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       typename LabelType::RegionType lung_bbox = label->GetRegion();
 536       axes[0] = 0.95*lung_bbox.GetSize()[0]*spacing[0]/2;
 537       axes[1] = 0.3*lung_bbox.GetSize()[1]*spacing[1]/2;
 538       axes[2] = 0.95*lung_bbox.GetSize()[2]*spacing[2]/2;
 539
 540       // ellipse's center is the center of the lungs' bounding box
 541       typename InternalImageType::PointType origin = lungs_low->GetOrigin();
 542       centerEllips[0] = origin[0] + (lung_bbox.GetIndex()[0] + lung_bbox.GetSize()[0]/2)*spacing[0];
 543       centerEllips[1] = origin[1] + (lung_bbox.GetIndex()[1] + lung_bbox.GetSize()[1]/2)*spacing[1];
 544       centerEllips[2] = origin[2] + (lung_bbox.GetIndex()[2] + lung_bbox.GetSize()[2]/2)*spacing[2];
 545
 546       if(m_Verbose) {
 547         std::cout << "Ellipse center at " << centerEllips << std::endl;
 548         std::cout << "Ellipse axes as " << axes << std::endl;
 549         std::cout << "Lung's bounding box (index,size) " << lung_bbox.GetIndex() << lung_bbox.GetSize() << std::endl;
 550       }
 551     }
 552     else {
 553       //---------------------------------
 554       // Offset from center
 555       //---------------------------------
 556       typename itk::Vector<double,Dimension> offset;
 557       if(m_ArgsInfo.offset_given== Dimension) {
 558         for(unsigned int i=0; i<Dimension; i++)
 559           offset[i]=m_ArgsInfo.offset_arg[i];
 560       } else {
 561         offset.Fill(0.);
 562         offset[1]=-50;
 563       }
 564       centerEllips=center+offset;
 565       if (m_Verbose) {
 566         std::cout<<"Placing the center of the initial ellipsoide at (mm) "<<std::endl;
 567         std::cout<<centerEllips[0];
 568         for (unsigned int i=1; i<Dimension; i++)
 569           std::cout<<" "<<centerEllips[i];
 570         std::cout<<std::endl;
 571       }
 572
 573       // Axes
 574       if (m_ArgsInfo.axes_given==Dimension)
 575         for(unsigned int i=0; i<Dimension; i++)
 576           axes[i]=m_ArgsInfo.axes_arg[i];
 577       else {
 578         axes[0]=100;
 579         axes[1]=30;
 580         axes[2]=150;
 581       }
 582     }
 583
 584     //---------------------------------
 585     // The ellips
 586     //---------------------------------
 587     ellips=InternalImageType::New();
 588     ellips->SetRegions (bones_low->GetLargestPossibleRegion());
 589     ellips->SetOrigin(bones_low->GetOrigin());
 590     ellips->SetSpacing(bones_low->GetSpacing());
 591     ellips->Allocate();
 592     ellips->FillBuffer(0);
 593
 594     // Draw an ellips
 595     IteratorType itEllips(ellips, ellips->GetLargestPossibleRegion());
 596     itEllips.GoToBegin();
 597     typename InternalImageType::PointType point;
 598     typename InternalImageType::IndexType index;
 599     double distance;
 600
 601     if (m_Verbose) std::cout<<"Drawing the initial ellipsoide..."<<std::endl;
 602     while (!itEllips.IsAtEnd()) {
 603       index=itEllips.GetIndex();
 604       ellips->TransformIndexToPhysicalPoint(index, point);
 605       distance=0.0;
 606       for(unsigned int i=0; i<Dimension; i++)
 607         distance+=powf( ( (centerEllips[i]-point[i])/axes[i] ), 2);
 608
 609       if (distance<1)
 610         itEllips.Set(1);
 611       ++itEllips;
 612     }
 613   }
 614
 615
 616   //---------------------------------
 617   // Write the ellips
 618   //---------------------------------
 619   if (m_ArgsInfo.writeEllips_given) {
 620     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
 621     caster->SetInput(ellips);
 622     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeEllips_arg, m_Verbose);
 623   }
 624
 625   return ellips;
 626
 627 }
 628
 629
 630 //-------------------------------------------------------------------
 631 // Update with the number of dimensions and the pixeltype
 632 //-------------------------------------------------------------------
 633 template <unsigned int Dimension, class  PixelType>
 634 void
 635 MotionMaskGenericFilter::UpdateWithDimAndPixelType()
 636 {
 637
 638   // ImageTypes
 639   typedef int InternalPixelType;
 640   typedef itk::Image<PixelType, Dimension> InputImageType;
 641   typedef itk::Image< InternalPixelType, Dimension> InternalImageType; //labeling doesn't work with unsigned char?
 642   typedef itk::Image< float, Dimension> LevelSetImageType; //labeling doesn't work with unsigned char?
