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   // DD(relabelFilter->GetNumberOfObjects());
 196   // DD(relabelFilter->GetOriginalNumberOfObjects());
 197   // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
 198
 199   // Return result
 200   typename ImageType::Pointer output = relabelFilter->GetOutput();
 201   return output;
 202 }
 203 //--------------------------------------------------------------------
 204
 205
 206 //--------------------------------------------------------------------
 207 /*
 208   Warning : in this cas, we consider outputType like inputType, not
 209   InternalImageType. Be sure it fits.
 210  */
 211 template<class ImageType>
 212 typename ImageType::Pointer
 213 clitk::LabelizeAndCountNumberOfObjects(const ImageType * input,
 214                                        typename ImageType::PixelType BG,
 215                                        bool isFullyConnected,
 216                                        int minimalComponentSize,
 217                                        int & nb) {
 218   // InternalImageType for storing large number of component
 219   typedef itk::Image<int, ImageType::ImageDimension> InternalImageType;
 220
 221   // Connected Component label
 222   typedef itk::ConnectedComponentImageFilter<ImageType, InternalImageType> ConnectFilterType;
 223   typename ConnectFilterType::Pointer connectFilter = ConnectFilterType::New();
 224   //  connectFilter->ReleaseDataFlagOn();
 225   connectFilter->SetInput(input);
 226   connectFilter->SetBackgroundValue(BG);
 227   connectFilter->SetFullyConnected(isFullyConnected);
 228
 229   // Sort by size and remove too small area.
 230   typedef itk::RelabelComponentImageFilter<InternalImageType, ImageType> RelabelFilterType;
 231   typename RelabelFilterType::Pointer relabelFilter = RelabelFilterType::New();
 232   //  relabelFilter->ReleaseDataFlagOn(); // if yes, fail when ExplosionControlledThresholdConnectedImageFilter ???
 233   relabelFilter->SetInput(connectFilter->GetOutput());
 234   relabelFilter->SetMinimumObjectSize(minimalComponentSize);
 235   relabelFilter->Update();
 236
 237   nb = relabelFilter->GetNumberOfObjects();
 238   // DD(relabelFilter->GetNumberOfObjects());
 239   // DD(relabelFilter->GetOriginalNumberOfObjects());
 240   // DD(relabelFilter->GetSizeOfObjectsInPhysicalUnits()[0]);
 241
 242   // Return result
 243   typename ImageType::Pointer output = relabelFilter->GetOutput();
 244   return output;
 245 }
 246 //--------------------------------------------------------------------
 247
 248
 249
 250 //--------------------------------------------------------------------
 251 template<class ImageType>
 252 typename ImageType::Pointer
 253 clitk::RemoveLabels(typename ImageType::Pointer input,
 254                     typename ImageType::PixelType BG,
 255                     std::vector<typename ImageType::PixelType> & labelsToRemove) {
 256   typename ImageType::Pointer working_image = input;
 257   for (unsigned int i=0; i <labelsToRemove.size(); i++) {
 258     typedef clitk::SetBackgroundImageFilter<ImageType, ImageType> SetBackgroundImageFilterType;
 259     typename SetBackgroundImageFilterType::Pointer setBackgroundFilter = SetBackgroundImageFilterType::New();
 260     setBackgroundFilter->SetInput(input);
 261     setBackgroundFilter->SetInput2(input);
 262     setBackgroundFilter->SetMaskValue(labelsToRemove[i]);
 263     setBackgroundFilter->SetOutsideValue(BG);
 264     setBackgroundFilter->Update();
 265     working_image = setBackgroundFilter->GetOutput();
 266   }
 267   return working_image;
 268 }
 269 //--------------------------------------------------------------------
 270
 271
 272 //--------------------------------------------------------------------
 273 template<class ImageType>
 274 typename ImageType::Pointer
 275 clitk::KeepLabels(const ImageType * input,
 276                   typename ImageType::PixelType BG,
 277                   typename ImageType::PixelType FG,
 278                   typename ImageType::PixelType firstKeep,
 279                   typename ImageType::PixelType lastKeep,
 280                   bool useLastKeep) {
