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