 643   typedef itk::Image<unsigned char, Dimension> OutputImageType;
 644
 645
 646   //----------------------------------------------------------------------------------------------------
 647   // Typedef for Processing
 648   //----------------------------------------------------------------------------------------------------
 649   typedef itk::ImageFileReader<InternalImageType> FeatureReaderType;
 650   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinarizeFilterType;
 651   typedef itk::BinaryThresholdImageFilter< LevelSetImageType,InternalImageType>    LevelSetBinarizeFilterType;
 652   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> InversionFilterType;
 653   typedef itk::ThresholdImageFilter<InternalImageType> ThresholdFilterType;
 654   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
 655   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
 656   typedef itk::MirrorPadImageFilter<InternalImageType, InternalImageType> MirrorPadImageFilterType;
 657   typedef itk::NearestNeighborInterpolateImageFunction<InternalImageType, double> InterpolatorType;
 658   typedef itk::ResampleImageFilter<InternalImageType, InternalImageType> ResampleImageFilterType;
 659   typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 660   typedef itk::GeodesicActiveContourLevelSetImageFilter<LevelSetImageType, InternalImageType> LevelSetImageFilterType;
 661   typedef itk::SignedDanielssonDistanceMapImageFilter<InternalImageType, LevelSetImageType> DistanceMapImageFilterType;
 662   typedef clitk::SetBackgroundImageFilter<InternalImageType,InternalImageType, InternalImageType> SetBackgroundFilterType;
 663   typedef itk::LabelStatisticsImageFilter<InternalImageType,InternalImageType> LabelStatisticsImageFilterType;
 664   typedef itk::CastImageFilter<InternalImageType,OutputImageType> CastImageFilterType;
 665
 666
 667   // Read the input
 668   typedef itk::ImageFileReader<InputImageType> InputReaderType;
 669   typename InputReaderType::Pointer reader = InputReaderType::New();
 670   reader->SetFileName( m_InputFileName);
 671   reader->Update();
 672   typename InputImageType::Pointer input= reader->GetOutput();
 673
 674   //     // globals for avi
 675   //     unsigned int number=0;
 676
 677
 678   if(m_Verbose) {
 679     std::cout<<std::endl;
 680     std::cout<<"=========================================="<<std::endl;
 681     std::cout<<"||         Making feature images        ||"<<std::endl;
 682     std::cout<<"=========================================="<<std::endl;
 683   }
 684
 685   //--------------------------------------------------------------------------------
 686   // Lungs
 687   //-------------------------------------------------------------------------------
 688   typename InternalImageType::Pointer lungs = this->GetLungsImage<Dimension, PixelType>(input);
 689
 690   //-------------------------------------------------------------------------------
 691   // Air
 692   //-------------------------------------------------------------------------------
 693   typename InternalImageType::Pointer air = this->GetAirImage<Dimension, PixelType>(input, lungs);
 694
 695   //-------------------------------------------------------------------------------
 696   // Bones
 697   //-------------------------------------------------------------------------------
 698   typename InternalImageType::Pointer bones = this->GetBonesImage<Dimension, PixelType>(input);
 699
 700   //----------------------------------------------------------------------------------------------------
 701   // Write feature images
 702   //----------------------------------------------------------------------------------------------------
 703   if(m_ArgsInfo.writeFeature_given) {
 704     typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
 705     setBackgroundFilter->SetInput(air);
 706     setBackgroundFilter->SetInput2(bones);
 707     setBackgroundFilter->SetMaskValue(0);
 708     setBackgroundFilter->SetOutsideValue(2);
 709     setBackgroundFilter->Update();
 710     typename InternalImageType::Pointer bones_air =setBackgroundFilter->GetOutput();
 711
 712     typename SetBackgroundFilterType::Pointer setBackgroundFilter2 = SetBackgroundFilterType::New();
 713     setBackgroundFilter2->SetInput(bones_air);
 714     setBackgroundFilter2->SetInput2(lungs);
 715     setBackgroundFilter2->SetMaskValue(0);
 716     setBackgroundFilter2->SetOutsideValue(3);
 717     setBackgroundFilter2->Update();
 718     typename InternalImageType::Pointer lungs_bones_air =setBackgroundFilter2->GetOutput();
 719
 720     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
 721     caster->SetInput(lungs_bones_air);
 722     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeFeature_arg, m_Verbose);
 723   }
 724
 725   //----------------------------------------------------------------------------------------------------
 726   // Low dimensional versions
 727   //----------------------------------------------------------------------------------------------------
 728   typename InternalImageType::Pointer bones_low =Resample<Dimension , PixelType>(bones);
 729   typename InternalImageType::Pointer lungs_low =Resample<Dimension , PixelType>(lungs);
 730   typename InternalImageType::Pointer air_low =Resample<Dimension , PixelType>(air);
 731
 732   //---------------------------------
 733   // Pad
 734   //---------------------------------
 735   if(m_ArgsInfo.pad_flag) {
 736     typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 737     IteratorType it(air_low, air_low->GetLargestPossibleRegion());
