segmentation/clitkMotionMaskGenericFilter.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 #ifndef clitkMotionMaskGenericFilter_txx
  19 #define clitkMotionMaskGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkMotionMaskGenericFilter.txx
  23  * @author
  24  * @date
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30 #include "itkLabelImageToShapeLabelMapFilter.h"
  31 #include "itkShapeLabelObject.h"
  32
  33 namespace clitk
  34 {
  35
  36 //-------------------------------------------------------------------
  37 // Update with the number of dimensions
  38 //-------------------------------------------------------------------
  39 template<unsigned int Dimension>
  40 void
  41 MotionMaskGenericFilter::UpdateWithDim(std::string PixelType)
  42 {
  43   if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  44
  45   if(PixelType == "short") {
  46     if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  47     UpdateWithDimAndPixelType<Dimension, signed short>();
  48   }
  49   //    else if(PixelType == "unsigned_short"){
  50   //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  51   //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  52   //     }
  53
  54   //     else if (PixelType == "unsigned_char"){
  55   //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  56   //       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  57   //     }
  58
  59   //     else if (PixelType == "char"){
  60   //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  61   //       UpdateWithDimAndPixelType<Dimension, signed char>();
  62   //     }
  63   else {
  64     if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  65     UpdateWithDimAndPixelType<Dimension, float>();
  66   }
  67 }
  68
  69 //-------------------------------------------------------------------
  70 // Air
  71 //-------------------------------------------------------------------
  72 template <unsigned int Dimension, class  PixelType>
  73 typename itk::Image<MotionMaskGenericFilter::InternalPixelType, Dimension>::Pointer
  74 MotionMaskGenericFilter::GetAirImage(typename itk::Image<PixelType, Dimension>::Pointer input,
  75                                      typename itk::Image<MotionMaskGenericFilter::InternalPixelType, Dimension>::Pointer lungs)
  76 {
  77
  78   // ImageTypes
  79   typedef int InternalPixelType;
  80   typedef itk::Image<PixelType, Dimension> InputImageType;
  81   typedef itk::Image< InternalPixelType, Dimension> InternalImageType; //labeling doesn't work with unsigned char?
  82
  83   //----------------------------------------------------------------------------------------------------
  84   // Typedef for Processing
  85   //----------------------------------------------------------------------------------------------------
  86   typedef itk::ImageFileReader<InternalImageType> FeatureReaderType;
  87   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinarizeFilterType;
  88   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> InversionFilterType;
  89   typedef itk::ThresholdImageFilter<InternalImageType> ThresholdFilterType;
  90   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
  91   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
  92   typedef itk::MirrorPadImageFilter<InternalImageType, InternalImageType> MirrorPadImageFilterType;
  93
  94
  95   typename InternalImageType::Pointer air;
  96   if (m_ArgsInfo.featureAir_given) {
  97     typename FeatureReaderType::Pointer featureReader =FeatureReaderType::New();
  98     featureReader->SetFileName(m_ArgsInfo.featureAir_arg);
  99     if (m_Verbose) std::cout<<"Reading the air feature image..."<<std::endl;
 100     featureReader->Update();
 101     air=featureReader->GetOutput();
 102
 103     //---------------------------------
 104     // Pad
 105     //---------------------------------
 106     if(m_ArgsInfo.pad_flag) {
 107       typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 108       IteratorType it(air, air->GetLargestPossibleRegion());
 109       typename InternalImageType::IndexType index;
 110       while(!it.IsAtEnd()) {
 111         index=it.GetIndex();
 112
 113         //Pad borders of all dimensions but 2 (cranio-caudal)
 114         for (unsigned int i=0; i<Dimension; i++){
 115           if(i==2)
 116             continue;
 117           if(index[i]==air->GetLargestPossibleRegion().GetIndex()[i]
 118               || index[i]==(unsigned int)air->GetLargestPossibleRegion().GetIndex()[i]+ (unsigned int) air->GetLargestPossibleRegion().GetSize()[i]-1)
 119             it.Set(1);
 120         }
 121         ++it;
 122       }
 123     }
 124   } else {
 125     if (m_Verbose) std::cout<<"Extracting the air feature image..."<<std::endl;
 126     //---------------------------------
 127     // Binarize the image
 128     //---------------------------------
 129     typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
 130     binarizeFilter->SetInput(input);
 131     binarizeFilter->SetLowerThreshold(static_cast<PixelType>(m_ArgsInfo.lowerThresholdAir_arg));
 132     binarizeFilter->SetUpperThreshold(static_cast<PixelType>(m_ArgsInfo.upperThresholdAir_arg));
 133     if (m_Verbose) std::cout<<"Binarizing the image using thresholds "<<m_ArgsInfo.lowerThresholdAir_arg
 134                               <<", "<<m_ArgsInfo.upperThresholdAir_arg<<"..."<<std::endl;
 135     binarizeFilter->Update();
 136     air = binarizeFilter->GetOutput();
 137
 138     //---------------------------------
 139     // Pad
 140     //---------------------------------
 141     if(m_ArgsInfo.pad_flag) {
 142       typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 143       IteratorType it(air, air->GetLargestPossibleRegion());
 144       typename InternalImageType::IndexType index;
 145       while(!it.IsAtEnd()) {
 146         index=it.GetIndex();
 147
 148         //Pad borders of all dimensions but 2 (cranio-caudal)
 149         for (unsigned int i=0; i<Dimension; i++){
 150           if(i==2)
 151             continue;
 152           if(index[i]==air->GetLargestPossibleRegion().GetIndex()[i]
 153               || index[i]==(unsigned int)air->GetLargestPossibleRegion().GetIndex()[i]+ (unsigned int) air->GetLargestPossibleRegion().GetSize()[i]-1)
 154             it.Set(binarizeFilter->GetInsideValue());
 155         }
 156         ++it;
 157       }
 158     }
 159
 160     //---------------------------------
 161     // Remove lungs (in place)
 162     //---------------------------------
 163     typedef itk::ImageRegionIterator<InternalImageType> IteratorType;
 164     IteratorType itAir(air, binarizeFilter->GetOutput()->GetLargestPossibleRegion());
 165     IteratorType itLungs(lungs, binarizeFilter->GetOutput()->GetLargestPossibleRegion()); //lungs padded, used air region
 166     itAir.GoToBegin();
 167     itLungs.GoToBegin();
 168     while(!itAir.IsAtEnd()) {
 169       if(!itLungs.Get())     // The lungs are set to 0 at that stage
 170         itAir.Set(0);
 171       ++itAir;
 172       ++itLungs;
 173     }
 174
 175     //---------------------------------
 176     // Label the connected components
 177     //---------------------------------
 178     typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 179     connectFilter->SetInput(binarizeFilter->GetOutput());
 180     connectFilter->SetBackgroundValue(0);
 181     connectFilter->SetFullyConnected(false);
 182     if (m_Verbose) std::cout<<"Labeling the connected components..."<<std::endl;
 183
 184     //---------------------------------
 185     // Sort the labels according to size
 186     //---------------------------------
 187     typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 188     relabelFilter->SetInput(connectFilter->GetOutput());
 189     if (m_Verbose) std::cout<<"Sorting the labels..."<<std::endl;
 190
 191     //---------------------------------
 192     // Keep the label
 193     //---------------------------------
 194     typename ThresholdFilterType::Pointer thresholdFilter=ThresholdFilterType::New();
 195     thresholdFilter->SetInput(relabelFilter->GetOutput());
 196     thresholdFilter->SetUpper(1);
 197     if (m_Verbose) std::cout<<"Keeping the first label..."<<std::endl;
 198     thresholdFilter->Update();
 199     air=thresholdFilter->GetOutput();
 200   }
 201
 202   //---------------------------------
 203   // Invert
 204   //---------------------------------
 205   typename InversionFilterType::Pointer inversionFilter=InversionFilterType::New();
 206   inversionFilter->SetInput(air);
 207   inversionFilter->SetLowerThreshold(0);
 208   inversionFilter->SetUpperThreshold(0);
 209   inversionFilter->SetInsideValue(1);
 210   inversionFilter->Update();
 211
 212   //---------------------------------
 213   // Mirror
 214   //---------------------------------
 215   typename MirrorPadImageFilterType::Pointer mirrorPadImageFilter=MirrorPadImageFilterType::New();
 216   mirrorPadImageFilter->SetInput(inversionFilter->GetOutput());
 217   typename InternalImageType::SizeType padSize;
 218   padSize.Fill(0);
 219   padSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
 220   mirrorPadImageFilter->SetPadLowerBound(padSize);
 221   if (m_Verbose) std::cout<<"Mirroring the entire image along the CC axis..."<<std::endl;
 222   mirrorPadImageFilter->Update();
 223   air=mirrorPadImageFilter->GetOutput();
 224   //writeImage<InternalImageType>(air,"/home/srit/tmp/air.mhd");
 225
 226   return air;
 227 }
 228
 229
 230 //-------------------------------------------------------------------
 231 // Bones
 232 //-------------------------------------------------------------------
 233 template <unsigned int Dimension, class  PixelType>
 234 typename itk::Image<MotionMaskGenericFilter::InternalPixelType, Dimension>::Pointer
 235 MotionMaskGenericFilter::GetBonesImage(typename itk::Image<PixelType, Dimension>::Pointer input )
 236 {
 237
 238   // ImageTypes
 239   typedef int InternalPixelType;
 240   typedef itk::Image<PixelType, Dimension> InputImageType;
 241   typedef itk::Image< InternalPixelType, Dimension> InternalImageType; //labeling doesn't work with unsigned char?
