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://oncora1.lyon.fnclcc.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
  36 namespace clitk {
  37
  38 //--------------------------------------------------------------------
  39 template<class ImageType>
  40 void ComputeBBFromImageRegion(typename ImageType::Pointer image,
  41                               typename ImageType::RegionType region,
  42                               typename itk::BoundingBox<unsigned long,
  43                               ImageType::ImageDimension>::Pointer bb) {
  44   typedef typename ImageType::IndexType IndexType;
  45   IndexType firstIndex;
  46   IndexType lastIndex;
  47   for(unsigned int i=0; i<image->GetImageDimension(); i++) {
  48     firstIndex[i] = region.GetIndex()[i];
  49     lastIndex[i] = firstIndex[i]+region.GetSize()[i];
  50   }
  51
  52   typedef itk::BoundingBox<unsigned long,
  53                            ImageType::ImageDimension> BBType;
  54   typedef typename BBType::PointType PointType;
  55   PointType lastPoint;
  56   PointType firstPoint;
  57   image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
  58   image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
  59
  60   bb->SetMaximum(lastPoint);
  61   bb->SetMinimum(firstPoint);
  62 }
  63 //--------------------------------------------------------------------
  64
  65
  66 //--------------------------------------------------------------------
  67 template<int Dimension>
  68 void ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  69                            typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  70                            typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
  71
  72   typedef itk::BoundingBox<unsigned long, Dimension> BBType;
  73   typedef typename BBType::PointType PointType;
  74   PointType lastPoint;
  75   PointType firstPoint;
  76
  77   for(unsigned int i=0; i<Dimension; i++) {
  78     firstPoint[i] = std::max(bbi1->GetMinimum()[i],
  79                              bbi2->GetMinimum()[i]);
  80     lastPoint[i] = std::min(bbi1->GetMaximum()[i],
  81                             bbi2->GetMaximum()[i]);
  82   }
  83
  84   bbo->SetMaximum(lastPoint);
  85   bbo->SetMinimum(firstPoint);
  86 }
  87 //--------------------------------------------------------------------
  88
  89
  90 //--------------------------------------------------------------------
  91 template<class ImageType>
  92 void ComputeRegionFromBB(typename ImageType::Pointer image,
  93                          const typename itk::BoundingBox<unsigned long,
  94                          ImageType::ImageDimension>::Pointer bb,
  95                          typename ImageType::RegionType & region) {
  96   // Types
  97   typedef typename ImageType::IndexType  IndexType;
  98   typedef typename ImageType::PointType  PointType;
  99   typedef typename ImageType::RegionType RegionType;
 100   typedef typename ImageType::SizeType   SizeType;
 101
 102   // Region starting point
 103   IndexType regionStart;
 104   PointType start = bb->GetMinimum();
 105   image->TransformPhysicalPointToIndex(start, regionStart);
 106
 107   // Region size
 108   SizeType regionSize;
 109   PointType maxs = bb->GetMaximum();
 110   PointType mins = bb->GetMinimum();
 111   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 112     // DD(maxs[i]);
 113     // DD(mins[i]);
 114     // DD((maxs[i] - mins[i])/image->GetSpacing()[i]);
 115     regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
 116     // DD(regionSize[i]);
 117   }
 118
 119   // Create region
 120   region.SetIndex(regionStart);
 121   region.SetSize(regionSize);
 122 }
 123 //--------------------------------------------------------------------
 124
 125 //--------------------------------------------------------------------
 126 template<class ImageType, class TMaskImageType>
 127 typename ImageType::Pointer
 128 SetBackground(const ImageType * input,
 129               const TMaskImageType * mask,
 130               typename TMaskImageType::PixelType maskBG,
 131               typename ImageType::PixelType outValue,
 132               bool inPlace) {
 133   typedef SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
 134     SetBackgroundImageFilterType;
 135   typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
 136     = SetBackgroundImageFilterType::New();
 137   //  if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
 138   setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
 139   setBackgroundFilter->SetInput(input);
 140   setBackgroundFilter->SetInput2(mask);
 141   setBackgroundFilter->SetMaskValue(maskBG);
 142   setBackgroundFilter->SetOutsideValue(outValue);
 143   setBackgroundFilter->Update();
 144   return setBackgroundFilter->GetOutput();
 145 }
 146 //--------------------------------------------------------------------
 147
 148
 149 //--------------------------------------------------------------------
 150 template<class ImageType>
 151 int GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
 152                                         typename ImageType::PixelType BG,
 153                                         bool isFullyConnected) {
 154   // Connected Component label
 155   typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
 156   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 157   connectFilter->SetInput(input);
 158   connectFilter->SetBackgroundValue(BG);
 159   connectFilter->SetFullyConnected(isFullyConnected);
 160   connectFilter->Update();
 161
 162   // Return result
 163   return connectFilter->GetObjectCount();
