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
  35 //--------------------------------------------------------------------
  36 template<class ImageType>
  37 void clitk::ComputeBBFromImageRegion(typename ImageType::Pointer image,
  38                                      typename ImageType::RegionType region,
  39                                      typename itk::BoundingBox<unsigned long,
  40                                                                ImageType::ImageDimension>::Pointer bb) {
  41   typedef typename ImageType::IndexType IndexType;
  42   IndexType firstIndex;
  43   IndexType lastIndex;
  44   for(unsigned int i=0; i<image->GetImageDimension(); i++) {
  45     firstIndex[i] = region.GetIndex()[i];
  46     lastIndex[i] = firstIndex[i]+region.GetSize()[i];
  47   }
  48
  49   typedef itk::BoundingBox<unsigned long,
  50                            ImageType::ImageDimension> BBType;
  51   typedef typename BBType::PointType PointType;
  52   PointType lastPoint;
  53   PointType firstPoint;
  54   image->TransformIndexToPhysicalPoint(firstIndex, firstPoint);
  55   image->TransformIndexToPhysicalPoint(lastIndex, lastPoint);
  56
  57   bb->SetMaximum(lastPoint);
  58   bb->SetMinimum(firstPoint);
  59 }
  60 //--------------------------------------------------------------------
  61
  62
  63 //--------------------------------------------------------------------
  64 template<int Dimension>
  65 void clitk::ComputeBBIntersection(typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbo,
  66                                   typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi1,
  67                                   typename itk::BoundingBox<unsigned long, Dimension>::Pointer bbi2) {
  68
  69   typedef itk::BoundingBox<unsigned long, Dimension> BBType;
  70   typedef typename BBType::PointType PointType;
  71   PointType lastPoint;
  72   PointType firstPoint;
  73
  74   for(unsigned int i=0; i<Dimension; i++) {
  75     firstPoint[i] = std::max(bbi1->GetMinimum()[i],
  76                              bbi2->GetMinimum()[i]);
  77     lastPoint[i] = std::min(bbi1->GetMaximum()[i],
  78                             bbi2->GetMaximum()[i]);
  79   }
  80
  81   bbo->SetMaximum(lastPoint);
  82   bbo->SetMinimum(firstPoint);
  83 }
  84 //--------------------------------------------------------------------
  85
  86
  87 //--------------------------------------------------------------------
  88 template<class ImageType>
  89 void clitk::ComputeRegionFromBB(typename ImageType::Pointer image,
  90                                 const typename itk::BoundingBox<unsigned long,
  91                                 ImageType::ImageDimension>::Pointer bb,
  92                                 typename ImageType::RegionType & region) {
  93   // Types
  94   typedef typename ImageType::IndexType  IndexType;
  95   typedef typename ImageType::PointType  PointType;
  96   typedef typename ImageType::RegionType RegionType;
  97   typedef typename ImageType::SizeType   SizeType;
  98
  99   // Region starting point
 100   IndexType regionStart;
 101   PointType start = bb->GetMinimum();
 102   image->TransformPhysicalPointToIndex(start, regionStart);
 103
 104   // Region size
 105   SizeType regionSize;
 106   PointType maxs = bb->GetMaximum();
 107   PointType mins = bb->GetMinimum();
 108   for(unsigned int i=0; i<ImageType::ImageDimension; i++) {
 109     // DD(maxs[i]);
 110     // DD(mins[i]);
 111     // DD((maxs[i] - mins[i])/image->GetSpacing()[i]);
 112     regionSize[i] = lrint((maxs[i] - mins[i])/image->GetSpacing()[i]);
 113     // DD(regionSize[i]);
 114   }
 115
 116   // Create region
 117   region.SetIndex(regionStart);
 118   region.SetSize(regionSize);
 119 }
 120 //--------------------------------------------------------------------
 121
 122 //--------------------------------------------------------------------
 123 template<class ImageType, class TMaskImageType>
 124 typename ImageType::Pointer
 125 clitk::SetBackground(const ImageType * input,
 126                      const TMaskImageType * mask,
 127                      typename TMaskImageType::PixelType maskBG,
 128                      typename ImageType::PixelType outValue,
 129                      bool inPlace) {
 130   typedef clitk::SetBackgroundImageFilter<ImageType, TMaskImageType, ImageType>