 738     typename InternalImageType::IndexType index;
 739     while(!it.IsAtEnd()) {
 740       index=it.GetIndex();
 741       for (unsigned int i=0; i<Dimension; i++)
 742         if(index[i]==air_low->GetLargestPossibleRegion().GetIndex()[i]
 743             || index[i]==(unsigned int)air_low->GetLargestPossibleRegion().GetIndex()[i]+ (unsigned int) air_low->GetLargestPossibleRegion().GetSize()[i]-1)
 744           it.Set(0);
 745       ++it;
 746     }
 747   }
 748
 749   //---------------------------------
 750   // Center
 751   //---------------------------------
 752   typename itk::Vector<double,Dimension> center;
 753   typedef itk::ImageMomentsCalculator<InternalImageType> MomentsCalculatorType;
 754   typename    MomentsCalculatorType::Pointer momentsCalculator=MomentsCalculatorType::New();
 755   momentsCalculator->SetImage(air);
 756   momentsCalculator->Compute();
 757   center=momentsCalculator->GetCenterOfGravity();
 758   if (m_Verbose) {
 759     std::cout<<"The center of gravity of the patient body is located at (mm) "<<std::endl;
 760     std::cout<<center[0];
 761     for (unsigned int i=1; i<Dimension; i++)
 762       std::cout<<" "<<center[i];
 763     std::cout<<std::endl;
 764   }
 765
 766   //----------------------------------------------------------------------------------------------------
 767   // Ellipsoide initialization
 768   //----------------------------------------------------------------------------------------------------
 769   typename InternalImageType::Pointer m_Ellips= InitializeEllips<Dimension, PixelType>(center,bones_low,lungs_low);
 770
 771   //----------------------------------------------------------------------------------------------------
 772   // Grow ellips
 773   //----------------------------------------------------------------------------------------------------
 774   typename InternalImageType::Pointer grownEllips;
 775   if (m_ArgsInfo.grownEllips_given || m_ArgsInfo.filledRibs_given) {
 776     if (m_ArgsInfo.grownEllips_given) {
 777
 778       typename FeatureReaderType::Pointer featureReader = FeatureReaderType::New();
 779       featureReader->SetFileName(m_ArgsInfo.grownEllips_arg);
 780       featureReader->Update();
 781       grownEllips=featureReader->GetOutput();
 782     }
 783   } else {
 784
 785     if(m_Verbose) {
 786       std::cout<<std::endl;
 787       std::cout<<"=========================================="<<std::endl;
 788       std::cout<<"||          Growing ellipsoide           ||"<<std::endl;
 789       std::cout<<"=========================================="<<std::endl;
 790     }
 791
 792     //---------------------------------
 793     // Detect abdomen
 794     //---------------------------------
 795     typename InternalImageType::PointType dPoint;
 796     if (m_ArgsInfo.detectionPoint_given) {
 797       for (unsigned int i=0; i<Dimension; i++)
 798         dPoint[i]=m_ArgsInfo.detectionPoint_arg[i];
 799     } else {
 800       typename InternalImageType::RegionType searchRegion=air->GetLargestPossibleRegion();
 801       typename InternalImageType::SizeType searchRegionSize = searchRegion.GetSize();
 802       typename InternalImageType::IndexType searchRegionIndex = searchRegion.GetIndex();
 803       searchRegionIndex[2]+=searchRegionSize[2]/2;
 804       searchRegionSize[2]=1;
 805       searchRegion.SetSize(searchRegionSize);
 806       searchRegion.SetIndex(searchRegionIndex);
 807       IteratorType itAbdomen(air, searchRegion);
 808       itAbdomen.GoToBegin();
 809
 810       typename InternalImageType::PointType aPoint;
 811       typename InternalImageType::IndexType aIndex;
 812
 813       if (m_Verbose) std::cout<<"Detecting the abdomen..."<<std::endl;
 814       while (!itAbdomen.IsAtEnd()) {
 815         if(itAbdomen.Get()) break;
 816         ++itAbdomen;
 817       }
 818       aIndex=itAbdomen.GetIndex();
 819       air->TransformIndexToPhysicalPoint(aIndex,aPoint);
 820       if (m_Verbose) std::cout<<"Detected the abdomen at "<<aPoint<<".."<<std::endl;
 821
 822
 823       //---------------------------------
 824       // Detect abdomen in additional images?
 825       //---------------------------------
 826       if (m_ArgsInfo.detectionPairs_given) {
 827         for (unsigned int i=0; i<m_ArgsInfo.detectionPairs_given; i++) {
 828           typename InternalImageType::Pointer airAdd;
 829           //---------------------------------
 830           // Read the input
 831           //--------------------------------
 832           typedef itk::ImageFileReader<InputImageType> InputReaderType;
 833           typename InputReaderType::Pointer reader = InputReaderType::New();
 834           reader->SetFileName( m_ArgsInfo.detectionPairs_arg[i]);
 835           reader->Update();
 836           typename InputImageType::Pointer additional= reader->GetOutput();
 837           if (m_Verbose) std::cout<<"Extracting the air from additional image "<< i<<"..."<<std::endl;
 838
 839           //---------------------------------
 840           // Binarize the image
 841           //---------------------------------
 842           typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
 843           binarizeFilter->SetInput(additional);
 844           binarizeFilter->SetLowerThreshold(static_cast<PixelType>(m_ArgsInfo.lowerThresholdAir_arg));
 845           binarizeFilter->SetUpperThreshold(static_cast<PixelType>(m_ArgsInfo.upperThresholdAir_arg));
 846           if (m_Verbose) std::cout<<"Binarizing the image using thresholds "<<m_ArgsInfo.lowerThresholdAir_arg
 847                                     <<", "<<m_ArgsInfo.upperThresholdAir_arg<<"..."<<std::endl;