 281   typedef itk::BinaryThresholdImageFilter<ImageType, ImageType> BinarizeFilterType;
 282   typename BinarizeFilterType::Pointer binarizeFilter = BinarizeFilterType::New();
 283   binarizeFilter->SetInput(input);
 284   binarizeFilter->SetLowerThreshold(firstKeep);
 285   if (useLastKeep) binarizeFilter->SetUpperThreshold(lastKeep);
 286   binarizeFilter->SetInsideValue(FG);
 287   binarizeFilter->SetOutsideValue(BG);
 288   binarizeFilter->Update();
 289   return binarizeFilter->GetOutput();
 290 }
 291 //--------------------------------------------------------------------
 292
 293
 294 //--------------------------------------------------------------------
 295 template<class ImageType>
 296 typename ImageType::Pointer
 297 clitk::LabelizeAndSelectLabels(typename ImageType::Pointer input,
 298                                typename ImageType::PixelType BG,
 299                                typename ImageType::PixelType FG,
 300                                bool isFullyConnected,
 301                                int minimalComponentSize,
 302                                LabelizeParameters<typename ImageType::PixelType> * param)
 303 {
 304   typename ImageType::Pointer working_image;
 305   working_image = Labelize<ImageType>(input, BG, isFullyConnected, minimalComponentSize);
 306   working_image = RemoveLabels<ImageType>(working_image, BG, param->GetLabelsToRemove());
 307   working_image = KeepLabels<ImageType>(working_image,
 308                                         BG, FG,
 309                                         param->GetFirstKeep(),
 310                                         param->GetLastKeep(),
 311                                         param->GetUseLastKeep());
 312   return working_image;
 313 }
 314 //--------------------------------------------------------------------
 315
 316
 317 //--------------------------------------------------------------------
 318 template<class ImageType>
 319 typename ImageType::Pointer
 320 clitk::ResizeImageLike(typename ImageType::Pointer input,
 321                        typename ImageType::Pointer like,
 322                        typename ImageType::PixelType backgroundValue)
 323 {
 324   typedef clitk::CropLikeImageFilter<ImageType> CropFilterType;
 325   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 326   cropFilter->SetInput(input);
 327   cropFilter->SetCropLikeImage(like);
 328   cropFilter->SetBackgroundValue(backgroundValue);
 329   cropFilter->Update();
 330   return cropFilter->GetOutput();
 331 }
 332 //--------------------------------------------------------------------
 333
 334
 335 //--------------------------------------------------------------------
 336 template<class MaskImageType>
 337 typename MaskImageType::Pointer
 338 clitk::SliceBySliceRelativePosition(const MaskImageType * input,
 339                                     const MaskImageType * object,
 340                                     int direction,
 341                                     double threshold,
 342                                     std::string orientation,
 343                                     bool uniqueConnectedComponent,
 344                                     double spacing,
 345                                     bool inverseflag)
 346 {
 347   typedef clitk::SliceBySliceRelativePositionFilter<MaskImageType> SliceRelPosFilterType;
 348   typename SliceRelPosFilterType::Pointer sliceRelPosFilter = SliceRelPosFilterType::New();
 349   sliceRelPosFilter->VerboseStepFlagOff();
 350   sliceRelPosFilter->WriteStepFlagOff();
 351   sliceRelPosFilter->SetInput(input);
 352   sliceRelPosFilter->SetInputObject(object);
 353   sliceRelPosFilter->SetDirection(direction);
 354   sliceRelPosFilter->SetFuzzyThreshold(threshold);
 355   sliceRelPosFilter->AddOrientationTypeString(orientation);
 356   sliceRelPosFilter->SetResampleBeforeRelativePositionFilter((spacing != -1));
 357   sliceRelPosFilter->SetIntermediateSpacing(spacing);
 358   sliceRelPosFilter->SetUniqueConnectedComponentBySlice(uniqueConnectedComponent);
 359   sliceRelPosFilter->SetInverseOrientationFlag(inverseflag);
 360   //  sliceRelPosFilter->SetAutoCropFlag(true); ??