 164 }
 165 //--------------------------------------------------------------------
 166
 167 //--------------------------------------------------------------------
 168 /*
 169   Warning : in this cas, we consider outputType like inputType, not
 170   InternalImageType. Be sure it fits.
 171  */
 172 template<class ImageType>
 173 typename ImageType::Pointer
 174 Labelize(const ImageType * input,
 175          typename ImageType::PixelType BG,
 176          bool isFullyConnected,
 177          int minimalComponentSize) {
 178   // InternalImageType for storing large number of component
 179   typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 180
 181   // Connected Component label
 182   typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 183   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 184   //  connectFilter->ReleaseDataFlagOn();
 185   connectFilter->SetInput(input);
 186   connectFilter->SetBackgroundValue(BG);
 187   connectFilter->SetFullyConnected(isFullyConnected);
 188
 189   // Sort by size and remove too small area.
 190   typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 191   typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 192   //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 193   relabelFilter->SetInput(connectFilter->GetOutput());
 194   relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 195   relabelFilter->Update();
 196
 197   // DD(relabelFilter->GetNumberOfObjects());
 198   // DD(relabelFilter->GetOriginalNumberOfObjects());
 199   // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
 200
 201   // Return result
 202   typename ImageType::Pointer output = relabelFilter->GetOutput();
 203   return output;
 204 }
 205 //--------------------------------------------------------------------
 206
 207
 208 //--------------------------------------------------------------------
 209 /*
 210   Warning : in this cas, we consider outputType like inputType, not
 211   InternalImageType. Be sure it fits.
 212  */
 213 template<class ImageType>
 214 typename ImageType::Pointer
 215 LabelizeAndCountNumberOfObjects(const ImageType * input,
 216                                 typename ImageType::PixelType BG,
 217                                 bool isFullyConnected,
 218                                 int minimalComponentSize,
 219                                 int & nb) {
 220   // InternalImageType for storing large number of component
 221   typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 222
 223   // Connected Component label
 224   typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 225   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 226   //  connectFilter->ReleaseDataFlagOn();
 227   connectFilter->SetInput(input);
 228   connectFilter->SetBackgroundValue(BG);
 229   connectFilter->SetFullyConnected(isFullyConnected);
 230
 231   // Sort by size and remove too small area.
 232   typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 233   typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 234   //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 235   relabelFilter->SetInput(connectFilter->GetOutput());
 236   relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 237   relabelFilter->Update();
 238
 239   nb = relabelFilter->GetNumberOfObjects();
 240   // DD(relabelFilter->GetNumberOfObjects());
 241   // DD(relabelFilter->GetOriginalNumberOfObjects());
 242   // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
 243
 244   // Return result
 245   typename ImageType::Pointer output = relabelFilter->GetOutput();
 246   return output;
 247 }
 248 //--------------------------------------------------------------------
 249
 250
 251
 252 //--------------------------------------------------------------------
 253 template<class ImageType>
 254 typename ImageType::Pointer
 255 RemoveLabels(typename ImageType::Pointer input,
 256              typename ImageType::PixelType BG,
 257              std::vector<typename ImageType::PixelType> & labelsToRemove) {
 258   typename ImageType::Pointer working_image = input;
 259   for (unsigned int i=0; i <labelsToRemove.size(); i++) {
 260     typedef SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
 261     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 262     setBackgroundFilter->SetInput(input);
 263     setBackgroundFilter->SetInput2(input);
 264     setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
 265     setBackgroundFilter->SetOutsideValue(BG);
 266     setBackgroundFilter->Update();
 267     working_image = setBackgroundFilter->GetOutput();
 268   }
 269   return working_image;
 270 }
 271 //--------------------------------------------------------------------
 272
 273
 274 //--------------------------------------------------------------------
 275 template<class ImageType>
 276 typename ImageType::Pointer
 277 KeepLabels(const ImageType * input,
 278            typename ImageType::PixelType BG,
 279            typename ImageType::PixelType FG,
 280            typename ImageType::PixelType firstKeep,
 281            typename ImageType::PixelType lastKeep,
 282            bool useLastKeep) {
 283   typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