 848
 849           //---------------------------------
 850           // Label the connected components
 851           //---------------------------------
 852           typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 853           connectFilter->SetInput(binarizeFilter->GetOutput());
 854           connectFilter->SetBackgroundValue(0);
 855           connectFilter->SetFullyConnected(false);
 856           if (m_Verbose) std::cout<<"Labeling the connected components..."<<std::endl;
 857
 858           //---------------------------------
 859           // Sort the labels according to size
 860           //---------------------------------
 861           typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 862           relabelFilter->SetInput(connectFilter->GetOutput());
 863           if (m_Verbose) std::cout<<"Sorting the labels..."<<std::endl;
 864
 865           //---------------------------------
 866           // Keep the label
 867           //---------------------------------
 868           typename ThresholdFilterType::Pointer thresholdFilter=ThresholdFilterType::New();
 869           thresholdFilter->SetInput(relabelFilter->GetOutput());
 870           thresholdFilter->SetUpper(1);
 871           if (m_Verbose) std::cout<<"Keeping the first label..."<<std::endl;
 872           thresholdFilter->Update();
 873           airAdd=thresholdFilter->GetOutput();
 874
 875
 876           //---------------------------------
 877           // Invert
 878           //---------------------------------
 879           typename InversionFilterType::Pointer inversionFilter=InversionFilterType::New();
 880           inversionFilter->SetInput(airAdd);
 881           inversionFilter->SetLowerThreshold(0);
 882           inversionFilter->SetUpperThreshold(0);
 883           inversionFilter->SetInsideValue(1);
 884           inversionFilter->Update();
 885
 886           //---------------------------------
 887           // Mirror
 888           //---------------------------------
 889           typename MirrorPadImageFilterType::Pointer mirrorPadImageFilter=MirrorPadImageFilterType::New();
 890           mirrorPadImageFilter->SetInput(inversionFilter->GetOutput());
 891           typename InternalImageType::SizeType padSize;
 892           padSize.Fill(0);
 893           padSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
 894           mirrorPadImageFilter->SetPadLowerBound(padSize);
 895           if (m_Verbose) std::cout<<"Mirroring the entire image along the CC axis..."<<std::endl;
 896           mirrorPadImageFilter->Update();
 897           airAdd=mirrorPadImageFilter->GetOutput();
 898
 899           //---------------------------------
 900           // Detect abdomen
 901           //---------------------------------
 902           typename InternalImageType::RegionType searchRegion=airAdd->GetLargestPossibleRegion();
 903           typename InternalImageType::SizeType searchRegionSize = searchRegion.GetSize();
 904           typename InternalImageType::IndexType searchRegionIndex = searchRegion.GetIndex();
 905           searchRegionIndex[2]+=searchRegionSize[2]/2;
 906           searchRegionSize[2]=1;
 907           searchRegion.SetSize(searchRegionSize);
 908           searchRegion.SetIndex(searchRegionIndex);
 909           IteratorType itAbdomen(airAdd, searchRegion);
 910           itAbdomen.GoToBegin();
 911
 912           typename InternalImageType::PointType additionalPoint;
 913           typename InternalImageType::IndexType aIndex;
 914
 915           if (m_Verbose) std::cout<<"Detecting the abdomen..."<<std::endl;
 916           while (!itAbdomen.IsAtEnd()) {
 917             if(itAbdomen.Get()) break;
 918             ++itAbdomen;
 919           }
 920           aIndex=itAbdomen.GetIndex();
 921           airAdd->TransformIndexToPhysicalPoint(aIndex,additionalPoint);
 922           if (m_Verbose) std::cout<<"Detected the abdomen in the additional image at "<<additionalPoint<<".."<<std::endl;
 923
 924           if(additionalPoint[1]< aPoint[1]) {
 925             aPoint=additionalPoint;
 926             if (m_Verbose) std::cout<<"Modifying the detected abdomen to "<<aPoint<<".."<<std::endl;
 927
 928           }
 929         }
 930       }
 931
 932
 933       // Determine the detection point
 934       dPoint.Fill(0.0);
 935       dPoint+=center;
 936       dPoint[1]=aPoint[1];
 937       if(m_ArgsInfo.offsetDetect_given==Dimension)
 938         for(unsigned int i=0; i <Dimension; i++)
 939           dPoint[i]+=m_ArgsInfo.offsetDetect_arg[i];
 940       else
 941         dPoint[1]+=-10;
 942
 943     }
 944     if (m_Verbose) std::cout<<"Setting the detection point to "<<dPoint<<".."<<std::endl;
 945
 946
 947     //---------------------------------
 948     // Pad the rib image and ellips image
 949     //---------------------------------
 950     typename InternalImageType::Pointer padded_ellips;
 951     typename InternalImageType::Pointer padded_bones_low;
 952
 953     // If detection point not inside the image: pad
 954     typename InternalImageType::IndexType dIndex;
 955     if (!bones_low->TransformPhysicalPointToIndex(dPoint, dIndex)) {
 956       typename InternalImageType::SizeType padSize;
 957       padSize.Fill(0);
 958       padSize[1]=abs(dIndex[1])+1;
 959       if (m_Verbose) std::cout<<"Padding the images with padding size "<<padSize<<" to include the detection point..."<<std::endl;
 960
 961       typename MirrorPadImageFilterType::Pointer padBonesFilter=MirrorPadImageFilterType::New();