 131     SetBackgroundImageFilterType;
 132   typename SetBackgroundImageFilterType::Pointer setBackgroundFilter
 133     = SetBackgroundImageFilterType::New();
 134   //  if (inPlace) setBackgroundFilter->ReleaseDataFlagOn(); // No seg fault
 135   setBackgroundFilter->SetInPlace(inPlace); // This is important to keep memory low
 136   setBackgroundFilter->SetInput(input);
 137   setBackgroundFilter->SetInput2(mask);
 138   setBackgroundFilter->SetMaskValue(maskBG);
 139   setBackgroundFilter->SetOutsideValue(outValue);
 140   setBackgroundFilter->Update();
 141   return setBackgroundFilter->GetOutput();
 142 }
 143 //--------------------------------------------------------------------
 144
 145
 146 //--------------------------------------------------------------------
 147 template<class ImageType>
 148 int clitk::GetNumberOfConnectedComponentLabels(typename ImageType::Pointer input,
 149                                                typename ImageType::PixelType BG,
 150                                                bool isFullyConnected) {
 151   // Connected Component label
 152   typedef itk::ConnectedComponentImageFilter<ImageType, ImageType> ConnectFilterType;
 153   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 154   connectFilter->SetInput(input);
 155   connectFilter->SetBackgroundValue(BG);
 156   connectFilter->SetFullyConnected(isFullyConnected);
 157   connectFilter->Update();
 158
 159   // Return result
 160   return connectFilter->GetObjectCount();
 161 }
 162 //--------------------------------------------------------------------
 163
 164 //--------------------------------------------------------------------
 165 /*
 166   Warning : in this cas, we consider outputType like inputType, not
 167   InternalImageType. Be sure it fits.
 168  */
 169 template<class ImageType>
 170 typename ImageType::Pointer
 171 clitk::Labelize(const ImageType * input,
 172                 typename ImageType::PixelType BG,
 173                 bool isFullyConnected,
 174                 int minimalComponentSize) {
 175   // InternalImageType for storing large number of component
 176   typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 177
 178   // Connected Component label
 179   typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 180   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 181   //  connectFilter->ReleaseDataFlagOn();
 182   connectFilter->SetInput(input);
 183   connectFilter->SetBackgroundValue(BG);
 184   connectFilter->SetFullyConnected(isFullyConnected);
 185
 186   // Sort by size and remove too small area.
 187   typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 188   typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 189   //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 190   relabelFilter->SetInput(connectFilter->GetOutput());
 191   relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 192   relabelFilter->Update();
 193
 194   // Return result
 195   typename ImageType::Pointer output = relabelFilter->GetOutput();
 196   return output;
 197 }
 198 //--------------------------------------------------------------------
 199
 200
 201 //--------------------------------------------------------------------
 202 template<class ImageType>
 203 typename ImageType::Pointer
 204 clitk::RemoveLabels(typename ImageType::Pointer input,
 205                     typename ImageType::PixelType BG,
 206                     std::vector<typename ImageType::PixelType> & labelsToRemove) {
 207   typename ImageType::Pointer working_image = input;
 208   for (unsigned int i=0; i <labelsToRemove.size(); i++) {
 209     typedef clitk::SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
 210     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 211     setBackgroundFilter->SetInput(input);
 212     setBackgroundFilter->SetInput2(input);
 213     setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
 214     setBackgroundFilter->SetOutsideValue(BG);
 215     setBackgroundFilter->Update();
 216     working_image = setBackgroundFilter->GetOutput();
 217   }
 218   return working_image;
 219 }
 220 //--------------------------------------------------------------------
 221
 222
 223 //--------------------------------------------------------------------
 224 template<class ImageType>