 284   typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 285   binarizeFilter->SetInput(input);
 286   binarizeFilter->SetLowerThreshold(firstKeep);
 287   if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 288   binarizeFilter->SetInsideValue(FG);
 289   binarizeFilter->SetOutsideValue(BG);
 290   binarizeFilter->Update();
 291   return binarizeFilter->GetOutput();
 292 }
 293 //--------------------------------------------------------------------
 294
 295
 296 //--------------------------------------------------------------------
 297 template<class ImageType>
 298 typename ImageType::Pointer
 299 LabelizeAndSelectLabels(typename ImageType::Pointer input,
 300                         typename ImageType::PixelType BG,
 301                         typename ImageType::PixelType FG,
 302                         bool isFullyConnected,
 303                         int minimalComponentSize,
 304                         LabelizeParameters<typename ImageType::PixelType> * param)
 305 {
 306   typename ImageType::Pointer working_image;
 307   working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
 308   working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
 309   working_image = KeepLabels<ImageType>(working_image,
 310                                         BG, FG,
 311                                         param->GetFirstKeep(),
 312                                         param->GetLastKeep(),
 313                                         param->GetUseLastKeep());
 314   return working_image;
 315 }
 316 //--------------------------------------------------------------------
 317
 318
 319 //--------------------------------------------------------------------
 320 template<class ImageType>
 321 typename ImageType::Pointer
 322 ResizeImageLike(typename ImageType::Pointer input,
 323                 typename ImageType::Pointer like,
 324                 typename ImageType::PixelType backgroundValue)
 325 {
 326   typedef CropLikeImageFilter<ImageType> CropFilterType;
 327   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 328   cropFilter->SetInput(input);
 329   cropFilter->SetCropLikeImage(like);
 330   cropFilter->SetBackgroundValue(backgroundValue);
 331   cropFilter->Update();
 332   return cropFilter->GetOutput();
 333 }
 334 //--------------------------------------------------------------------
 335
 336
 337 //--------------------------------------------------------------------
 338 template<class MaskImageType>
 339 typename MaskImageType::Pointer
 340 SliceBySliceRelativePosition(const MaskImageType * input,
 341                              const MaskImageType * object,
 342                              int direction,
 343                              double threshold,
 344                              std::string orientation,
 345                              bool uniqueConnectedComponent,
 346                              double spacing,
 347                              bool inverseflag)
 348 {
 349   typedef SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 350   typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 351   sliceRelPosFilter->VerboseStepFlagOff();
 352   sliceRelPosFilter->WriteStepFlagOff();
 353   sliceRelPosFilter->SetInput(input);
 354   sliceRelPosFilter->SetInputObject(object);
 355   sliceRelPosFilter->SetDirection(direction);
 356   sliceRelPosFilter->SetFuzzyThreshold(threshold);
 357   sliceRelPosFilter->AddOrientationTypeString(orientation);
 358   sliceRelPosFilter->SetResampleBeforeRelativePositionFilter((spacing != -1));
 359   sliceRelPosFilter->SetIntermediateSpacing(spacing);
 360   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
 361   sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 362   //  sliceRelPosFilter->SetAutoCropFlag(true); ??
 363   sliceRelPosFilter->Update();
 364   return sliceRelPosFilter->GetOutput();
 365 }
 366 //--------------------------------------------------------------------
 367
 368 //--------------------------------------------------------------------
 369 template<class ImageType>
 370 bool
 371 FindExtremaPointInAGivenDirection(const ImageType * input,
 372                                   typename ImageType::PixelType bg,
 373                                   int direction, bool opposite,
 374                                   typename ImageType::PointType & point)
 375 {
 376   typename ImageType::PointType dummy;
 377   return FindExtremaPointInAGivenDirection(input, bg, direction,
 378                                            opposite, dummy, 0, point);
 379 }
 380 //--------------------------------------------------------------------
 381
 382 //--------------------------------------------------------------------
 383 template<class ImageType>
 384 bool
 385 FindExtremaPointInAGivenDirection(const ImageType * input,
 386                                   typename ImageType::PixelType bg,
 387                                   int direction, bool opposite,
 388                                   typename ImageType::PointType refpoint,
 389                                   double distanceMax,
 390                                   typename ImageType::PointType & point)
 391 {
 392   /*
 393     loop over input pixels, store the index in the fg that is max
 394     according to the given direction.
