itk/clitkAddRelativePositionConstraintToLabelImageFilter.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://www.centreleonberard.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ===========================================================================**/
  18
  19 // clitk
  20 #include "clitkCommon.h"
  21 #include "clitkBooleanOperatorLabelImageFilter.h"
  22 #include "clitkAutoCropFilter.h"
  23 #include "clitkResampleImageWithOptionsFilter.h"
  24 #include "clitkBooleanOperatorLabelImageFilter.h"
  25 #include "clitkCropLikeImageFilter.h"
  26
  27 // itk
  28 #include <deque>
  29 #include <itkStatisticsLabelMapFilter.h>
  30 #include <itkLabelImageToStatisticsLabelMapFilter.h>
  31 #include <itkRegionOfInterestImageFilter.h>
  32 #include <itkBinaryThresholdImageFilter.h>
  33 #include <itkBinaryErodeImageFilter.h>
  34 #include <itkBinaryBallStructuringElement.h>
  35 #include <itkAddImageFilter.h>
  36 #if ITK_VERSION_MAJOR >= 4
  37   #include <itkDivideImageFilter.h>
  38 #else
  39   #include <itkDivideByConstantImageFilter.h>
  40 #endif
  41
  42 // itk [Bloch et al]
  43 #include "RelativePositionPropImageFilter.h"
  44
  45 //--------------------------------------------------------------------
  46 template <class ImageType>
  47 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
  48 AddRelativePositionConstraintToLabelImageFilter():
  49   clitk::FilterBase(),
  50   itk::ImageToImageFilter<ImageType, ImageType>()
  51 {
  52   this->SetNumberOfRequiredInputs(2);
  53   SetFuzzyThreshold(0.6);
  54   SetBackgroundValue(0);
  55   SetObjectBackgroundValue(0);
  56   ClearOrientationType();
  57   IntermediateSpacingFlagOn();
  58   SetIntermediateSpacing(10);
  59   AutoCropFlagOn();
  60   InverseOrientationFlagOff();
  61   RemoveObjectFlagOn();
  62   CombineWithOrFlagOff();
  63   VerboseStepFlagOff();
  64   WriteStepFlagOff();
  65   FuzzyMapOnlyFlagOff();
  66   FastFlagOff();
  67   SetRadius(2.0);
  68 }
  69 //--------------------------------------------------------------------
  70
  71
  72 //--------------------------------------------------------------------
  73 template <class ImageType>
  74 void
  75 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
  76 SetInput(const ImageType * image)
  77 {
  78   // Process object is not const-correct so the const casting is required.
  79   this->SetNthInput(0, const_cast<ImageType *>(image));
  80 }
  81 //--------------------------------------------------------------------
  82
  83
  84 //--------------------------------------------------------------------
  85 template <class ImageType>
  86 void
  87 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
  88 SetInputObject(const ImageType * image)
  89 {
  90   // Process object is not const-correct so the const casting is required.
  91   this->SetNthInput(1, const_cast<ImageType *>(image));
  92 }
  93 //--------------------------------------------------------------------
  94
  95
  96 //--------------------------------------------------------------------
  97 template <class ImageType>
  98 void
  99 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 100 ClearOrientationType()
 101 {
 102   m_OrientationTypeString.clear();
 103   m_OrientationType.clear();
 104   m_Angle1.clear();
 105   m_Angle2.clear();
 106 }
 107 //--------------------------------------------------------------------
 108
 109
 110 //--------------------------------------------------------------------
 111 template <class ImageType>
 112 int
 113 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 114 GetNumberOfAngles()
 115 {
 116   return m_OrientationType.size();
 117 }
 118 //--------------------------------------------------------------------
 119
 120
 121 //--------------------------------------------------------------------
 122 template <class ImageType>
 123 void
 124 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 125 AddOrientationTypeString(std::string t)
 126 {
 127   m_OrientationTypeString.push_back(t);
 128
 129   if (t == "LeftTo") { AddOrientationType(LeftTo); return; }
 130   if (t == "RightTo") { AddOrientationType(RightTo); return; }
