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://oncora1.lyon.fnclcc.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17   ======================================================================-====*/
  18
  19 // clitk
  20 #include "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 #include <itkDivideByConstantImageFilter.h>
  36
  37 // itk [Bloch et al]
  38 #include "RelativePositionPropImageFilter.h"
  39
  40 //--------------------------------------------------------------------
  41 template <class ImageType>
  42 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
  43 AddRelativePositionConstraintToLabelImageFilter():
  44   clitk::FilterBase(),
  45   itk::ImageToImageFilter<ImageType, ImageType>()
  46 {
  47   this->SetNumberOfRequiredInputs(2);
  48   SetFuzzyThreshold(0.6);
  49   SetBackgroundValue(0);
  50   SetObjectBackgroundValue(0);
  51   ClearOrientationType();
  52   ResampleBeforeRelativePositionFilterOn();
  53   SetIntermediateSpacing(10);
  54   AutoCropFlagOn();
  55   InverseOrientationFlagOff();
  56   RemoveObjectFlagOn();
  57   CombineWithOrFlagOff();
  58 }
  59 //--------------------------------------------------------------------
  60
  61
  62 //--------------------------------------------------------------------
  63 template <class ImageType>
  64 void
  65 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
  66 SetInput(const ImageType * image)
  67 {
  68   // Process object is not const-correct so the const casting is required.
  69   this->SetNthInput(0, const_cast<ImageType *>(image));
  70 }
  71 //--------------------------------------------------------------------
  72
  73
  74 //--------------------------------------------------------------------
  75 template <class ImageType>
  76 void
  77 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
  78 SetInputObject(const ImageType * image)
  79 {
  80   // Process object is not const-correct so the const casting is required.
  81   this->SetNthInput(1, const_cast<ImageType *>(image));
  82 }
  83 //--------------------------------------------------------------------
  84
  85
  86 //--------------------------------------------------------------------
  87 template <class ImageType>
  88 void
  89 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
  90 ClearOrientationType()
  91 {
  92   m_OrientationTypeString.clear();
  93   m_OrientationType.clear();
  94   m_Angle1.clear();
  95   m_Angle2.clear();
  96 }
  97 //--------------------------------------------------------------------
  98
  99
 100 //--------------------------------------------------------------------
 101 template <class ImageType>
 102 int
 103 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 104 GetNumberOfAngles()
 105 {
 106   return m_OrientationType.size();
 107 }
 108 //--------------------------------------------------------------------
 109
 110
 111 //--------------------------------------------------------------------
 112 template <class ImageType>
 113 void
 114 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 115 AddOrientationTypeString(std::string t)
 116 {
 117   m_OrientationTypeString.push_back(t);
 118   switch (t[0]) {
 119   case 'L' : AddOrientationType(LeftTo); break;
 120   case 'R' : AddOrientationType(RightTo);break;
 121   case 'A' : AddOrientationType(AntTo);break;
 122   case 'P' : AddOrientationType(PostTo);break;
 123   case 'S' : AddOrientationType(SupTo);break;
 124   case 'I' : AddOrientationType(InfTo);break;
 125   default: clitkExceptionMacro("Error, you must provide L,R or A,P or S,I");
 126   }
 127 }
 128 //--------------------------------------------------------------------
 129
 130
 131 //--------------------------------------------------------------------
 132 template <class ImageType>
 133 void
 134 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 135 GenerateOutputInformation()
 136 {
 137   ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
 138   ImagePointer outputImage = this->GetOutput(0);
 139   outputImage->SetRegions(outputImage->GetLargestPossibleRegion());
 140 }
 141 //--------------------------------------------------------------------
