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       typename InternalImageType::RegionType region, region_before = lungs_low->GetLargestPossibleRegion();
 524       typename InternalImageType::SizeType size = region_before.GetSize();
 525       size[2] /= 2;
 526       region.SetSize(size);
 527       lungs_low->SetRegions(region);
 528
 529       // compute statistics of the (mirroed) lung region in order to guess the params of the ellipse
 530       typedef itk::LabelImageToShapeLabelMapFilter<InternalImageType>  LabelImageToShapeLabelMapFilter;
 531       typename LabelImageToShapeLabelMapFilter::Pointer label_filter = LabelImageToShapeLabelMapFilter::New();
 532       label_filter->SetInput(lungs_low);
 533       label_filter->Update();
 534
 535       typename InternalImageType::SpacingType spacing = lungs_low->GetSpacing();
 536       typedef typename LabelImageToShapeLabelMapFilter::OutputImageType::LabelObjectType LabelType;
 537       const LabelType* label = dynamic_cast<LabelType*>(label_filter->GetOutput()->GetNthLabelObject(0));
 538
 539       // lungs' barycenter
 540       typename LabelType::CentroidType lung_centroid = label->GetCentroid();
 541
 542       // try to guess ideal ellipse axes from the lungs' bounding box and centroid
 543       // with some hard-coded "magic" constants...
 544       typename LabelType::RegionType lung_bbox = label->GetBoundingBox();
 545
 546       axes[0] = 0.95*lung_bbox.GetSize()[0]*spacing[0]/2;
 547       axes[1] = 0.3*lung_bbox.GetSize()[1]*spacing[1]/2;
 548       axes[2] = 1.25*fabs(lung_centroid[2] - center[2]);
 549
 550       // ellipse's center in XY is the center of the lungs' bounding box
 551       typename InternalImageType::PointType origin = lungs_low->GetOrigin();
 552       centerEllips[0] = origin[0] + (lung_bbox.GetIndex()[0] + lung_bbox.GetSize()[0]/2)*spacing[0];
 553       centerEllips[1] = origin[1] + (lung_bbox.GetIndex()[1] + lung_bbox.GetSize()[1]/2)*spacing[1];
 554       centerEllips[2] = center[2];
 555
 556       lungs_low->SetRegions(region_before);
 557
 558       if(m_Verbose) {
 559         std::cout << "Lungs'centroid at " << lung_centroid << std::endl;
 560         std::cout << "Ellipse center at " << centerEllips << std::endl;
 561         std::cout << "Ellipse axes as " << axes << std::endl;
 562         std::cout << "Lung's bounding box (index,size) " << lung_bbox.GetIndex() << lung_bbox.GetSize() << std::endl;
 563       }
 564     }
 565     else {
 566       //---------------------------------
 567       // Offset from center
 568       //---------------------------------
 569       typename itk::Vector<double,Dimension> offset;
 570       if(m_ArgsInfo.offset_given== Dimension) {
 571         for(unsigned int i=0; i<Dimension; i++)
 572           offset[i]=m_ArgsInfo.offset_arg[i];
 573       } else {
 574         offset.Fill(0.);
 575         offset[1]=-50;
 576       }
 577       centerEllips=center+offset;
 578       if (m_Verbose) {
 579         std::cout<<"Placing the center of the initial ellipsoide at (mm) "<<std::endl;
 580         std::cout<<centerEllips[0];
 581         for (unsigned int i=1; i<Dimension; i++)
 582           std::cout<<" "<<centerEllips[i];
 583         std::cout<<std::endl;
 584       }
 585
 586       // Axes
 587       if (m_ArgsInfo.axes_given==Dimension)
 588         for(unsigned int i=0; i<Dimension; i++)
 589           axes[i]=m_ArgsInfo.axes_arg[i];
 590       else {
 591         axes[0]=100;
 592         axes[1]=30;
 593         axes[2]=150;
 594       }
 595     }
 596
 597     //---------------------------------
 598     // The ellips
 599     //---------------------------------
 600     ellips=InternalImageType::New();
 601     ellips->SetRegions (bones_low->GetLargestPossibleRegion());
 602     ellips->SetOrigin(bones_low->GetOrigin());
 603     ellips->SetSpacing(bones_low->GetSpacing());
 604     ellips->Allocate();
 605     ellips->FillBuffer(0);
 606
 607     // Draw an ellips
 608     IteratorType itEllips(ellips, ellips->GetLargestPossibleRegion());
 609     itEllips.GoToBegin();
 610     typename InternalImageType::PointType point;
 611     typename InternalImageType::IndexType index;
 612     double distance;
 613
 614     if (m_Verbose) std::cout<<"Drawing the initial ellipsoide..."<<std::endl;
 615     while (!itEllips.IsAtEnd()) {
 616       index=itEllips.GetIndex();
 617       ellips->TransformIndexToPhysicalPoint(index, point);
 618       distance=0.0;
 619       for(unsigned int i=0; i<Dimension; i++)
 620         distance+=powf( ( (centerEllips[i]-point[i])/axes[i] ), 2);
 621
 622       if (distance<1)
 623         itEllips.Set(1);
 624       ++itEllips;
 625     }
 626   }
 627
 628
 629   //---------------------------------
 630   // Write the ellips
 631   //---------------------------------
 632   if (m_ArgsInfo.writeEllips_given) {
 633     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
 634     caster->SetInput(ellips);
 635     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeEllips_arg, m_Verbose);
 636   }
 637
 638   return ellips;
 639
 640 }
 641
 642
 643 //-------------------------------------------------------------------
 644 // Update with the number of dimensions and the pixeltype
 645 //-------------------------------------------------------------------
 646 template <unsigned int Dimension, class  PixelType>
 647 void
 648 MotionMaskGenericFilter::UpdateWithDimAndPixelType()
 649 {
 650
 651   // ImageTypes
 652   typedef int InternalPixelType;
 653   typedef itk::Image<PixelType, Dimension> InputImageType;
 654   typedef itk::Image< InternalPixelType, Dimension> InternalImageType; //labeling doesn't work with unsigned char?
