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 //--------------------------------------------------------------------
  37 template<class ImageType>
  38 void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image,
  39                                      typename ImageType::RegionType region,
  40                                      typename itk::BoundingBox<unsigned long,
  41                                                                ImageType::ImageDimension>::Pointer bb) {
  42   typedef typename ImageType::IndexType IndexType;
  43   IndexType firstIndex;
  44   IndexType lastIndex;
  45   for(unsigned int i=0; i<image->GetImageDimension(); i++) {
  46     firstIndex[i] = region.GetIndex()[i];
  47     lastIndex[i] = firstIndex[i]+region.GetSize()[i];
  48   }
  49
  50   typedef itk::BoundingBox<unsigned long,
  51                            ImageType::ImageDimension> BBType;
  52   typedef typename BBType::PointType PointType;
  53   PointType lastPoint;
  54   PointType firstPoint;
  55   image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
  56   image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
  57
  58   bb->SetMaximum(lastPoint);
  59   bb->SetMinimum(firstPoint);
  60 }
  61 //--------------------------------------------------------------------
  62
  63
  64 //--------------------------------------------------------------------
  65 template<int Dimension>
  66 void clitk::ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  67                                   typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  68                                   typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
  69
  70   typedef itk::BoundingBox<unsigned long, Dimension> BBType;
  71   typedef typename BBType::PointType PointType;
  72   PointType lastPoint;
  73   PointType firstPoint;
  74
  75   for(unsigned int i=0; i<Dimension; i++) {
  76     firstPoint[i] = std::max(bbi1->GetMinimum()[i],
  77                              bbi2->GetMinimum()[i]);
  78     lastPoint[i] = std::min(bbi1->GetMaximum()[i],
  79                             bbi2->GetMaximum()[i]);
  80   }
  81
  82   bbo->SetMaximum(lastPoint);
  83   bbo->SetMinimum(firstPoint);
  84 }
  85 //--------------------------------------------------------------------
  86
  87
  88 //--------------------------------------------------------------------
  89 template<class ImageType>
  90 void clitk::ComputeRegionFromBB(typename ImageType::Pointer image,
  91                                 const typename itk::BoundingBox<unsigned long,
  92                                 ImageType::ImageDimension>::Pointer bb,
  93                                 typename ImageType::RegionType & region) {
  94   // Types
  95   typedef typename ImageType::IndexType  IndexType;
  96   typedef typename ImageType::PointType  PointType;
  97   typedef typename ImageType::RegionType RegionType;
  98   typedef typename ImageType::SizeType   SizeType;
  99
 100   // Region starting point
 101   IndexType regionStart;
 102   PointType start = bb->GetMinimum();
 103   image->TransformPhysicalPointToIndex(start, regionStart);
 104
 105   // Region size
 106   SizeType regionSize;
 107   PointType maxs = bb->GetMaximum();
 108   PointType mins = bb->GetMinimum();
 109   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 110     // DD(maxs[i]);
 111     // DD(mins[i]);
 112     // DD((maxs[i] - mins[i])/image->GetSpacing()[i]);
 113     regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
 114     // DD(regionSize[i]);
 115   }
 116
 117   // Create region
 118   region.SetIndex(regionStart);
 119   region.SetSize(regionSize);
 120 }
 121 //--------------------------------------------------------------------
 122
 123 //--------------------------------------------------------------------
 124 template<class ImageType, class TMaskImageType>
 125 typename ImageType::Pointer
 126 clitk::SetBackground(const ImageType * input,
 127                      const TMaskImageType * mask,
 128                      typename TMaskImageType::PixelType maskBG,
 129                      typename ImageType::PixelType outValue,
 130                      bool inPlace) {
 131   typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
 132     SetBackgroundImageFilterType;
 133   typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
 134     = SetBackgroundImageFilterType::New();
 135   //  if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
 136   setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
 137   setBackgroundFilter->SetInput(input);
 138   setBackgroundFilter->SetInput2(mask);
 139   setBackgroundFilter->SetMaskValue(maskBG);
 140   setBackgroundFilter->SetOutsideValue(outValue);
 141   setBackgroundFilter->Update();
 142   return setBackgroundFilter->GetOutput();
 143 }
 144 //--------------------------------------------------------------------
 145
 146
 147 //--------------------------------------------------------------------
 148 template<class ImageType>
 149 int clitk::GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
 150                                                typename ImageType::PixelType BG,
 151                                                bool isFullyConnected) {
 152   // Connected Component label
 153   typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
 154   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 155   connectFilter->SetInput(input);
 156   connectFilter->SetBackgroundValue(BG);
 157   connectFilter->SetFullyConnected(isFullyConnected);
 158   connectFilter->Update();
 159
 160   // Return result
 161   return connectFilter->GetObjectCount();
