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 /* =================================================
  25  * @file   clitkImageStatisticsGenericFilter.txx
  26  * @author
  27  * @date
  28  *
  29  * @brief
  30  *
  31  ===================================================*/
  32 #include "clitkImageStatisticsGenericFilter.h"
  33
  34
  35 namespace clitk
  36 {
  37
  38   //-------------------------------------------------------------------
  39   // Update with the number of dimensions
  40   //-------------------------------------------------------------------
  41   template<unsigned int Dimension, unsigned int Components>
  42   void
  43   ImageStatisticsGenericFilter::UpdateWithDim(std::string PixelType)
  44   {
  45     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<" with " << Components << " channel(s)..."<<std::endl;
  46
  47     if(PixelType == "short"){
  48       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  49       UpdateWithDimAndPixelType<Dimension, signed short, Components>();
  50     }
  51     else if(PixelType == "unsigned_short"){
  52       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  53       UpdateWithDimAndPixelType<Dimension, unsigned short, Components>();
  54     }
  55
  56     else if (PixelType == "unsigned_char"){
  57       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  58       UpdateWithDimAndPixelType<Dimension, unsigned char, Components>();
  59     }
  60
  61 //     else if (PixelType == "unsigned_int"){
  62 //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_int..." << std::endl;
  63 //       UpdateWithDimAndPixelType<Dimension, unsigned int, Components>();
  64 //     }
  65     //     else if (PixelType == "char"){
  66     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  67     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  68     //     }
  69     else if(PixelType == "double"){
  70       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl;
  71       UpdateWithDimAndPixelType<Dimension, double, Components>();
  72     }
  73     else {
  74       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  75       UpdateWithDimAndPixelType<Dimension, float, Components>();
  76     }
  77   }
  78
  79
  80   //-------------------------------------------------------------------
  81   // Update with the number of dimensions and the pixeltype
  82   //-------------------------------------------------------------------
  83   template <unsigned int Dimension, class  PixelType, unsigned int Components>
  84   void
  85   ImageStatisticsGenericFilter::UpdateWithDimAndPixelType()
  86   {
  87
  88     // ImageTypes
  89     typedef unsigned char LabelPixelType;
  90     typedef itk::Image<itk::Vector<PixelType, Components>, Dimension> InputImageType;
  91     typedef itk::Image<LabelPixelType, Dimension> LabelImageType;
  92
  93     // Read the input
  94     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  95     typename InputReaderType::Pointer reader = InputReaderType::New();
  96     reader->SetFileName( m_InputFileName);
  97     reader->Update();
  98     typename InputImageType::Pointer input= reader->GetOutput();
  99
 100     typedef itk::NthElementImageAdaptor<InputImageType, PixelType> InputImageAdaptorType;
 101     typedef itk::Image<PixelType, Dimension> OutputImageType;
 102
 103     typename InputImageAdaptorType::Pointer input_adaptor = InputImageAdaptorType::New();
 104     input_adaptor->SetImage(input);
 105
 106     // Filter
 107     typedef itk::LabelStatisticsImageFilter<InputImageAdaptorType, LabelImageType> StatisticsImageFilterType;
 108     typename StatisticsImageFilterType::Pointer statisticsFilter=StatisticsImageFilterType::New();
 109     statisticsFilter->SetInput(input_adaptor);
 110
 111     // Label image
 112     typename LabelImageType::Pointer labelImage;
 113     if (m_ArgsInfo.mask_given) {
 114       int maskDimension, maskComponents;
 115       std::string maskPixelType;
 116       ReadImageDimensionAndPixelType(m_ArgsInfo.mask_arg, maskDimension, maskPixelType, maskComponents);
 117       if (maskDimension == Dimension - 1) {
 118         // Due to a limitation of filter itk::LabelStatisticsImageFilter, InputImageType and LabelImageType
 119         // must have the same image dimension. However, we want to support label images with Dl = Di - 1,
 120         // so we need to replicate the label image as many times as the size along dimension Di.