 131   if (t == "AntTo") { AddOrientationType(AntTo); return; }
 132   if (t == "PostTo") { AddOrientationType(PostTo); return; }
 133   if (t == "SupTo") { AddOrientationType(SupTo); return; }
 134   if (t == "InfTo") { AddOrientationType(InfTo); return; }
 135
 136   if (t == "NotLeftTo") { AddOrientationType(LeftTo); InverseOrientationFlagOn(); return; }
 137   if (t == "NotRightTo") { AddOrientationType(RightTo); InverseOrientationFlagOn(); return; }
 138   if (t == "NotAntTo") { AddOrientationType(AntTo); InverseOrientationFlagOn(); return; }
 139   if (t == "NotPostTo") { AddOrientationType(PostTo); InverseOrientationFlagOn(); return; }
 140   if (t == "NotSupTo") { AddOrientationType(SupTo); InverseOrientationFlagOn(); return; }
 141   if (t == "NotInfTo") { AddOrientationType(InfTo); InverseOrientationFlagOn(); return; }
 142
 143   if (t == "Angle") return;
 144
 145   clitkExceptionMacro("Error, you must provide LeftTo,RightTo or AntTo,PostTo or SupTo,InfTo (or NotLeftTo, NotRightTo etc) but you give " << t);
 146 }
 147 //--------------------------------------------------------------------
 148
 149
 150 //--------------------------------------------------------------------
 151 template <class ImageType>
 152 void
 153 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 154 GenerateOutputInformation()
 155 {
 156   ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
 157   ImagePointer outputImage = this->GetOutput(0);
 158   outputImage->SetRegions(outputImage->GetLargestPossibleRegion());
 159 }
 160 //--------------------------------------------------------------------
 161
 162
 163 //--------------------------------------------------------------------
 164 template <class ImageType>
 165 void
 166 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 167 GenerateInputRequestedRegion()
 168 {
 169   // Call default
 170   itk::ImageToImageFilter<ImageType, ImageType>::GenerateInputRequestedRegion();
 171   // Get input pointers and set requested region to common region
 172   ImagePointer input1 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
 173   ImagePointer input2 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
 174   input1->SetRequestedRegion(input1->GetLargestPossibleRegion());
 175   input2->SetRequestedRegion(input2->GetLargestPossibleRegion());
 176 }
 177 //--------------------------------------------------------------------
 178
 179
 180 //--------------------------------------------------------------------
 181 template <class ImageType>
 182 void
 183 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 184 AddAnglesInRad(double a, double b)
 185 {
 186   m_OrientationTypeString.push_back("Angle");
 187   m_OrientationType.push_back(Angle);
 188   m_Angle1.push_back(a);
 189   m_Angle2.push_back(b);
 190 }
 191 //--------------------------------------------------------------------
 192
 193
 194 //--------------------------------------------------------------------
 195 template <class ImageType>
 196 void
 197 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 198 AddAnglesInDeg(double a, double b)
 199 {
 200   AddAnglesInRad(clitk::deg2rad(a), clitk::deg2rad(b));
 201 }
 202 //--------------------------------------------------------------------
 203
 204
 205 //--------------------------------------------------------------------
 206 template <class ImageType>
 207 void
 208 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 209 AddOrientationType(OrientationTypeEnumeration orientation)
 210 {
 211   m_OrientationType.push_back(orientation);
 212   switch (orientation) {
 213   case RightTo:
 214     m_Angle1.push_back(clitk::deg2rad(0));
 215     m_Angle2.push_back(clitk::deg2rad(0));
 216     break;
 217   case LeftTo:
 218     m_Angle1.push_back(clitk::deg2rad(180));
 219     m_Angle2.push_back(clitk::deg2rad(0));
 220     break;
 221   case AntTo:
 222     m_Angle1.push_back(clitk::deg2rad(90));
 223     m_Angle2.push_back(clitk::deg2rad(0));
 224     break;
 225   case PostTo:
 226     m_Angle1.push_back(clitk::deg2rad(-90));
 227     m_Angle2.push_back(clitk::deg2rad(0));
 228     break;
 229   case InfTo:
 230     m_Angle1.push_back(clitk::deg2rad(0));
 231     m_Angle2.push_back(clitk::deg2rad(90));
 232     break;
 233   case SupTo:
 234     m_Angle1.push_back(clitk::deg2rad(0));
 235     m_Angle2.push_back(clitk::deg2rad(-90));
 236     break;
 237   case Angle:  break;
 238   }
 239   /*         A1   A2
 240              Left      0    0
 241              Right   180    0
 242              Ant      90    0
 243              Post    -90    0
 244              Inf       0   90
 245              Sup       0  -90
 246   */
 247 }
 248 //--------------------------------------------------------------------
 249
 250
 251 //--------------------------------------------------------------------
 252 template <class ImageType>
 253 void
 254 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 255 PrintOptions()
 256 {
 257   DD((int)this->GetBackgroundValue());
 258   DD((int)this->GetObjectBackgroundValue());
 259   DDV(this->GetOrientationTypeString(), (uint)this->GetNumberOfAngles());
 260   DD(this->GetIntermediateSpacingFlag());
 261   DD(this->GetIntermediateSpacing());
 262   DD(this->GetFuzzyThreshold());
 263   DD(this->GetAutoCropFlag());
 264   DD(this->GetInverseOrientationFlag());
 265   DD(this->GetRemoveObjectFlag());
 266   DD(this->GetCombineWithOrFlag());
 267 }
 268 //--------------------------------------------------------------------
 269
 270
 271 //--------------------------------------------------------------------
 272 template <class ImageType>
 273 void
 274 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 275 GenerateData()
 276 {
 277   if (GetNumberOfAngles() <1) {
 278     clitkExceptionMacro("Add at least one orientation type");
 279   }
 280
 281   if (GetVerboseOptionFlag()) {
 282     for(int i=0; i<GetNumberOfAngles(); i++) {
 283         std::cout << "Orientation    \t:" << GetOrientationTypeString(i) << std::endl;
 284     }
 285     std::cout << "Interm Spacing \t:" << GetIntermediateSpacingFlag() << " " << GetIntermediateSpacing() << "mm" << std::endl;
 286     std::cout << "Fuzzy threshold\t:" << GetFuzzyThreshold() << std::endl;
 287     std::cout << "AutoCrop       \t:" << GetAutoCropFlag() << std::endl;
 288     std::cout << "InverseOrient  \t:" << GetInverseOrientationFlag() << std::endl;
 289     std::cout << "RemoveObject   \t:" << GetRemoveObjectFlag() << std::endl;
 290     std::cout << "CombineWithOr  \t:" << GetCombineWithOrFlag() << std::endl;
 291   }
 292
 293   // Get input pointer
 294   input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
 295   object = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
 296   static const unsigned int dim = ImageType::ImageDimension;
 297
 298   // Step 2: object pad to input image -> we want to compute the
 299   // relative position for each point belonging to the input image
 300   // domain, so we have to extend (pad) the object image to fit the
 301   // domain size
 302   working_image = object;
 303   if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, working_image)) {
 304     StartNewStep("Pad (resize) object to input size");
 305
 306     if (0) { // OLD VERSION (TO REMOVE)
 307       StartNewStep("Pad object to image size");
 308       typename ImageType::Pointer output = ImageType::New();
 309       SizeType size;
 310       for(unsigned int i=0; i<dim; i++) {
 311         size[i] = lrint((input->GetLargestPossibleRegion().GetSize()[i]*
 312                          input->GetSpacing()[i])/(double)working_image->GetSpacing()[i]);
 313       }
 314
 315       // The index of the input is not necessarily zero, so we have to
 316       // take it into account (not done)
 317       RegionType region;
 318       IndexType index = input->GetLargestPossibleRegion().GetIndex();
 319       region.SetSize(size);
 320       for(unsigned int i=0; i<dim; i++) {
 321         if (index[i] != 0) {
 322           std::cerr << "Index diff from zero : " << index << ". not done yet !" << std::endl;
 323           exit(0);
 324         }
 325       }
 326       // output->SetLargestPossibleRegion(region);
 327       output->SetRegions(region);
 328       output->SetSpacing(working_image->GetSpacing());