 162 }
 163 //--------------------------------------------------------------------
 164
 165 //--------------------------------------------------------------------
 166 /*
 167   Warning : in this cas, we consider outputType like inputType, not
 168   InternalImageType. Be sure it fits.
 169  */
 170 template<class ImageType>
 171 typename ImageType::Pointer
 172 clitk::Labelize(const ImageType * input,
 173                 typename ImageType::PixelType BG,
 174                 bool isFullyConnected,
 175                 int minimalComponentSize) {
 176   // InternalImageType for storing large number of component
 177   typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 178
 179   // Connected Component label
 180   typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 181   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 182   //  connectFilter->ReleaseDataFlagOn();
 183   connectFilter->SetInput(input);
 184   connectFilter->SetBackgroundValue(BG);
 185   connectFilter->SetFullyConnected(isFullyConnected);
 186
 187   // Sort by size and remove too small area.
 188   typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 189   typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 190   //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 191   relabelFilter->SetInput(connectFilter->GetOutput());
 192   relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 193   relabelFilter->Update();
 194
 195   // Return result
 196   typename ImageType::Pointer output = relabelFilter->GetOutput();
 197   return output;
 198 }
 199 //--------------------------------------------------------------------
 200
 201
 202 //--------------------------------------------------------------------
 203 template<class ImageType>
 204 typename ImageType::Pointer
 205 clitk::RemoveLabels(typename ImageType::Pointer input,
 206                     typename ImageType::PixelType BG,
 207                     std::vector<typename ImageType::PixelType> & labelsToRemove) {
 208   typename ImageType::Pointer working_image = input;
 209   for (unsigned int i=0; i <labelsToRemove.size(); i++) {
 210     typedef clitk::SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
 211     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 212     setBackgroundFilter->SetInput(input);
 213     setBackgroundFilter->SetInput2(input);
 214     setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
 215     setBackgroundFilter->SetOutsideValue(BG);
 216     setBackgroundFilter->Update();
 217     working_image = setBackgroundFilter->GetOutput();
 218   }
 219   return working_image;
 220 }
 221 //--------------------------------------------------------------------
 222
 223
 224 //--------------------------------------------------------------------
 225 template<class ImageType>
 226 typename ImageType::Pointer
 227 clitk::KeepLabels(const ImageType * input,
 228                   typename ImageType::PixelType BG,
 229                   typename ImageType::PixelType FG,
 230                   typename ImageType::PixelType firstKeep,
 231                   typename ImageType::PixelType lastKeep,
 232                   bool useLastKeep) {
 233   typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
 234   typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 235   binarizeFilter->SetInput(input);
 236   binarizeFilter->SetLowerThreshold(firstKeep);
 237   if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 238   binarizeFilter->SetInsideValue(FG);
 239   binarizeFilter->SetOutsideValue(BG);
 240   binarizeFilter->Update();
 241   return binarizeFilter->GetOutput();
 242 }
 243 //--------------------------------------------------------------------
 244
 245
 246 //--------------------------------------------------------------------
 247 template<class ImageType>
 248 typename ImageType::Pointer
 249 clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
 250                                typename ImageType::PixelType BG,
 251                                typename ImageType::PixelType FG,
 252                                bool isFullyConnected,
 253                                int minimalComponentSize,
 254                                LabelizeParameters<typename ImageType::PixelType> * param)
 255 {
 256   typename ImageType::Pointer working_image;
 257   working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
