tools/clitkImageStatisticsGenericFilter.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 clitkImageStatisticsGenericFilter_txx
  19 #define clitkImageStatisticsGenericFilter_txx
  20
  21 #include "itkNthElementImageAdaptor.h"
  22 #include "itkJoinSeriesImageFilter.h"
  23 #include "itkImageRegionConstIterator.h"
  24
  25 #include "clitkImageStatisticsGenericFilter.h"
  26 #include "clitkCropLikeImageFilter.h"
  27 #include "clitkResampleImageWithOptionsFilter.h"
  28
  29 namespace clitk
  30 {
  31
  32   //-------------------------------------------------------------------
  33   // Update with the number of dimensions
  34   //-------------------------------------------------------------------
  35   template<unsigned int Dimension, unsigned int Components>
  36   void
  37   ImageStatisticsGenericFilter::UpdateWithDim(std::string PixelType)
  38   {
  39     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<" with " << Components << " channel(s)..."<<std::endl;
  40
  41     if(PixelType == "short"){
  42       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  43       UpdateWithDimAndPixelType<Dimension, signed short, Components>();
  44     }
  45     else if(PixelType == "unsigned_short"){
  46       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  47       UpdateWithDimAndPixelType<Dimension, unsigned short, Components>();
  48     }
  49
  50     else if (PixelType == "unsigned_char"){
  51       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  52       UpdateWithDimAndPixelType<Dimension, unsigned char, Components>();
  53     }
  54
  55     else if(PixelType == "double"){
  56       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
  57       UpdateWithDimAndPixelType<Dimension, double, Components>();
  58     }
  59     else {
  60       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  61       UpdateWithDimAndPixelType<Dimension, float, Components>();
  62     }
  63   }
  64
  65
  66   //-------------------------------------------------------------------
  67   // Update with the number of dimensions and the pixeltype
  68   //-------------------------------------------------------------------
  69   template <unsigned int Dimension, class  PixelType, unsigned int Components>
  70   void
  71   ImageStatisticsGenericFilter::UpdateWithDimAndPixelType()
  72   {
  73
  74     // ImageTypes
  75     typedef unsigned char LabelPixelType;
  76     typedef itk::Image<itk::Vector<PixelType, Components>, Dimension> InputImageType;
  77     typedef itk::Image<LabelPixelType, Dimension> LabelImageType;
  78
  79     // Read the input
  80     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  81     typename InputReaderType::Pointer reader = InputReaderType::New();
  82     reader->SetFileName( m_InputFileName);
  83     reader->Update();
  84     typename InputImageType::Pointer input= reader->GetOutput();
  85
  86     typedef itk::NthElementImageAdaptor<InputImageType, PixelType> InputImageAdaptorType;
  87     typedef itk::Image<PixelType, Dimension> OutputImageType;
  88
  89     typename InputImageAdaptorType::Pointer input_adaptor = InputImageAdaptorType::New();
  90     input_adaptor->SetImage(input);
  91
  92     // Filter
  93     typedef itk::LabelStatisticsImageFilter<InputImageAdaptorType, LabelImageType> StatisticsImageFilterType;
  94     typename StatisticsImageFilterType::Pointer statisticsFilter=StatisticsImageFilterType::New();
  95     statisticsFilter->SetInput(input_adaptor);
  96
  97     // Label image
  98     typename LabelImageType::Pointer labelImage;
  99     if (m_ArgsInfo.mask_given) {
 100       int maskDimension, maskComponents;
 101       std::string maskPixelType;
 102       ReadImageDimensionAndPixelType(m_ArgsInfo.mask_arg, maskDimension, maskPixelType, maskComponents);
 103
 104       if (maskDimension == Dimension - 1) {
 105         // Due to a limitation of filter itk::LabelStatisticsImageFilter, InputImageType and LabelImageType
 106         // must have the same image dimension. However, we want to support label images with Dl = Di - 1,
 107         // so we need to replicate the label image as many times as the size along dimension Di.