 142
 143
 144 //--------------------------------------------------------------------
 145 template <class ImageType>
 146 void
 147 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 148 GenerateInputRequestedRegion()
 149 {
 150   // Call default
 151   itk::ImageToImageFilter<ImageType, ImageType>::GenerateInputRequestedRegion();
 152   // Get input pointers and set requested region to common region
 153   ImagePointer input1 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
 154   ImagePointer input2 = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
 155   input1->SetRequestedRegion(input1->GetLargestPossibleRegion());
 156   input2->SetRequestedRegion(input2->GetLargestPossibleRegion());
 157 }
 158 //--------------------------------------------------------------------
 159
 160
 161 //--------------------------------------------------------------------
 162 template <class ImageType>
 163 void
 164 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 165 AddAngles(double a, double b)
 166 {
 167   AddOrientationTypeString("Angle");
 168   m_Angle1.push_back(a);
 169   m_Angle2.push_back(b);
 170 }
 171 //--------------------------------------------------------------------
 172
 173
 174 //--------------------------------------------------------------------
 175 template <class ImageType>
 176 void
 177 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 178 AddOrientationType(OrientationTypeEnumeration orientation)
 179 {
 180   m_OrientationType.push_back(orientation);
 181   switch (orientation) {
 182   case LeftTo:
 183     m_Angle1.push_back(clitk::deg2rad(0));
 184     m_Angle2.push_back(clitk::deg2rad(0));
 185     break;
 186   case RightTo:
 187     m_Angle1.push_back(clitk::deg2rad(180));
 188     m_Angle2.push_back(clitk::deg2rad(0));
 189     break;
 190   case AntTo:
 191     m_Angle1.push_back(clitk::deg2rad(90));
 192     m_Angle2.push_back(clitk::deg2rad(0));
 193     break;
 194   case PostTo:
 195     m_Angle1.push_back(clitk::deg2rad(-90));
 196     m_Angle2.push_back(clitk::deg2rad(0));
 197     break;
 198   case InfTo:
 199     m_Angle1.push_back(clitk::deg2rad(0));
 200     m_Angle2.push_back(clitk::deg2rad(90));
 201     break;
 202   case SupTo:
 203     m_Angle1.push_back(clitk::deg2rad(0));
 204     m_Angle2.push_back(clitk::deg2rad(-90));
 205     break;
 206   case Angle:  break;
 207   }
 208   /*         A1   A2
 209              Left      0    0
 210              Right   180    0
 211              Ant      90    0
 212              Post    -90    0
 213              Inf       0   90
 214              Sup       0  -90
 215   */
 216 }
 217 //--------------------------------------------------------------------
 218
 219
 220 //--------------------------------------------------------------------
 221 template <class ImageType>
 222 void
 223 clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>::
 224 GenerateData()
 225 {
 226   if (GetNumberOfAngles() <1) {
 227     clitkExceptionMacro("Add at least one orientation type");
 228   }
 229
 230   // Get input pointer
 231   input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
 232   object = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
 233
 234   //--------------------------------------------------------------------
 235   //--------------------------------------------------------------------
 236   static const unsigned int dim = ImageType::ImageDimension;
 237   StartNewStep("Initial resample");
 238   // Step 1 : resample
 239   if (m_ResampleBeforeRelativePositionFilter) {
 240     typedef clitk::ResampleImageWithOptionsFilter<ImageType> ResampleFilterType;
 241     typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
 242     resampleFilter->SetInput(object);
 243     resampleFilter->SetOutputIsoSpacing(m_IntermediateSpacing);
 244     resampleFilter->SetGaussianFilteringEnabled(false);
 245     //    resampleFilter->SetVerboseOptions(true);
 246     resampleFilter->Update();
 247     working_image = resampleFilter->GetOutput();
 248   }
 249   else {
 250     working_image = object;
 251   }
 252   StopCurrentStep<ImageType>(working_image);