 242
 243   //----------------------------------------------------------------------------------------------------
 244   // Typedef for Processing
 245   //----------------------------------------------------------------------------------------------------
 246   typedef itk::ImageFileReader<InternalImageType> FeatureReaderType;
 247   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinarizeFilterType;
 248   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> InversionFilterType;
 249   typedef itk::ThresholdImageFilter<InternalImageType> ThresholdFilterType;
 250   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
 251   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
 252   typedef itk::MirrorPadImageFilter<InternalImageType, InternalImageType> MirrorPadImageFilterType;
 253
 254
 255   typename InternalImageType::Pointer bones;
 256   if (m_ArgsInfo.featureBones_given) {
 257     typename FeatureReaderType::Pointer featureReader =FeatureReaderType::New();
 258     featureReader->SetFileName(m_ArgsInfo.featureBones_arg);
 259     if (m_Verbose) std::cout<<"Reading the bones feature image..."<<std::endl;
 260     featureReader->Update();
 261     bones=featureReader->GetOutput();
 262   } else {
 263     if (m_Verbose) std::cout<<"Extracting the bones feature image..."<<std::endl;
 264     //---------------------------------
 265     // Binarize the image
 266     //---------------------------------
 267     typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
 268     binarizeFilter->SetInput(input);
 269     binarizeFilter->SetLowerThreshold(static_cast<PixelType>(m_ArgsInfo.lowerThresholdBones_arg));
 270     binarizeFilter->SetUpperThreshold(static_cast<PixelType>(m_ArgsInfo.upperThresholdBones_arg));
 271     if (m_Verbose) std::cout<<"Binarizing the image using thresholds "<<m_ArgsInfo.lowerThresholdBones_arg
 272                               <<", "<<m_ArgsInfo.upperThresholdBones_arg<<"..."<<std::endl;
 273
 274     //---------------------------------
 275     // Label the connected components
 276     //---------------------------------
 277     typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 278     connectFilter->SetInput(binarizeFilter->GetOutput());
 279     connectFilter->SetBackgroundValue(0);
 280     connectFilter->SetFullyConnected(false);
 281     if (m_Verbose) std::cout<<"Labeling the connected components..."<<std::endl;
 282
 283     //---------------------------------
 284     // Sort the labels according to size
 285     //---------------------------------
 286     typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 287     relabelFilter->SetInput(connectFilter->GetOutput());
 288     if (m_Verbose) std::cout<<"Sorting the labels..."<<std::endl;
 289
 290     //---------------------------------
 291     // Keep the label
 292     //---------------------------------
 293     typename ThresholdFilterType::Pointer thresholdFilter=ThresholdFilterType::New();
 294     thresholdFilter->SetInput(relabelFilter->GetOutput());
 295     thresholdFilter->SetUpper(1);
 296     if (m_Verbose) std::cout<<"Keeping the first label..."<<std::endl;
 297     thresholdFilter->Update();
 298     bones=thresholdFilter->GetOutput();
 299
 300   }
 301
 302   //---------------------------------
 303   // Invert
 304   //---------------------------------
 305   typename InversionFilterType::Pointer inversionFilter=InversionFilterType::New();
 306   inversionFilter->SetInput(bones);
 307   inversionFilter->SetLowerThreshold(0);
 308   inversionFilter->SetUpperThreshold(0);
 309   inversionFilter->SetInsideValue(1);
 310   inversionFilter->Update();
 311
 312   //---------------------------------
 313   // Mirror
 314   //---------------------------------
 315   typename MirrorPadImageFilterType::Pointer mirrorPadImageFilter=MirrorPadImageFilterType::New();
 316   mirrorPadImageFilter->SetInput(inversionFilter->GetOutput());
 317   typename InternalImageType::SizeType padSize;
 318   padSize.Fill(0);
 319   padSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
 320   mirrorPadImageFilter->SetPadLowerBound(padSize);
 321   if (m_Verbose) std::cout<<"Mirroring the entire image along the CC axis..."<<std::endl;
 322   mirrorPadImageFilter->Update();
 323   bones=mirrorPadImageFilter->GetOutput();
 324   // writeImage<InternalImageType>(bones,"/home/jef/tmp/bones.mhd");
 325
 326   return bones;
 327 }
 328
 329
 330
 331
 332 //-------------------------------------------------------------------
 333 // Lungs
 334 //-------------------------------------------------------------------
 335 template <unsigned int Dimension, class  PixelType>
 336 typename itk::Image<MotionMaskGenericFilter::InternalPixelType, Dimension>::Pointer
 337 MotionMaskGenericFilter::GetLungsImage(typename itk::Image<PixelType, Dimension>::Pointer input )
 338 {
 339   // ImageTypes
 340   typedef int InternalPixelType;
 341   typedef itk::Image<PixelType, Dimension> InputImageType;
 342   typedef itk::Image< InternalPixelType, Dimension> InternalImageType; //labeling doesn't work with unsigned char?
