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