segmentation/clitkDecomposeAndReconstructGenericFilter.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://oncora1.lyon.fnclcc.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 clitkDecomposeAndReconstructGenericFilter_txx
  19 #define clitkDecomposeAndReconstructGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkDecomposeAndReconstructGenericFilter.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   DecomposeAndReconstructGenericFilter::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       std::cout  << "WARNING: Working in unsigned pixelType, remember to set the Erosion Padding Value to a suitable value!"<< std::endl;
  55       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  56
  57     }
  58
  59     //     else if (PixelType == "char"){
  60     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  61     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  62     //     }
  63     else {
  64       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  65       UpdateWithDimAndPixelType<Dimension, float>();
  66     }
  67   }
  68
  69
  70   //-------------------------------------------------------------------
  71   // Update with the number of dimensions and the pixeltype
  72   //-------------------------------------------------------------------
  73   template <unsigned int Dimension, class  PixelType>
  74   void
  75   DecomposeAndReconstructGenericFilter::UpdateWithDimAndPixelType()
  76   {
  77
  78     // ImageTypes
  79     typedef itk::Image<PixelType, Dimension> InputImageType;
  80     typedef itk::Image<int, Dimension> InternalImageType;
  81     typedef itk::Image<PixelType, Dimension> OutputImageType;
  82
  83     // Read the input
  84     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  85     typename InputReaderType::Pointer reader = InputReaderType::New();
  86     reader->SetFileName( m_InputFileName);
  87     reader->Update();
  88     typename InputImageType::Pointer input= reader->GetOutput();
  89
  90     // Structuring element radius
  91     typename InputImageType::SizeType radius;
  92     if (m_ArgsInfo.radius_given==Dimension)
  93       for (unsigned int i=0;i<Dimension;i++)
  94         {radius[i]=m_ArgsInfo.radius_arg[i];}
  95     else
  96       for (unsigned int i=0;i<Dimension;i++)
  97         radius[i]=m_ArgsInfo.radius_arg[0];
  98
  99     // Cast
 100     typedef itk::CastImageFilter<InputImageType, InternalImageType> InputCastImageFilterType;
 101     typename InputCastImageFilterType::Pointer inputCaster= InputCastImageFilterType::New();
 102     inputCaster->SetInput(input);
 103     inputCaster->Update();
 104
 105     // Filter
 106     typedef itk::ImageToImageFilter<InternalImageType, InternalImageType> ImageToImageFilterType;
 107     typename ImageToImageFilterType::Pointer filter;
 108
 109     switch (m_ArgsInfo.type_arg)
 110       {
 111       case 0:
 112         {
 113           typedef clitk::DecomposeThroughErosionImageFilter<InternalImageType,InternalImageType> FilterType;
 114           typename FilterType::Pointer f=FilterType::New();
 115           f->SetVerbose(m_Verbose);
 116           f->SetFullyConnected(m_ArgsInfo.full_flag);
 117           f->SetErosionPaddingValue(m_ArgsInfo.pad_arg);
 118           f->SetMinimumNumberOfIterations(m_ArgsInfo.min_arg);
 119           f->SetMinimumObjectSize(m_ArgsInfo.minSize_arg);
 120           f->SetRadius(radius);
 121           f->SetNumberOfNewLabels(m_ArgsInfo.new_arg);
 122           if(m_Verbose) std::cout<<"Using the DecomposeThroughErosionImageFilter..."<<std::endl;
 123           filter=f;
 124           break;
 125         }
 126
 127       case 1:
 128         {
 129           typedef clitk::ReconstructThroughDilationImageFilter<InternalImageType,InternalImageType> FilterType;
 130           typename FilterType::Pointer f=FilterType::New();
 131           f->SetVerbose(m_Verbose);
 132           f->SetErosionPaddingValue(m_ArgsInfo.pad_arg);
 133           f->SetRadius(radius);
 134           f->SetMaximumNumberOfLabels(m_ArgsInfo.max_arg);
 135           f->SetBackgroundValue(m_ArgsInfo.bg_arg);
 136           f->SetForegroundValue(m_ArgsInfo.fg_arg);
 137           if(m_Verbose) std::cout<<"Using the ReconstructThroughDilationImageFilter..."<<std::endl;
 138           filter=f;
 139           break;
 140         }
 141       case 2:
 142         {
 143           typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> FilterType;
 144           typename FilterType::Pointer f=FilterType::New();
 145           f->SetVerbose(m_Verbose);
 146           f->SetRadius(radius);
 147           f->SetMaximumNumberOfLabels(m_ArgsInfo.max_arg);
 148           f->SetMinimumNumberOfIterations(m_ArgsInfo.min_arg);
 149           f->SetBackgroundValue(m_ArgsInfo.bg_arg);
 150           f->SetForegroundValue(m_ArgsInfo.fg_arg);
 151           f->SetFullyConnected(m_ArgsInfo.full_flag);
 152           f->SetNumberOfNewLabels(m_ArgsInfo.new_arg);
 153           f->SetMinimumObjectSize(m_ArgsInfo.minSize_arg);
 154           if(m_Verbose) std::cout<<"Using the DecomposeAndReconstructImageFilter..."<<std::endl;
 155           filter=f;
 156           break;
 157         }
 158       }
 159
 160     filter->SetInput(inputCaster->GetOutput());
 161     filter->Update();
 162     typename InternalImageType::Pointer output= filter->GetOutput();
 163
 164     // Cast
 165     typedef itk::CastImageFilter<InternalImageType, OutputImageType> OutputCastImageFilterType;
 166     typename OutputCastImageFilterType::Pointer outputCaster= OutputCastImageFilterType::New();
 167     outputCaster->SetInput(output);
 168     outputCaster->Update();
 169
 170     // Output
 171     typedef itk::ImageFileWriter<OutputImageType> WriterType;
 172     typename WriterType::Pointer writer = WriterType::New();
 173     writer->SetFileName(m_ArgsInfo.output_arg);
 174     writer->SetInput(outputCaster->GetOutput());
 175     writer->Update();
 176
 177   }
 178
 179
 180 }//end clitk
 181
 182 #endif //#define clitkDecomposeAndReconstructGenericFilter_txx