 343
 344   //----------------------------------------------------------------------------------------------------
 345   // Typedef for Processing
 346   //----------------------------------------------------------------------------------------------------
 347   typedef itk::ImageFileReader<InternalImageType> FeatureReaderType;
 348   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinarizeFilterType;
 349   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> InversionFilterType;
 350   typedef itk::ThresholdImageFilter<InternalImageType> ThresholdFilterType;
 351   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
 352   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
 353   typedef itk::MirrorPadImageFilter<InternalImageType, InternalImageType> MirrorPadImageFilterType;
 354
 355   typename InternalImageType::Pointer lungs;
 356   if (m_ArgsInfo.featureLungs_given) {
 357     typename FeatureReaderType::Pointer featureReader =FeatureReaderType::New();
 358     featureReader->SetFileName(m_ArgsInfo.featureLungs_arg);
 359     if (m_Verbose) std::cout<<"Reading the lungs feature image..."<<std::endl;
 360     featureReader->Update();
 361     lungs=featureReader->GetOutput();
 362   } else {
 363     if (m_Verbose) std::cout<<"Extracting the lungs feature image..."<<std::endl;
 364     //---------------------------------
 365     // Binarize the image
 366     //---------------------------------
 367     typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
 368     binarizeFilter->SetInput(input);
 369     binarizeFilter->SetLowerThreshold(static_cast<PixelType>(m_ArgsInfo.lowerThresholdLungs_arg));
 370     binarizeFilter->SetUpperThreshold(static_cast<PixelType>(m_ArgsInfo.upperThresholdLungs_arg));
 371     if (m_Verbose) std::cout<<"Binarizing the image using a threshold "<<m_ArgsInfo.lowerThresholdLungs_arg
 372                               <<", "<<m_ArgsInfo.upperThresholdLungs_arg<<"..."<<std::endl;
 373
 374     //---------------------------------
 375     // Label the connected components
 376     //---------------------------------
 377     typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 378     connectFilter->SetInput(binarizeFilter->GetOutput());
 379     connectFilter->SetBackgroundValue(0);
 380     connectFilter->SetFullyConnected(true);
 381     if (m_Verbose) std::cout<<"Labeling the connected components..."<<std::endl;
 382     connectFilter->Update();
 383     if (m_Verbose) std::cout<<"found "<< connectFilter->GetObjectCount() << std::endl;
 384
 385     //---------------------------------
 386     // Sort the labels according to size
 387     //---------------------------------
 388     typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 389     relabelFilter->SetInput(connectFilter->GetOutput());
 390     if (m_Verbose) std::cout<<"Sorting the labels..."<<std::endl;
 391     // writeImage<InternalImageType> (relabelFilter->GetOutput(), "/home/vdelmon/tmp/labels.mhd");
 392
 393     //---------------------------------
 394     // Keep the label
 395     //---------------------------------
 396     typename ThresholdFilterType::Pointer thresholdFilter=ThresholdFilterType::New();
 397     thresholdFilter->SetInput(relabelFilter->GetOutput());
 398     thresholdFilter->SetLower(1);
 399     thresholdFilter->SetUpper(2);
 400     if (m_Verbose) std::cout<<"Keeping the first two labels..."<<std::endl;
 401     thresholdFilter->Update();
 402     lungs=thresholdFilter->GetOutput();
 403
 404   }
 405
 406
 407   //---------------------------------
 408   // Invert
 409   //---------------------------------
 410   typename InversionFilterType::Pointer inversionFilter=InversionFilterType::New();
 411   inversionFilter->SetInput(lungs);
 412   inversionFilter->SetLowerThreshold(0);
 413   inversionFilter->SetUpperThreshold(0);
 414   inversionFilter->SetInsideValue(1);
 415   inversionFilter->Update();
 416
 417   //---------------------------------
 418   // Mirror
 419   //---------------------------------
 420   typename MirrorPadImageFilterType::Pointer mirrorPadImageFilter=MirrorPadImageFilterType::New();
 421   mirrorPadImageFilter->SetInput(inversionFilter->GetOutput());
 422   typename InternalImageType::SizeType padSize;
 423   padSize.Fill(0);
 424   padSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
 425   mirrorPadImageFilter->SetPadLowerBound(padSize);
 426   if (m_Verbose) std::cout<<"Mirroring the entire image along the CC axis..."<<std::endl;
 427   mirrorPadImageFilter->Update();
 428   lungs=mirrorPadImageFilter->GetOutput();
 429   // writeImage<InternalImageType>(lungs,"/home/jef/tmp/lungs.mhd");
 430
 431   return lungs;
 432 }
 433
 434 //-------------------------------------------------------------------
 435 // Resample
 436 //-------------------------------------------------------------------
 437 template <unsigned int Dimension, class  PixelType>
 438 typename itk::Image<MotionMaskGenericFilter::InternalPixelType, Dimension>::Pointer
 439 MotionMaskGenericFilter::Resample( typename itk::Image<InternalPixelType,Dimension>::Pointer input )
 440 {
 441
 442   typedef int InternalPixelType;
 443   typedef itk::Image<PixelType, Dimension> InputImageType;
 444   typedef itk::Image< InternalPixelType, Dimension> InternalImageType; //labeling doesn't work with unsigned char?
 445
 446   //---------------------------------
 447   // Resample to new spacing
 448   //---------------------------------
 449   typename InternalImageType::SizeType size_low;
 450   typename InternalImageType::SpacingType spacing_low;
 451   for (unsigned int i=0; i<Dimension; i++)
 452     if (m_ArgsInfo.spacing_given==Dimension)
 453       for (unsigned int i=0; i<Dimension; i++) {
 454         spacing_low[i]=m_ArgsInfo.spacing_arg[i];
 455         size_low[i]=ceil(input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i]/spacing_low[i]);
 456       }
 457     else
 458       for (unsigned int i=0; i<Dimension; i++) {
 459         spacing_low[i]=m_ArgsInfo.spacing_arg[0];
 460         size_low[i]=ceil(input->GetLargestPossibleRegion().GetSize()[i]*input->GetSpacing()[i]/spacing_low[i]);
 461       }
 462
 463   typename InternalImageType::PointType origin;
 464   input->TransformIndexToPhysicalPoint(input->GetLargestPossibleRegion().GetIndex(), origin);
 465   typedef itk::ResampleImageFilter<InternalImageType, InternalImageType> ResampleImageFilterType;
 466   typename ResampleImageFilterType::Pointer resampler =ResampleImageFilterType::New();
 467   typedef itk::NearestNeighborInterpolateImageFunction<InternalImageType, double> InterpolatorType;
 468   typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
 469   resampler->SetInterpolator(interpolator);
 470   resampler->SetOutputOrigin(origin);
 471   resampler->SetOutputSpacing(spacing_low);
 472   resampler->SetSize(size_low);
 473   resampler->SetInput(input);
 474   resampler->Update();
 475   typename InternalImageType::Pointer output =resampler->GetOutput();
 476   return output;
 477 }
 478
 479
 480 //-------------------------------------------------------------------
 481 // Initialize ellips
 482 //-------------------------------------------------------------------
 483 template <unsigned int Dimension, class  PixelType>
 484 typename itk::Image<MotionMaskGenericFilter::InternalPixelType, Dimension>::Pointer
 485 MotionMaskGenericFilter::InitializeEllips( typename itk::Vector<double,Dimension> center, typename itk::Image<InternalPixelType,Dimension>::Pointer bones_low, typename itk::Image<InternalPixelType,Dimension>::Pointer lungs_low )
 486 {
 487
 488   // ImageTypes
 489   typedef int InternalPixelType;
 490   typedef itk::Image<PixelType, Dimension> InputImageType;
 491   typedef itk::Image< InternalPixelType, Dimension> InternalImageType; //labeling doesn't work with unsigned char?
 492   typedef itk::Image< unsigned char , Dimension> OutputImageType;
 493   typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 494   typedef clitk::SetBackgroundImageFilter<InternalImageType,InternalImageType, InternalImageType> SetBackgroundFilterType;
 495   typedef itk::LabelStatisticsImageFilter<InternalImageType,InternalImageType> LabelStatisticsImageFilterType;
 496   typedef itk::CastImageFilter<InternalImageType,OutputImageType> CastImageFilterType;
 497
 498
 499   typename InternalImageType::Pointer ellips;
 500   if (m_ArgsInfo.ellips_given || m_ArgsInfo.grownEllips_given || m_ArgsInfo.filledRibs_given) {
 501     if(m_ArgsInfo.ellips_given) {
 502       typedef itk::ImageFileReader<InternalImageType> FeatureReaderType;
 503       typename FeatureReaderType::Pointer featureReader = FeatureReaderType::New();
 504       featureReader->SetFileName(m_ArgsInfo.ellips_arg);
 505       featureReader->Update();
 506       ellips=featureReader->GetOutput();
 507     }
 508   } else {
 509     if(m_Verbose) {
 510       std::cout<<std::endl;
 511       std::cout<<"=========================================="<<std::endl;
