.GetSize();
1252     typename SliceType::IndexType index = region.GetIndex();
1253
1254     // Loop from slice A to slice B
1255     for(uint i=0; i<A.size(); i++) {
1256       input->TransformPhysicalPointToIndex(A[i], Ap);
1257       uint sliceIndex = Ap[2] - input->GetLargestPossibleRegion().GetIndex()[2];
1258       if ((sliceIndex < 0) || (sliceIndex >= slices.size())) {
1259         continue; // do not consider this slice
1260       }
1261
1262       // Compute region for BG
1263       if (removeGreaterThanXFlag) {
1264         index[0] = Ap[0];
1265         size[0] = region.GetSize()[0]-(index[0]-region.GetIndex()[0]);
1266       }
1267       else {
1268         index[0] = region.GetIndex()[0];
1269         size[0] = Ap[0] - index[0];
1270       }
1271
1272       if (removeGreaterThanYFlag) {
1273         index[1] = Ap[1];
1274         size[1] = region.GetSize()[1]-(index[1]-region.GetIndex()[1]);
1275       }
1276       else {
1277         index[1] = region.GetIndex()[1];
1278         size[1] = Ap[1] - index[1];
1279       }
1280
1281       // Set region
1282       region.SetSize(size);
1283       region.SetIndex(index);
1284
1285       // Fill region with BG (simple region iterator)
1286       FillRegionWithValue<SliceType>(slices[sliceIndex], BG, region);
1287       // Loop
1288     }
1289
1290     // Merge slices
1291     typename ImageType::Pointer output;
1292     output = clitk::JoinSlices<ImageType>(slices, input, sliceDim);
1293     return output;
1294   }
1295   //--------------------------------------------------------------------
1296
1297
1298   //--------------------------------------------------------------------
1299   template<class ImageType>
1300   void
1301   FillRegionWithValue(ImageType * input, typename ImageType::PixelType value, typename ImageType::RegionType & region)
1302   {
1303     typedef itk::ImageRegionIterator<ImageType> IteratorType;
1304     IteratorType iter(input, region);
1305     iter.GoToBegin();
1306     while (!iter.IsAtEnd()) {
1307       iter.Set(value);
1308       ++iter;
1309     }
1310   }
1311   //--------------------------------------------------------------------
1312
1313
1314   //--------------------------------------------------------------------
1315   template<class ImageType>
1316   void
1317   GetMinMaxBoundary(ImageType * input, typename ImageType::PointType & min,
1318                     typename ImageType::PointType & max)
1319   {
1320     typedef typename ImageType::PointType PointType;
1321     typedef typename ImageType::IndexType IndexType;
1322     IndexType min_i, max_i;
1323     min_i = input->GetLargestPossibleRegion().GetIndex();
1324     for(uint i=0; i<ImageType::ImageDimension; i++)
1325       max_i[i] = input->GetLargestPossibleRegion().GetSize()[i] + min_i[i];
1326     input->TransformIndexToPhysicalPoint(min_i, min);
1327     input->TransformIndexToPhysicalPoint(max_i, max);
1328   }
1329   //--------------------------------------------------------------------
1330
1331
1332   //--------------------------------------------------------------------
1333   template<class ImageType>
1334   typename itk::Image<float, ImageType::ImageDimension>::Pointer
1335   DistanceMap(const ImageType * input, typename ImageType::PixelType BG)//,
1336   //              typename itk::Image<float, ImageType::ImageDimension>::Pointer dmap)
1337   {
1338     typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
1339     typedef itk::SignedMaurerDistanceMapImageFilter<ImageType, FloatImageType> DistanceMapFilterType;
1340     typename DistanceMapFilterType::Pointer filter = DistanceMapFilterType::New();
1341     filter->SetInput(input);
1342     filter->SetUseImageSpacing(true);
1343     filter->SquaredDistanceOff();
1344     filter->SetBackgroundValue(BG);
1345     filter->Update();
1346     return filter->GetOutput();
1347   }
1348   //--------------------------------------------------------------------
1349
1350
1351   //--------------------------------------------------------------------
1352   template<class ImageType>
1353   void
1354   SliceBySliceBuildLineSegmentAccordingToMinimalDistanceBetweenStructures(const ImageType * S1,
1355                                                                           const ImageType * S2,