 108         if (m_Verbose)
 109           std::cout << "Replicating label image to match input image's dimension... " << std::endl;
 110
 111         typedef itk::Image<LabelPixelType, Dimension - 1> ReducedLabelImageType;
 112         typedef itk::ImageFileReader<ReducedLabelImageType> LabelImageReaderType;
 113         typedef itk::JoinSeriesImageFilter<ReducedLabelImageType, LabelImageType> JoinImageFilterType;
 114
 115         typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
 116         labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
 117         labelImageReader->Update();
 118
 119         typename JoinImageFilterType::Pointer joinFilter = JoinImageFilterType::New();
 120         typename InputImageType::SizeType size = input->GetLargestPossibleRegion().GetSize();
 121         for (unsigned int i = 0; i < size[Dimension - 1]; i++)
 122           joinFilter->PushBackInput(labelImageReader->GetOutput());
 123
 124         joinFilter->Update();
 125         labelImage = joinFilter->GetOutput();
 126       }
 127       else {
 128         typedef itk::ImageFileReader<LabelImageType> LabelImageReaderType;
 129         typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
 130         labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
 131         labelImageReader->Update();
 132         labelImage= labelImageReader->GetOutput();
 133
 134         // Check mask sampling/size
 135         if (!HaveSameSizeAndSpacing<LabelImageType, InputImageType>(labelImage, input)) {
 136           if (m_ArgsInfo.allow_resize_flag) {
 137             if (m_ArgsInfo.verbose_flag) {
 138               std::cout << "Resize mask image like input" << std::endl;
 139             }
 140             typedef clitk::ResampleImageWithOptionsFilter<LabelImageType> ResamplerType;
 141             typename ResamplerType::Pointer resampler = ResamplerType::New();
 142             resampler->SetInput(labelImage);
 143             resampler->SetOutputSpacing(input->GetSpacing());
 144             resampler->SetOutputOrigin(labelImage->GetOrigin());
 145             resampler->SetGaussianFilteringEnabled(false);
 146             resampler->Update();
 147             labelImage = resampler->GetOutput();
 148             //writeImage<LabelImageType>(labelImage, "test1.mha");
 149
 150             typedef clitk::CropLikeImageFilter<LabelImageType> FilterType;
 151             typename FilterType::Pointer crop = FilterType::New();
 152             crop->SetInput(labelImage);
 153             crop->SetCropLikeImage(input);
 154             crop->Update();
 155             labelImage = crop->GetOutput();
 156             //writeImage<LabelImageType>(labelImage, "test2.mha");
 157
 158           }
 159           else {
 160             std::cerr << "Mask image has a different size/spacing than input. Abort. (Use option to resize)" << std::endl;
 161             exit(-1);
 162           }
 163         }
 164
 165       }
 166
 167     }
 168     else {
 169       labelImage=LabelImageType::New();
 170       labelImage->SetDirection(input->GetDirection());
 171       labelImage->SetRegions(input->GetLargestPossibleRegion());
 172       labelImage->SetOrigin(input->GetOrigin());
 173       labelImage->SetSpacing(input->GetSpacing());
 174       labelImage->SetDirection(input->GetDirection());
 175       labelImage->Allocate();
 176       labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
 177     }
 178     statisticsFilter->SetLabelInput(labelImage);
 179
 180     // Check/compute spacing
 181     const typename LabelImageType::SpacingType& spacing = input->GetSpacing();
 182     double spacing_cc = (spacing[0]*spacing[1]*spacing[2])/1000;
 183     // std::cout<<"Spacing x : " << spacing[0]<<std::endl;
 184     // std::cout<<"Spacing y :  " << spacing[1]<<std::endl;
 185     // std::cout<<"Spacing z :  " << spacing[2]<<std::endl;
 186     // std::cout <<"spacing_cc : " << spacing_cc << std::endl;
 187
 188
 189     // For each Label
 190     typename LabelImageType::PixelType label;
 191     unsigned int numberOfLabels;
 192     if (m_ArgsInfo.label_given)
 193       numberOfLabels=m_ArgsInfo.label_given;
 194     else
 195       numberOfLabels=1;
 196
 197     unsigned int firstComponent = 0, lastComponent = 0;
 198     if (m_ArgsInfo.channel_arg == -1) {
 199       firstComponent = 0;
 200       lastComponent = Components - 1;
 201     }
 202     else {
 203       firstComponent = m_ArgsInfo.channel_arg;
 204       lastComponent = m_ArgsInfo.channel_arg;