 395   */
 396   typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
 397   IteratorType iter(input, input->GetLargestPossibleRegion());
 398   iter.GoToBegin();
 399   typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
 400   if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
 401   bool found=false;
 402   while (!iter.IsAtEnd()) {
 403     if (iter.Get() != bg) {
 404       bool test = iter.GetIndex()[direction] >  max[direction];
 405       if (opposite) test = !test;
 406       if (test) {
 407         typename ImageType::PointType p;
 408         input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
 409         if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
 410           max = iter.GetIndex();
 411           found = true;
 412         }
 413       }
 414     }
 415     ++iter;
 416   }
 417   if (!found) return false;
 418   input->TransformIndexToPhysicalPoint(max, point);
 419   return true;
 420 }
 421 //--------------------------------------------------------------------
 422
 423
 424 //--------------------------------------------------------------------
 425 template<class ImageType>
 426 typename ImageType::Pointer
 427 CropImageAbove(typename ImageType::Pointer image,
 428                int dim, double min,
 429                bool autoCrop,
 430                typename ImageType::PixelType BG)
 431 {
 432   return CropImageAlongOneAxis<ImageType>(image, dim,
 433                                           image->GetOrigin()[dim],
 434                                           min,
 435                                           autoCrop, BG);
 436 }
 437 //--------------------------------------------------------------------
 438
 439
 440 //--------------------------------------------------------------------
 441 template<class ImageType>
 442 typename ImageType::Pointer
 443 CropImageBelow(typename ImageType::Pointer image,
 444                int dim, double max,
 445                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(typename ImageType::Pointer image,
 460                       int dim, double min, double max,
 461                       bool autoCrop,
 462                       typename ImageType::PixelType BG)
 463 {
 464   // Compute region size
 465   typename ImageType::RegionType region;
 466   typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 467   typename ImageType::PointType p = image->GetOrigin();
 468   p[dim] = min;
 469   typename ImageType::IndexType start;
 470   image->TransformPhysicalPointToIndex(p, start);
 471   p[dim] = max;
 472   typename ImageType::IndexType end;
 473   image->TransformPhysicalPointToIndex(p, end);
 474   size[dim] = fabs(end[dim]-start[dim]);
 475   region.SetIndex(start);
 476   region.SetSize(size);
 477
 478   // Perform Crop
 479   typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 480   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 481   cropFilter->SetInput(image);
 482   cropFilter->SetRegionOfInterest(region);
 483   cropFilter->Update();
 484   typename ImageType::Pointer result = cropFilter->GetOutput();
 485
 486   // Auto Crop
 487   if (autoCrop) {
 488     result = AutoCrop<ImageType>(result, BG);
 489   }
 490   return result;
 491 }
 492 //--------------------------------------------------------------------
 493
 494
 495 //--------------------------------------------------------------------
 496 template<class ImageType>
 497 void
 498 ComputeCentroids(typename ImageType::Pointer image,
 499                         typename ImageType::PixelType BG,
 500                         std::vector<typename ImageType::PointType> & centroids)
 501 {
 502   typedef long LabelType;
 503   static const unsigned int Dim = ImageType::ImageDimension;
 504   typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 505   typedef itk::LabelMap< LabelObjectType > LabelMapType;
 506   typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 507   typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 508   typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 509   typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 510   imageToLabelFilter->SetBackgroundValue(BG);
 511   imageToLabelFilter->SetInput(image);
 512   statFilter->SetInput(imageToLabelFilter->GetOutput());
 513   statFilter->Update();
 514   typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 515
 516   centroids.clear();
 517   typename ImageType::PointType dummy;
 518   centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 519   for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 520     centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 521   }
 522 }
 523 //--------------------------------------------------------------------
 524
 525
 526 //--------------------------------------------------------------------
 527 template<class ImageType>
 528 void
 529 ExtractSlices(typename ImageType::Pointer image,
 530               int direction,
 531               std::vector<typename itk::Image<typename ImageType::PixelType,
 532               ImageType::ImageDimension-1>::Pointer > & slices)
 533 {
 534   typedef ExtractSliceFilter<ImageType> ExtractSliceFilterType;
 535   typedef typename ExtractSliceFilterType::SliceType SliceType;