 225 typename ImageType::Pointer
 226 clitk::KeepLabels(const ImageType * input,
 227                   typename ImageType::PixelType BG,
 228                   typename ImageType::PixelType FG,
 229                   typename ImageType::PixelType firstKeep,
 230                   typename ImageType::PixelType lastKeep,
 231                   bool useLastKeep) {
 232   typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
 233   typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 234   binarizeFilter->SetInput(input);
 235   binarizeFilter->SetLowerThreshold(firstKeep);
 236   if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 237   binarizeFilter->SetInsideValue(FG);
 238   binarizeFilter->SetOutsideValue(BG);
 239   binarizeFilter->Update();
 240   return binarizeFilter->GetOutput();
 241 }
 242 //--------------------------------------------------------------------
 243
 244
 245 //--------------------------------------------------------------------
 246 template<class ImageType>
 247 typename ImageType::Pointer
 248 clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
 249                                typename ImageType::PixelType BG,
 250                                typename ImageType::PixelType FG,
 251                                bool isFullyConnected,
 252                                int minimalComponentSize,
 253                                LabelizeParameters<typename ImageType::PixelType> * param)
 254 {
 255   typename ImageType::Pointer working_image;
 256   working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
 257   working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
 258   working_image = KeepLabels<ImageType>(working_image,
 259                                         BG, FG,
 260                                         param->GetFirstKeep(),
 261                                         param->GetLastKeep(),
 262                                         param->GetUseLastKeep());
 263   return working_image;
 264 }
 265 //--------------------------------------------------------------------
 266
 267
 268 //--------------------------------------------------------------------
 269 template<class ImageType>
 270 typename ImageType::Pointer
 271 clitk::ResizeImageLike(typename ImageType::Pointer input,
 272                        typename ImageType::Pointer like,
 273                        typename ImageType::PixelType backgroundValue)
 274 {
 275   typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
 276   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 277   cropFilter->SetInput(input);
 278   cropFilter->SetCropLikeImage(like);
 279   cropFilter->SetBackgroundValue(backgroundValue);
 280   cropFilter->Update();
 281   return cropFilter->GetOutput();
 282 }
 283 //--------------------------------------------------------------------
 284
 285
 286 //--------------------------------------------------------------------
 287 template<class MaskImageType>
 288 typename MaskImageType::Pointer
 289 clitk::SliceBySliceRelativePosition(const MaskImageType * input,
 290                                     const MaskImageType * object,
 291                                     int direction,
 292                                     double threshold,
 293                                     std::string orientation,
 294                                     bool uniqueConnectedComponent,
 295                                     double spacing,
 296                                     bool inverseflag)
 297 {
 298   typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 299   typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 300   sliceRelPosFilter->VerboseStepFlagOff();
 301   sliceRelPosFilter->WriteStepFlagOff();
 302   sliceRelPosFilter->SetInput(input);
 303   sliceRelPosFilter->SetInputObject(object);
 304   sliceRelPosFilter->SetDirection(direction);
 305   sliceRelPosFilter->SetFuzzyThreshold(threshold);
 306   sliceRelPosFilter->AddOrientationTypeString(orientation);
 307   sliceRelPosFilter->SetResampleBeforeRelativePositionFilter((spacing != -1));
 308   sliceRelPosFilter->SetIntermediateSpacing(spacing);
 309   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
 310   sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 311   //  sliceRelPosFilter->SetAutoCropFlag(true); ??