 205     }
 206
 207     for (unsigned int c=firstComponent; c<=lastComponent; c++) {
 208       if (m_Verbose) std::cout << std::endl << "Processing channel " << c << std::endl;
 209
 210       input_adaptor->SelectNthElement(c);
 211       input_adaptor->Update();
 212
 213       for (unsigned int k=0; k< numberOfLabels; k++) {
 214         label=m_ArgsInfo.label_arg[k];
 215
 216         std::cout<<std::endl;
 217         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 218         if (m_Verbose) std::cout<<"| Label: "<< (int) label<<"  |"<<std::endl;
 219         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 220
 221         // Histograms
 222         if (m_ArgsInfo.histogram_given) {
 223           statisticsFilter->SetUseHistograms(true);
 224           statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
 225         }
 226
 227         // DVH
 228         if(m_ArgsInfo.dvhistogram_given)
 229         {
 230           statisticsFilter->SetUseHistograms(true);
 231           statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
 232         }
 233
 234         statisticsFilter->Update();
 235
 236         //find localization for max and min (the last pixel found)
 237         typename InputImageType::IndexType minIndex, maxIndex;
 238         if (m_Verbose && m_Localize) {
 239           itk::ImageRegionConstIterator<InputImageAdaptorType> imageIterator(input_adaptor,input_adaptor->GetLargestPossibleRegion());
 240           while(!imageIterator.IsAtEnd()) {
 241             if (imageIterator.Get() == statisticsFilter->GetMinimum(label))
 242               minIndex = imageIterator.GetIndex();
 243             if (imageIterator.Get() == statisticsFilter->GetMaximum(label))
 244               maxIndex = imageIterator.GetIndex();
 245             ++imageIterator;
 246           }
 247         }
 248
 249         // Output
 250         if (m_Verbose) std::cout<<"N° of pixels: ";
 251         std::cout<<statisticsFilter->GetCount(label)<<std::endl;
 252         if (m_Verbose) std::cout<<"Mean: ";
 253         std::cout<<statisticsFilter->GetMean(label)<<std::endl;
 254         if (m_Verbose) std::cout<<"SD: ";
 255         std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
 256         if (m_Verbose) std::cout<<"Variance: ";
 257         std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
 258         if (m_Verbose) std::cout<<"Min: ";
 259         std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
 260         if (m_Verbose && m_Localize) {
 261           std::cout<<"        in voxel of index: ";
 262           std::cout<<minIndex<<std::endl;
 263         }
 264         if (m_Verbose) std::cout<<"Max: ";
 265         std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
 266         if (m_Verbose && m_Localize) {
 267           std::cout<<"        in voxel of index: ";
 268           std::cout<<maxIndex<<std::endl;
 269         }
 270         if (m_Verbose) std::cout<<"Sum: ";
 271         std::cout<<statisticsFilter->GetSum(label)<<std::endl;
 272         if (m_Verbose) std::cout<<"Volume (cc): ";
 273         std::cout<<statisticsFilter->GetCount(label)*spacing_cc<<std::endl;
 274         if (m_Verbose) std::cout<<"Bounding box: ";
 275         for(unsigned int i =0; i <statisticsFilter->GetBoundingBox(label).size(); i++)
 276             std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
 277         std::cout<<std::endl;
 278
 279         // Histogram
 280         if (m_ArgsInfo.histogram_given)
 281         {
 282           if (m_Verbose) std::cout<<"Median: ";
 283           std::cout<<statisticsFilter->GetMedian(label)<<std::endl;
 284
 285           typename StatisticsImageFilterType::HistogramPointer histogram =statisticsFilter->GetHistogram(label);
 286
 287           // Screen
 288           if (m_Verbose) std::cout<<"Histogram: "<<std::endl;
 289             std::cout<<"# MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
 290           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 291             std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
 292
 293           // Add to the file
 294           std::ofstream histogramFile(m_ArgsInfo.histogram_arg);
 295           histogramFile<<"#Histogram: "<<std::endl;
 296           histogramFile<<"#MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
 297           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 298             histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