 962       padBonesFilter->SetInput(bones_low);
 963       padBonesFilter->SetPadLowerBound(padSize);
 964       padBonesFilter->Update();
 965       padded_bones_low=padBonesFilter->GetOutput();
 966
 967       typename MirrorPadImageFilterType::Pointer padEllipsFilter=MirrorPadImageFilterType::New();
 968       padEllipsFilter->SetInput(m_Ellips);
 969       padEllipsFilter->SetPadLowerBound(padSize);
 970       padEllipsFilter->Update();
 971       padded_ellips=padEllipsFilter->GetOutput();
 972     }
 973
 974     else {
 975       padded_bones_low=bones_low;
 976       padded_ellips=m_Ellips;
 977     }
 978
 979
 980     //---------------------------------
 981     // Calculate distance map
 982     //---------------------------------
 983     typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
 984     distanceMapImageFilter->SetInput(padded_ellips);
 985     distanceMapImageFilter->SetInsideIsPositive(false);
 986     if (m_Verbose) std::cout<<"Calculating the distance map..."<<std::endl;
 987     distanceMapImageFilter->Update();
 988     if (m_ArgsInfo.writeDistMap_given) {
 989       writeImage<LevelSetImageType>(distanceMapImageFilter->GetOutput(), m_ArgsInfo.writeDistMap_arg, m_Verbose);
 990
 991     }
 992
 993     //---------------------------------
 994     // Grow while monitoring detection point
 995     //---------------------------------
 996     typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
 997     levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
 998     levelSetFilter->SetFeatureImage( padded_bones_low );
 999     levelSetFilter->SetPropagationScaling( 1 );
1000     levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve1_arg );
1001     levelSetFilter->SetAdvectionScaling( 0 );
1002     levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS1_arg );
1003     levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter1_arg );
1004     levelSetFilter->SetUseImageSpacing(true);
1005
1006     //  //---------------------------------
1007     //  // Script for making movie
1008     //  //---------------------------------
1009     //          std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1010
1011
1012     if (m_Verbose) std::cout<<"Starting level set segmentation..."<<std::endl;
1013     unsigned int totalNumberOfIterations=0;
1014     while (true) {
1015       levelSetFilter->Update();
1016       totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1017
1018       if ( levelSetFilter->GetOutput()->GetPixel(dIndex) < 0 ) {
1019         if (m_Verbose) std::cout<<"Detection point reached!"<<std::endl;
1020         break;
1021       } else {
1022         if (m_Verbose) std::cout<<"Detection point not reached after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1023         levelSetFilter->SetInput(levelSetFilter->GetOutput());
1024         if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg, m_Verbose);
1025
1026         //              // script
1027         //              std::ostringstream number_str;
1028         //              number_str << number;
1029         //              std::string param =  number_str.str();
1030         //              system((script+param).c_str());
1031         //              number+=1;
1032
1033       }
1034       if ( (totalNumberOfIterations> 10000) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS1_arg) ) break;
1035     }
1036
1037     // Output values
1038     if (m_Verbose) std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1039     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1040     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1041
1042     // Threshold
1043     typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1044     thresholder->SetUpperThreshold( 0.0 );
1045     thresholder->SetOutsideValue( 0 );
1046     thresholder->SetInsideValue( 1 );
1047     thresholder->SetInput( levelSetFilter->GetOutput() );
1048     if (m_Verbose) std::cout<<"Thresholding the output level set..."<<std::endl;
1049     thresholder->Update();
1050     grownEllips=thresholder->GetOutput();
1051   }
1052
1053   //---------------------------------
1054   // Write the grown ellips
1055   //---------------------------------
1056   if (m_ArgsInfo.writeGrownEllips_given) {
1057     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1058     caster->SetInput(grownEllips);
1059     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeGrownEllips_arg, m_Verbose);
1060   }
1061
1062
1063   //----------------------------------------------------------------------------------------------------
1064   // Grow inside ribs
1065   //----------------------------------------------------------------------------------------------------
1066   typename InternalImageType::Pointer filledRibs;
1067   if (m_ArgsInfo.filledRibs_given) {
1068     typename FeatureReaderType::Pointer featureReader = FeatureReaderType::New();
1069     featureReader->SetFileName(m_ArgsInfo.filledRibs_arg);
1070     if (m_Verbose) std::cout<<"Reading filled ribs mask..."<<std::endl;
1071     featureReader->Update();
1072     filledRibs=featureReader->GetOutput();
1073   } else {
1074     if(m_Verbose) {
1075       std::cout<<std::endl;
1076       std::cout<<"=========================================="<<std::endl;
1077       std::cout<<"||        Filling the ribs image         ||"<<std::endl;
1078       std::cout<<"=========================================="<<std::endl;
1079     }
1080     //---------------------------------
1081     // Make feature image air+bones
1082     //---------------------------------
1083     typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