 329       PointType origin = input->GetOrigin();
 330       for(unsigned int i=0; i<dim; i++) {
 331         origin[i] = index[i]*input->GetSpacing()[i] + input->GetOrigin()[i];
 332       }
 333       output->SetOrigin(origin);
 334       //    output->SetOrigin(input->GetOrigin());
 335
 336       output->Allocate();
 337       output->FillBuffer(m_BackgroundValue);
 338       typename PasteFilterType::Pointer padFilter = PasteFilterType::New();
 339       // typename PasteFilterType::InputImageIndexType index;
 340       for(unsigned int i=0; i<dim; i++) {
 341         index[i] = -index[i]*input->GetSpacing()[i]/(double)working_image->GetSpacing()[i]
 342           + lrint((working_image->GetOrigin()[i] - input->GetOrigin()[i])/working_image->GetSpacing()[i]);
 343       }
 344       padFilter->SetSourceImage(working_image);
 345       padFilter->SetDestinationImage(output);
 346       padFilter->SetDestinationIndex(index);
 347       padFilter->SetSourceRegion(working_image->GetLargestPossibleRegion());
 348       padFilter->Update();
 349       working_image = padFilter->GetOutput();
 350     }
 351
 352     // Resize object like input
 353     working_image = clitk::ResizeImageLike<ImageType>(working_image, input, GetBackgroundValue());
 354     StopCurrentStep<ImageType>(working_image);
 355   }
 356
 357   //--------------------------------------------------------------------
 358   //--------------------------------------------------------------------
 359   // Step 1 : resample
 360   if (m_IntermediateSpacingFlag) {
 361     StartNewStep("Resample object to intermediate spacing");
 362     typedef clitk::ResampleImageWithOptionsFilter<ImageType> ResampleFilterType;
 363     typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
 364     resampleFilter->SetInput(working_image);
 365     resampleFilter->SetDefaultPixelValue(0);
 366     resampleFilter->SetOutputIsoSpacing(m_IntermediateSpacing);
 367     resampleFilter->SetGaussianFilteringEnabled(false);
 368     //    resampleFilter->SetVerboseOptions(true);
 369     resampleFilter->Update();
 370     working_image = resampleFilter->GetOutput();
 371     StopCurrentStep<ImageType>(working_image);
 372   }
 373
 374   // Keep object image (with resampline and pad)
 375   object_resampled = working_image;
 376
 377   // Step 3: compute rel pos in object
 378   StartNewStep("Relative Position Map");
 379   typedef itk::RelativePositionPropImageFilter<ImageType, FloatImageType> RelPosFilterType;
 380   typename RelPosFilterType::Pointer relPosFilter;
 381
 382   for(int i=0; i<GetNumberOfAngles(); i++) {
 383     // Compute fuzzy map
 384     relPosFilter = RelPosFilterType::New();
 385     relPosFilter->SetFast(GetFastFlag());
 386     relPosFilter->SetRadius(GetRadius());
 387     relPosFilter->SetInput(working_image);
 388     relPosFilter->SetAlpha1(m_Angle1[i]); // xy plane
 389     relPosFilter->SetAlpha2(m_Angle2[i]);
 390     relPosFilter->SetK1(M_PI/2.0); // Opening parameter, default = pi/2
 391
 392     // relPosFilter->SetFast(true);
 393     // relPosFilter->SetRadius(1); // seems sufficient in this case
 394
 395     // relPosFilter->SetVerboseProgress(true);
 396     relPosFilter->Update();
 397     relPos = relPosFilter->GetOutput();
 398
 399     if (GetNumberOfAngles() != 1) {
 400       // Creation of the first m_FuzzyMap
 401       if (i==0) {
 402         m_FuzzyMap = clitk::NewImageLike<FloatImageType>(relPos, true);
 403         m_FuzzyMap->FillBuffer(0.0);
 404       }
 405
 406       // Add to current fuzzy map
 407       typedef itk::AddImageFilter<FloatImageType, FloatImageType, FloatImageType> AddImageFilter;
 408       typename AddImageFilter::Pointer addFilter = AddImageFilter::New();
 409       addFilter->SetInput1(m_FuzzyMap);
 410       addFilter->SetInput2(relPos);
 411       addFilter->Update();
 412       m_FuzzyMap = addFilter->GetOutput();
 413     }
 414     else m_FuzzyMap = relPos;
 415   }
 416
 417   // Divide by the number of relpos
 418   if (GetNumberOfAngles() != 1) {
 419 #if ITK_VERSION_MAJOR >= 4
 420     typedef itk::DivideImageFilter<FloatImageType, FloatImageType, FloatImageType> DivideFilter;