 361   sliceRelPosFilter->Update();
 362   return sliceRelPosFilter->GetOutput();
 363 }
 364 //--------------------------------------------------------------------
 365
 366 //--------------------------------------------------------------------
 367 template<class ImageType>
 368 bool
 369 clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
 370                                          typename ImageType::PixelType bg,
 371                                          int direction, bool opposite,
 372                                          typename ImageType::PointType & point)
 373 {
 374   typename ImageType::PointType dummy;
 375   return clitk::FindExtremaPointInAGivenDirection(input, bg, direction,
 376                                                   opposite, dummy, 0, point);
 377 }
 378 //--------------------------------------------------------------------
 379
 380 //--------------------------------------------------------------------
 381 template<class ImageType>
 382 bool
 383 clitk::FindExtremaPointInAGivenDirection(const ImageType * input,
 384                                          typename ImageType::PixelType bg,
 385                                          int direction, bool opposite,
 386                                          typename ImageType::PointType refpoint,
 387                                          double distanceMax,
 388                                          typename ImageType::PointType & point)
 389 {
 390   /*
 391     loop over input pixels, store the index in the fg that is max
 392     according to the given direction.
 393   */
 394   typedef itk::ImageRegionConstIteratorWithIndex<ImageType> IteratorType;
 395   IteratorType iter(input, input->GetLargestPossibleRegion());
 396   iter.GoToBegin();
 397   typename ImageType::IndexType max = input->GetLargestPossibleRegion().GetIndex();
 398   if (opposite) max = max+input->GetLargestPossibleRegion().GetSize();
 399   bool found=false;
 400   while (!iter.IsAtEnd()) {
 401     if (iter.Get() != bg) {
 402       bool test = iter.GetIndex()[direction] >  max[direction];
 403       if (opposite) test = !test;
 404       if (test) {
 405         typename ImageType::PointType p;
 406         input->TransformIndexToPhysicalPoint(iter.GetIndex(), p);
 407         if ((distanceMax==0) || (p.EuclideanDistanceTo(refpoint) < distanceMax)) {
 408           max = iter.GetIndex();
 409           found = true;
 410         }
 411       }
 412     }
 413     ++iter;
 414   }
 415   if (!found) return false;
 416   input->TransformIndexToPhysicalPoint(max, point);
 417   return true;
 418 }
 419 //--------------------------------------------------------------------
 420
 421
 422 //--------------------------------------------------------------------
 423 template<class ImageType>
 424 typename ImageType::Pointer
 425 clitk::CropImageAbove(typename ImageType::Pointer image,
 426                       int dim, double min,
 427                       bool autoCrop,
 428                       typename ImageType::PixelType BG)
 429 {
 430   return clitk::CropImageAlongOneAxis<ImageType>(image, dim,
 431                                                  image->GetOrigin()[dim],
 432                                                  min,
 433                                                  autoCrop, BG);
 434 }
 435 //--------------------------------------------------------------------
 436
 437
 438 //--------------------------------------------------------------------
 439 template<class ImageType>
 440 typename ImageType::Pointer
 441 clitk::CropImageBelow(typename ImageType::Pointer image,
 442                       int dim, double max,
 443                       bool autoCrop,
 444                       typename ImageType::PixelType BG)
 445 {
 446   typename ImageType::PointType p;
 447   image->TransformIndexToPhysicalPoint(image->GetLargestPossibleRegion().GetIndex()+
 448                                        image->GetLargestPossibleRegion().GetSize(), p);
 449   return clitk::CropImageAlongOneAxis<ImageType>(image, dim, max, p[dim], autoCrop, BG);
 450 }
 451 //--------------------------------------------------------------------
 452
 453
 454 //--------------------------------------------------------------------
 455 template<class ImageType>
 456 typename ImageType::Pointer
 457 clitk::CropImageAlongOneAxis(typename ImageType::Pointer image,
 458                              int dim, double min, double max,
 459                              bool autoCrop,
 460                              typename ImageType::PixelType BG)
 461 {
 462   // Compute region size
 463   typename ImageType::RegionType region;