1084     setBackgroundFilter->SetInput(air_low);
1085     setBackgroundFilter->SetInput2(bones_low);
1086     setBackgroundFilter->SetMaskValue(0);
1087     setBackgroundFilter->SetOutsideValue(0);
1088     setBackgroundFilter->Update();
1089     typename InternalImageType::Pointer bones_air_low =setBackgroundFilter->GetOutput();
1090
1091     //---------------------------------
1092     // Resampling previous solution
1093     //---------------------------------
1094     if (m_Verbose) std::cout<<"Resampling previous solution..."<<std::endl;
1095     typename ResampleImageFilterType::Pointer resampler =ResampleImageFilterType::New();
1096     typename InternalImageType::PointType origin;
1097     bones_low->TransformIndexToPhysicalPoint(bones_low->GetLargestPossibleRegion().GetIndex(), origin);
1098     resampler->SetOutputOrigin(origin);
1099     resampler->SetOutputSpacing(bones_low->GetSpacing());
1100     typename InternalImageType::SizeType size_low= bones_low->GetLargestPossibleRegion().GetSize();
1101     resampler->SetSize(size_low);
1102     typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
1103     resampler->SetInterpolator(interpolator);
1104     resampler->SetInput(grownEllips);
1105     resampler->Update();
1106     typename InternalImageType::Pointer grownEllips =resampler->GetOutput();
1107
1108
1109     //---------------------------------
1110     // Calculate Distance Map
1111     //---------------------------------
1112     typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
1113     distanceMapImageFilter->SetInput(grownEllips);
1114     distanceMapImageFilter->SetInsideIsPositive(false);
1115     if (m_Verbose) std::cout<<"Calculating distance map..."<<std::endl;
1116     distanceMapImageFilter->Update();
1117     if (m_ArgsInfo.writeDistMap_given) {
1118       writeImage<LevelSetImageType>(distanceMapImageFilter->GetOutput(), m_ArgsInfo.writeDistMap_arg, m_Verbose);
1119
1120     }
1121
1122     //---------------------------------
1123     // Grow while monitoring lung volume coverage
1124     //---------------------------------
1125     typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
1126     levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
1127     levelSetFilter->SetFeatureImage( bones_air_low );
1128     levelSetFilter->SetPropagationScaling( 1 );
1129     levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve2_arg );
1130     levelSetFilter->SetAdvectionScaling( 0 );
1131     levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS2_arg );
1132     levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter2_arg );
1133     levelSetFilter->SetUseImageSpacing(true);
1134
1135     //---------------------------------
1136     // Invert lung mask
1137     //---------------------------------
1138     typename InversionFilterType::Pointer invertor= InversionFilterType::New();
1139     invertor->SetInput(lungs_low);
1140     invertor->SetLowerThreshold(0);
1141     invertor->SetUpperThreshold(0);
1142     invertor->SetInsideValue(1);
1143     invertor->Update();
1144     typename InternalImageType::Pointer lungs_low_inv=invertor->GetOutput();
1145
1146     //---------------------------------
1147     // Calculate lung volume
1148     //---------------------------------
1149     typename LabelStatisticsImageFilterType::Pointer statisticsFilter= LabelStatisticsImageFilterType::New();
1150     statisticsFilter->SetInput(lungs_low_inv);
1151     statisticsFilter->SetLabelInput(lungs_low);
1152     statisticsFilter->Update();
1153     unsigned int volume=statisticsFilter->GetSum(0);
1154
1155     // Prepare threshold
1156     typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1157     thresholder->SetUpperThreshold(     0.0 );
1158     thresholder->SetOutsideValue(  0  );
1159     thresholder->SetInsideValue(  1 );
1160
1161
1162     // Start monitoring
1163     unsigned int totalNumberOfIterations=0;
1164     unsigned int coverage=0;
1165
1166
1167     //  //---------------------------------
1168     //  // Script for making movie
1169     //  //---------------------------------
1170     //          std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1171
1172     while (true) {
1173       levelSetFilter->Update();
1174       totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1175
1176       thresholder->SetInput( levelSetFilter->GetOutput() );
1177       thresholder->Update();
1178       statisticsFilter->SetInput(thresholder->GetOutput());
1179       statisticsFilter->Update();
1180       coverage=statisticsFilter->GetSum(0);
1181
1182       // Compare the volumes
1183       if ( coverage >= m_ArgsInfo.fillingLevel_arg * volume/100 ) {
1184         if (m_Verbose) std::cout<<"Lungs filled for "<< m_ArgsInfo.fillingLevel_arg<<"% !"<<std::endl;
1185         break;
1186       } else {
1187         if (m_Verbose) std::cout<<"After "<<totalNumberOfIterations<<" iterations, lungs are covered for "
1188                                   <<(double)coverage/volume*100.0<<"%..."<<std::endl;
1189         levelSetFilter->SetInput(levelSetFilter->GetOutput());
1190         if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg, m_Verbose);
1191
1192         //              // script
1193         //              std::ostringstream number_str;
1194         //              number_str << number;
1195         //              std::string param =  number_str.str();
1196         //              system((script+param).c_str());
1197         //              number+=1;
1198
1199       }
1200       if ( (totalNumberOfIterations> 30000) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS2_arg) ) break;