 655   typedef itk::Image< float, Dimension> LevelSetImageType; //labeling doesn't work with unsigned char?
 656   typedef itk::Image<unsigned char, Dimension> OutputImageType;
 657
 658
 659   //----------------------------------------------------------------------------------------------------
 660   // Typedef for Processing
 661   //----------------------------------------------------------------------------------------------------
 662   typedef itk::ImageFileReader<InternalImageType> FeatureReaderType;
 663   typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> InputBinarizeFilterType;
 664   typedef itk::BinaryThresholdImageFilter< LevelSetImageType,InternalImageType>    LevelSetBinarizeFilterType;
 665   typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> InversionFilterType;
 666   typedef itk::ThresholdImageFilter<InternalImageType> ThresholdFilterType;
 667   typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
 668   typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
 669   typedef itk::MirrorPadImageFilter<InternalImageType, InternalImageType> MirrorPadImageFilterType;
 670   typedef itk::NearestNeighborInterpolateImageFunction<InternalImageType, double> InterpolatorType;
 671   typedef itk::ResampleImageFilter<InternalImageType, InternalImageType> ResampleImageFilterType;
 672   typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 673   typedef itk::GeodesicActiveContourLevelSetImageFilter<LevelSetImageType, InternalImageType> LevelSetImageFilterType;
 674   typedef itk::SignedDanielssonDistanceMapImageFilter<InternalImageType, LevelSetImageType> DistanceMapImageFilterType;
 675   typedef clitk::SetBackgroundImageFilter<InternalImageType,InternalImageType, InternalImageType> SetBackgroundFilterType;
 676   typedef itk::LabelStatisticsImageFilter<InternalImageType,InternalImageType> LabelStatisticsImageFilterType;
 677   typedef itk::CastImageFilter<InternalImageType,OutputImageType> CastImageFilterType;
 678
 679
 680   // Read the input
 681   typedef itk::ImageFileReader<InputImageType> InputReaderType;
 682   typename InputReaderType::Pointer reader = InputReaderType::New();
 683   reader->SetFileName( m_InputFileName);
 684   reader->Update();
 685   typename InputImageType::Pointer input= reader->GetOutput();
 686
 687   //     // globals for avi
 688   //     unsigned int number=0;
 689
 690
 691   if(m_Verbose) {
 692     std::cout<<std::endl;
 693     std::cout<<"=========================================="<<std::endl;
 694     std::cout<<"||         Making feature images        ||"<<std::endl;
 695     std::cout<<"=========================================="<<std::endl;
 696   }
 697
 698   //--------------------------------------------------------------------------------
 699   // Lungs
 700   //-------------------------------------------------------------------------------
 701   typename InternalImageType::Pointer lungs = this->GetLungsImage<Dimension, PixelType>(input);
 702
 703   //-------------------------------------------------------------------------------
 704   // Air
 705   //-------------------------------------------------------------------------------
 706   typename InternalImageType::Pointer air = this->GetAirImage<Dimension, PixelType>(input, lungs);
 707
 708   //-------------------------------------------------------------------------------
 709   // Bones
 710   //-------------------------------------------------------------------------------
 711   typename InternalImageType::Pointer bones = this->GetBonesImage<Dimension, PixelType>(input);
 712
 713   //----------------------------------------------------------------------------------------------------
 714   // Write feature images
 715   //----------------------------------------------------------------------------------------------------
 716   if(m_ArgsInfo.writeFeature_given) {
 717     typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
 718     setBackgroundFilter->SetInput(air);
 719     setBackgroundFilter->SetInput2(bones);
 720     setBackgroundFilter->SetMaskValue(0);
 721     setBackgroundFilter->SetOutsideValue(2);
 722     setBackgroundFilter->Update();
 723     typename InternalImageType::Pointer bones_air =setBackgroundFilter->GetOutput();
 724
 725     typename SetBackgroundFilterType::Pointer setBackgroundFilter2 = SetBackgroundFilterType::New();
 726     setBackgroundFilter2->SetInput(bones_air);
 727     setBackgroundFilter2->SetInput2(lungs);
 728     setBackgroundFilter2->SetMaskValue(0);
 729     setBackgroundFilter2->SetOutsideValue(3);
 730     setBackgroundFilter2->Update();
 731     typename InternalImageType::Pointer lungs_bones_air =setBackgroundFilter2->GetOutput();
 732
 733     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
 734     caster->SetInput(lungs_bones_air);
 735     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeFeature_arg, m_Verbose);
 736   }
 737