 258   working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
 259   working_image = KeepLabels<ImageType>(working_image,
 260                                         BG, FG,
 261                                         param->GetFirstKeep(),
 262                                         param->GetLastKeep(),
 263                                         param->GetUseLastKeep());
 264   return working_image;
 265 }
 266 //--------------------------------------------------------------------
 267
 268
 269 //--------------------------------------------------------------------
 270 template<class ImageType>
 271 typename ImageType::Pointer
 272 clitk::ResizeImageLike(typename ImageType::Pointer input,
 273                        typename ImageType::Pointer like,
 274                        typename ImageType::PixelType backgroundValue)
 275 {
 276   typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
 277   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 278   cropFilter->SetInput(input);
 279   cropFilter->SetCropLikeImage(like);
 280   cropFilter->SetBackgroundValue(backgroundValue);
 281   cropFilter->Update();
 282   return cropFilter->GetOutput();
 283 }
 284 //--------------------------------------------------------------------
 285
 286
 287 //--------------------------------------------------------------------
 288 template<class MaskImageType>
 289 typename MaskImageType::Pointer
 290 clitk::SliceBySliceRelativePosition(const MaskImageType * input,
 291                                     const MaskImageType * object,
 292                                     int direction,
 293                                     double threshold,
 294                                     std::string orientation,
 295                                     bool uniqueConnectedComponent,
 296                                     double spacing,
 297                                     bool inverseflag)
 298 {
 299   typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 300   typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 301   sliceRelPosFilter->VerboseStepFlagOff();
 302   sliceRelPosFilter->WriteStepFlagOff();
 303   sliceRelPosFilter->SetInput(input);
 304   sliceRelPosFilter->SetInputObject(object);
 305   sliceRelPosFilter->SetDirection(direction);
 306   sliceRelPosFilter->SetFuzzyThreshold(threshold);
 307   sliceRelPosFilter->AddOrientationTypeString(orientation);
 308   sliceRelPosFilter->SetResampleBeforeRelativePositionFilter((spacing != -1));
 309   sliceRelPosFilter->SetIntermediateSpacing(spacing);
 310   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
 311   sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 312   //  sliceRelPosFilter->SetAutoCropFlag(true); ??
 313   sliceRelPosFilter->Update();
 314   return sliceRelPosFilter->GetOutput();
 315 }
 316 //--------------------------------------------------------------------
 317
 318 //--------------------------------------------------------------------
 319 template<class ImageType>
 320 bool
 321 clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
 322                                          typename ImageType::PixelType bg,
 323                                          int direction, bool opposite,
 324                                          typename ImageType::PointType & point)
 325 {
 326   typename ImageType::PointType dummy;
 327   return clitk::FindExtremaPointInAGivenDirection(input, bg, direction,
 328                                                   opposite, dummy, 0, point);
 329 }
 330 //--------------------------------------------------------------------
 331
 332 //--------------------------------------------------------------------
 333 template<class ImageType>
 334 bool
 335 clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
 336                                          typename ImageType::PixelType bg,
 337                                          int direction, bool opposite,
 338                                          typename ImageType::PointType refpoint,
 339                                          double distanceMax,
 340                                          typename ImageType::PointType & point)
 341 {
 342   /*
 343     loop over input pixels, store the index in the fg that is max
 344     according to the given direction.