 464   typename ImageType::SizeType size = image->GetLargestPossibleRegion().GetSize();
 465   typename ImageType::PointType p = image->GetOrigin();
 466   p[dim] = min;
 467   typename ImageType::IndexType start;
 468   image->TransformPhysicalPointToIndex(p, start);
 469   p[dim] = max;
 470   typename ImageType::IndexType end;
 471   image->TransformPhysicalPointToIndex(p, end);
 472   size[dim] = fabs(end[dim]-start[dim]);
 473   region.SetIndex(start);
 474   region.SetSize(size);
 475
 476   // Perform Crop
 477   typedef itk::RegionOfInterestImageFilter<ImageType, ImageType> CropFilterType;
 478   typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 479   cropFilter->SetInput(image);
 480   cropFilter->SetRegionOfInterest(region);
 481   cropFilter->Update();
 482   typename ImageType::Pointer result = cropFilter->GetOutput();
 483
 484   // Auto Crop
 485   if (autoCrop) {
 486     result = clitk::AutoCrop<ImageType>(result, BG);
 487   }
 488   return result;
 489 }
 490 //--------------------------------------------------------------------
 491
 492
 493 //--------------------------------------------------------------------
 494 template<class ImageType>
 495 void
 496 clitk::ComputeCentroids(typename ImageType::Pointer image,
 497                         typename ImageType::PixelType BG,
 498                         std::vector<typename ImageType::PointType> & centroids)
 499 {
 500   typedef long LabelType;
 501   static const unsigned int Dim = ImageType::ImageDimension;
 502   typedef itk::ShapeLabelObject< LabelType, Dim > LabelObjectType;
 503   typedef itk::LabelMap< LabelObjectType > LabelMapType;
 504   typedef itk::LabelImageToLabelMapFilter<ImageType, LabelMapType> ImageToMapFilterType;
 505   typename ImageToMapFilterType::Pointer imageToLabelFilter = ImageToMapFilterType::New();
 506   typedef itk::ShapeLabelMapFilter<LabelMapType, ImageType> ShapeFilterType;
 507   typename ShapeFilterType::Pointer statFilter = ShapeFilterType::New();
 508   imageToLabelFilter->SetBackgroundValue(BG);
 509   imageToLabelFilter->SetInput(image);
 510   statFilter->SetInput(imageToLabelFilter->GetOutput());
 511   statFilter->Update();
 512   typename LabelMapType::Pointer labelMap = statFilter->GetOutput();
 513
 514   centroids.clear();
 515   typename ImageType::PointType dummy;
 516   centroids.push_back(dummy); // label 0 -> no centroid, use dummy point
 517   for(uint i=1; i<labelMap->GetNumberOfLabelObjects()+1; i++) {
 518     centroids.push_back(labelMap->GetLabelObject(i)->GetCentroid());
 519   }
 520 }
 521 //--------------------------------------------------------------------
 522
 523
 524 //--------------------------------------------------------------------
 525 template<class ImageType>
 526 void
 527 clitk::ExtractSlices(typename ImageType::Pointer image,
 528                      int direction,
 529                      std::vector<typename itk::Image<typename ImageType::PixelType,
 530                      ImageType::ImageDimension-1>::Pointer > & slices)
 531 {
 532   typedef clitk::ExtractSliceFilter<ImageType> ExtractSliceFilterType;
 533   typedef typename ExtractSliceFilterType::SliceType SliceType;
 534   typename ExtractSliceFilterType::Pointer
 535     extractSliceFilter = ExtractSliceFilterType::New();
 536   extractSliceFilter->SetInput(image);
 537   extractSliceFilter->SetDirection(direction);
 538   extractSliceFilter->Update();
 539   extractSliceFilter->GetOutputSlices(slices);
 540 }
 541 //--------------------------------------------------------------------
 542
 543
 544 //--------------------------------------------------------------------
 545 template<class ImageType>
 546 typename ImageType::Pointer
 547 clitk::JoinSlices(std::vector<typename itk::Image<typename ImageType::PixelType,
 548                   ImageType::ImageDimension-1>::Pointer > & slices,
 549                   typename ImageType::Pointer input,
 550                   int direction) {
 551   typedef typename itk::Image<typename ImageType::PixelType, ImageType::ImageDimension-1> SliceType;
 552   typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
 553   typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
 554   joinFilter->SetOrigin(input->GetOrigin()[direction]);
 555   joinFilter->SetSpacing(input->GetSpacing()[direction]);
 556   for(unsigned int i=0; i<slices.size(); i++) {
 557     joinFilter->PushBackInput(slices[i]);
 558   }
 559   joinFilter->Update();
 560   return joinFilter->GetOutput();
 561 }
 562 //--------------------------------------------------------------------
 563
 564
 565 //--------------------------------------------------------------------
 566 template<class ImageType>
 567 void