 512       std::cout<<"||       Initializing ellipsoide        ||"<<std::endl;
 513       std::cout<<"=========================================="<<std::endl;
 514     }
 515
 516     itk::Vector<double,Dimension> centerEllips;
 517     typename itk::Vector<double, Dimension> axes;
 518     if (m_ArgsInfo.ellipseAutoDetect_flag) {
 519       if(m_Verbose) {
 520         std::cout<<"Auto-detecting intial ellipse..."<<std::endl;
 521       }
 522
 523       // compute statistics of the (mirroed) lung region in order to guess the params of the ellipse
 524       typedef itk::LabelImageToShapeLabelMapFilter<InternalImageType>  LabelImageToShapeLabelMapFilter;
 525       typename LabelImageToShapeLabelMapFilter::Pointer label_filter = LabelImageToShapeLabelMapFilter::New();
 526       label_filter->SetInput(lungs_low);
 527       label_filter->Update();
 528
 529       typename InternalImageType::SpacingType spacing = lungs_low->GetSpacing();
 530       typedef typename LabelImageToShapeLabelMapFilter::OutputImageType::LabelObjectType LabelType;
 531       const LabelType* label = dynamic_cast<LabelType*>(label_filter->GetOutput()->GetNthLabelObject(0));
 532
 533
 534       // try to guess ideal ellipse axes from the lungs' bounding box
 535 #if ITK_VERSION_MAJOR >= 4
 536       typename LabelType::RegionType lung_bbox = label->GetBoundingBox();
 537 #else
 538       typename LabelType::RegionType lung_bbox = label->GetRegion();
 539 #endif
 540       axes[0] = 0.95*lung_bbox.GetSize()[0]*spacing[0]/2;
 541       axes[1] = 0.3*lung_bbox.GetSize()[1]*spacing[1]/2;
 542       axes[2] = 0.95*lung_bbox.GetSize()[2]*spacing[2]/2;
 543
 544       // ellipse's center is the center of the lungs' bounding box
 545       typename InternalImageType::PointType origin = lungs_low->GetOrigin();
 546       centerEllips[0] = origin[0] + (lung_bbox.GetIndex()[0] + lung_bbox.GetSize()[0]/2)*spacing[0];
 547       centerEllips[1] = origin[1] + (lung_bbox.GetIndex()[1] + lung_bbox.GetSize()[1]/2)*spacing[1];
 548       centerEllips[2] = origin[2] + (lung_bbox.GetIndex()[2] + lung_bbox.GetSize()[2]/2)*spacing[2];
 549
 550       if(m_Verbose) {
 551         std::cout << "Ellipse center at " << centerEllips << std::endl;
 552         std::cout << "Ellipse axes as " << axes << std::endl;
 553         std::cout << "Lung's bounding box (index,size) " << lung_bbox.GetIndex() << lung_bbox.GetSize() << std::endl;
 554       }
 555     }
 556     else {
 557       //---------------------------------
 558       // Offset from center
 559       //---------------------------------
 560       typename itk::Vector<double,Dimension> offset;
 561       if(m_ArgsInfo.offset_given== Dimension) {
 562         for(unsigned int i=0; i<Dimension; i++)
 563           offset[i]=m_ArgsInfo.offset_arg[i];
 564       } else {
 565         offset.Fill(0.);
 566         offset[1]=-50;
 567       }
 568       centerEllips=center+offset;
 569       if (m_Verbose) {
 570         std::cout<<"Placing the center of the initial ellipsoide at (mm) "<<std::endl;
 571         std::cout<<centerEllips[0];
 572         for (unsigned int i=1; i<Dimension; i++)
 573           std::cout<<" "<<centerEllips[i];
 574         std::cout<<std::endl;
 575       }
 576
 577       // Axes
 578       if (m_ArgsInfo.axes_given==Dimension)
 579         for(unsigned int i=0; i<Dimension; i++)
 580           axes[i]=m_ArgsInfo.axes_arg[i];
 581       else {
 582         axes[0]=100;
 583         axes[1]=30;
 584         axes[2]=150;
 585       }
 586     }
 587
 588     //---------------------------------
 589     // The ellips
 590     //---------------------------------
 591     ellips=InternalImageType::New();
 592     ellips->SetRegions (bones_low->GetLargestPossibleRegion());
 593     ellips->SetOrigin(bones_low->GetOrigin());
 594     ellips->SetSpacing(bones_low->GetSpacing());
 595     ellips->Allocate();
 596     ellips->FillBuffer(0);
 597
 598     // Draw an ellips
 599     IteratorType itEllips(ellips, ellips->GetLargestPossibleRegion());
 600     itEllips.GoToBegin();
 601     typename InternalImageType::PointType point;
 602     typename InternalImageType::IndexType index;
 603     double distance;
 604
 605     if (m_Verbose) std::cout<<"Drawing the initial ellipsoide..."<<std::endl;
 606     while (!itEllips.IsAtEnd()) {
 607       index=itEllips.GetIndex();
 608       ellips->TransformIndexToPhysicalPoint(index, point);
 609       distance=0.0;
 610       for(unsigned int i=0; i<Dimension; i++)
 611         distance+=powf( ( (centerEllips[i]-point[i])/axes[i] ), 2);
 612
 613       if (distance<1)
 614         itEllips.Set(1);
 615       ++itEllips;
 616     }
 617   }
 618
 619
 620   //---------------------------------
 621   // Write the ellips
 622   //---------------------------------
 623   if (m_ArgsInfo.writeEllips_given) {
 624     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
 625     caster->SetInput(ellips);
 626     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeEllips_arg, m_Verbose);
 627   }
 628
 629   return ellips;
 630
 631 }
 632
 633
 634 //-------------------------------------------------------------------
 635 // Update with the number of dimensions and the pixeltype
 636 //-------------------------------------------------------------------
 637 template <unsigned int Dimension, class  PixelType>
 638 void
 639 MotionMaskGenericFilter::UpdateWithDimAndPixelType()
 640 {
 641
 642   // ImageTypes
 643   typedef int InternalPixelType;
 644   typedef itk::Image<PixelType, Dimension> InputImageType;
 645   typedef itk::Image< InternalPixelType, Dimension> InternalImageType; //labeling doesn't work with unsigned char?
 646   typedef itk::Image< float, Dimension> LevelSetImageType; //labeling doesn't work with unsigned char?
 647   typedef itk::Image<unsigned char, Dimension> OutputImageType;
 648
 649
 650   //----------------------------------------------------------------------------------------------------
 651   // Typedef for Processing
 652   //----------------------------------------------------------------------------------------------------
 653   typedef itk::ImageFileReader<InternalImageType> FeatureReaderType;
 654   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinarizeFilterType;
 655   typedef itk::BinaryThresholdImageFilter< LevelSetImageType,InternalImageType>    LevelSetBinarizeFilterType;
 656   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> InversionFilterType;
 657   typedef itk::ThresholdImageFilter<InternalImageType> ThresholdFilterType;
 658   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
 659   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
 660   typedef itk::MirrorPadImageFilter<InternalImageType, InternalImageType> MirrorPadImageFilterType;
 661   typedef itk::NearestNeighborInterpolateImageFunction<InternalImageType, double> InterpolatorType;
 662   typedef itk::ResampleImageFilter<InternalImageType, InternalImageType> ResampleImageFilterType;
 663   typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 664   typedef itk::GeodesicActiveContourLevelSetImageFilter<LevelSetImageType, InternalImageType> LevelSetImageFilterType;
 665   typedef itk::SignedDanielssonDistanceMapImageFilter<InternalImageType, LevelSetImageType> DistanceMapImageFilterType;
 666   typedef clitk::SetBackgroundImageFilter<InternalImageType,InternalImageType, InternalImageType> SetBackgroundFilterType;
 667   typedef itk::LabelStatisticsImageFilter<InternalImageType,InternalImageType> LabelStatisticsImageFilterType;
 668   typedef itk::CastImageFilter<InternalImageType,OutputImageType> CastImageFilterType;
 669
 670
 671   // Read the input
 672   typedef itk::ImageFileReader<InputImageType> InputReaderType;
 673   typename InputReaderType::Pointer reader = InputReaderType::New();
 674   reader->SetFileName( m_InputFileName);
 675   reader->Update();
 676   typename InputImageType::Pointer input= reader->GetOutput();
 677
 678   //     // globals for avi
 679   //     unsigned int number=0;
 680
 681
 682   if(m_Verbose) {
 683     std::cout<<std::endl;
 684     std::cout<<"=========================================="<<std::endl;
 685     std::cout<<"||         Making feature images        ||"<<std::endl;
 686     std::cout<<"=========================================="<<std::endl;
 687   }
 688
 689   //--------------------------------------------------------------------------------
 690   // Lungs
 691   //-------------------------------------------------------------------------------
 692   typename InternalImageType::Pointer lungs = this->GetLungsImage<Dimension, PixelType>(input);
 693
 694   //-------------------------------------------------------------------------------
 695   // Air
 696   //-------------------------------------------------------------------------------
 697   typename InternalImageType::Pointer air = this->GetAirImage<Dimension, PixelType>(input, lungs);
 698
 699   //-------------------------------------------------------------------------------