 345   */
 346   typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
 347   IteratorType iter(input, input->GetLargestPossibleRegion());
 348   iter.GoToBegin();
 349   typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
 350   if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
 351   bool found=false;
 352   while (!iter.IsAtEnd()) {
 353     if (iter.Get() != bg) {
 354       bool test = iter.GetIndex()[direction] >  max[direction];
 355       if (opposite) test = !test;
 356       if (test) {
 357         typename ImageType::PointType p;
 358         input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
 359         if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
 360           max = iter.GetIndex();
 361           found = true;
 362         }
 363       }
 364     }
 365     ++iter;
 366   }
 367   if (!found) return false;
 368   input->TransformIndexToPhysicalPoint(max, point);
 369   return true;
 370 }
 371 //--------------------------------------------------------------------
 372
 373
 374 //--------------------------------------------------------------------
 375 template<class ImageType>
 376 typename ImageType::Pointer
 377 clitk::CropImageAbove(typename ImageType::Pointer image,
 378                       int dim, double min,
 379                       bool autoCrop,
 380                       typename ImageType::PixelType BG)
 381 {
 382   return clitk::CropImageAlongOneAxis<ImageType>(image, dim,
 383                                                  image->GetOrigin()[dim],
 384                                                  min,
 385                                                  autoCrop, BG);
 386 }
 387 //--------------------------------------------------------------------
 388
 389
 390 //--------------------------------------------------------------------
 391 template<class ImageType>
 392 typename ImageType::Pointer
 393 clitk::CropImageBelow(typename ImageType::Pointer image,
 394                       int dim, double max,
 395                       bool autoCrop,
 396                       typename ImageType::PixelType BG)
 397 {
 398   typename ImageType::PointType p;
 399   image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
 400                                        image->GetLargestPossibleRegion().GetSize(), p);
 401   return clitk::CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
 402 }
 403 //--------------------------------------------------------------------
 404
 405
 406 //--------------------------------------------------------------------
 407 template<class ImageType>
 408 typename ImageType::Pointer
 409 clitk::CropImageAlongOneAxis(typename ImageType::Pointer image,
 410                              int dim, double min, double max,
 411                              bool autoCrop,
 412                              typename ImageType::PixelType BG)
 413 {
 414   // Compute region size
 415   typename ImageType::RegionType region;
 416   typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 417   typename ImageType::PointType p = image->GetOrigin();
 418   p[dim] = min;
 419   typename ImageType::IndexType start;
 420   image->TransformPhysicalPointToIndex(p, start);
 421   p[dim] = max;
 422   typename ImageType::IndexType end;
 423   image->TransformPhysicalPointToIndex(p, end);
 424   size[dim] = fabs(end[dim]-start[dim]);
 425   region.SetIndex(start);
 426   region.SetSize(size);
 427
 428   // Perform Crop
 429   typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 430   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 431   cropFilter->SetInput(image);
 432   cropFilter->SetRegionOfInterest(region);
 433   cropFilter->Update();
 434   typename ImageType::Pointer result = cropFilter->GetOutput();
 435
 436   // Auto Crop
 437   if (autoCrop) {
 438     result = clitk::AutoCrop<ImageType>(result, BG);
 439   }
 440   return result;
 441 }
 442 //--------------------------------------------------------------------
 443
 444
 445 //--------------------------------------------------------------------
 446 template<class ImageType>
 447 void
 448 clitk::ComputeCentroids(typename ImageType::Pointer image,
 449                         typename ImageType::PixelType BG,
 450                         std::vector<typename ImageType::PointType> & centroids)
 451 {
 452   typedef long LabelType;
 453   static const unsigned int Dim = ImageType::ImageDimension;
 454   typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 455   typedef itk::LabelMap< LabelObjectType > LabelMapType;
 456   typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 457   typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 458   typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 459   typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 460   imageToLabelFilter->SetBackgroundValue(BG);
 461   imageToLabelFilter->SetInput(image);
 462   statFilter->SetInput(imageToLabelFilter->GetOutput());
 463   statFilter->Update();
 464   typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 465
 466   centroids.clear();
 467   typename ImageType::PointType dummy;
 468   centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 469   for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 470     centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 471   }
 472 }
 473 //--------------------------------------------------------------------
 474
 475
 476 //--------------------------------------------------------------------
 477 template<class ImageType>
 478 void
 479 clitk::ExtractSlices(typename ImageType::Pointer image,