1201     }
1202
1203     // Output values
1204     if (m_Verbose) std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1205     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1206     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1207
1208     // Threshold
1209     thresholder->SetInput( levelSetFilter->GetOutput() );
1210     thresholder->Update();
1211     filledRibs=thresholder->GetOutput();
1212     // writeImage<InternalImageType>(filledRibs,"/home/jef/tmp/filled_ribs_before.mhd", m_Verbose);
1213
1214   }
1215
1216   //---------------------------------
1217   // Write the filled ribs
1218   //---------------------------------
1219   if (m_ArgsInfo.writeFilledRibs_given) {
1220     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1221     caster->SetInput(filledRibs);
1222     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeFilledRibs_arg, m_Verbose);
1223   }
1224
1225
1226   //----------------------------------------------------------------------------------------------------
1227   // Collapse to the lungs
1228   //----------------------------------------------------------------------------------------------------
1229   if(m_Verbose) {
1230     std::cout<<std::endl;
1231     std::cout<<"=========================================="<<std::endl;
1232     std::cout<<"||     Collapsing to the lung image     ||"<<std::endl;
1233     std::cout<<"=========================================="<<std::endl;
1234   }
1235
1236   //---------------------------------
1237   // Make feature image air+bones
1238   //---------------------------------
1239   if (m_Verbose) std::cout<<"Making feature images..."<<std::endl;
1240   typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
1241   setBackgroundFilter->SetInput(air);
1242   setBackgroundFilter->SetInput2(bones);
1243   setBackgroundFilter->SetMaskValue(0);
1244   setBackgroundFilter->SetOutsideValue(0);
1245   setBackgroundFilter->Update();
1246   typename InternalImageType::Pointer bones_air =setBackgroundFilter->GetOutput();
1247
1248   typename SetBackgroundFilterType::Pointer setBackgroundFilter2 = SetBackgroundFilterType::New();
1249   setBackgroundFilter2->SetInput(bones_air);
1250   setBackgroundFilter2->SetInput2(lungs);
1251   setBackgroundFilter2->SetMaskValue(0);
1252   setBackgroundFilter2->SetOutsideValue(0);
1253   setBackgroundFilter2->Update();
1254   typename InternalImageType::Pointer lungs_bones_air =setBackgroundFilter2->GetOutput();
1255
1256   //---------------------------------
1257   // Prepare previous solution
1258   //---------------------------------
1259   if (m_Verbose) std::cout<<"Resampling previous solution..."<<std::endl;
1260   typename ResampleImageFilterType::Pointer resampler =ResampleImageFilterType::New();
1261   typedef itk::NearestNeighborInterpolateImageFunction<InternalImageType, double> InterpolatorType;
1262   typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
1263   resampler->SetOutputStartIndex(bones->GetLargestPossibleRegion().GetIndex());
1264   resampler->SetInput(filledRibs);
1265   resampler->SetInterpolator(interpolator);
1266   resampler->SetOutputParametersFromImage(bones);
1267   resampler->Update();
1268   filledRibs =resampler->GetOutput();
1269
1270   if (m_Verbose) std::cout<<"Setting lungs to 1..."<<std::endl;
1271   typename SetBackgroundFilterType::Pointer setBackgroundFilter3 = SetBackgroundFilterType::New();
1272   setBackgroundFilter3->SetInput(filledRibs);
1273   setBackgroundFilter3->SetInput2(lungs);
1274   setBackgroundFilter3->SetMaskValue(0);
1275   setBackgroundFilter3->SetOutsideValue(1);
1276   setBackgroundFilter3->Update();
1277   filledRibs=setBackgroundFilter3->GetOutput();
1278
1279   if (m_Verbose) std::cout<<"Removing overlap with bones..."<<std::endl;
1280   typename SetBackgroundFilterType::Pointer setBackgroundFilter4 = SetBackgroundFilterType::New();
1281   setBackgroundFilter4->SetInput(filledRibs);
1282   setBackgroundFilter4->SetInput2(bones);
1283   setBackgroundFilter4->SetMaskValue(0);
1284   setBackgroundFilter4->SetOutsideValue(0);
1285   setBackgroundFilter4->Update();
1286   filledRibs =setBackgroundFilter4->GetOutput();
1287   //   writeImage<InternalImageType>(filledRibs,"/home/jef/tmp/filledRibs_pp.mhd");
1288   //---------------------------------
1289   // Calculate Distance Map
1290   //---------------------------------
1291   //  typedef  itk::ApproximateSignedDistanceMapImageFilter <InternalImageType, LevelSetImageType> DistanceMapImageFilterType2;
1292   typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
1293   distanceMapImageFilter->SetInput(filledRibs);
1294   distanceMapImageFilter->SetInsideIsPositive(false);
1295   // distanceMapImageFilter->SetInsideValue(0);
1296 //     distanceMapImageFilter->SetOutsideValue(1);
1297   if (m_Verbose) std::cout<<"Calculating distance map..."<<std::endl;
1298   distanceMapImageFilter->Update();
1299
1300   //---------------------------------
1301   // Collapse
1302   //---------------------------------
1303   typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
1304   levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
1305   levelSetFilter->SetFeatureImage( lungs_bones_air );
1306   levelSetFilter->SetPropagationScaling(m_ArgsInfo.prop3_arg);
1307   levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve3_arg );
1308   levelSetFilter->SetAdvectionScaling( 0 );
1309   levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS3_arg );
1310   levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter3_arg );