 299         }
 300
 301         // DVH
 302         if(m_ArgsInfo.dvhistogram_given)
 303         {
 304             typename StatisticsImageFilterType::HistogramPointer dvhistogram = statisticsFilter->GetHistogram(label);
 305             double totalVolumeCC = ((statisticsFilter->GetCount(label))*spacing_cc);
 306             double totalVolume = statisticsFilter->GetCount(label);
 307
 308             // Screen
 309             std::cout<<"# Total volume : ";
 310             std::cout<<totalVolume<<" [No. of voxels]"<<std::endl;
 311             std::cout<<"# Total volume : ";
 312             std::cout<<totalVolumeCC<<" [cc]"<<std::endl;
 313             std::cout<<"# Dose mean: ";
 314             std::cout<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
 315             std::cout<<"# Dose min: ";
 316             std::cout<<statisticsFilter->GetMinimum(label)<<" [Gy]"<<std::endl;
 317             std::cout<<"# Dose max: ";
 318             std::cout<<statisticsFilter->GetMaximum(label)<<" [Gy]"<<std::endl;
 319             std::cout<<" "<<std::endl;
 320             std::cout<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
 321             for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 322             {
 323               double popCumulativeVolume = 0;
 324               for(int j=0; j<i; j++)
 325               {
 326                  popCumulativeVolume+=(dvhistogram->GetFrequency(j));
 327               }
 328               double cumulativeVolume = (totalVolume - (popCumulativeVolume + (dvhistogram->GetFrequency(i))));
 329               double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label)) ;
 330               double ccCumulativeVolume = (totalVolumeCC -((popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc));
 331               double percentDiffVolume = dvhistogram->GetFrequency(i)*100/(statisticsFilter->GetCount(label));
 332               std::cout<<dvhistogram->GetBinMax(0,i)<<"\t  "<<dvhistogram->GetFrequency(i)<<"\t  "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<"\t "<<cumulativeVolume<<"\t  "<<percentCumulativeVolume<<"\t  "<<ccCumulativeVolume<<"\t "<<std::endl;
 333             }
 334
 335             // Add to the file
 336             std::ofstream dvhistogramFile(m_ArgsInfo.dvhistogram_arg);
 337             dvhistogramFile<<"# Total volume : ";
 338             dvhistogramFile<<statisticsFilter->GetCount(label)<<" [No. of voxels]"<<std::endl;
 339             dvhistogramFile<<"# Total volume : ";
 340             dvhistogramFile<<totalVolumeCC<<" [cc]"<<std::endl;
 341             dvhistogramFile<<"# Dose mean: ";
 342             dvhistogramFile<<statisticsFilter->GetMean(label)<<" [Gy]"<<std::endl;
 343             dvhistogramFile<<"# Dose min: ";
 344             dvhistogramFile<<statisticsFilter->GetMinimum(label)<<" [Gy]"<<std::endl;
 345             dvhistogramFile<<"# Dose max: ";
 346             dvhistogramFile<<statisticsFilter->GetMaximum(label)<<" [Gy]"<<std::endl;
 347             dvhistogramFile<<"  "<<std::endl;
 348             dvhistogramFile<<"#Dose_diff[Gy] Volume_diff[No. of voxels] Volume_diff[%] Volume_diff[cc] Volume_cumul[No. of voxels] Volume_cumul[%] Volume_cumul[cc]"<<std::endl;
 349             for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 350             {
 351                double popCumulativeVolume = 0;
 352                for(int j=0; j<i; j++)
 353                {
 354                  popCumulativeVolume+=(dvhistogram->GetFrequency(j));
 355                }
 356                double cumulativeVolume = (totalVolume - (popCumulativeVolume + (dvhistogram->GetFrequency(i))));
 357                double percentCumulativeVolume =(cumulativeVolume*100)/(statisticsFilter->GetCount(label));
 358                double ccCumulativeVolume = (totalVolumeCC -((popCumulativeVolume + (dvhistogram->GetFrequency(i)))*spacing_cc));
 359                double percentDiffVolume = ((dvhistogram->GetFrequency(i))*100)/(statisticsFilter->GetCount(label));
 360                dvhistogramFile<<dvhistogram->GetBinMax(0,i)<<"\t  "<<dvhistogram->GetFrequency(i)<<"\t  "<<percentDiffVolume<<"\t "<<((dvhistogram->GetFrequency(i))*spacing_cc)<<"\t "<<cumulativeVolume<<"\t "<<percentCumulativeVolume<<"\t  "<<ccCumulativeVolume<<std::endl;
 361            }
 362         }
 363       }
 364     }
 365
 366     return;
 367
 368   }
 369
 370
 371 }//end clitk
 372
 373 #endif //#define clitkImageStatisticsGenericFilter_txx