 253
 254   // Step 2: object pad to input image -> we want to compute the
 255   // relative position for each point belonging to the input image
 256   // domain, so we have to extend (pad) the object image to fit the
 257   // domain size
 258   if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(input, working_image)) {
 259     StartNewStep("Pad object to image size");
 260     typename ImageType::Pointer output = ImageType::New();
 261     SizeType size;
 262     for(unsigned int i=0; i<dim; i++) {
 263       size[i] = lrint((input->GetLargestPossibleRegion().GetSize()[i]*
 264                        input->GetSpacing()[i])/(double)working_image->GetSpacing()[i]);
 265     }
 266
 267     // The index of the input is not necessarily zero, so we have to
 268     // take it into account (not done)
 269     RegionType region;
 270     IndexType index = input->GetLargestPossibleRegion().GetIndex();
 271     region.SetSize(size);
 272     for(unsigned int i=0; i<dim; i++) {
 273       if (index[i] != 0) {
 274         std::cerr << "Index diff from zero : " << index << ". not done yet !" << std::endl;
 275         exit(0);
 276       }
 277     }
 278     // output->SetLargestPossibleRegion(region);
 279     output->SetRegions(region);
 280     output->SetSpacing(working_image->GetSpacing());
 281     PointType origin = input->GetOrigin();
 282     for(unsigned int i=0; i<dim; i++) {
 283       origin[i] = index[i]*input->GetSpacing()[i] + input->GetOrigin()[i];
 284     }
 285     output->SetOrigin(origin);
 286     //    output->SetOrigin(input->GetOrigin());
 287
 288     output->Allocate();
 289     output->FillBuffer(m_BackgroundValue);
 290     typename PadFilterType::Pointer padFilter = PadFilterType::New();
 291     // typename PadFilterType::InputImageIndexType index;
 292     for(unsigned int i=0; i<dim; i++) {
 293       index[i] = -index[i]*input->GetSpacing()[i]/(double)working_image->GetSpacing()[i]
 294         + lrint((working_image->GetOrigin()[i] - input->GetOrigin()[i])/working_image->GetSpacing()[i]);
 295     }
 296     padFilter->SetSourceImage(working_image);
 297     padFilter->SetDestinationImage(output);
 298     padFilter->SetDestinationIndex(index);
 299     padFilter->SetSourceRegion(working_image->GetLargestPossibleRegion());
 300     padFilter->Update();
 301     working_image = padFilter->GetOutput();
 302     StopCurrentStep<ImageType>(working_image);
 303   }
 304   else {
 305     // DD("[debug] RelPos : same size and spacing : no padding");
 306   }
 307   // Keep object image (with resampline and pad)
 308   object_resampled = working_image;
 309   //  StopCurrentStep<ImageType>(working_image);
 310
 311   // Step 3: compute rel pos in object
 312   StartNewStep("Relative Position Map");
 313   typedef itk::RelativePositionPropImageFilter<ImageType, FloatImageType> RelPosFilterType;
 314   typename RelPosFilterType::Pointer relPosFilter;
 315
 316   typename FloatImageType::Pointer m_FuzzyMap;
 317   for(int i=0; i<GetNumberOfAngles(); i++) {
 318     // Compute fuzzy map
 319     relPosFilter = RelPosFilterType::New();
 320     relPosFilter->SetInput(working_image);
 321     relPosFilter->SetAlpha1(m_Angle1[i]); // xy plane
 322     relPosFilter->SetAlpha2(m_Angle2[i]);
 323     relPosFilter->SetK1(M_PI/2.0); // Opening parameter, default = pi/2
 324     relPosFilter->SetFast(true);
 325     relPosFilter->SetRadius(1); // seems sufficient in this case
 326     // relPosFilter->SetVerboseProgress(true);
 327     relPosFilter->Update();
 328     relPos = relPosFilter->GetOutput();
 329
 330     if (GetNumberOfAngles() != 1) {
 331       // Creation of the first m_FuzzyMap
 332       if (i==0) {
 333         m_FuzzyMap = clitk::NewImageLike<FloatImageType>(relPos, true);
 334         m_FuzzyMap->FillBuffer(0.0);
 335       }
 336
 337       // Add to current fuzzy map
 338       typedef itk::AddImageFilter<FloatImageType, FloatImageType, FloatImageType> AddImageFilter;
 339       typename AddImageFilter::Pointer addFilter = AddImageFilter::New();
 340       addFilter->SetInput1(m_FuzzyMap);
 341       addFilter->SetInput2(relPos);