1311   levelSetFilter->SetUseImageSpacing(true);
1312
1313   //     //script
1314   //     std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1315
1316   // Start monitoring
1317   if (m_Verbose) std::cout<<"Starting the levelset..."<<std::endl;
1318   unsigned int totalNumberOfIterations=0;
1319   while (true) {
1320     levelSetFilter->Update();
1321
1322     // monitor state
1323     totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1324     levelSetFilter->SetInput(levelSetFilter->GetOutput());
1325     if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg);
1326     std::cout << "After "<<totalNumberOfIterations<<" iteration the RMS change is " << levelSetFilter->GetRMSChange() <<"..."<< std::endl;
1327
1328     //  // script
1329     //  std::ostringstream number_str;
1330     //  number_str << number;
1331     //  std::string param =  number_str.str();
1332     //  system((script+param).c_str());
1333     //  number+=1;
1334
1335     // stopping condition
1336     if ( (totalNumberOfIterations>= (unsigned int) m_ArgsInfo.maxIter3_arg) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS3_arg) ) break;
1337     levelSetFilter->SetNumberOfIterations( std::min ((unsigned int) m_ArgsInfo.iter3_arg, (unsigned int) m_ArgsInfo.maxIter3_arg-totalNumberOfIterations ) );
1338   }
1339
1340   // Output values
1341   if (m_Verbose) {
1342     std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1343     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1344     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1345   }
1346
1347   // Threshold
1348   typedef itk::BinaryThresholdImageFilter< LevelSetImageType,InternalImageType>    LevelSetBinarizeFilterType;
1349   typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1350   thresholder->SetUpperThreshold( 0.0 );
1351   thresholder->SetOutsideValue( 0 );
1352   thresholder->SetInsideValue( 1 );
1353   thresholder->SetInput( levelSetFilter->GetOutput() );
1354   thresholder->Update();
1355   typename InternalImageType::Pointer output = thresholder->GetOutput();
1356
1357
1358   //----------------------------------------------------------------------------------------------------
1359   // Prepare the output
1360   //----------------------------------------------------------------------------------------------------
1361
1362   //---------------------------------
1363   // Set Air to zero
1364   //---------------------------------
1365   if (m_Verbose) std::cout<<"Removing overlap mask with air..."<<std::endl;
1366   typename SetBackgroundFilterType::Pointer setBackgroundFilter5 = SetBackgroundFilterType::New();
1367   setBackgroundFilter5->SetInput(output);
1368   setBackgroundFilter5->SetInput2(air);
1369   setBackgroundFilter5->SetMaskValue(0);
1370   setBackgroundFilter5->SetOutsideValue(0);
1371   setBackgroundFilter5->Update();
1372   output=setBackgroundFilter5->GetOutput();
1373
1374   //---------------------------------
1375   // Open & close  to cleanup
1376   //---------------------------------
1377   if ( m_ArgsInfo.openClose_flag) {
1378
1379     //---------------------------------
1380     // Structuring element
1381     //---------------------------------
1382     typedef itk::BinaryBallStructuringElement<InternalPixelType,Dimension > KernelType;
1383     KernelType structuringElement;
1384     structuringElement.SetRadius(1);
1385     structuringElement.CreateStructuringElement();
1386
1387     //---------------------------------
1388     // Open
1389     //---------------------------------
1390     typedef itk::BinaryMorphologicalOpeningImageFilter<InternalImageType, InternalImageType , KernelType> OpenFilterType;
1391     typename OpenFilterType::Pointer openFilter = OpenFilterType::New();
1392     openFilter->SetInput(output);
1393     openFilter->SetBackgroundValue(0);
1394     openFilter->SetForegroundValue(1);
1395     openFilter->SetKernel(structuringElement);
1396     if(m_Verbose) std::cout<<"Opening the output image..."<<std::endl;
1397
1398     //---------------------------------
1399     // Close
1400     //---------------------------------
1401     typedef itk::BinaryMorphologicalClosingImageFilter<InternalImageType, InternalImageType , KernelType> CloseFilterType;
1402     typename CloseFilterType::Pointer closeFilter = CloseFilterType::New();
1403     closeFilter->SetInput(openFilter->GetOutput());
1404     closeFilter->SetSafeBorder(true);
1405     closeFilter->SetForegroundValue(1);
1406     closeFilter->SetKernel(structuringElement);
1407     if(m_Verbose) std::cout<<"Closing the output image..."<<std::endl;
1408     closeFilter->Update();
1409     output=closeFilter->GetOutput();
1410
1411   }
1412   //writeImage<InternalImageType>(output,"/home/jef/tmp/mm_double.mhd");
1413
1414   // Extract the upper part
1415   typedef  itk::CropImageFilter<InternalImageType, InternalImageType> CropImageFilterType;
1416   typename CropImageFilterType::Pointer cropFilter=CropImageFilterType::New();
1417   cropFilter->SetInput(output);
1418   typename InputImageType::SizeType lSize, uSize;
1419   uSize.Fill(0);
1420   lSize.Fill(0);
1421   lSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
1422   cropFilter->SetLowerBoundaryCropSize(lSize);
1423   cropFilter->SetUpperBoundaryCropSize(uSize);
1424   cropFilter->Update();
1425
1426   // Output
1427   typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1428   caster->SetInput(cropFilter->GetOutput());
1429   writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.output_arg, m_Verbose);
1430
1431 }
1432
1433 }//end clitk
1434
1435 #endif //#define clitkMotionMaskGenericFilter_txx