 738   //----------------------------------------------------------------------------------------------------
 739   // Low dimensional versions
 740   //----------------------------------------------------------------------------------------------------
 741   typename InternalImageType::Pointer bones_low =Resample<Dimension , PixelType>(bones);
 742   typename InternalImageType::Pointer lungs_low =Resample<Dimension , PixelType>(lungs);
 743   typename InternalImageType::Pointer air_low =Resample<Dimension , PixelType>(air);
 744
 745   //---------------------------------
 746   // Pad
 747   //---------------------------------
 748   if(m_ArgsInfo.pad_flag) {
 749     typedef itk::ImageRegionIteratorWithIndex<InternalImageType> IteratorType;
 750     IteratorType it(air_low, air_low->GetLargestPossibleRegion());
 751     typename InternalImageType::IndexType index;
 752     while(!it.IsAtEnd()) {
 753       index=it.GetIndex();
 754       for (unsigned int i=0; i<Dimension; i++)
 755         if(index[i]==air_low->GetLargestPossibleRegion().GetIndex()[i]
 756             || index[i]==(unsigned int)air_low->GetLargestPossibleRegion().GetIndex()[i]+ (unsigned int) air_low->GetLargestPossibleRegion().GetSize()[i]-1)
 757           it.Set(0);
 758       ++it;
 759     }
 760   }
 761
 762   //---------------------------------
 763   // Center
 764   //---------------------------------
 765   typename itk::Vector<double,Dimension> center;
 766   typedef itk::ImageMomentsCalculator<InternalImageType> MomentsCalculatorType;
 767   typename    MomentsCalculatorType::Pointer momentsCalculator=MomentsCalculatorType::New();
 768   momentsCalculator->SetImage(air);
 769   momentsCalculator->Compute();
 770   center=momentsCalculator->GetCenterOfGravity();
 771   if (m_Verbose) {
 772     std::cout<<"The center of gravity of the patient body is located at (mm) "<<std::endl;
 773     std::cout<<center[0];
 774     for (unsigned int i=1; i<Dimension; i++)
 775       std::cout<<" "<<center[i];
 776     std::cout<<std::endl;
 777   }
 778
 779   //----------------------------------------------------------------------------------------------------
 780   // Ellipsoide initialization
 781   //----------------------------------------------------------------------------------------------------
 782   typename InternalImageType::Pointer m_Ellips= InitializeEllips<Dimension, PixelType>(center,bones_low,lungs_low);
 783
 784   //----------------------------------------------------------------------------------------------------
 785   // Grow ellips
 786   //----------------------------------------------------------------------------------------------------
 787   typename InternalImageType::Pointer grownEllips;
 788   if (m_ArgsInfo.grownEllips_given || m_ArgsInfo.filledRibs_given) {
 789     if (m_ArgsInfo.grownEllips_given) {
 790
 791       typename FeatureReaderType::Pointer featureReader = FeatureReaderType::New();
 792       featureReader->SetFileName(m_ArgsInfo.grownEllips_arg);
 793       featureReader->Update();
 794       grownEllips=featureReader->GetOutput();
 795     }
 796   } else {
 797
 798     if(m_Verbose) {
 799       std::cout<<std::endl;
 800       std::cout<<"=========================================="<<std::endl;
 801       std::cout<<"||          Growing ellipsoide           ||"<<std::endl;
 802       std::cout<<"=========================================="<<std::endl;
 803     }
 804
 805     //---------------------------------
 806     // Detect abdomen
 807     //---------------------------------
 808     typename InternalImageType::PointType dPoint;
 809     if (m_ArgsInfo.detectionPoint_given) {
 810       for (unsigned int i=0; i<Dimension; i++)
 811         dPoint[i]=m_ArgsInfo.detectionPoint_arg[i];
 812     } else {
 813       typename InternalImageType::RegionType searchRegion=air->GetLargestPossibleRegion();
 814       typename InternalImageType::SizeType searchRegionSize = searchRegion.GetSize();
 815       typename InternalImageType::IndexType searchRegionIndex = searchRegion.GetIndex();
 816       searchRegionIndex[2]+=searchRegionSize[2]/2;
 817       searchRegionSize[2]=1;
 818       searchRegion.SetSize(searchRegionSize);
 819       searchRegion.SetIndex(searchRegionIndex);
 820       IteratorType itAbdomen(air, searchRegion);
 821       itAbdomen.GoToBegin();
 822
 823       typename InternalImageType::PointType aPoint;
 824       typename InternalImageType::IndexType aIndex;
 825
 826       if (m_Verbose) std::cout<<"Detecting the abdomen..."<<std::endl;
 827       while (!itAbdomen.IsAtEnd()) {
 828         if(itAbdomen.Get()) break;
 829         ++itAbdomen;
 830       }
 831       aIndex=itAbdomen.GetIndex();
 832       air->TransformIndexToPhysicalPoint(aIndex,aPoint);
 833       if (m_Verbose) std::cout<<"Detected the abdomen at "<<aPoint<<".."<<std::endl;
 834
 835
 836       //---------------------------------
 837       // Detect abdomen in additional images?
