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