 421     typename DivideFilter::Pointer divideFilter = DivideFilter::New();
 422     divideFilter->SetConstant2(GetNumberOfAngles());
 423 #else
 424     typedef itk::DivideByConstantImageFilter<FloatImageType, float, FloatImageType> DivideFilter;
 425     typename DivideFilter::Pointer divideFilter = DivideFilter::New();
 426     divideFilter->SetConstant(GetNumberOfAngles());
 427 #endif
 428     divideFilter->SetInput(m_FuzzyMap);
 429     divideFilter->Update();
 430     m_FuzzyMap = divideFilter->GetOutput();
 431   }
 432
 433   relPos = m_FuzzyMap;
 434   StopCurrentStep<FloatImageType>(relPos);
 435   if (GetFuzzyMapOnlyFlag()) return;
 436
 437   //--------------------------------------------------------------------
 438   //--------------------------------------------------------------------
 439   StartNewStep("Map Threshold");
 440   // Step 1: threshold
 441   typedef itk::BinaryThresholdImageFilter<FloatImageType, ImageType> BinaryThresholdImageFilterType;
 442   typename BinaryThresholdImageFilterType::Pointer thresholdFilter = BinaryThresholdImageFilterType::New();
 443   thresholdFilter->SetInput(relPos);
 444   thresholdFilter->SetOutsideValue(m_BackgroundValue);
 445   thresholdFilter->SetInsideValue(m_BackgroundValue+1);
 446   thresholdFilter->SetLowerThreshold(m_FuzzyThreshold);
 447   thresholdFilter->Update();
 448   working_image = thresholdFilter->GetOutput();
 449   StopCurrentStep<ImageType>(working_image);
 450
 451   //--------------------------------------------------------------------
 452   //--------------------------------------------------------------------
 453   StartNewStep("Post Processing: erosion with initial mask");
 454   // Step 2 : erosion with initial mask to exclude pixels that were
 455   // inside the resampled version and outside the original mask
 456   typedef itk::BinaryBallStructuringElement<unsigned int, ImageDimension> StructuringElementType;
 457   StructuringElementType kernel;
 458   kernel.SetRadius(1);
 459   kernel.CreateStructuringElement();
 460   typedef itk::BinaryErodeImageFilter<ImageType, ImageType, StructuringElementType> ErodeFilterType;
 461   typename ErodeFilterType::Pointer erodeFilter = ErodeFilterType::New();
 462   erodeFilter->SetInput(working_image);
 463   erodeFilter->SetKernel(kernel);
 464   erodeFilter->SetBackgroundValue(m_BackgroundValue);
 465   erodeFilter->SetErodeValue(m_BackgroundValue+1);
 466   erodeFilter->Update();
 467   working_image = erodeFilter->GetOutput();
 468   StopCurrentStep<ImageType>(working_image);
 469
 470   //--------------------------------------------------------------------
 471   //--------------------------------------------------------------------
 472   // Step 5: resample to initial spacing
 473   if (m_IntermediateSpacingFlag) {
 474     StartNewStep("Resample to come back to the same sampling than input");
 475     typedef clitk::ResampleImageWithOptionsFilter<ImageType> ResampleFilterType;
 476     typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
 477     resampleFilter->SetDefaultPixelValue(m_BackgroundValue);
 478     resampleFilter->SetInput(working_image);
 479     resampleFilter->SetOutputSpacing(input->GetSpacing());
 480     resampleFilter->SetGaussianFilteringEnabled(false);
 481     // resampleFilter->SetVerboseOptions(true);
 482     resampleFilter->Update();
 483     working_image = resampleFilter->GetOutput();
 484     StopCurrentStep<ImageType>(working_image);
 485   }
 486
 487   //--------------------------------------------------------------------
 488   //--------------------------------------------------------------------
 489   // Pre Step 6: pad if not the same size : it can occur when downsample and upsample
 490   //if (!HaveSameSizeAndSpacing(working_image, input)) {
 491   if (working_image->GetLargestPossibleRegion() != input->GetLargestPossibleRegion()) {
 492     StartNewStep("Pad to get the same size than input");
 493     typename ImageType::Pointer temp = ImageType::New();
 494     temp->CopyInformation(input);
 495     temp->SetRegions(input->GetLargestPossibleRegion()); // Do not forget !!