1356                                                                           typename ImageType::PixelType BG,
1357                                                                           int sliceDimension,
1358                                                                           std::vector<typename ImageType::PointType> & A,
1359                                                                           std::vector<typename ImageType::PointType> & B)
1360   {
1361     // Extract slices
1362     typedef typename itk::Image<typename ImageType::PixelType, 2> SliceType;
1363     typedef typename SliceType::Pointer SlicePointer;
1364     std::vector<SlicePointer> slices_s1;
1365     std::vector<SlicePointer> slices_s2;
1366     clitk::ExtractSlices<ImageType>(S1, sliceDimension, slices_s1);
1367     clitk::ExtractSlices<ImageType>(S2, sliceDimension, slices_s2);
1368
1369     assert(slices_s1.size() == slices_s2.size());
1370
1371     // Prepare dmap
1372     typedef itk::Image<float,2> FloatImageType;
1373     typedef itk::SignedMaurerDistanceMapImageFilter<SliceType, FloatImageType> DistanceMapFilterType;
1374     std::vector<typename FloatImageType::Pointer> dmaps1;
1375     std::vector<typename FloatImageType::Pointer> dmaps2;
1376     typename FloatImageType::Pointer dmap;
1377
1378     // loop on slices
1379     for(uint i=0; i<slices_s1.size(); i++) {
1380       // Compute dmap for S1 *TO PUT IN FONCTION*
1381       dmap = clitk::DistanceMap<SliceType>(slices_s1[i], BG);
1382       dmaps1.push_back(dmap);
1383       writeImage<FloatImageType>(dmap, "dmap1.mha");
1384       // Compute dmap for S2
1385       dmap = clitk::DistanceMap<SliceType>(slices_s2[i], BG);
1386       dmaps2.push_back(dmap);
1387       writeImage<FloatImageType>(dmap, "dmap2.mha");
1388
1389       // Look in S2 for the point the closest to S1
1390       typename SliceType::PointType p = ComputeClosestPoint<SliceType>(slices_s1[i], dmaps2[i], BG);
1391       typename ImageType::PointType p3D;
1392       clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S1, i, p3D);
1393       A.push_back(p3D);
1394
1395       // Look in S2 for the point the closest to S1
1396       p = ComputeClosestPoint<SliceType>(slices_s2[i], dmaps1[i], BG);
1397       clitk::PointsUtils<ImageType>::Convert2DTo3D(p, S2, i, p3D);
1398       B.push_back(p3D);
1399
1400     }
1401
1402     // Debug dmap
1403     /*
1404       typedef itk::Image<float,3> FT;
1405       FT::Pointer f = FT::New();
1406       typename FT::Pointer d1 = clitk::JoinSlices<FT>(dmaps1, S1, 2);
1407       typename FT::Pointer d2 = clitk::JoinSlices<FT>(dmaps2, S2, 2);
1408       writeImage<FT>(d1, "d1.mha");
1409       writeImage<FT>(d2, "d2.mha");
1410     */
1411   }
1412   //--------------------------------------------------------------------
1413
1414
1415   //--------------------------------------------------------------------
1416   template<class ImageType>
1417   typename ImageType::PointType
1418   ComputeClosestPoint(const ImageType * input,
1419                       const itk::Image<float, ImageType::ImageDimension> * dmap,
1420                       typename ImageType::PixelType & BG)
1421   {
1422     // Loop dmap + S2, if FG, get min
1423     typedef itk::Image<float,ImageType::ImageDimension> FloatImageType;
1424     typedef itk::ImageRegionConstIteratorWithIndex<ImageType> ImageIteratorType;
1425     typedef itk::ImageRegionConstIterator<FloatImageType> DMapIteratorType;
1426     ImageIteratorType iter1(input, input->GetLargestPossibleRegion());
1427     DMapIteratorType iter2(dmap, dmap->GetLargestPossibleRegion());
1428
1429     iter1.GoToBegin();
1430     iter2.GoToBegin();
1431     double dmin = 100000.0;
1432     typename ImageType::IndexType indexmin;
1433     while (!iter1.IsAtEnd()) {
1434       if (iter1.Get() != BG) {
1435         double d = iter2.Get();
1436         if (d<dmin) {
1437           indexmin = iter1.GetIndex();
1438           dmin = d;
1439         }
1440       }
1441       ++iter1;
1442       ++iter2;
1443     }
1444
1445     // Convert in Point
1446     typename ImageType::PointType p;
1447     input->TransformIndexToPhysicalPoint(indexmin, p);
1448     return p;
1449   }
1450   //--------------------------------------------------------------------
1451
1452
1453
1454
1455 } // end of namespace
1456