 121         if (m_Verbose)
 122           std::cout << "Replicating label image to match input image's dimension... " << std::endl;
 123
 124         typedef itk::Image<LabelPixelType, Dimension - 1> ReducedLabelImageType;
 125         typedef itk::ImageFileReader<ReducedLabelImageType> LabelImageReaderType;
 126         typedef itk::JoinSeriesImageFilter<ReducedLabelImageType, LabelImageType> JoinImageFilterType;
 127
 128         typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
 129         labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
 130         labelImageReader->Update();
 131
 132         typename JoinImageFilterType::Pointer joinFilter = JoinImageFilterType::New();
 133         typename InputImageType::SizeType size = input->GetLargestPossibleRegion().GetSize();
 134         for (unsigned int i = 0; i < size[Dimension - 1]; i++)
 135           joinFilter->PushBackInput(labelImageReader->GetOutput());
 136
 137         joinFilter->Update();
 138         labelImage = joinFilter->GetOutput();
 139       }
 140       else {
 141         typedef itk::ImageFileReader<LabelImageType> LabelImageReaderType;
 142         typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
 143         labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
 144         labelImageReader->Update();
 145         labelImage= labelImageReader->GetOutput();
 146       }
 147
 148     }
 149     else {
 150       labelImage=LabelImageType::New();
 151       labelImage->SetRegions(input->GetLargestPossibleRegion());
 152       labelImage->SetOrigin(input->GetOrigin());
 153       labelImage->SetSpacing(input->GetSpacing());
 154       labelImage->Allocate();
 155       labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
 156     }
 157     statisticsFilter->SetLabelInput(labelImage);
 158
 159     // For each Label
 160     typename LabelImageType::PixelType label;
 161     unsigned int numberOfLabels;
 162     if (m_ArgsInfo.label_given)
 163       numberOfLabels=m_ArgsInfo.label_given;
 164     else
 165       numberOfLabels=1;
 166
 167     unsigned int firstComponent = 0, lastComponent = 0;
 168     if (m_ArgsInfo.channel_arg == -1) {
 169       firstComponent = 0;
 170       lastComponent = Components - 1;
 171     }
 172     else {
 173       firstComponent = m_ArgsInfo.channel_arg;
 174       lastComponent = m_ArgsInfo.channel_arg;
 175     }
 176
 177     for (unsigned int c=firstComponent; c<=lastComponent; c++) {
 178       if (m_Verbose) std::cout << std::endl << "Processing channel " << c << std::endl;
 179
 180       input_adaptor->SelectNthElement(c);
 181       input_adaptor->Update();
 182
 183       for (unsigned int k=0; k< numberOfLabels; k++) {
 184         label=m_ArgsInfo.label_arg[k];
 185
 186         std::cout<<std::endl;
 187         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 188         if (m_Verbose) std::cout<<"| Label: "<<label<<"  |"<<std::endl;
 189         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 190
 191         // Histograms
 192         if (m_ArgsInfo.histogram_given) {
 193           statisticsFilter->SetUseHistograms(true);
 194           statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
 195         }
 196         statisticsFilter->Update();
 197
 198         // Output
 199         if (m_Verbose) std::cout<<"N° of pixels: ";
 200           std::cout<<statisticsFilter->GetCount(label)<<std::endl;
 201
 202         if (m_Verbose) std::cout<<"Mean: ";
 203           std::cout<<statisticsFilter->GetMean(label)<<std::endl;
 204
 205         if (m_Verbose) std::cout<<"SD: ";
 206           std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
 207
 208         if (m_Verbose) std::cout<<"Variance: ";
 209           std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
 210
 211         if (m_Verbose) std::cout<<"Min: ";
 212           std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
 213
 214         if (m_Verbose) std::cout<<"Max: ";
 215           std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
 216
 217         if (m_Verbose) std::cout<<"Sum: ";
 218           std::cout<<statisticsFilter->GetSum(label)<<std::endl;
 219
 220         if (m_Verbose) std::cout<<"Bounding box: ";
 221
 222         for(unsigned int i =0; i <statisticsFilter->GetBoundingBox(label).size(); i++)
 223           std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
 224         std::cout<<std::endl;
 225
 226         // Histogram
 227         if (m_ArgsInfo.histogram_given)
 228         {
 229           if (m_Verbose) std::cout<<"Median: ";
 230           std::cout<<statisticsFilter->GetMedian(label)<<std::endl;
 231
 232           typename StatisticsImageFilterType::HistogramPointer histogram =statisticsFilter->GetHistogram(label);
 233
 234           // Screen
 235           if (m_Verbose) std::cout<<"Histogram: "<<std::endl;
 236             std::cout<<"# MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
 237           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 238             std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
 239
 240           // Add to the file
 241           std::ofstream histogramFile(m_ArgsInfo.histogram_arg);
 242           histogramFile<<"#Histogram: "<<std::endl;
 243           histogramFile<<"#MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
 244           for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 245             histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
 246         }
 247       }
 248     }
 249
 250     return;
 251
 252   }
 253
 254
 255 }//end clitk
 256
 257 #endif //#define clitkImageStatisticsGenericFilter_txx