 700   // Bones
 701   //-------------------------------------------------------------------------------
 702   typename InternalImageType::Pointer bones = this->GetBonesImage<Dimension, PixelType>(input);
 703
 704   //----------------------------------------------------------------------------------------------------
 705   // Write feature images
 706   //----------------------------------------------------------------------------------------------------
 707   if(m_ArgsInfo.writeFeature_given) {
 708     typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
 709     setBackgroundFilter->SetInput(air);
 710     setBackgroundFilter->SetInput2(bones);
 711     setBackgroundFilter->SetMaskValue(0);
 712     setBackgroundFilter->SetOutsideValue(2);
 713     setBackgroundFilter->Update();
 714     typename InternalImageType::Pointer bones_air =setBackgroundFilter->GetOutput();
 715
 716     typename SetBackgroundFilterType::Pointer setBackgroundFilter2 = SetBackgroundFilterType::New();
 717     setBackgroundFilter2->SetInput(bones_air);
 718     setBackgroundFilter2->SetInput2(lungs);
 719     setBackgroundFilter2->SetMaskValue(0);
 720     setBackgroundFilter2->SetOutsideValue(3);
 721     setBackgroundFilter2->Update();
 722     typename InternalImageType::Pointer lungs_bones_air =setBackgroundFilter2->GetOutput();
 723
 724     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
 725     caster->SetInput(lungs_bones_air);
 726     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeFeature_arg, m_Verbose);
 727   }
 728
 729   //----------------------------------------------------------------------------------------------------
 730   // Low dimensional versions
 731   //----------------------------------------------------------------------------------------------------
 732   typename InternalImageType::Pointer bones_low =Resample<Dimension , PixelType>(bones);
 733   typename InternalImageType::Pointer lungs_low =Resample<Dimension , PixelType>(lungs);
 734   typename InternalImageType::Pointer air_low =Resample<Dimension , PixelType>(air);
 735
 736   //---------------------------------
 737   // Pad
 738   //---------------------------------
 739   if(m_ArgsInfo.pad_flag) {
 740     typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 741     IteratorType it(air_low, air_low->GetLargestPossibleRegion());
 742     typename InternalImageType::IndexType index;
 743     while(!it.IsAtEnd()) {
 744       index=it.GetIndex();
 745       for (unsigned int i=0; i<Dimension; i++)
 746         if(index[i]==air_low->GetLargestPossibleRegion().GetIndex()[i]
 747             || index[i]==(unsigned int)air_low->GetLargestPossibleRegion().GetIndex()[i]+ (unsigned int) air_low->GetLargestPossibleRegion().GetSize()[i]-1)
 748           it.Set(0);
 749       ++it;
 750     }
 751   }
 752
 753   //---------------------------------
 754   // Center
 755   //---------------------------------
 756   typename itk::Vector<double,Dimension> center;
 757   typedef itk::ImageMomentsCalculator<InternalImageType> MomentsCalculatorType;
 758   typename    MomentsCalculatorType::Pointer momentsCalculator=MomentsCalculatorType::New();
 759   momentsCalculator->SetImage(air);
 760   momentsCalculator->Compute();
 761   center=momentsCalculator->GetCenterOfGravity();
 762   if (m_Verbose) {
 763     std::cout<<"The center of gravity of the patient body is located at (mm) "<<std::endl;
 764     std::cout<<center[0];
 765     for (unsigned int i=1; i<Dimension; i++)
 766       std::cout<<" "<<center[i];
 767     std::cout<<std::endl;
 768   }
 769
 770   //----------------------------------------------------------------------------------------------------
 771   // Ellipsoide initialization
 772   //----------------------------------------------------------------------------------------------------
 773   typename InternalImageType::Pointer m_Ellips= InitializeEllips<Dimension, PixelType>(center,bones_low,lungs_low);
 774
 775   //----------------------------------------------------------------------------------------------------
 776   // Grow ellips
 777   //----------------------------------------------------------------------------------------------------
 778   typename InternalImageType::Pointer grownEllips;
 779   if (m_ArgsInfo.grownEllips_given || m_ArgsInfo.filledRibs_given) {
 780     if (m_ArgsInfo.grownEllips_given) {
 781
 782       typename FeatureReaderType::Pointer featureReader = FeatureReaderType::New();
 783       featureReader->SetFileName(m_ArgsInfo.grownEllips_arg);
 784       featureReader->Update();
 785       grownEllips=featureReader->GetOutput();
 786     }
 787   } else {
 788
 789     if(m_Verbose) {
 790       std::cout<<std::endl;
 791       std::cout<<"=========================================="<<std::endl;
 792       std::cout<<"||          Growing ellipsoide           ||"<<std::endl;
 793       std::cout<<"=========================================="<<std::endl;
 794     }
 795
 796     //---------------------------------
 797     // Detect abdomen
 798     //---------------------------------
 799     typename InternalImageType::PointType dPoint;
 800     if (m_ArgsInfo.detectionPoint_given) {
 801       for (unsigned int i=0; i<Dimension; i++)
 802         dPoint[i]=m_ArgsInfo.detectionPoint_arg[i];
 803     } else {
 804       typename InternalImageType::RegionType searchRegion=air->GetLargestPossibleRegion();
 805       typename InternalImageType::SizeType searchRegionSize = searchRegion.GetSize();
 806       typename InternalImageType::IndexType searchRegionIndex = searchRegion.GetIndex();
 807       searchRegionIndex[2]+=searchRegionSize[2]/2;
 808       searchRegionSize[2]=1;
 809       searchRegion.SetSize(searchRegionSize);
 810       searchRegion.SetIndex(searchRegionIndex);
 811       IteratorType itAbdomen(air, searchRegion);
 812       itAbdomen.GoToBegin();
 813
 814       typename InternalImageType::PointType aPoint;
 815       typename InternalImageType::IndexType aIndex;
 816
 817       if (m_Verbose) std::cout<<"Detecting the abdomen..."<<std::endl;
 818       while (!itAbdomen.IsAtEnd()) {
 819         if(itAbdomen.Get()) break;
 820         ++itAbdomen;
 821       }
 822       aIndex=itAbdomen.GetIndex();
 823       air->TransformIndexToPhysicalPoint(aIndex,aPoint);
 824       if (m_Verbose) std::cout<<"Detected the abdomen at "<<aPoint<<".."<<std::endl;
 825
 826
 827       //---------------------------------
 828       // Detect abdomen in additional images?
 829       //---------------------------------
 830       if (m_ArgsInfo.detectionPairs_given) {
 831         for (unsigned int i=0; i<m_ArgsInfo.detectionPairs_given; i++) {
 832           typename InternalImageType::Pointer airAdd;
 833           //---------------------------------
 834           // Read the input
 835           //--------------------------------
 836           typedef itk::ImageFileReader<InputImageType> InputReaderType;
 837           typename InputReaderType::Pointer reader = InputReaderType::New();
 838           reader->SetFileName( m_ArgsInfo.detectionPairs_arg[i]);
 839           reader->Update();
 840           typename InputImageType::Pointer additional= reader->GetOutput();
 841           if (m_Verbose) std::cout<<"Extracting the air from additional image "<< i<<"..."<<std::endl;
 842
 843           //---------------------------------
 844           // Binarize the image
 845           //---------------------------------
 846           typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
 847           binarizeFilter->SetInput(additional);
 848           binarizeFilter->SetLowerThreshold(static_cast<PixelType>(m_ArgsInfo.lowerThresholdAir_arg));
 849           binarizeFilter->SetUpperThreshold(static_cast<PixelType>(m_ArgsInfo.upperThresholdAir_arg));
 850           if (m_Verbose) std::cout<<"Binarizing the image using thresholds "<<m_ArgsInfo.lowerThresholdAir_arg
 851                                     <<", "<<m_ArgsInfo.upperThresholdAir_arg<<"..."<<std::endl;
 852
 853           //---------------------------------
 854           // Label the connected components
 855           //---------------------------------
 856           typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 857           connectFilter->SetInput(binarizeFilter->GetOutput());
 858           connectFilter->SetBackgroundValue(0);
 859           connectFilter->SetFullyConnected(false);
 860           if (m_Verbose) std::cout<<"Labeling the connected components..."<<std::endl;
 861
 862           //---------------------------------
 863           // Sort the labels according to size
 864           //---------------------------------
 865           typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 866           relabelFilter->SetInput(connectFilter->GetOutput());
 867           if (m_Verbose) std::cout<<"Sorting the labels..."<<std::endl;
 868
 869           //---------------------------------
 870           // Keep the label
