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