 312   sliceRelPosFilter->Update();
 313   return sliceRelPosFilter->GetOutput();
 314 }
 315 //--------------------------------------------------------------------
 316
 317 //--------------------------------------------------------------------
 318 template<class ImageType>
 319 bool
 320 clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
 321                                          typename ImageType::PixelType bg,
 322                                          int direction, bool opposite,
 323                                          typename ImageType::PointType & point)
 324 {
 325   typename ImageType::PointType dummy;
 326   return clitk::FindExtremaPointInAGivenDirection(input, bg, direction,
 327                                                   opposite, dummy, 0, point);
 328 }
 329 //--------------------------------------------------------------------
 330
 331 //--------------------------------------------------------------------
 332 template<class ImageType>
 333 bool
 334 clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
 335                                          typename ImageType::PixelType bg,
 336                                          int direction, bool opposite,
 337                                          typename ImageType::PointType refpoint,
 338                                          double distanceMax,
 339                                          typename ImageType::PointType & point)
 340 {
 341   /*
 342     loop over input pixels, store the index in the fg that is max
 343     according to the given direction.
 344   */
 345   typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
 346   IteratorType iter(input, input->GetLargestPossibleRegion());
 347   iter.GoToBegin();
 348   typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
 349   if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
 350   bool found=false;
 351   while (!iter.IsAtEnd()) {
 352     if (iter.Get() != bg) {
 353       bool test = iter.GetIndex()[direction] >  max[direction];
 354       if (opposite) test = !test;
 355       if (test) {
 356         typename ImageType::PointType p;
 357         input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
 358         if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
 359           max = iter.GetIndex();
 360           found = true;
 361         }
 362       }
 363     }
 364     ++iter;
 365   }
 366   if (!found) return false;
 367   input->TransformIndexToPhysicalPoint(max, point);
 368   return true;
 369 }
 370 //--------------------------------------------------------------------
 371
 372
 373 //--------------------------------------------------------------------
 374 template<class ImageType>
 375 typename ImageType::Pointer
 376 clitk::CropImageAbove(typename ImageType::Pointer image,
 377                       int dim, double min,
 378                       bool autoCrop,
 379                       typename ImageType::PixelType BG)
 380 {
 381   return clitk::CropImageAlongOneAxis<ImageType>(image, dim,
 382                                                  image->GetOrigin()[dim],
 383                                                  min,
 384                                                  autoCrop, BG);
 385 }
 386 //--------------------------------------------------------------------
 387
 388
 389 //--------------------------------------------------------------------
 390 template<class ImageType>
 391 typename ImageType::Pointer
 392 clitk::CropImageBelow(typename ImageType::Pointer image,
 393                       int dim, double max,
 394                       bool autoCrop,
 395                       typename ImageType::PixelType BG)
 396 {
 397   typename ImageType::PointType p;
 398   image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
 399                                        image->GetLargestPossibleRegion().GetSize(), p);
 400   return clitk::CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
 401 }
 402 //--------------------------------------------------------------------
 403
 404
 405 //--------------------------------------------------------------------
 406 template<class ImageType>
 407 typename ImageType::Pointer
 408 clitk::CropImageAlongOneAxis(typename ImageType::Pointer image,
 409                              int dim, double min, double max,
 410                              bool autoCrop,
 411                              typename ImageType::PixelType BG)
 412 {
 413   // Compute region size
 414   typename ImageType::RegionType region;
 415   typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 416   typename ImageType::PointType p = image->GetOrigin();
 417   p[dim] = min;
 418   typename ImageType::IndexType start;
 419   image->TransformPhysicalPointToIndex(p, start);
 420   p[dim] = max;
 421   typename ImageType::IndexType end;
 422   image->TransformPhysicalPointToIndex(p, end);
 423   size[dim] = fabs(end[dim]-start[dim]);
 424   region.SetIndex(start);
 425   region.SetSize(size);
 426