 480                      int direction,
 481                      std::vector<typename itk::Image<typename ImageType::PixelType,
 482                      ImageType::ImageDimension-1>::Pointer > & slices)
 483 {
 484   typedef clitk::ExtractSliceFilter<ImageType> ExtractSliceFilterType;
 485   typedef typename ExtractSliceFilterType::SliceType SliceType;
 486   typename ExtractSliceFilterType::Pointer
 487     extractSliceFilter = ExtractSliceFilterType::New();
 488   extractSliceFilter->SetInput(image);
 489   extractSliceFilter->SetDirection(direction);
 490   extractSliceFilter->Update();
 491   extractSliceFilter->GetOutputSlices(slices);
 492 }
 493 //--------------------------------------------------------------------
 494
 495
 496 //--------------------------------------------------------------------
 497 template<class ImageType>
 498 typename ImageType::Pointer
 499 clitk::JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
 500                   ImageType::ImageDimension-1>::Pointer > & slices,
 501                   typename ImageType::Pointer input,
 502                   int direction) {
 503   typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
 504   typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
 505   typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
 506   joinFilter->SetOrigin(input->GetOrigin()[direction]);
 507   joinFilter->SetSpacing(input->GetSpacing()[direction]);
 508   for(unsigned int i=0; i<slices.size(); i++) {
 509     joinFilter->PushBackInput(slices[i]);
 510   }
 511   joinFilter->Update();
 512   return joinFilter->GetOutput();
 513 }
 514 //--------------------------------------------------------------------
 515
 516
 517 //--------------------------------------------------------------------
 518 template<class ImageType>
 519 void
 520 clitk::PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p,
 521                                              ImagePointer image,
 522                                              const int slice,
 523                                              PointType3D & p3D)
 524 {
 525   p3D[0] = p[0];
 526   p3D[1] = p[1];
 527   p3D[2] = (image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 528     + image->GetOrigin()[2];
 529 }
 530 //--------------------------------------------------------------------
 531
 532
 533 //--------------------------------------------------------------------
 534 template<class ImageType>
 535 void
 536 clitk::PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map,
 537                                                  ImagePointer image,
 538                                                  VectorPoint3DType & list)
 539 {
 540   typename MapPoint2DType::const_iterator iter = map.begin();
 541   while (iter != map.end()) {
 542     PointType3D p;
 543     Convert2DTo3D(iter->second, image, iter->first, p);
 544     list.push_back(p);
 545     ++iter;
 546   }
 547 }
 548 //--------------------------------------------------------------------
 549
 550 //--------------------------------------------------------------------
 551 template<class ImageType>
 552 void
 553 clitk::WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 554                             std::string filename)
 555 {
 556   std::ofstream os;
 557   openFileForWriting(os, filename);
 558   os << "LANDMARKS1" << std::endl;
 559   for(uint i=0; i<points.size(); i++) {
 560     const typename ImageType::PointType & p = points[i];
 561     // Write it in the file
 562     os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 563   }
 564   os.close();
 565 }
 566 //--------------------------------------------------------------------
 567
 568
 569 //--------------------------------------------------------------------
 570 template<class ImageType>
 571 typename ImageType::Pointer
 572 clitk::Dilate(typename ImageType::Pointer image,
 573               double radiusInMM,
 574               typename ImageType::PixelType BG,
 575               typename ImageType::PixelType FG,
 576               bool extendSupport)
 577 {
 578   typename ImageType::SizeType r;
 579   for(uint i=0; i<ImageType::ImageDimension; i++)
 580     r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 581   return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
 582 }
 583 //--------------------------------------------------------------------
 584
 585
 586 //--------------------------------------------------------------------
 587 template<class ImageType>
 588 typename ImageType::Pointer
 589 clitk::Dilate(typename ImageType::Pointer image,
 590               typename ImageType::PointType radiusInMM,
 591               typename ImageType::PixelType BG,
 592               typename ImageType::PixelType FG,
 593               bool extendSupport)
 594 {
 595   typename ImageType::SizeType r;
 596   for(uint i=0; i<ImageType::ImageDimension; i++)
 597     r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 598   return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
 599 }
 600 //--------------------------------------------------------------------
 601
 602
 603 //--------------------------------------------------------------------
 604 template<class ImageType>
 605 typename ImageType::Pointer
 606 clitk::Dilate(typename ImageType::Pointer image,
 607               typename ImageType::SizeType radius,
 608               typename ImageType::PixelType BG,
 609               typename ImageType::PixelType FG,
 610               bool extendSupport)
 611 {
 612   // Create kernel for dilatation