 536   typename ExtractSliceFilterType::Pointer
 537     extractSliceFilter = ExtractSliceFilterType::New();
 538   extractSliceFilter->SetInput(image);
 539   extractSliceFilter->SetDirection(direction);
 540   extractSliceFilter->Update();
 541   extractSliceFilter->GetOutputSlices(slices);
 542 }
 543 //--------------------------------------------------------------------
 544
 545
 546 //--------------------------------------------------------------------
 547 template<class ImageType>
 548 typename ImageType::Pointer
 549 JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
 550            ImageType::ImageDimension-1>::Pointer > & slices,
 551            typename ImageType::Pointer input,
 552            int direction) {
 553   typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
 554   typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
 555   typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
 556   joinFilter->SetOrigin(input->GetOrigin()[direction]);
 557   joinFilter->SetSpacing(input->GetSpacing()[direction]);
 558   for(unsigned int i=0; i<slices.size(); i++) {
 559     joinFilter->PushBackInput(slices[i]);
 560   }
 561   joinFilter->Update();
 562   return joinFilter->GetOutput();
 563 }
 564 //--------------------------------------------------------------------
 565
 566
 567 //--------------------------------------------------------------------
 568 template<class ImageType>
 569 void
 570 PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p,
 571                                       ImagePointer image,
 572                                       const int slice,
 573                                       PointType3D & p3D)
 574 {
 575   p3D[0] = p[0];
 576   p3D[1] = p[1];
 577   p3D[2] = (image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 578     + image->GetOrigin()[2];
 579 }
 580 //--------------------------------------------------------------------
 581
 582
 583 //--------------------------------------------------------------------
 584 template<class ImageType>
 585 void
 586 PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map,
 587                                           ImagePointer image,
 588                                           VectorPoint3DType & list)
 589 {
 590   typename MapPoint2DType::const_iterator iter = map.begin();
 591   while (iter != map.end()) {
 592     PointType3D p;
 593     Convert2DTo3D(iter->second, image, iter->first, p);
 594     list.push_back(p);
 595     ++iter;
 596   }
 597 }
 598 //--------------------------------------------------------------------
 599
 600 //--------------------------------------------------------------------
 601 template<class ImageType>
 602 void
 603 WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 604                      std::string filename)
 605 {
 606   std::ofstream os;
 607   openFileForWriting(os, filename);
 608   os << "LANDMARKS1" << std::endl;
 609   for(uint i=0; i<points.size(); i++) {
 610     const typename ImageType::PointType & p = points[i];
 611     // Write it in the file
 612     os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 613   }
 614   os.close();
 615 }
 616 //--------------------------------------------------------------------
 617
 618
 619 //--------------------------------------------------------------------
 620 template<class ImageType>
 621 typename ImageType::Pointer
 622 Dilate(typename ImageType::Pointer image,
 623        double radiusInMM,
 624        typename ImageType::PixelType BG,
 625        typename ImageType::PixelType FG,
 626        bool extendSupport)
 627 {
 628   typename ImageType::SizeType r;
 629   for(uint i=0; i<ImageType::ImageDimension; i++)
 630     r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 631   return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 632 }
 633 //--------------------------------------------------------------------
 634
 635
 636 //--------------------------------------------------------------------
 637 template<class ImageType>
 638 typename ImageType::Pointer
 639 Dilate(typename ImageType::Pointer image,
 640        typename ImageType::PointType radiusInMM,
 641        typename ImageType::PixelType BG,
 642        typename ImageType::PixelType FG,
 643        bool extendSupport)
 644 {
 645   typename ImageType::SizeType r;
 646   for(uint i=0; i<ImageType::ImageDimension; i++)
 647     r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 648   return Dilate<ImageType>(image, r, BG, FG, extendSupport);
 649 }
 650 //--------------------------------------------------------------------
 651
 652
 653 //--------------------------------------------------------------------
 654 template<class ImageType>
 655 typename ImageType::Pointer
 656 Dilate(typename ImageType::Pointer image,
 657        typename ImageType::SizeType radius,
 658        typename ImageType::PixelType BG,
 659        typename ImageType::PixelType FG,
 660        bool extendSupport)
 661 {
 662   // Create kernel for dilatation
 663   typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 664                                             ImageType::ImageDimension> KernelType;
 665   KernelType structuringElement;