 342       addFilter->Update();
 343       m_FuzzyMap = addFilter->GetOutput();
 344     }
 345     else m_FuzzyMap = relPos;
 346   }
 347
 348   // Divide by the number of relpos
 349   if (GetNumberOfAngles() != 1) {
 350     typedef itk::DivideByConstantImageFilter<FloatImageType, float, FloatImageType> DivideFilter;
 351     typename DivideFilter::Pointer divideFilter = DivideFilter::New();
 352     divideFilter->SetInput(m_FuzzyMap);
 353     divideFilter->SetConstant(GetNumberOfAngles());
 354     divideFilter->Update();
 355     m_FuzzyMap = divideFilter->GetOutput();
 356   }
 357
 358   relPos = m_FuzzyMap;
 359   StopCurrentStep<FloatImageType>(relPos);
 360
 361   //--------------------------------------------------------------------
 362   //--------------------------------------------------------------------
 363   StartNewStep("Map Threshold");
 364   // Step 1: threshold
 365   typedef itk::BinaryThresholdImageFilter<FloatImageType, ImageType> BinaryThresholdImageFilterType;
 366   typename BinaryThresholdImageFilterType::Pointer thresholdFilter = BinaryThresholdImageFilterType::New();
 367   thresholdFilter->SetInput(relPos);
 368   thresholdFilter->SetOutsideValue(m_BackgroundValue);
 369   thresholdFilter->SetInsideValue(m_BackgroundValue+1);
 370   thresholdFilter->SetLowerThreshold(m_FuzzyThreshold);
 371   thresholdFilter->Update();
 372   working_image = thresholdFilter->GetOutput();
 373   StopCurrentStep<ImageType>(working_image);
 374
 375   //--------------------------------------------------------------------
 376   //--------------------------------------------------------------------
 377   StartNewStep("Post Processing: erosion with initial mask");
 378   // Step 2 : erosion with initial mask to exclude pixels that were
 379   // inside the resampled version and outside the original mask
 380   typedef itk::BinaryBallStructuringElement<unsigned int, ImageDimension> StructuringElementType;
 381   StructuringElementType kernel;
 382   kernel.SetRadius(1);
 383   kernel.CreateStructuringElement();
 384   typedef itk::BinaryErodeImageFilter<ImageType, ImageType, StructuringElementType> ErodeFilterType;
 385   typename ErodeFilterType::Pointer erodeFilter = ErodeFilterType::New();
 386   erodeFilter->SetInput(working_image);
 387   erodeFilter->SetKernel(kernel);
 388   erodeFilter->SetBackgroundValue(m_BackgroundValue);
 389   erodeFilter->SetErodeValue(m_BackgroundValue+1);
 390   erodeFilter->Update();
 391   working_image = erodeFilter->GetOutput();
 392   StopCurrentStep<ImageType>(working_image);
 393
 394   //--------------------------------------------------------------------
 395   //--------------------------------------------------------------------
 396   // Step 5: resample to initial spacing
 397   if (m_ResampleBeforeRelativePositionFilter) {
 398     StartNewStep("Resample to get the same sampling than input");
 399     typedef clitk::ResampleImageWithOptionsFilter<ImageType> ResampleFilterType;
 400     typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
 401     resampleFilter->SetDefaultPixelValue(m_BackgroundValue);
 402     resampleFilter->SetInput(working_image);
 403     resampleFilter->SetOutputSpacing(input->GetSpacing());
 404     resampleFilter->SetGaussianFilteringEnabled(false);
 405     // resampleFilter->SetVerboseOptions(true);
 406     resampleFilter->Update();
 407     working_image = resampleFilter->GetOutput();
 408     StopCurrentStep<ImageType>(working_image);
 409   }
 410
 411   //--------------------------------------------------------------------
 412   //--------------------------------------------------------------------
 413   // Pre Step 6: pad if not the same size : it can occur when downsample and upsample
 414   //if (!HaveSameSizeAndSpacing(working_image, input)) {
 415   if (working_image->GetLargestPossibleRegion() != input->GetLargestPossibleRegion()) {
 416     StartNewStep("Pad to get the same size than input");
 417     typename ImageType::Pointer temp = ImageType::New();
 418     temp->CopyInformation(input);
 419     temp->SetRegions(input->GetLargestPossibleRegion()); // Do not forget !!