 871           //---------------------------------
 872           typename ThresholdFilterType::Pointer thresholdFilter=ThresholdFilterType::New();
 873           thresholdFilter->SetInput(relabelFilter->GetOutput());
 874           thresholdFilter->SetUpper(1);
 875           if (m_Verbose) std::cout<<"Keeping the first label..."<<std::endl;
 876           thresholdFilter->Update();
 877           airAdd=thresholdFilter->GetOutput();
 878
 879
 880           //---------------------------------
 881           // Invert
 882           //---------------------------------
 883           typename InversionFilterType::Pointer inversionFilter=InversionFilterType::New();
 884           inversionFilter->SetInput(airAdd);
 885           inversionFilter->SetLowerThreshold(0);
 886           inversionFilter->SetUpperThreshold(0);
 887           inversionFilter->SetInsideValue(1);
 888           inversionFilter->Update();
 889
 890           //---------------------------------
 891           // Mirror
 892           //---------------------------------
 893           typename MirrorPadImageFilterType::Pointer mirrorPadImageFilter=MirrorPadImageFilterType::New();
 894           mirrorPadImageFilter->SetInput(inversionFilter->GetOutput());
 895           typename InternalImageType::SizeType padSize;
 896           padSize.Fill(0);
 897           padSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
 898           mirrorPadImageFilter->SetPadLowerBound(padSize);
 899           if (m_Verbose) std::cout<<"Mirroring the entire image along the CC axis..."<<std::endl;
 900           mirrorPadImageFilter->Update();
 901           airAdd=mirrorPadImageFilter->GetOutput();
 902
 903           //---------------------------------
 904           // Detect abdomen
 905           //---------------------------------
 906           typename InternalImageType::RegionType searchRegion=airAdd->GetLargestPossibleRegion();
 907           typename InternalImageType::SizeType searchRegionSize = searchRegion.GetSize();
 908           typename InternalImageType::IndexType searchRegionIndex = searchRegion.GetIndex();
 909           searchRegionIndex[2]+=searchRegionSize[2]/2;
 910           searchRegionSize[2]=1;
 911           searchRegion.SetSize(searchRegionSize);
 912           searchRegion.SetIndex(searchRegionIndex);
 913           IteratorType itAbdomen(airAdd, searchRegion);
 914           itAbdomen.GoToBegin();
 915
 916           typename InternalImageType::PointType additionalPoint;
 917           typename InternalImageType::IndexType aIndex;
 918
 919           if (m_Verbose) std::cout<<"Detecting the abdomen..."<<std::endl;
 920           while (!itAbdomen.IsAtEnd()) {
 921             if(itAbdomen.Get()) break;
 922             ++itAbdomen;
 923           }
 924           aIndex=itAbdomen.GetIndex();
 925           airAdd->TransformIndexToPhysicalPoint(aIndex,additionalPoint);
 926           if (m_Verbose) std::cout<<"Detected the abdomen in the additional image at "<<additionalPoint<<".."<<std::endl;
 927
 928           if(additionalPoint[1]< aPoint[1]) {
 929             aPoint=additionalPoint;
 930             if (m_Verbose) std::cout<<"Modifying the detected abdomen to "<<aPoint<<".."<<std::endl;
 931
 932           }
 933         }
 934       }
 935
 936
 937       // Determine the detection point
 938       dPoint.Fill(0.0);
 939       dPoint+=center;
 940       dPoint[1]=aPoint[1];
 941       if(m_ArgsInfo.offsetDetect_given==Dimension)
 942         for(unsigned int i=0; i <Dimension; i++)
 943           dPoint[i]+=m_ArgsInfo.offsetDetect_arg[i];
 944       else
 945         dPoint[1]+=-10;
 946
 947     }
 948     if (m_Verbose) std::cout<<"Setting the detection point to "<<dPoint<<".."<<std::endl;
 949
 950
 951     //---------------------------------
 952     // Pad the rib image and ellips image
 953     //---------------------------------
 954     typename InternalImageType::Pointer padded_ellips;
 955     typename InternalImageType::Pointer padded_bones_low;
 956
 957     // If detection point not inside the image: pad
 958     typename InternalImageType::IndexType dIndex;
 959     if (!bones_low->TransformPhysicalPointToIndex(dPoint, dIndex)) {
 960       typename InternalImageType::SizeType padSize;
 961       padSize.Fill(0);
 962       padSize[1]=abs(dIndex[1])+1;
 963       if (m_Verbose) std::cout<<"Padding the images with padding size "<<padSize<<" to include the detection point..."<<std::endl;
 964
 965       typename MirrorPadImageFilterType::Pointer padBonesFilter=MirrorPadImageFilterType::New();
 966       padBonesFilter->SetInput(bones_low);
 967       padBonesFilter->SetPadLowerBound(padSize);
 968       padBonesFilter->Update();
 969       padded_bones_low=padBonesFilter->GetOutput();
 970
 971       typename MirrorPadImageFilterType::Pointer padEllipsFilter=MirrorPadImageFilterType::New();
 972       padEllipsFilter->SetInput(m_Ellips);
 973       padEllipsFilter->SetPadLowerBound(padSize);
 974       padEllipsFilter->Update();
 975       padded_ellips=padEllipsFilter->GetOutput();
 976     }
 977
 978     else {
 979       padded_bones_low=bones_low;
 980       padded_ellips=m_Ellips;
 981     }
 982
 983
 984     //---------------------------------
 985     // Calculate distance map
 986     //---------------------------------
 987     typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
 988     distanceMapImageFilter->SetInput(padded_ellips);
 989     distanceMapImageFilter->SetInsideIsPositive(false);
 990     if (m_Verbose) std::cout<<"Calculating the distance map..."<<std::endl;
 991     distanceMapImageFilter->Update();
 992     if (m_ArgsInfo.writeDistMap_given) {
 993       writeImage<LevelSetImageType>(distanceMapImageFilter->GetOutput(), m_ArgsInfo.writeDistMap_arg, m_Verbose);
 994
 995     }
 996
 997     //---------------------------------
 998     // Grow while monitoring detection point
 999     //---------------------------------
1000     typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
1001     levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
1002     levelSetFilter->SetFeatureImage( padded_bones_low );
1003     levelSetFilter->SetPropagationScaling( 1 );
1004     levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve1_arg );
1005     levelSetFilter->SetAdvectionScaling( 0 );
1006     levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS1_arg );
1007     levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter1_arg );
1008     levelSetFilter->SetUseImageSpacing(true);
1009
1010     //  //---------------------------------
1011     //  // Script for making movie
1012     //  //---------------------------------
1013     //          std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1014
1015
1016     if (m_Verbose) std::cout<<"Starting level set segmentation..."<<std::endl;
1017     unsigned int totalNumberOfIterations=0;
1018     while (true) {
1019       levelSetFilter->Update();
1020       totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1021
1022       if ( levelSetFilter->GetOutput()->GetPixel(dIndex) < 0 ) {
1023         if (m_Verbose) std::cout<<"Detection point reached!"<<std::endl;
1024         break;
1025       } else {
1026         if (m_Verbose) std::cout<<"Detection point not reached after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1027         levelSetFilter->SetInput(levelSetFilter->GetOutput());
1028         if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg, m_Verbose);
1029
1030         //              // script
1031         //              std::ostringstream number_str;
1032         //              number_str << number;
1033         //              std::string param =  number_str.str();
1034         //              system((script+param).c_str());
1035         //              number+=1;
1036
1037       }
1038       if ( (totalNumberOfIterations> 10000) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS1_arg) ) break;
1039     }
1040
1041     // Output values
1042     if (m_Verbose) std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1043     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1044     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1045
1046     // Threshold
1047     typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1048     thresholder->SetUpperThreshold( 0.0 );
1049     thresholder->SetOutsideValue( 0 );
1050     thresholder->SetInsideValue( 1 );
1051     thresholder->SetInput( levelSetFilter->GetOutput() );
1052     if (m_Verbose) std::cout<<"Thresholding the output level set..."<<std::endl;
1053     thresholder->Update();
1054     grownEllips=thresholder->GetOutput();
1055   }
1056
1057   //---------------------------------
1058   // Write the grown ellips
1059   //---------------------------------
1060   if (m_ArgsInfo.writeGrownEllips_given) {
1061     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1062     caster->SetInput(grownEllips);
1063     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeGrownEllips_arg, m_Verbose);