 568 clitk::PointsUtils<ImageType>::Convert2DTo3D(const PointType2D & p,
 569                                              ImagePointer image,
 570                                              const int slice,
 571                                              PointType3D & p3D)
 572 {
 573   p3D[0] = p[0];
 574   p3D[1] = p[1];
 575   p3D[2] = (image->GetLargestPossibleRegion().GetIndex()[2]+slice)*image->GetSpacing()[2]
 576     + image->GetOrigin()[2];
 577 }
 578 //--------------------------------------------------------------------
 579
 580
 581 //--------------------------------------------------------------------
 582 template<class ImageType>
 583 void
 584 clitk::PointsUtils<ImageType>::Convert2DTo3DList(const MapPoint2DType & map,
 585                                                  ImagePointer image,
 586                                                  VectorPoint3DType & list)
 587 {
 588   typename MapPoint2DType::const_iterator iter = map.begin();
 589   while (iter != map.end()) {
 590     PointType3D p;
 591     Convert2DTo3D(iter->second, image, iter->first, p);
 592     list.push_back(p);
 593     ++iter;
 594   }
 595 }
 596 //--------------------------------------------------------------------
 597
 598 //--------------------------------------------------------------------
 599 template<class ImageType>
 600 void
 601 clitk::WriteListOfLandmarks(std::vector<typename ImageType::PointType> points,
 602                             std::string filename)
 603 {
 604   std::ofstream os;
 605   openFileForWriting(os, filename);
 606   os << "LANDMARKS1" << std::endl;
 607   for(uint i=0; i<points.size(); i++) {
 608     const typename ImageType::PointType & p = points[i];
 609     // Write it in the file
 610     os << i << " " << p[0] << " " << p[1] << " " << p[2] << " 0 0 " << std::endl;
 611   }
 612   os.close();
 613 }
 614 //--------------------------------------------------------------------
 615
 616
 617 //--------------------------------------------------------------------
 618 template<class ImageType>
 619 typename ImageType::Pointer
 620 clitk::Dilate(typename ImageType::Pointer image,
 621               double radiusInMM,
 622               typename ImageType::PixelType BG,
 623               typename ImageType::PixelType FG,
 624               bool extendSupport)
 625 {
 626   typename ImageType::SizeType r;
 627   for(uint i=0; i<ImageType::ImageDimension; i++)
 628     r[i] = (uint)lrint(radiusInMM/image->GetSpacing()[i]);
 629   return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
 630 }
 631 //--------------------------------------------------------------------
 632
 633
 634 //--------------------------------------------------------------------
 635 template<class ImageType>
 636 typename ImageType::Pointer
 637 clitk::Dilate(typename ImageType::Pointer image,
 638               typename ImageType::PointType radiusInMM,
 639               typename ImageType::PixelType BG,
 640               typename ImageType::PixelType FG,
 641               bool extendSupport)
 642 {
 643   typename ImageType::SizeType r;
 644   for(uint i=0; i<ImageType::ImageDimension; i++)
 645     r[i] = (uint)lrint(radiusInMM[i]/image->GetSpacing()[i]);
 646   return clitk::Dilate<ImageType>(image, r, BG, FG, extendSupport);
 647 }
 648 //--------------------------------------------------------------------
 649
 650
 651 //--------------------------------------------------------------------
 652 template<class ImageType>
 653 typename ImageType::Pointer
 654 clitk::Dilate(typename ImageType::Pointer image,
 655               typename ImageType::SizeType radius,
 656               typename ImageType::PixelType BG,
 657               typename ImageType::PixelType FG,
 658               bool extendSupport)
 659 {
 660   // Create kernel for dilatation
 661   typedef itk::BinaryBallStructuringElement<typename ImageType::PixelType,
 662                                             ImageType::ImageDimension> KernelType;
 663   KernelType structuringElement;
 664   structuringElement.SetRadius(radius);
 665   structuringElement.CreateStructuringElement();
 666
 667   if (extendSupport) {
 668     typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
 669     typename PadFilterType::Pointer padFilter = PadFilterType::New();
 670     padFilter->SetInput(image);
 671     typename ImageType::SizeType lower;
 672     typename ImageType::SizeType upper;
 673     for(uint i=0; i<3; i++) {
 674       lower[i] = upper[i] = 2*(radius[i]+1);
 675     }
 676     padFilter->SetPadLowerBound(lower);
 677     padFilter->SetPadUpperBound(upper);
 678     padFilter->Update();
 679     image = padFilter->GetOutput();
 680   }
 681
 682   // Dilate  filter