 427   // Perform Crop
 428   typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 429   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 430   cropFilter->SetInput(image);
 431   cropFilter->SetRegionOfInterest(region);
 432   cropFilter->Update();
 433   typename ImageType::Pointer result = cropFilter->GetOutput();
 434
 435   // Auto Crop
 436   if (autoCrop) {
 437     result = clitk::AutoCrop<ImageType>(result, BG);
 438   }
 439   return result;
 440 }
 441 //--------------------------------------------------------------------
 442
 443
 444 //--------------------------------------------------------------------
 445 template<class ImageType>
 446 void
 447 clitk::ComputeCentroids(typename ImageType::Pointer image,
 448                         typename ImageType::PixelType BG,
 449                         std::vector<typename ImageType::PointType> & centroids)
 450 {
 451   typedef long LabelType;
 452   static const unsigned int Dim = ImageType::ImageDimension;
 453   typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 454   typedef itk::LabelMap< LabelObjectType > LabelMapType;
 455   typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 456   typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 457   typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 458   typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 459   imageToLabelFilter->SetBackgroundValue(BG);
 460   imageToLabelFilter->SetInput(image);
 461   statFilter->SetInput(imageToLabelFilter->GetOutput());
 462   statFilter->Update();
 463   typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 464
 465   centroids.clear();
 466   typename ImageType::PointType dummy;
 467   centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 468   for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 469     centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 470   }
 471 }
 472 //--------------------------------------------------------------------
 473
 474
 475 //--------------------------------------------------------------------
 476 template<class ImageType>
 477 void
 478 clitk::ExtractSlices(typename ImageType::Pointer image,
 479                      int direction,
 480                      std::vector<typename itk::Image<typename ImageType::PixelType,
 481                      ImageType::ImageDimension-1>::Pointer > & slices)
 482 {
 483   typedef clitk::ExtractSliceFilter<ImageType> ExtractSliceFilterType;
 484   typedef typename ExtractSliceFilterType::SliceType SliceType;
 485   typename ExtractSliceFilterType::Pointer
 486     extractSliceFilter = ExtractSliceFilterType::New();
 487   extractSliceFilter->SetInput(image);
 488   extractSliceFilter->SetDirection(direction);
 489   extractSliceFilter->Update();
 490   extractSliceFilter->GetOutputSlices(slices);
 491 }
 492 //--------------------------------------------------------------------
 493
 494
 495 //--------------------------------------------------------------------
 496 template<class ImageType>
 497 typename ImageType::Pointer
 498 clitk::JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
 499                   ImageType::ImageDimension-1>::Pointer > & slices,
 500                   typename ImageType::Pointer input,
 501                   int direction) {
 502   typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
 503   typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
 504   typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
 505   joinFilter->SetOrigin(input->GetOrigin()[direction]);
 506   joinFilter->SetSpacing(input->GetSpacing()[direction]);
 507   for(unsigned int i=0; i<slices.size(); i++) {
 508     joinFilter->PushBackInput(slices[i]);
 509   }
 510   joinFilter->Update();
 511   return joinFilter->GetOutput();
 512 }
 513 //--------------------------------------------------------------------
 514
 515
 516 //--------------------------------------------------------------------
 517 template<class ImageType>
 518 void
 519 clitk::PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p,
 520                                              ImagePointer image,
 521                                              const int slice,
 522                                              PointType3D & p3D)
 523 {
 524   p3D[0] = p[0];
 525   p3D[1] = p[1];
 526   p3D[2] = (image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 527     + image->GetOrigin()[2];
 528 }
 529 //--------------------------------------------------------------------
 530
 531
 532 //--------------------------------------------------------------------
 533 template<class ImageType>
 534 void
 535 clitk::PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map,
 536                                                  ImagePointer image,
 537                                                  VectorPoint3DType & list)
 538 {
 539   typename MapPoint2DType::const_iterator iter = map.begin();
 540   while (iter != map.end()) {
 541     PointType3D p;
 542     Convert2DTo3D(iter->second, image, iter->first, p);