1064   }
1065
1066
1067   //----------------------------------------------------------------------------------------------------
1068   // Grow inside ribs
1069   //----------------------------------------------------------------------------------------------------
1070   typename InternalImageType::Pointer filledRibs;
1071   if (m_ArgsInfo.filledRibs_given) {
1072     typename FeatureReaderType::Pointer featureReader = FeatureReaderType::New();
1073     featureReader->SetFileName(m_ArgsInfo.filledRibs_arg);
1074     if (m_Verbose) std::cout<<"Reading filled ribs mask..."<<std::endl;
1075     featureReader->Update();
1076     filledRibs=featureReader->GetOutput();
1077   } else {
1078     if(m_Verbose) {
1079       std::cout<<std::endl;
1080       std::cout<<"=========================================="<<std::endl;
1081       std::cout<<"||        Filling the ribs image         ||"<<std::endl;
1082       std::cout<<"=========================================="<<std::endl;
1083     }
1084     //---------------------------------
1085     // Make feature image air+bones
1086     //---------------------------------
1087     typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
1088     setBackgroundFilter->SetInput(air_low);
1089     setBackgroundFilter->SetInput2(bones_low);
1090     setBackgroundFilter->SetMaskValue(0);
1091     setBackgroundFilter->SetOutsideValue(0);
1092     setBackgroundFilter->Update();
1093     typename InternalImageType::Pointer bones_air_low =setBackgroundFilter->GetOutput();
1094
1095     //---------------------------------
1096     // Resampling previous solution
1097     //---------------------------------
1098     if (m_Verbose) std::cout<<"Resampling previous solution..."<<std::endl;
1099     typename ResampleImageFilterType::Pointer resampler =ResampleImageFilterType::New();
1100     typename InternalImageType::PointType origin;
1101     bones_low->TransformIndexToPhysicalPoint(bones_low->GetLargestPossibleRegion().GetIndex(), origin);
1102     resampler->SetOutputOrigin(origin);
1103     resampler->SetOutputSpacing(bones_low->GetSpacing());
1104     typename InternalImageType::SizeType size_low= bones_low->GetLargestPossibleRegion().GetSize();
1105     resampler->SetSize(size_low);
1106     typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
1107     resampler->SetInterpolator(interpolator);
1108     resampler->SetInput(grownEllips);
1109     resampler->Update();
1110     typename InternalImageType::Pointer grownEllips =resampler->GetOutput();
1111
1112
1113     //---------------------------------
1114     // Calculate Distance Map
1115     //---------------------------------
1116     typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
1117     distanceMapImageFilter->SetInput(grownEllips);
1118     distanceMapImageFilter->SetInsideIsPositive(false);
1119     if (m_Verbose) std::cout<<"Calculating distance map..."<<std::endl;
1120     distanceMapImageFilter->Update();
1121     if (m_ArgsInfo.writeDistMap_given) {
1122       writeImage<LevelSetImageType>(distanceMapImageFilter->GetOutput(), m_ArgsInfo.writeDistMap_arg, m_Verbose);
1123
1124     }
1125
1126     //---------------------------------
1127     // Grow while monitoring lung volume coverage
1128     //---------------------------------
1129     typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
1130     levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
1131     levelSetFilter->SetFeatureImage( bones_air_low );
1132     levelSetFilter->SetPropagationScaling( 1 );
1133     levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve2_arg );
1134     levelSetFilter->SetAdvectionScaling( 0 );
1135     levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS2_arg );
1136     levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter2_arg );
1137     levelSetFilter->SetUseImageSpacing(true);
1138
1139     //---------------------------------
1140     // Invert lung mask
1141     //---------------------------------
1142     typename InversionFilterType::Pointer invertor= InversionFilterType::New();
1143     invertor->SetInput(lungs_low);
1144     invertor->SetLowerThreshold(0);
1145     invertor->SetUpperThreshold(0);
1146     invertor->SetInsideValue(1);
1147     invertor->Update();
1148     typename InternalImageType::Pointer lungs_low_inv=invertor->GetOutput();
1149
1150     //---------------------------------
1151     // Calculate lung volume
1152     //---------------------------------
1153     typename LabelStatisticsImageFilterType::Pointer statisticsFilter= LabelStatisticsImageFilterType::New();
1154     statisticsFilter->SetInput(lungs_low_inv);
1155     statisticsFilter->SetLabelInput(lungs_low);
1156     statisticsFilter->Update();
1157     unsigned int volume=statisticsFilter->GetSum(0);
1158
1159     // Prepare threshold
1160     typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1161     thresholder->SetUpperThreshold(     0.0 );
1162     thresholder->SetOutsideValue(  0  );
1163     thresholder->SetInsideValue(  1 );
1164
1165
1166     // Start monitoring
1167     unsigned int totalNumberOfIterations=0;
1168     unsigned int coverage=0;
1169
1170
1171     //  //---------------------------------
1172     //  // Script for making movie
1173     //  //---------------------------------
1174     //          std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1175
1176     while (true) {
1177       levelSetFilter->Update();
1178       totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1179
1180       thresholder->SetInput( levelSetFilter->GetOutput() );
1181       thresholder->Update();
1182       statisticsFilter->SetInput(thresholder->GetOutput());
1183       statisticsFilter->Update();
1184       coverage=statisticsFilter->GetSum(0);
1185
1186       // Compare the volumes
1187       if ( coverage >= m_ArgsInfo.fillingLevel_arg * volume/100 ) {
1188         if (m_Verbose) std::cout<<"Lungs filled for "<< m_ArgsInfo.fillingLevel_arg<<"% !"<<std::endl;
1189         break;
1190       } else {
1191         if (m_Verbose) std::cout<<"After "<<totalNumberOfIterations<<" iterations, lungs are covered for "
1192                                   <<(double)coverage/volume*100.0<<"%..."<<std::endl;
1193         levelSetFilter->SetInput(levelSetFilter->GetOutput());
1194         if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg, m_Verbose);
1195
1196         //              // script
1197         //              std::ostringstream number_str;
1198         //              number_str << number;
1199         //              std::string param =  number_str.str();
1200         //              system((script+param).c_str());
1201         //              number+=1;
1202
1203       }
1204       if ( (totalNumberOfIterations> 30000) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS2_arg) ) break;
1205     }
1206
1207     // Output values
1208     if (m_Verbose) std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1209     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1210     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1211
1212     // Threshold
1213     thresholder->SetInput( levelSetFilter->GetOutput() );
1214     thresholder->Update();
1215     filledRibs=thresholder->GetOutput();
1216     // writeImage<InternalImageType>(filledRibs,"/home/jef/tmp/filled_ribs_before.mhd", m_Verbose);
1217
1218   }
1219
1220   //---------------------------------
1221   // Write the filled ribs
1222   //---------------------------------
1223   if (m_ArgsInfo.writeFilledRibs_given) {
1224     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1225     caster->SetInput(filledRibs);
1226     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeFilledRibs_arg, m_Verbose);
1227   }
1228
1229
1230   //----------------------------------------------------------------------------------------------------
1231   // Collapse to the lungs
1232   //----------------------------------------------------------------------------------------------------
1233   if(m_Verbose) {
1234     std::cout<<std::endl;
1235     std::cout<<"=========================================="<<std::endl;
1236     std::cout<<"||     Collapsing to the lung image     ||"<<std::endl;
1237     std::cout<<"=========================================="<<std::endl;
1238   }
1239
1240   //---------------------------------
1241   // Make feature image air+bones
1242   //---------------------------------
1243   if (m_Verbose) std::cout<<"Making feature images..."<<std::endl;
1244   typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
1245   setBackgroundFilter->SetInput(air);
1246   setBackgroundFilter->SetInput2(bones);
1247   setBackgroundFilter->SetMaskValue(0);
1248   setBackgroundFilter->SetOutsideValue(0);
1249   setBackgroundFilter->Update();
1250   typename InternalImageType::Pointer bones_air =setBackgroundFilter->GetOutput();
1251
1252   typename SetBackgroundFilterType::Pointer setBackgroundFilter2 = SetBackgroundFilterType::New();