 838       //---------------------------------
 839       if (m_ArgsInfo.detectionPairs_given) {
 840         for (unsigned int i=0; i<m_ArgsInfo.detectionPairs_given; i++) {
 841           typename InternalImageType::Pointer airAdd;
 842           //---------------------------------
 843           // Read the input
 844           //--------------------------------
 845           typedef itk::ImageFileReader<InputImageType> InputReaderType;
 846           typename InputReaderType::Pointer reader = InputReaderType::New();
 847           reader->SetFileName( m_ArgsInfo.detectionPairs_arg[i]);
 848           reader->Update();
 849           typename InputImageType::Pointer additional= reader->GetOutput();
 850           if (m_Verbose) std::cout<<"Extracting the air from additional image "<< i<<"..."<<std::endl;
 851
 852           //---------------------------------
 853           // Binarize the image
 854           //---------------------------------
 855           typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
 856           binarizeFilter->SetInput(additional);
 857           binarizeFilter->SetLowerThreshold(static_cast<PixelType>(m_ArgsInfo.lowerThresholdAir_arg));
 858           binarizeFilter->SetUpperThreshold(static_cast<PixelType>(m_ArgsInfo.upperThresholdAir_arg));
 859           if (m_Verbose) std::cout<<"Binarizing the image using thresholds "<<m_ArgsInfo.lowerThresholdAir_arg
 860                                     <<", "<<m_ArgsInfo.upperThresholdAir_arg<<"..."<<std::endl;
 861
 862           //---------------------------------
 863           // Label the connected components
 864           //---------------------------------
 865           typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
 866           connectFilter->SetInput(binarizeFilter->GetOutput());
 867           connectFilter->SetBackgroundValue(0);
 868           connectFilter->SetFullyConnected(false);
 869           if (m_Verbose) std::cout<<"Labeling the connected components..."<<std::endl;
 870
 871           //---------------------------------
 872           // Sort the labels according to size
 873           //---------------------------------
 874           typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
 875           relabelFilter->SetInput(connectFilter->GetOutput());
 876           if (m_Verbose) std::cout<<"Sorting the labels..."<<std::endl;
 877
 878           //---------------------------------
 879           // Keep the label
 880           //---------------------------------
 881           typename ThresholdFilterType::Pointer thresholdFilter=ThresholdFilterType::New();
 882           thresholdFilter->SetInput(relabelFilter->GetOutput());
 883           thresholdFilter->SetUpper(1);
 884           if (m_Verbose) std::cout<<"Keeping the first label..."<<std::endl;
 885           thresholdFilter->Update();
 886           airAdd=thresholdFilter->GetOutput();
 887
 888
 889           //---------------------------------
 890           // Invert
 891           //---------------------------------
 892           typename InversionFilterType::Pointer inversionFilter=InversionFilterType::New();
 893           inversionFilter->SetInput(airAdd);
 894           inversionFilter->SetLowerThreshold(0);
 895           inversionFilter->SetUpperThreshold(0);
 896           inversionFilter->SetInsideValue(1);
 897           inversionFilter->Update();
 898
 899           //---------------------------------
 900           // Mirror
 901           //---------------------------------
 902           typename MirrorPadImageFilterType::Pointer mirrorPadImageFilter=MirrorPadImageFilterType::New();
 903           mirrorPadImageFilter->SetInput(inversionFilter->GetOutput());
 904           typename InternalImageType::SizeType padSize;
 905           padSize.Fill(0);
 906           padSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
 907           mirrorPadImageFilter->SetPadLowerBound(padSize);
 908           if (m_Verbose) std::cout<<"Mirroring the entire image along the CC axis..."<<std::endl;
 909           mirrorPadImageFilter->Update();
 910           airAdd=mirrorPadImageFilter->GetOutput();
 911
 912           //---------------------------------
 913           // Detect abdomen
 914           //---------------------------------
 915           typename InternalImageType::RegionType searchRegion=airAdd->GetLargestPossibleRegion();
 916           typename InternalImageType::SizeType searchRegionSize = searchRegion.GetSize();
 917           typename InternalImageType::IndexType searchRegionIndex = searchRegion.GetIndex();
 918           searchRegionIndex[2]+=searchRegionSize[2]/2;
 919           searchRegionSize[2]=1;
 920           searchRegion.SetSize(searchRegionSize);
 921           searchRegion.SetIndex(searchRegionIndex);
 922           IteratorType itAbdomen(airAdd, searchRegion);
 923           itAbdomen.GoToBegin();
 924
 925           typename InternalImageType::PointType additionalPoint;
 926           typename InternalImageType::IndexType aIndex;
 927
 928           if (m_Verbose) std::cout<<"Detecting the abdomen..."<<std::endl;
 929           while (!itAbdomen.IsAtEnd()) {
 930             if(itAbdomen.Get()) break;
 931             ++itAbdomen;
 932           }
 933           aIndex=itAbdomen.GetIndex();
 934           airAdd->TransformIndexToPhysicalPoint(aIndex,additionalPoint);
 935           if (m_Verbose) std::cout<<"Detected the abdomen in the additional image at "<<additionalPoint<<".."<<std::endl;
 936
 937           if(additionalPoint[1]< aPoint[1]) {
 938             aPoint=additionalPoint;
 939             if (m_Verbose) std::cout<<"Modifying the detected abdomen to "<<aPoint<<".."<<std::endl;
 940
 941           }
 942         }
 943       }
 944
 945
 946       // Determine the detection point
 947       dPoint.Fill(0.0);
 948       dPoint+=center;
 949       dPoint[1]=aPoint[1];
 950       if(m_ArgsInfo.offsetDetect_given==Dimension)