 683   typedef itk::BinaryDilateImageFilter<ImageType, ImageType , KernelType> DilateFilterType;
 684   typename DilateFilterType::Pointer dilateFilter = DilateFilterType::New();
 685   dilateFilter->SetBackgroundValue(BG);
 686   dilateFilter->SetForegroundValue(FG);
 687   dilateFilter->SetBoundaryToForeground(false);
 688   dilateFilter->SetKernel(structuringElement);
 689   dilateFilter->SetInput(image);
 690   dilateFilter->Update();
 691   return image = dilateFilter->GetOutput();
 692 }
 693 //--------------------------------------------------------------------
 694
 695
 696 //--------------------------------------------------------------------
 697 template<class ValueType, class VectorType>
 698 void clitk::ConvertOption(std::string optionName, uint given,
 699                           ValueType * values, VectorType & p,
 700                           uint dim, bool required)
 701 {
 702   if (required && (given == 0)) {
 703     clitkExceptionMacro("The option --" << optionName << " must be set and have 1 or "
 704                         << dim << " values.");
 705   }
 706   if (given == 1) {
 707     for(uint i=0; i<dim; i++) p[i] = values[0];
 708     return;
 709   }
 710   if (given == dim) {
 711     for(uint i=0; i<dim; i++) p[i] = values[i];
 712     return;
 713   }
 714   if (given == 0) return;
 715   clitkExceptionMacro("The option --" << optionName << " must have 1 or "
 716                       << dim << " values.");
 717 }
 718 //--------------------------------------------------------------------
 719
 720
 721 //--------------------------------------------------------------------
 722 /*
 723   http://www.gamedev.net/community/forums/topic.asp?topic_id=542870
 724   Assuming the points are (Ax,Ay) (Bx,By) and (Cx,Cy), you need to compute:
 725   (Bx - Ax) * (Cy - Ay) - (By - Ay) * (Cx - Ax)
 726   This will equal zero if the point C is on the line formed by
 727   points A and B, and will have a different sign depending on the
 728   side. Which side this is depends on the orientation of your (x,y)
 729   coordinates, but you can plug test values for A,B and C into this
 730   formula to determine whether negative values are to the left or to
 731   the right.
 732   => to accelerate, start with formula, when change sign -> stop and fill
 733 */
 734 template<class ImageType>
 735 void
 736 clitk::SliceBySliceSetBackgroundFromLineSeparation(typename ImageType::Pointer input,
 737                                                    std::vector<typename ImageType::PointType> & lA,
 738                                                    std::vector<typename ImageType::PointType> & lB,
 739                                                    typename ImageType::PixelType BG,
 740                                                    int mainDirection,
 741                                                    double offsetToKeep)
 742 {
 743
 744   typedef itk::ImageSliceIteratorWithIndex<ImageType> SliceIteratorType;
 745   SliceIteratorType siter = SliceIteratorType(input,
 746                                               input->GetLargestPossibleRegion());
 747   siter.SetFirstDirection(0);
 748   siter.SetSecondDirection(1);
 749   siter.GoToBegin();
 750   int i=0;
 751   typename ImageType::PointType A;
 752   typename ImageType::PointType B;
 753   typename ImageType::PointType C;
 754   while (!siter.IsAtEnd()) {
 755     // Check that the current slice correspond to the current point
 756     input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 757     if (C[2] != lA[i][2]) {
 758       // DD(C);
 759       // DD(lA[i]);
 760     }
 761     else {
 762       // Define A,B,C points
 763       A = lA[i];
 764       B = lB[i];
 765       C = A;
 766       C[mainDirection] += offsetToKeep; // I know I must keep this point
 767       double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 768       bool isPositive = s<0;
 769       while (!siter.IsAtEndOfSlice()) {
 770         while (!siter.IsAtEndOfLine()) {
 771           // Very slow, I know ... but image should be very small
 772           input->TransformIndexToPhysicalPoint(siter.GetIndex(), C);
 773           double s = (B[0] - A[0]) * (C[1] - A[1]) - (B[1] - A[1]) * (C[0] - A[0]);
 774           if (s == 0) siter.Set(BG); // on the line, we decide to remove
 775           if (isPositive) {
 776             if (s > 0) siter.Set(BG);
 777           }
 778           else {
 779             if (s < 0) siter.Set(BG);
 780           }
 781           ++siter;
 782         }
 783         siter.NextLine();
 784       }
 785       ++i;
 786     }
 787     siter.NextSlice();
 788   }
 789 }
 790 //--------------------------------------------------------------------