 496     temp->Allocate();
 497     temp->FillBuffer(m_BackgroundValue);
 498     typename PasteFilterType::Pointer padFilter2 = PasteFilterType::New();
 499     padFilter2->SetSourceImage(working_image);
 500     padFilter2->SetDestinationImage(temp);
 501     padFilter2->SetDestinationIndex(input->GetLargestPossibleRegion().GetIndex());
 502     padFilter2->SetSourceRegion(working_image->GetLargestPossibleRegion());
 503     padFilter2->Update();
 504     working_image = padFilter2->GetOutput();
 505     StopCurrentStep<ImageType>(working_image);
 506   }
 507   else {
 508     //DD("[debug] Rel Pos : no padding after");
 509   }
 510
 511   //--------------------------------------------------------------------
 512   //--------------------------------------------------------------------
 513   // Step 6: combine input+thresholded relpos
 514   StartNewStep("Combine with initial input (boolean And)");
 515   typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 516   typename BoolFilterType::Pointer combineFilter = BoolFilterType::New();
 517   combineFilter->SetBackgroundValue(m_BackgroundValue);
 518   combineFilter->SetBackgroundValue1(m_BackgroundValue);
 519   combineFilter->SetBackgroundValue2(m_BackgroundValue);
 520   combineFilter->SetForegroundValue(m_BackgroundValue+1);
 521   combineFilter->SetInput1(input);
 522   combineFilter->SetInput2(working_image);
 523   if (GetInverseOrientationFlag())
 524     combineFilter->SetOperationType(BoolFilterType::AndNot);
 525   else {
 526     if (GetCombineWithOrFlag())
 527       combineFilter->SetOperationType(BoolFilterType::Or);
 528     else
 529       combineFilter->SetOperationType(BoolFilterType::And);
 530   }
 531   combineFilter->InPlaceOff(); // Do not modify initial input (!)
 532   combineFilter->Update();
 533   working_image = combineFilter->GetOutput();
 534
 535   // Remove (if needed the object from the support)
 536   if (GetRemoveObjectFlag()) {
 537     combineFilter = BoolFilterType::New();
 538     combineFilter->SetInput1(working_image);
 539     combineFilter->SetInput2(object);
 540     combineFilter->SetOperationType(BoolFilterType::AndNot);
 541     combineFilter->InPlaceOn();
 542     combineFilter->Update();
 543     working_image = combineFilter->GetOutput();
 544   }
 545   // In the other case, we must *add* the initial object to keep it
 546   // but not more than the initial support
 547   else {
 548     combineFilter = BoolFilterType::New();
 549     combineFilter->SetInput1(working_image);
 550     combineFilter->SetInput2(object);
 551     combineFilter->SetOperationType(BoolFilterType::Or);
 552     combineFilter->InPlaceOn();
 553     combineFilter->Update();
 554     working_image = combineFilter->GetOutput(); // not needed because InPlaceOn ?
 555     combineFilter = BoolFilterType::New();
 556     combineFilter->SetInput1(working_image);
 557     combineFilter->SetInput2(input);
 558     combineFilter->SetOperationType(BoolFilterType::And);
 559     combineFilter->InPlaceOn();
 560     combineFilter->Update();
 561     working_image = combineFilter->GetOutput();
 562   }
 563
 564   StopCurrentStep<ImageType>(working_image);
 565
 566   //--------------------------------------------------------------------
 567   //--------------------------------------------------------------------
 568   // Step 7: autocrop
 569   if (GetAutoCropFlag()) {
 570     StartNewStep("Final AutoCrop");
 571     typedef clitk::AutoCropFilter<ImageType> CropFilterType;
 572     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 573     cropFilter->SetInput(working_image);
 574     cropFilter->ReleaseDataFlagOff();
 575     cropFilter->Update();
 576     working_image = cropFilter->GetOutput();
 577     StopCurrentStep<ImageType>(working_image);
 578   }
 579
 580   //--------------------------------------------------------------------
 581   //--------------------------------------------------------------------
 582
 583   // Final Step -> set output
 584   this->SetNthOutput(0, working_image);
 585   //  this->GraftOutput(working_image);
 586 }
 587 //--------------------------------------------------------------------
 588