 951         for(unsigned int i=0; i <Dimension; i++)
 952           dPoint[i]+=m_ArgsInfo.offsetDetect_arg[i];
 953       else
 954         dPoint[1]+=-10;
 955
 956     }
 957     if (m_Verbose) std::cout<<"Setting the detection point to "<<dPoint<<".."<<std::endl;
 958
 959
 960     //---------------------------------
 961     // Pad the rib image and ellips image
 962     //---------------------------------
 963     typename InternalImageType::Pointer padded_ellips;
 964     typename InternalImageType::Pointer padded_bones_low;
 965
 966     // If detection point not inside the image: pad
 967     typename InternalImageType::IndexType dIndex;
 968     if (!bones_low->TransformPhysicalPointToIndex(dPoint, dIndex)) {
 969       typename InternalImageType::SizeType padSize;
 970       padSize.Fill(0);
 971       padSize[1]=abs(dIndex[1])+1;
 972       if (m_Verbose) std::cout<<"Padding the images with padding size "<<padSize<<" to include the detection point..."<<std::endl;
 973
 974       typename MirrorPadImageFilterType::Pointer padBonesFilter=MirrorPadImageFilterType::New();
 975       padBonesFilter->SetInput(bones_low);
 976       padBonesFilter->SetPadLowerBound(padSize);
 977       padBonesFilter->Update();
 978       padded_bones_low=padBonesFilter->GetOutput();
 979
 980       typename MirrorPadImageFilterType::Pointer padEllipsFilter=MirrorPadImageFilterType::New();
 981       padEllipsFilter->SetInput(m_Ellips);
 982       padEllipsFilter->SetPadLowerBound(padSize);
 983       padEllipsFilter->Update();
 984       padded_ellips=padEllipsFilter->GetOutput();
 985     }
 986
 987     else {
 988       padded_bones_low=bones_low;
 989       padded_ellips=m_Ellips;
 990     }
 991
 992
 993     //---------------------------------
 994     // Calculate distance map
 995     //---------------------------------
 996     typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
 997     distanceMapImageFilter->SetInput(padded_ellips);
 998     distanceMapImageFilter->SetInsideIsPositive(false);
 999     if (m_Verbose) std::cout<<"Calculating the distance map..."<<std::endl;
1000     distanceMapImageFilter->Update();
1001     if (m_ArgsInfo.writeDistMap_given) {
1002       writeImage<LevelSetImageType>(distanceMapImageFilter->GetOutput(), m_ArgsInfo.writeDistMap_arg, m_Verbose);
1003
1004     }
1005
1006     //---------------------------------
1007     // Grow while monitoring detection point
1008     //---------------------------------
1009     typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
1010     levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
1011     levelSetFilter->SetFeatureImage( padded_bones_low );
1012     levelSetFilter->SetPropagationScaling( 1 );
1013     levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve1_arg );
1014     levelSetFilter->SetAdvectionScaling( 0 );
1015     levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS1_arg );
1016     levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter1_arg );
1017     levelSetFilter->SetUseImageSpacing(true);
1018
1019     //  //---------------------------------
1020     //  // Script for making movie
1021     //  //---------------------------------
1022     //          std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1023
1024
1025     if (m_Verbose) std::cout<<"Starting level set segmentation..."<<std::endl;
1026     unsigned int totalNumberOfIterations=0;
1027     while (true) {
1028       levelSetFilter->Update();
1029       totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1030
1031       if ( levelSetFilter->GetOutput()->GetPixel(dIndex) < 0 ) {
1032         if (m_Verbose) std::cout<<"Detection point reached!"<<std::endl;
1033         break;
1034       } else {
1035         if (m_Verbose) std::cout<<"Detection point not reached after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1036         levelSetFilter->SetInput(levelSetFilter->GetOutput());
1037         if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg, m_Verbose);
1038
1039         //              // script
1040         //              std::ostringstream number_str;
1041         //              number_str << number;
1042         //              std::string param =  number_str.str();
1043         //              system((script+param).c_str());
1044         //              number+=1;
1045
1046       }
1047       if ( (totalNumberOfIterations> 10000) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS1_arg) ) break;
1048     }
1049
1050     // Output values
1051     if (m_Verbose) std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1052     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1053     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1054
1055     // Threshold
1056     typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1057     thresholder->SetUpperThreshold( 0.0 );
1058     thresholder->SetOutsideValue( 0 );
1059     thresholder->SetInsideValue( 1 );
1060     thresholder->SetInput( levelSetFilter->GetOutput() );
1061     if (m_Verbose) std::cout<<"Thresholding the output level set..."<<std::endl;
1062     thresholder->Update();
1063     grownEllips=thresholder->GetOutput();
1064   }
1065
1066   //---------------------------------
1067   // Write the grown ellips
1068   //---------------------------------
1069   if (m_ArgsInfo.writeGrownEllips_given) {
1070     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1071     caster->SetInput(grownEllips);
1072     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeGrownEllips_arg, m_Verbose);
1073   }
1074
1075
1076   //----------------------------------------------------------------------------------------------------
1077   // Grow inside ribs
1078   //----------------------------------------------------------------------------------------------------
1079   typename InternalImageType::Pointer filledRibs;
1080   if (m_ArgsInfo.filledRibs_given) {
1081     typename FeatureReaderType::Pointer featureReader = FeatureReaderType::New();