 420     temp->Allocate();
 421     temp->FillBuffer(m_BackgroundValue);
 422     typename PadFilterType::Pointer padFilter2 = PadFilterType::New();
 423     padFilter2->SetSourceImage(working_image);
 424     padFilter2->SetDestinationImage(temp);
 425     // DD(input->GetLargestPossibleRegion().GetIndex());
 426     padFilter2->SetDestinationIndex(input->GetLargestPossibleRegion().GetIndex());
 427     padFilter2->SetSourceRegion(working_image->GetLargestPossibleRegion());
 428     padFilter2->Update();
 429     working_image = padFilter2->GetOutput();
 430     StopCurrentStep<ImageType>(working_image);
 431   }
 432   else {
 433     //DD("[debug] Rel Pos : no padding after");
 434   }
 435
 436   //--------------------------------------------------------------------
 437   //--------------------------------------------------------------------
 438   // Step 6: combine input+thresholded relpos
 439   StartNewStep("Combine with initial input (boolean And)");
 440   typedef clitk::BooleanOperatorLabelImageFilter<ImageType> BoolFilterType;
 441   typename BoolFilterType::Pointer combineFilter = BoolFilterType::New();
 442   combineFilter->SetBackgroundValue(m_BackgroundValue);
 443   combineFilter->SetBackgroundValue1(m_BackgroundValue);
 444   combineFilter->SetBackgroundValue2(m_BackgroundValue);
 445   combineFilter->SetForegroundValue(m_BackgroundValue+1);
 446   combineFilter->SetInput1(input);
 447   combineFilter->SetInput2(working_image);
 448   if (GetInverseOrientationFlag())
 449     combineFilter->SetOperationType(BoolFilterType::AndNot);
 450   else {
 451     if (GetCombineWithOrFlag())
 452       combineFilter->SetOperationType(BoolFilterType::Or);
 453     else
 454       combineFilter->SetOperationType(BoolFilterType::And);
 455   }
 456   combineFilter->InPlaceOff(); // Do not modify initial input (!)
 457   combineFilter->Update();
 458   working_image = combineFilter->GetOutput();
 459
 460   // Remove (if needed the object from the support)
 461   if (GetRemoveObjectFlag()) {
 462     combineFilter = BoolFilterType::New();
 463     combineFilter->SetInput1(working_image);
 464     combineFilter->SetInput2(object);
 465     combineFilter->SetOperationType(BoolFilterType::AndNot);
 466     combineFilter->InPlaceOn();
 467     combineFilter->Update();
 468     working_image = combineFilter->GetOutput();
 469   }
 470   // In the other case, we must *add* the initial object to keep it
 471   // but not more than the initial support
 472   else {
 473     combineFilter = BoolFilterType::New();
 474     combineFilter->SetInput1(working_image);
 475     combineFilter->SetInput2(object);
 476     combineFilter->SetOperationType(BoolFilterType::Or);
 477     combineFilter->InPlaceOn();
 478     combineFilter->Update();
 479     working_image = combineFilter->GetOutput(); // not needed because InPlaceOn ?
 480     combineFilter = BoolFilterType::New();
 481     combineFilter->SetInput1(working_image);
 482     combineFilter->SetInput2(input);
 483     combineFilter->SetOperationType(BoolFilterType::And);
 484     combineFilter->InPlaceOn();
 485     combineFilter->Update();
 486     working_image = combineFilter->GetOutput();
 487   }
 488
 489   StopCurrentStep<ImageType>(working_image);
 490
 491   //--------------------------------------------------------------------
 492   //--------------------------------------------------------------------
 493   // Step 7: autocrop
 494   if (GetAutoCropFlag()) {
 495     StartNewStep("Final AutoCrop");
 496     typedef clitk::AutoCropFilter<ImageType> CropFilterType;
 497     typename CropFilterType::Pointer cropFilter = CropFilterType::New();
 498     cropFilter->SetInput(working_image);
 499     cropFilter->ReleaseDataFlagOff();
 500     cropFilter->Update();
 501     working_image = cropFilter->GetOutput();
 502     StopCurrentStep<ImageType>(working_image);
 503   }
 504
 505   //--------------------------------------------------------------------
 506   //--------------------------------------------------------------------
 507
 508   // Final Step -> set output
 509   this->SetNthOutput(0, working_image);
 510   //  this->GraftOutput(working_image);
 511 }
 512 //--------------------------------------------------------------------
 513