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 /* =================================================
  22  * @file   clitkImageStatisticsGenericFilter.txx
  23  * @author
  24  * @date
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30
  31 namespace clitk
  32 {
  33
  34   //-------------------------------------------------------------------
  35   // Update with the number of dimensions
  36   //-------------------------------------------------------------------
  37   template<unsigned int Dimension>
  38   void
  39   ImageStatisticsGenericFilter::UpdateWithDim(std::string PixelType)
  40   {
  41     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  42
  43     if(PixelType == "short"){
  44       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  45       UpdateWithDimAndPixelType<Dimension, signed short>();
  46     }
  47     //    else if(PixelType == "unsigned_short"){
  48     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  49     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  50     //     }
  51
  52     else if (PixelType == "unsigned_char"){
  53       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  54       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  55     }
  56
  57     //     else if (PixelType == "char"){
  58     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  59     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  60     //     }
  61     else {
  62       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  63       UpdateWithDimAndPixelType<Dimension, float>();
  64     }
  65   }
  66
  67
  68   //-------------------------------------------------------------------
  69   // Update with the number of dimensions and the pixeltype
  70   //-------------------------------------------------------------------
  71   template <unsigned int Dimension, class  PixelType>
  72   void
  73   ImageStatisticsGenericFilter::UpdateWithDimAndPixelType()
  74   {
  75
  76     // ImageTypes
  77     typedef itk::Image<PixelType, Dimension> InputImageType;
  78     typedef itk::Image<unsigned int, Dimension> LabelImageType;
  79     typedef itk::Image<PixelType, Dimension> OutputImageType;
  80
  81     // Read the input
  82     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  83     typename InputReaderType::Pointer reader = InputReaderType::New();
  84     reader->SetFileName( m_InputFileName);
  85     reader->Update();
  86     typename InputImageType::Pointer input= reader->GetOutput();
  87
  88     // Filter
  89     typedef itk::LabelStatisticsImageFilter<InputImageType, LabelImageType> StatisticsImageFilterType;
  90     typename StatisticsImageFilterType::Pointer statisticsFilter=StatisticsImageFilterType::New();
  91     statisticsFilter->SetInput(input);
  92
  93     // Label image
  94     typename LabelImageType::Pointer labelImage;
  95     if (m_ArgsInfo.mask_given)
  96       {
  97         typedef itk::ImageFileReader<LabelImageType> LabelImageReaderType;
  98         typename LabelImageReaderType::Pointer labelImageReader=LabelImageReaderType::New();
  99         labelImageReader->SetFileName(m_ArgsInfo.mask_arg);
 100         labelImageReader->Update();
 101         labelImage= labelImageReader->GetOutput();
 102       }
 103     else
 104       {
 105         labelImage=LabelImageType::New();
 106         labelImage->SetRegions(input->GetLargestPossibleRegion());
 107         labelImage->SetOrigin(input->GetOrigin());
 108         labelImage->SetSpacing(input->GetSpacing());
 109         labelImage->Allocate();
 110         labelImage->FillBuffer(m_ArgsInfo.label_arg[0]);
 111       }
 112     statisticsFilter->SetLabelInput(labelImage);
 113
 114     // For each Label
 115     typename LabelImageType::PixelType label;
 116     unsigned int numberOfLabels;
 117     if (m_ArgsInfo.label_given)
 118       numberOfLabels=m_ArgsInfo.label_given;
 119     else
 120       numberOfLabels=1;
 121
 122     for (unsigned int k=0; k< numberOfLabels; k++)
 123       {
 124         label=m_ArgsInfo.label_arg[k];
 125
 126         std::cout<<std::endl;
 127         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 128         if (m_Verbose) std::cout<<"| Label: "<<label<<"  |"<<std::endl;
 129         if (m_Verbose) std::cout<<"-------------"<<std::endl;
 130
 131         // Histograms
 132         if (m_ArgsInfo.histogram_given)
 133           {
 134             statisticsFilter->SetUseHistograms(true);
 135             statisticsFilter->SetHistogramParameters(m_ArgsInfo.bins_arg, m_ArgsInfo.lower_arg, m_ArgsInfo.upper_arg);
 136           }
 137         statisticsFilter->Update();
 138
 139
 140         // Output
 141         if (m_Verbose) std::cout<<"N° of pixels: ";
 142         std::cout<<statisticsFilter->GetCount(label)<<std::endl;
 143
 144         if (m_Verbose) std::cout<<"Mean: ";
 145         std::cout<<statisticsFilter->GetMean(label)<<std::endl;
 146
 147         if (m_Verbose) std::cout<<"SD: ";
 148         std::cout<<statisticsFilter->GetSigma(label)<<std::endl;
 149
 150         if (m_Verbose) std::cout<<"Variance: ";
 151         std::cout<<statisticsFilter->GetVariance(label)<<std::endl;
 152
 153         if (m_Verbose) std::cout<<"Min: ";
 154         std::cout<<statisticsFilter->GetMinimum(label)<<std::endl;
 155
 156         if (m_Verbose) std::cout<<"Max: ";
 157         std::cout<<statisticsFilter->GetMaximum(label)<<std::endl;
 158
 159         if (m_Verbose) std::cout<<"Sum: ";
 160         std::cout<<statisticsFilter->GetSum(label)<<std::endl;
 161
 162         if (m_Verbose) std::cout<<"Bounding box: ";
 163         for(unsigned int i =0; i <statisticsFilter->GetBoundingBox(label).size(); i++)
 164           std::cout<<statisticsFilter->GetBoundingBox(label)[i]<<" ";
 165         std::cout<<std::endl;
 166
 167
 168         // Histogram
 169         if (m_ArgsInfo.histogram_given)
 170           {
 171             if (m_Verbose) std::cout<<"Median: ";
 172             std::cout<<statisticsFilter->GetMedian(label)<<std::endl;
 173
 174             typename StatisticsImageFilterType::HistogramPointer histogram =statisticsFilter->GetHistogram(label);
 175
 176             // Screen
 177             if (m_Verbose) std::cout<<"Histogram: "<<std::endl;
 178             std::cout<<"# MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
 179             for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 180               std::cout<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
 181
 182             // Add to the file
 183             std::ofstream histogramFile(m_ArgsInfo.histogram_arg);
 184             histogramFile<<"#Histogram: "<<std::endl;
 185             histogramFile<<"#MinBin\tMidBin\tMaxBin\tFrequency"<<std::endl;
 186             for( int i =0; i <m_ArgsInfo.bins_arg; i++)
 187               histogramFile<<histogram->GetBinMin(0,i)<<"\t"<<histogram->GetMeasurement(i,0)<<"\t"<<histogram->GetBinMax(0,i)<<"\t"<<histogram->GetFrequency(i)<<std::endl;
 188           }
 189       }
 190
 191     return;
 192
 193   }
 194
 195
 196 }//end clitk
 197
 198 #endif //#define clitkImageStatisticsGenericFilter_txx