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>();
  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 == "char"){
  55     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  56     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  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->Update();
 144             labelImage = resampler->GetOutput();
 145
 146             typename itk::ImageBase<LabelImageType::ImageDimension>::RegionType reg
 147               = input->GetLargestPossibleRegion();
 148             labelImage = ResizeImageLike<LabelImageType>(labelImage, &reg, 0);
 149           }
 150           else {
 151             std::cerr << "Mask image has a different size/spacing than input. Abort" << std::endl;
 152             exit(-1);
 153           }
 154         }
 155
 156       }
 157
 158     }
 159     else {
 160       labelImage=LabelImageType::New();
 161       labelImage->SetRegions(input->GetLargestPossibleRegion());
 162       labelImage->SetOrigin(input->GetOrigin());
 163       labelImage->SetSpacing(input->GetSpacing());
 164       labelImage->Allocate();
 165       labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
 166     }
 167     statisticsFilter->SetLabelInput(labelImage);
 168
 169     // For each Label
 170     typename LabelImageType::PixelType label;
 171     unsigned int numberOfLabels;
 172     if (m_ArgsInfo.label_given)
 173       numberOfLabels=m_ArgsInfo.label_given;
 174     else
 175       numberOfLabels=1;
 176
 177     unsigned int firstComponent = 0, lastComponent = 0;
 178     if (m_ArgsInfo.channel_arg == -1) {
 179       firstComponent = 0;
 180       lastComponent = Components - 1;
 181     }
 182     else {
 183       firstComponent = m_ArgsInfo.channel_arg;
 184       lastComponent = m_ArgsInfo.channel_arg;
 185     }
 186
 187     for (unsigned int c=firstComponent; c<=lastComponent; c++) {
 188       if (m_Verbose) std::cout << std::endl << "Processing channel " << c << std::endl;
 189
 190       input_adaptor->SelectNthElement(c);
 191       input_adaptor->Update();
 192
 193       for (unsigned int k=0; k< numberOfLabels; k++) {
 194         label=m_ArgsInfo.label_arg[k];
 195
 196         std::cout<<std::endl;
 197         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 198         if (m_Verbose) std::cout<<"| Label: "<<label<<"  |"<<std::endl;
 199         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 200
 201         // Histograms
 202         if (m_ArgsInfo.histogram_given) {
 203           statisticsFilter->SetUseHistograms(true);
 204           statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
 205         }
 206         statisticsFilter->Update();
 207
 208         // Output
 209         if (m_Verbose) std::cout<<"N° of pixels: ";
 210           std::cout<<statisticsFilter->GetCount(label)<<std::endl;
 211
 212         if (m_Verbose) std::cout<<"Mean: ";
 213           std::cout<<statisticsFilter->GetMean(label)<<std::endl;
 214
 215         if (m_Verbose) std::cout<<"SD: ";
 216           std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
 217
 218         if (m_Verbose) std::cout<<"Variance: ";
 219           std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
 220
 221         if (m_Verbose) std::cout<<"Min: ";
 222           std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
 223
 224         if (m_Verbose) std::cout<<"Max: ";
 225           std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
 226
 227         if (m_Verbose) std::cout<<"Sum: ";
 228           std::cout<<statisticsFilter->GetSum(label)<<std::endl;
 229
 230         if (m_Verbose) std::cout<<"Bounding box: ";
 231
 232         for(unsigned int i =0; i <statisticsFilter->GetBoundingBox(label).size(); i++)
 233           std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
 234         std::cout<<std::endl;
 235
 236         // Histogram
 237         if (m_ArgsInfo.histogram_given)
 238         {
 239           if (m_Verbose) std::cout<<"Median: ";
 240           std::cout<<statisticsFilter->GetMedian(label)<<std::endl;
 241
 242           typename StatisticsImageFilterType::HistogramPointer histogram =statisticsFilter->GetHistogram(label);
 243
 244           // Screen
 245           if (m_Verbose) std::cout<<"Histogram: "<<std::endl;
 246             std::cout<<"# MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
 247           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 248             std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
 249
 250           // Add to the file
 251           std::ofstream histogramFile(m_ArgsInfo.histogram_arg);
 252           histogramFile<<"#Histogram: "<<std::endl;
 253           histogramFile<<"#MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
 254           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 255             histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
 256         }
 257       }
 258     }
 259
 260     return;
 261
 262   }
 263
 264
 265 }//end clitk
 266
 267 #endif //#define clitkImageStatisticsGenericFilter_txx