1082     featureReader->SetFileName(m_ArgsInfo.filledRibs_arg);
1083     if (m_Verbose) std::cout<<"Reading filled ribs mask..."<<std::endl;
1084     featureReader->Update();
1085     filledRibs=featureReader->GetOutput();
1086   } else {
1087     if(m_Verbose) {
1088       std::cout<<std::endl;
1089       std::cout<<"=========================================="<<std::endl;
1090       std::cout<<"||        Filling the ribs image         ||"<<std::endl;
1091       std::cout<<"=========================================="<<std::endl;
1092     }
1093     //---------------------------------
1094     // Make feature image air+bones
1095     //---------------------------------
1096     typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
1097     setBackgroundFilter->SetInput(air_low);
1098     setBackgroundFilter->SetInput2(bones_low);
1099     setBackgroundFilter->SetMaskValue(0);
1100     setBackgroundFilter->SetOutsideValue(0);
1101     setBackgroundFilter->Update();
1102     typename InternalImageType::Pointer bones_air_low =setBackgroundFilter->GetOutput();
1103
1104     //---------------------------------
1105     // Resampling previous solution
1106     //---------------------------------
1107     if (m_Verbose) std::cout<<"Resampling previous solution..."<<std::endl;
1108     typename ResampleImageFilterType::Pointer resampler =ResampleImageFilterType::New();
1109     typename InternalImageType::PointType origin;
1110     bones_low->TransformIndexToPhysicalPoint(bones_low->GetLargestPossibleRegion().GetIndex(), origin);
1111     resampler->SetOutputOrigin(origin);
1112     resampler->SetOutputSpacing(bones_low->GetSpacing());
1113     typename InternalImageType::SizeType size_low= bones_low->GetLargestPossibleRegion().GetSize();
1114     resampler->SetSize(size_low);
1115     typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
1116     resampler->SetInterpolator(interpolator);
1117     resampler->SetInput(grownEllips);
1118     resampler->Update();
1119     typename InternalImageType::Pointer grownEllips =resampler->GetOutput();
1120
1121
1122     //---------------------------------
1123     // Calculate Distance Map
1124     //---------------------------------
1125     typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
1126     distanceMapImageFilter->SetInput(grownEllips);
1127     distanceMapImageFilter->SetInsideIsPositive(false);
1128     if (m_Verbose) std::cout<<"Calculating distance map..."<<std::endl;
1129     distanceMapImageFilter->Update();
1130     if (m_ArgsInfo.writeDistMap_given) {
1131       writeImage<LevelSetImageType>(distanceMapImageFilter->GetOutput(), m_ArgsInfo.writeDistMap_arg, m_Verbose);
1132
1133     }
1134
1135     //---------------------------------
1136     // Grow while monitoring lung volume coverage
1137     //---------------------------------
1138     typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
1139     levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
1140     levelSetFilter->SetFeatureImage( bones_air_low );
1141     levelSetFilter->SetPropagationScaling( 1 );
1142     levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve2_arg );
1143     levelSetFilter->SetAdvectionScaling( 0 );
1144     levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS2_arg );
1145     levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter2_arg );
1146     levelSetFilter->SetUseImageSpacing(true);
1147
1148     //---------------------------------
1149     // Invert lung mask
1150     //---------------------------------
1151     typename InversionFilterType::Pointer invertor= InversionFilterType::New();
1152     invertor->SetInput(lungs_low);
1153     invertor->SetLowerThreshold(0);
1154     invertor->SetUpperThreshold(0);
1155     invertor->SetInsideValue(1);
1156     invertor->Update();
1157     typename InternalImageType::Pointer lungs_low_inv=invertor->GetOutput();
1158
1159     //---------------------------------
1160     // Calculate lung volume
1161     //---------------------------------
1162     typename LabelStatisticsImageFilterType::Pointer statisticsFilter= LabelStatisticsImageFilterType::New();
1163     statisticsFilter->SetInput(lungs_low_inv);
1164     statisticsFilter->SetLabelInput(lungs_low);
1165     statisticsFilter->Update();
1166     unsigned int volume=statisticsFilter->GetSum(0);
1167
1168     // Prepare threshold
1169     typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1170     thresholder->SetUpperThreshold(     0.0 );
1171     thresholder->SetOutsideValue(  0  );
1172     thresholder->SetInsideValue(  1 );
1173
1174
1175     // Start monitoring
1176     unsigned int totalNumberOfIterations=0;
1177     unsigned int coverage=0;
1178
1179
1180     //  //---------------------------------
1181     //  // Script for making movie
1182     //  //---------------------------------
1183     //          std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1184
1185     while (true) {
1186       levelSetFilter->Update();
1187       totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1188
1189       thresholder->SetInput( levelSetFilter->GetOutput() );
1190       thresholder->Update();
1191       statisticsFilter->SetInput(thresholder->GetOutput());
1192       statisticsFilter->Update();
1193       coverage=statisticsFilter->GetSum(0);
1194
1195       // Compare the volumes
1196       if ( coverage >= m_ArgsInfo.fillingLevel_arg * volume/100 ) {
1197         if (m_Verbose) std::cout<<"Lungs filled for "<< m_ArgsInfo.fillingLevel_arg<<"% !"<<std::endl;
1198         break;
1199       } else {
1200         if (m_Verbose) std::cout<<"After "<<totalNumberOfIterations<<" iterations, lungs are covered for "
1201                                   <<(double)coverage/volume*100.0<<"%..."<<std::endl;
1202         levelSetFilter->SetInput(levelSetFilter->GetOutput());
1203         if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg, m_Verbose);
1204
1205         //              // script