 613   typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 614                                             ImageType::ImageDimension> KernelType;
 615   KernelType structuringElement;
 616   structuringElement.SetRadius(radius);
 617   structuringElement.CreateStructuringElement();
 618
 619   if (extendSupport) {
 620     typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 621     typename PadFilterType::Pointer padFilter = PadFilterType::New();
 622     padFilter->SetInput(image);
 623     typename ImageType::SizeType lower;
 624     typename ImageType::SizeType upper;
 625     for(uint i=0; i<3; i++) {
 626       lower[i] = upper[i] = 2*(radius[i]+1);
 627     }
 628     padFilter->SetPadLowerBound(lower);
 629     padFilter->SetPadUpperBound(upper);
 630     padFilter->Update();
 631     image = padFilter->GetOutput();
 632   }
 633
 634   // Dilate  filter
 635   typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 636   typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 637   dilateFilter->SetBackgroundValue(BG);
 638   dilateFilter->SetForegroundValue(FG);
 639   dilateFilter->SetBoundaryToForeground(false);
 640   dilateFilter->SetKernel(structuringElement);
 641   dilateFilter->SetInput(image);
 642   dilateFilter->Update();
 643   return image = dilateFilter->GetOutput();
 644 }
 645 //--------------------------------------------------------------------
 646
 647
 648 //--------------------------------------------------------------------
 649 template<class ValueType, class VectorType>
 650 void clitk::ConvertOption(std::string optionName, uint given,
 651                           ValueType * values, VectorType & p,
 652                           uint dim, bool required)
 653 {
 654   if (required && (given == 0)) {
 655     clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 656                         << dim << " values.");
 657   }
 658   if (given == 1) {
 659     for(uint i=0; i<dim; i++) p[i] = values[0];
 660     return;
 661   }
 662   if (given == dim) {
 663     for(uint i=0; i<dim; i++) p[i] = values[i];
 664     return;
 665   }
 666   if (given == 0) return;
 667   clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 668                       << dim << " values.");
 669 }
 670 //--------------------------------------------------------------------
 671
 672
 673 //--------------------------------------------------------------------
 674 /*
 675   http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
 676   Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
 677   (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
 678   This will equal zero if the point C is on the line formed by
 679   points A and B, and will have a different sign depending on the
 680   side. Which side this is depends on the orientation of your (x,y)
 681   coordinates, but you can plug test values for A,B and C into this
 682   formula to determine whether negative values are to the left or to
 683   the right.
 684   => to accelerate, start with formula, when change sign -> stop and fill
 685 */
 686 template<class ImageType>
 687 void
 688 clitk::SliceBySliceSetBackgroundFromLineSeparation(typename ImageType::Pointer input,
 689                                                    std::vector<typename ImageType::PointType> & lA,
 690                                                    std::vector<typename ImageType::PointType> & lB,
 691                                                    typename ImageType::PixelType BG,
 692                                                    int mainDirection,
 693                                                    double offsetToKeep)
 694 {
 695
 696   typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
 697   SliceIteratorType siter = SliceIteratorType(input,
 698                                               input->GetLargestPossibleRegion());
 699   siter.SetFirstDirection(0);
 700   siter.SetSecondDirection(1);
 701   siter.GoToBegin();
 702   uint i=0;
 703   typename ImageType::PointType A;
 704   typename ImageType::PointType B;
 705   typename ImageType::PointType C;
 706   assert(lA.size() == B.size());
 707   //  DD(lA.size());
 708   //DD(input->GetLargestPossibleRegion().GetSize());
 709   while ((i<lA.size()) && (!siter.IsAtEnd())) {
 710     // Check that the current slice correspond to the current point
 711     input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 712     if (C[2] != lA[i][2]) {
 713       // DD(C);
 714       // DD(lA[i]);
 715     }
 716     else {
 717       // Define A,B,C points
 718       A = lA[i];
 719       B = lB[i];
 720       C = A;
 721       C[mainDirection] += offsetToKeep; // I know I must keep this point
 722       double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 723       bool isPositive = s<0;
 724       while (!siter.IsAtEndOfSlice()) {
 725         while (!siter.IsAtEndOfLine()) {
 726           // Very slow, I know ... but image should be very small
 727           input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 728           double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 729           if (s == 0) siter.Set(BG); // on the line, we decide to remove
 730           if (isPositive) {
 731             if (s > 0) siter.Set(BG);
 732           }
 733           else {
 734             if (s < 0) siter.Set(BG);
 735           }
 736           ++siter;
 737         }
 738         siter.NextLine();
 739       }
 740       ++i;
 741     }
 742     siter.NextSlice();
 743   }
 744 }
 745 //--------------------------------------------------------------------