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