 543     list.push_back(p);
 544     ++iter;
 545   }
 546 }
 547 //--------------------------------------------------------------------
 548
 549 //--------------------------------------------------------------------
 550 template<class ImageType>
 551 void
 552 clitk::WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 553                             std::string filename)
 554 {
 555   std::ofstream os;
 556   openFileForWriting(os, filename);
 557   os << "LANDMARKS1" << std::endl;
 558   for(uint i=0; i<points.size(); i++) {
 559     const typename ImageType::PointType & p = points[i];
 560     // Write it in the file
 561     os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 562   }
 563   os.close();
 564 }
 565 //--------------------------------------------------------------------
 566
 567
 568 //--------------------------------------------------------------------
 569 template<class ImageType>
 570 typename ImageType::Pointer
 571 clitk::Dilate(typename ImageType::Pointer image,
 572               double radiusInMM,
 573               typename ImageType::PixelType BG,
 574               typename ImageType::PixelType FG,
 575               bool extendSupport)
 576 {
 577   typename ImageType::SizeType r;
 578   for(uint i=0; i<ImageType::ImageDimension; i++)
 579     r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 580   return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
 581 }
 582 //--------------------------------------------------------------------
 583
 584
 585 //--------------------------------------------------------------------
 586 template<class ImageType>
 587 typename ImageType::Pointer
 588 clitk::Dilate(typename ImageType::Pointer image,
 589               typename ImageType::PointType radiusInMM,
 590               typename ImageType::PixelType BG,
 591               typename ImageType::PixelType FG,
 592               bool extendSupport)
 593 {
 594   typename ImageType::SizeType r;
 595   for(uint i=0; i<ImageType::ImageDimension; i++)
 596     r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 597   return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
 598 }
 599 //--------------------------------------------------------------------
 600
 601
 602 //--------------------------------------------------------------------
 603 template<class ImageType>
 604 typename ImageType::Pointer
 605 clitk::Dilate(typename ImageType::Pointer image,
 606               typename ImageType::SizeType radius,
 607               typename ImageType::PixelType BG,
 608               typename ImageType::PixelType FG,
 609               bool extendSupport)
 610 {
 611   // Create kernel for dilatation
 612   typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 613                                             ImageType::ImageDimension> KernelType;
 614   KernelType structuringElement;
 615   structuringElement.SetRadius(radius);
 616   structuringElement.CreateStructuringElement();
 617
 618   if (extendSupport) {
 619     typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 620     typename PadFilterType::Pointer padFilter = PadFilterType::New();
 621     padFilter->SetInput(image);
 622     typename ImageType::SizeType lower;
 623     typename ImageType::SizeType upper;
 624     for(uint i=0; i<3; i++) {
 625       lower[i] = upper[i] = 2*(radius[i]+1);
 626     }
 627     padFilter->SetPadLowerBound(lower);
 628     padFilter->SetPadUpperBound(upper);
 629     padFilter->Update();
 630     image = padFilter->GetOutput();
 631   }
 632
 633   // Dilate  filter
 634   typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 635   typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 636   dilateFilter->SetBackgroundValue(BG);
 637   dilateFilter->SetForegroundValue(FG);
 638   dilateFilter->SetBoundaryToForeground(false);
 639   dilateFilter->SetKernel(structuringElement);
 640   dilateFilter->SetInput(image);
 641   dilateFilter->Update();
 642   return image = dilateFilter->GetOutput();
 643 }
 644 //--------------------------------------------------------------------
 645
 646
 647 //--------------------------------------------------------------------
 648 template<class ValueType, class VectorType>
 649 void clitk::ConvertOption(std::string optionName, uint given,
 650                           ValueType * values, VectorType & p,
 651                           uint dim, bool required)
 652 {
 653   if (required && (given == 0)) {
 654     clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 655                         << dim << " values.");
 656   }
 657   if (given == 1) {
 658     for(uint i=0; i<dim; i++) p[i] = values[0];
 659     return;
 660   }
 661   if (given == dim) {
 662     for(uint i=0; i<dim; i++) p[i] = values[i];
 663     return;
 664   }
 665   if (given == 0) return;
 666   clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 667                       << dim << " values.");
 668 }
 669 //--------------------------------------------------------------------
 670
 671