1206         //              std::ostringstream number_str;
1207         //              number_str << number;
1208         //              std::string param =  number_str.str();
1209         //              system((script+param).c_str());
1210         //              number+=1;
1211
1212       }
1213       if ( (totalNumberOfIterations> 30000) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS2_arg) ) break;
1214     }
1215
1216     // Output values
1217     if (m_Verbose) std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1218     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1219     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1220
1221     // Threshold
1222     thresholder->SetInput( levelSetFilter->GetOutput() );
1223     thresholder->Update();
1224     filledRibs=thresholder->GetOutput();
1225     // writeImage<InternalImageType>(filledRibs,"/home/jef/tmp/filled_ribs_before.mhd", m_Verbose);
1226
1227   }
1228
1229   //---------------------------------
1230   // Write the filled ribs
1231   //---------------------------------
1232   if (m_ArgsInfo.writeFilledRibs_given) {
1233     typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1234     caster->SetInput(filledRibs);
1235     writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.writeFilledRibs_arg, m_Verbose);
1236   }
1237
1238
1239   //----------------------------------------------------------------------------------------------------
1240   // Collapse to the lungs
1241   //----------------------------------------------------------------------------------------------------
1242   if(m_Verbose) {
1243     std::cout<<std::endl;
1244     std::cout<<"=========================================="<<std::endl;
1245     std::cout<<"||     Collapsing to the lung image     ||"<<std::endl;
1246     std::cout<<"=========================================="<<std::endl;
1247   }
1248
1249   //---------------------------------
1250   // Make feature image air+bones
1251   //---------------------------------
1252   if (m_Verbose) std::cout<<"Making feature images..."<<std::endl;
1253   typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
1254   setBackgroundFilter->SetInput(air);
1255   setBackgroundFilter->SetInput2(bones);
1256   setBackgroundFilter->SetMaskValue(0);
1257   setBackgroundFilter->SetOutsideValue(0);
1258   setBackgroundFilter->Update();
1259   typename InternalImageType::Pointer bones_air =setBackgroundFilter->GetOutput();
1260
1261   typename SetBackgroundFilterType::Pointer setBackgroundFilter2 = SetBackgroundFilterType::New();
1262   setBackgroundFilter2->SetInput(bones_air);
1263   setBackgroundFilter2->SetInput2(lungs);
1264   setBackgroundFilter2->SetMaskValue(0);
1265   setBackgroundFilter2->SetOutsideValue(0);
1266   setBackgroundFilter2->Update();
1267   typename InternalImageType::Pointer lungs_bones_air =setBackgroundFilter2->GetOutput();
1268
1269   //---------------------------------
1270   // Prepare previous solution
1271   //---------------------------------
1272   if (m_Verbose) std::cout<<"Resampling previous solution..."<<std::endl;
1273   typename ResampleImageFilterType::Pointer resampler =ResampleImageFilterType::New();
1274   typedef itk::NearestNeighborInterpolateImageFunction<InternalImageType, double> InterpolatorType;
1275   typename InterpolatorType::Pointer interpolator=InterpolatorType::New();
1276   resampler->SetOutputStartIndex(bones->GetLargestPossibleRegion().GetIndex());
1277   resampler->SetInput(filledRibs);
1278   resampler->SetInterpolator(interpolator);
1279   resampler->SetOutputParametersFromImage(bones);
1280   resampler->Update();
1281   filledRibs =resampler->GetOutput();
1282
1283   if (m_Verbose) std::cout<<"Setting lungs to 1..."<<std::endl;
1284   typename SetBackgroundFilterType::Pointer setBackgroundFilter3 = SetBackgroundFilterType::New();
1285   setBackgroundFilter3->SetInput(filledRibs);
1286   setBackgroundFilter3->SetInput2(lungs);
1287   setBackgroundFilter3->SetMaskValue(0);
1288   setBackgroundFilter3->SetOutsideValue(1);
1289   setBackgroundFilter3->Update();
1290   filledRibs=setBackgroundFilter3->GetOutput();
1291
1292   if (m_Verbose) std::cout<<"Removing overlap with bones..."<<std::endl;
1293   typename SetBackgroundFilterType::Pointer setBackgroundFilter4 = SetBackgroundFilterType::New();
1294   setBackgroundFilter4->SetInput(filledRibs);
1295   setBackgroundFilter4->SetInput2(bones);
1296   setBackgroundFilter4->SetMaskValue(0);
1297   setBackgroundFilter4->SetOutsideValue(0);
1298   setBackgroundFilter4->Update();
1299   filledRibs =setBackgroundFilter4->GetOutput();
1300   //   writeImage<InternalImageType>(filledRibs,"/home/jef/tmp/filledRibs_pp.mhd");
1301   //---------------------------------
1302   // Calculate Distance Map
1303   //---------------------------------
1304   //  typedef  itk::ApproximateSignedDistanceMapImageFilter <InternalImageType, LevelSetImageType> DistanceMapImageFilterType2;
1305   typename DistanceMapImageFilterType::Pointer distanceMapImageFilter = DistanceMapImageFilterType::New();
1306   distanceMapImageFilter->SetInput(filledRibs);
1307   distanceMapImageFilter->SetInsideIsPositive(false);
1308   // distanceMapImageFilter->SetInsideValue(0);
1309 //     distanceMapImageFilter->SetOutsideValue(1);
1310   if (m_Verbose) std::cout<<"Calculating distance map..."<<std::endl;
1311   distanceMapImageFilter->Update();
1312
1313   //---------------------------------
1314   // Collapse
1315   //---------------------------------
1316   typename LevelSetImageFilterType::Pointer levelSetFilter=LevelSetImageFilterType::New();
1317   levelSetFilter->SetInput(  distanceMapImageFilter->GetOutput() );
1318   levelSetFilter->SetFeatureImage( lungs_bones_air );
1319   levelSetFilter->SetPropagationScaling(m_ArgsInfo.prop3_arg);
1320   levelSetFilter->SetCurvatureScaling( m_ArgsInfo.curve3_arg );
1321   levelSetFilter->SetAdvectionScaling( 0 );
1322   levelSetFilter->SetMaximumRMSError( m_ArgsInfo.maxRMS3_arg );