 666   structuringElement.SetRadius(radius);
 667   structuringElement.CreateStructuringElement();
 668
 669   if (extendSupport) {
 670     typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 671     typename PadFilterType::Pointer padFilter = PadFilterType::New();
 672     padFilter->SetInput(image);
 673     typename ImageType::SizeType lower;
 674     typename ImageType::SizeType upper;
 675     for(uint i=0; i<3; i++) {
 676       lower[i] = upper[i] = 2*(radius[i]+1);
 677     }
 678     padFilter->SetPadLowerBound(lower);
 679     padFilter->SetPadUpperBound(upper);
 680     padFilter->Update();
 681     image = padFilter->GetOutput();
 682   }
 683
 684   // Dilate  filter
 685   typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 686   typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 687   dilateFilter->SetBackgroundValue(BG);
 688   dilateFilter->SetForegroundValue(FG);
 689   dilateFilter->SetBoundaryToForeground(false);
 690   dilateFilter->SetKernel(structuringElement);
 691   dilateFilter->SetInput(image);
 692   dilateFilter->Update();
 693   return image = dilateFilter->GetOutput();
 694 }
 695 //--------------------------------------------------------------------
 696
 697
 698 //--------------------------------------------------------------------
 699 template<class ValueType, class VectorType>
 700 void ConvertOption(std::string optionName, uint given,
 701                    ValueType * values, VectorType & p,
 702                    uint dim, bool required)
 703 {
 704   if (required && (given == 0)) {
 705     clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 706                         << dim << " values.");
 707   }
 708   if (given == 1) {
 709     for(uint i=0; i<dim; i++) p[i] = values[0];
 710     return;
 711   }
 712   if (given == dim) {
 713     for(uint i=0; i<dim; i++) p[i] = values[i];
 714     return;
 715   }
 716   if (given == 0) return;
 717   clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 718                       << dim << " values.");
 719 }
 720 //--------------------------------------------------------------------
 721
 722
 723 //--------------------------------------------------------------------
 724 /*
 725   http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
 726   Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
 727   (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
 728   This will equal zero if the point C is on the line formed by
 729   points A and B, and will have a different sign depending on the
 730   side. Which side this is depends on the orientation of your (x,y)
 731   coordinates, but you can plug test values for A,B and C into this
 732   formula to determine whether negative values are to the left or to
 733   the right.
 734   => to accelerate, start with formula, when change sign -> stop and fill
 735 */
 736 template<class ImageType>
 737 void
 738 SliceBySliceSetBackgroundFromLineSeparation(typename ImageType::Pointer input,
 739                                             std::vector<typename ImageType::PointType> & lA,
 740                                             std::vector<typename ImageType::PointType> & lB,
 741                                             typename ImageType::PixelType BG,
 742                                             int mainDirection,
 743                                             double offsetToKeep)
 744 {
 745
 746   typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
 747   SliceIteratorType siter = SliceIteratorType(input,
 748                                               input->GetLargestPossibleRegion());
 749   siter.SetFirstDirection(0);
 750   siter.SetSecondDirection(1);
 751   siter.GoToBegin();
 752   int i=0;
 753   typename ImageType::PointType A;
 754   typename ImageType::PointType B;
 755   typename ImageType::PointType C;
 756   while (!siter.IsAtEnd()) {
 757     // Check that the current slice correspond to the current point
 758     input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 759     if (C[2] != lA[i][2]) {
 760       // DD(C);
 761       // DD(lA[i]);
 762     }
 763     else {
 764       // Define A,B,C points
 765       A = lA[i];
 766       B = lB[i];
 767       C = A;
 768       C[mainDirection] += offsetToKeep; // I know I must keep this point
 769       double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 770       bool isPositive = s<0;
 771       while (!siter.IsAtEndOfSlice()) {
 772         while (!siter.IsAtEndOfLine()) {
 773           // Very slow, I know ... but image should be very small
 774           input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 775           double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 776           if (s == 0) siter.Set(BG); // on the line, we decide to remove
 777           if (isPositive) {
 778             if (s > 0) siter.Set(BG);
 779           }
 780           else {
 781             if (s < 0) siter.Set(BG);
 782           }
 783           ++siter;
 784         }
 785         siter.NextLine();
 786       }
 787       ++i;
 788     }
 789     siter.NextSlice();
 790   }
 791 }
 792 //--------------------------------------------------------------------
 793 }