1253   setBackgroundFilter2->SetInput(bones_air);
1254   setBackgroundFilter2->SetInput2(lungs);
1255   setBackgroundFilter2->SetMaskValue(0);
1256   setBackgroundFilter2->SetOutsideValue(0);
1257   setBackgroundFilter2->Update();
1258   typename InternalImageType::Pointer lungs_bones_air =setBackgroundFilter2->GetOutput();
1259
1260   //---------------------------------
1261   // Prepare previous solution
1262   //---------------------------------
1263   if (m_Verbose) std::cout<<"Resampling previous solution..."<<std::endl;
1264   typename ResampleImageFilterType::Pointer resampler =ResampleImageFilterType::New();
1265   typedef itk::NearestNeighborInterpolateImageFunction<InternalImageType, double> InterpolatorType;
1266   typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
1267   resampler->SetOutputStartIndex(bones->GetLargestPossibleRegion().GetIndex());
1268   resampler->SetInput(filledRibs);
1269   resampler->SetInterpolator(interpolator);
1270   resampler->SetOutputParametersFromImage(bones);
1271   resampler->Update();
1272   filledRibs =resampler->GetOutput();
1273
1274   if (m_Verbose) std::cout<<"Setting lungs to 1..."<<std::endl;
1275   typename SetBackgroundFilterType::Pointer setBackgroundFilter3 = SetBackgroundFilterType::New();
1276   setBackgroundFilter3->SetInput(filledRibs);
1277   setBackgroundFilter3->SetInput2(lungs);
1278   setBackgroundFilter3->SetMaskValue(0);
1279   setBackgroundFilter3->SetOutsideValue(1);
1280   setBackgroundFilter3->Update();
1281   filledRibs=setBackgroundFilter3->GetOutput();
1282
1283   if (m_Verbose) std::cout<<"Removing overlap with bones..."<<std::endl;
1284   typename SetBackgroundFilterType::Pointer setBackgroundFilter4 = SetBackgroundFilterType::New();
1285   setBackgroundFilter4->SetInput(filledRibs);
1286   setBackgroundFilter4->SetInput2(bones);
1287   setBackgroundFilter4->SetMaskValue(0);
1288   setBackgroundFilter4->SetOutsideValue(0);
1289   setBackgroundFilter4->Update();
1290   filledRibs =setBackgroundFilter4->GetOutput();
1291   //   writeImage<InternalImageType>(filledRibs,"/home/jef/tmp/filledRibs_pp.mhd");
1292   //---------------------------------
1293   // Calculate Distance Map
1294   //---------------------------------
1295   //  typedef  itk::ApproximateSignedDistanceMapImageFilter <InternalImageType, LevelSetImageType> DistanceMapImageFilterType2;
1296   typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
1297   distanceMapImageFilter->SetInput(filledRibs);
1298   distanceMapImageFilter->SetInsideIsPositive(false);
1299   // distanceMapImageFilter->SetInsideValue(0);
1300 //     distanceMapImageFilter->SetOutsideValue(1);
1301   if (m_Verbose) std::cout<<"Calculating distance map..."<<std::endl;
1302   distanceMapImageFilter->Update();
1303
1304   //---------------------------------
1305   // Collapse
1306   //---------------------------------
1307   typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
1308   levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
1309   levelSetFilter->SetFeatureImage( lungs_bones_air );
1310   levelSetFilter->SetPropagationScaling(m_ArgsInfo.prop3_arg);
1311   levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve3_arg );
1312   levelSetFilter->SetAdvectionScaling( 0 );
1313   levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS3_arg );
1314   levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter3_arg );
1315   levelSetFilter->SetUseImageSpacing(true);
1316
1317   //     //script
1318   //     std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1319
1320   // Start monitoring
1321   if (m_Verbose) std::cout<<"Starting the levelset..."<<std::endl;
1322   unsigned int totalNumberOfIterations=0;
1323   while (true) {
1324     levelSetFilter->Update();
1325
1326     // monitor state
1327     totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1328     levelSetFilter->SetInput(levelSetFilter->GetOutput());
1329     if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg);
1330     std::cout << "After "<<totalNumberOfIterations<<" iteration the RMS change is " << levelSetFilter->GetRMSChange() <<"..."<< std::endl;
1331
1332     //  // script
1333     //  std::ostringstream number_str;
1334     //  number_str << number;
1335     //  std::string param =  number_str.str();
1336     //  system((script+param).c_str());
1337     //  number+=1;
1338
1339     // stopping condition
1340     if ( (totalNumberOfIterations>= (unsigned int) m_ArgsInfo.maxIter3_arg) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS3_arg) ) break;
1341     levelSetFilter->SetNumberOfIterations( std::min ((unsigned int) m_ArgsInfo.iter3_arg, (unsigned int) m_ArgsInfo.maxIter3_arg-totalNumberOfIterations ) );
1342   }
1343
1344   // Output values
1345   if (m_Verbose) {
1346     std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1347     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1348     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1349   }
1350
1351   // Threshold
1352   typedef itk::BinaryThresholdImageFilter< LevelSetImageType,InternalImageType>    LevelSetBinarizeFilterType;
1353   typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1354   thresholder->SetUpperThreshold( 0.0 );
1355   thresholder->SetOutsideValue( 0 );
1356   thresholder->SetInsideValue( 1 );
1357   thresholder->SetInput( levelSetFilter->GetOutput() );
1358   thresholder->Update();
1359   typename InternalImageType::Pointer output = thresholder->GetOutput();
1360
1361
1362   //----------------------------------------------------------------------------------------------------
1363   // Prepare the output
1364   //----------------------------------------------------------------------------------------------------
1365
1366   //---------------------------------
1367   // Set Air to zero
1368   //---------------------------------
1369   if (m_Verbose) std::cout<<"Removing overlap mask with air..."<<std::endl;
1370   typename SetBackgroundFilterType::Pointer setBackgroundFilter5 = SetBackgroundFilterType::New();
1371   setBackgroundFilter5->SetInput(output);
1372   setBackgroundFilter5->SetInput2(air);
1373   setBackgroundFilter5->SetMaskValue(0);
1374   setBackgroundFilter5->SetOutsideValue(0);
1375   setBackgroundFilter5->Update();
1376   output=setBackgroundFilter5->GetOutput();
1377
1378   //---------------------------------
1379   // Open & close  to cleanup
1380   //---------------------------------
1381   if ( m_ArgsInfo.openClose_flag) {
1382
1383     //---------------------------------
1384     // Structuring element
1385     //---------------------------------
1386     typedef itk::BinaryBallStructuringElement<InternalPixelType,Dimension > KernelType;
1387     KernelType structuringElement;
1388     structuringElement.SetRadius(1);
1389     structuringElement.CreateStructuringElement();
1390
1391     //---------------------------------
1392     // Open
1393     //---------------------------------
1394     typedef itk::BinaryMorphologicalOpeningImageFilter<InternalImageType, InternalImageType , KernelType> OpenFilterType;
1395     typename OpenFilterType::Pointer openFilter = OpenFilterType::New();
1396     openFilter->SetInput(output);
1397     openFilter->SetBackgroundValue(0);
1398     openFilter->SetForegroundValue(1);
1399     openFilter->SetKernel(structuringElement);
1400     if(m_Verbose) std::cout<<"Opening the output image..."<<std::endl;
1401
1402     //---------------------------------
1403     // Close
1404     //---------------------------------
1405     typedef itk::BinaryMorphologicalClosingImageFilter<InternalImageType, InternalImageType , KernelType> CloseFilterType;
1406     typename CloseFilterType::Pointer closeFilter = CloseFilterType::New();
1407     closeFilter->SetInput(openFilter->GetOutput());
1408     closeFilter->SetSafeBorder(true);
1409     closeFilter->SetForegroundValue(1);
1410     closeFilter->SetKernel(structuringElement);
1411     if(m_Verbose) std::cout<<"Closing the output image..."<<std::endl;
1412     closeFilter->Update();
1413     output=closeFilter->GetOutput();
1414
1415   }
1416   //writeImage<InternalImageType>(output,"/home/jef/tmp/mm_double.mhd");
1417
1418   // Extract the upper part
1419   typedef  itk::CropImageFilter<InternalImageType, InternalImageType> CropImageFilterType;
1420   typename CropImageFilterType::Pointer cropFilter=CropImageFilterType::New();
1421   cropFilter->SetInput(output);
1422   typename InputImageType::SizeType lSize, uSize;
1423   uSize.Fill(0);
1424   lSize.Fill(0);
1425   lSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
1426   cropFilter->SetLowerBoundaryCropSize(lSize);
1427   cropFilter->SetUpperBoundaryCropSize(uSize);
1428   cropFilter->Update();
1429
1430   // Output
1431   typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1432   caster->SetInput(cropFilter->GetOutput());
1433   writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.output_arg, m_Verbose);
1434
1435 }
1436
1437 }//end clitk
1438
1439 #endif //#define clitkMotionMaskGenericFilter_txx