1323   levelSetFilter->SetNumberOfIterations( m_ArgsInfo.iter3_arg );
1324   levelSetFilter->SetUseImageSpacing(true);
1325
1326   //     //script
1327   //     std::string script="source /home/jef/thesis/presentations/20091014_JDD/videos/motionmask/make_motion_mask_movie_4mm.sh ";
1328
1329   // Start monitoring
1330   if (m_Verbose) std::cout<<"Starting the levelset..."<<std::endl;
1331   unsigned int totalNumberOfIterations=0;
1332   while (true) {
1333     levelSetFilter->Update();
1334
1335     // monitor state
1336     totalNumberOfIterations+=levelSetFilter->GetElapsedIterations();
1337     levelSetFilter->SetInput(levelSetFilter->GetOutput());
1338     if(m_ArgsInfo.monitor_given) writeImage<LevelSetImageType>(levelSetFilter->GetOutput(), m_ArgsInfo.monitor_arg);
1339     std::cout << "After "<<totalNumberOfIterations<<" iteration the RMS change is " << levelSetFilter->GetRMSChange() <<"..."<< std::endl;
1340
1341     //  // script
1342     //  std::ostringstream number_str;
1343     //  number_str << number;
1344     //  std::string param =  number_str.str();
1345     //  system((script+param).c_str());
1346     //  number+=1;
1347
1348     // stopping condition
1349     if ( (totalNumberOfIterations>= (unsigned int) m_ArgsInfo.maxIter3_arg) || (levelSetFilter->GetRMSChange()< m_ArgsInfo.maxRMS3_arg) ) break;
1350     levelSetFilter->SetNumberOfIterations( std::min ((unsigned int) m_ArgsInfo.iter3_arg, (unsigned int) m_ArgsInfo.maxIter3_arg-totalNumberOfIterations ) );
1351   }
1352
1353   // Output values
1354   if (m_Verbose) {
1355     std::cout<<"Level set segmentation stopped after "<<totalNumberOfIterations<<" iterations..."<<std::endl;
1356     std::cout << "Max. RMS error: " << levelSetFilter->GetMaximumRMSError() << std::endl;
1357     std::cout << "RMS change: " << levelSetFilter->GetRMSChange() << std::endl;
1358   }
1359
1360   // Threshold
1361   typedef itk::BinaryThresholdImageFilter< LevelSetImageType,InternalImageType>    LevelSetBinarizeFilterType;
1362   typename LevelSetBinarizeFilterType::Pointer thresholder = LevelSetBinarizeFilterType::New();
1363   thresholder->SetUpperThreshold( 0.0 );
1364   thresholder->SetOutsideValue( 0 );
1365   thresholder->SetInsideValue( 1 );
1366   thresholder->SetInput( levelSetFilter->GetOutput() );
1367   thresholder->Update();
1368   typename InternalImageType::Pointer output = thresholder->GetOutput();
1369
1370
1371   //----------------------------------------------------------------------------------------------------
1372   // Prepare the output
1373   //----------------------------------------------------------------------------------------------------
1374
1375   //---------------------------------
1376   // Set Air to zero
1377   //---------------------------------
1378   if (m_Verbose) std::cout<<"Removing overlap mask with air..."<<std::endl;
1379   typename SetBackgroundFilterType::Pointer setBackgroundFilter5 = SetBackgroundFilterType::New();
1380   setBackgroundFilter5->SetInput(output);
1381   setBackgroundFilter5->SetInput2(air);
1382   setBackgroundFilter5->SetMaskValue(0);
1383   setBackgroundFilter5->SetOutsideValue(0);
1384   setBackgroundFilter5->Update();
1385   output=setBackgroundFilter5->GetOutput();
1386
1387   //---------------------------------
1388   // Open & close  to cleanup
1389   //---------------------------------
1390   if ( m_ArgsInfo.openClose_flag) {
1391
1392     //---------------------------------
1393     // Structuring element
1394     //---------------------------------
1395     typedef itk::BinaryBallStructuringElement<InternalPixelType,Dimension > KernelType;
1396     KernelType structuringElement;
1397     structuringElement.SetRadius(1);
1398     structuringElement.CreateStructuringElement();
1399
1400     //---------------------------------
1401     // Open
1402     //---------------------------------
1403     typedef itk::BinaryMorphologicalOpeningImageFilter<InternalImageType, InternalImageType , KernelType> OpenFilterType;
1404     typename OpenFilterType::Pointer openFilter = OpenFilterType::New();
1405     openFilter->SetInput(output);
1406     openFilter->SetBackgroundValue(0);
1407     openFilter->SetForegroundValue(1);
1408     openFilter->SetKernel(structuringElement);
1409     if(m_Verbose) std::cout<<"Opening the output image..."<<std::endl;
1410
1411     //---------------------------------
1412     // Close
1413     //---------------------------------
1414     typedef itk::BinaryMorphologicalClosingImageFilter<InternalImageType, InternalImageType , KernelType> CloseFilterType;
1415     typename CloseFilterType::Pointer closeFilter = CloseFilterType::New();
1416     closeFilter->SetInput(openFilter->GetOutput());
1417     closeFilter->SetSafeBorder(true);
1418     closeFilter->SetForegroundValue(1);
1419     closeFilter->SetKernel(structuringElement);
1420     if(m_Verbose) std::cout<<"Closing the output image..."<<std::endl;
1421     closeFilter->Update();
1422     output=closeFilter->GetOutput();
1423
1424   }
1425   //writeImage<InternalImageType>(output,"/home/jef/tmp/mm_double.mhd");
1426
1427   // Extract the upper part
1428   typedef  itk::CropImageFilter<InternalImageType, InternalImageType> CropImageFilterType;
1429   typename CropImageFilterType::Pointer cropFilter=CropImageFilterType::New();
1430   cropFilter->SetInput(output);
1431   typename InputImageType::SizeType lSize, uSize;
1432   uSize.Fill(0);
1433   lSize.Fill(0);
1434   lSize[2]=input->GetLargestPossibleRegion().GetSize()[2];
1435   cropFilter->SetLowerBoundaryCropSize(lSize);
1436   cropFilter->SetUpperBoundaryCropSize(uSize);
1437   cropFilter->Update();
1438
1439   // Output
1440   typename CastImageFilterType::Pointer caster=CastImageFilterType::New();
1441   caster->SetInput(cropFilter->GetOutput());
1442   writeImage<OutputImageType>(caster->GetOutput(), m_ArgsInfo.output_arg, m_Verbose);
1443
1444 }
1445
1446 }//end clitk
1447
1448 #endif //#define clitkMotionMaskGenericFilter_txx