tools/clitkSetBackgroundGenericFilter.txx

   1 #ifndef clitkSetBackgroundGenericFilter_txx
   2 #define clitkSetBackgroundGenericFilter_txx
   3
   4 /* =================================================
   5  * @file   clitkSetBackgroundGenericFilter.txx
   6  * @author
   7  * @date
   8  *
   9  * @brief
  10  *
  11  ===================================================*/
  12
  13
  14 namespace clitk
  15 {
  16
  17   //-------------------------------------------------------------------
  18   // Update with the number of dimensions
  19   //-------------------------------------------------------------------
  20   template<unsigned int Dimension>
  21   void
  22   SetBackgroundGenericFilter::UpdateWithDim(std::string PixelType)
  23   {
  24     if (m_Verbose) std::cout << "Image was detected to be "<<Dimension<<"D and "<< PixelType<<"..."<<std::endl;
  25
  26     if(PixelType == "short"){
  27       if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl;
  28       UpdateWithDimAndPixelType<Dimension, signed short>();
  29     }
  30     //    else if(PixelType == "unsigned_short"){
  31     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl;
  32     //       UpdateWithDimAndPixelType<Dimension, unsigned short>();
  33     //     }
  34
  35     else if (PixelType == "unsigned_char"){
  36       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl;
  37       UpdateWithDimAndPixelType<Dimension, unsigned char>();
  38     }
  39
  40     //     else if (PixelType == "char"){
  41     //       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl;
  42     //       UpdateWithDimAndPixelType<Dimension, signed char>();
  43     //     }
  44     else {
  45       if (m_Verbose) std::cout  << "Launching filter in "<< Dimension <<"D and float..." << std::endl;
  46       UpdateWithDimAndPixelType<Dimension, float>();
  47     }
  48   }
  49
  50
  51   //-------------------------------------------------------------------
  52   // Update with the number of dimensions and the pixeltype
  53   //-------------------------------------------------------------------
  54   template <unsigned int Dimension, class  PixelType>
  55   void
  56   SetBackgroundGenericFilter::UpdateWithDimAndPixelType()
  57   {
  58
  59   // ImageTypes
  60     typedef itk::Image<PixelType, Dimension> InputImageType;
  61     typedef itk::Image<float, Dimension> MaskImageType;
  62
  63     // Read the input
  64     typedef itk::ImageFileReader<InputImageType> InputReaderType;
  65     typename InputReaderType::Pointer reader = InputReaderType::New();
  66     reader->SetFileName( m_InputFileName);
  67     typename InputImageType::Pointer input= reader->GetOutput();
  68
  69     // Read the mask
  70     typedef itk::ImageFileReader<MaskImageType> MaskReaderType;
  71     typename MaskReaderType::Pointer maskReader = MaskReaderType::New();
  72     maskReader->SetFileName( m_ArgsInfo.mask_arg);
  73     typename MaskImageType::Pointer mask= maskReader->GetOutput();
  74
  75     // Filter setting background
  76     typedef clitk::SetBackgroundImageFilter<InputImageType,MaskImageType, InputImageType> SetBackgroundFilterType;
  77     typename SetBackgroundFilterType::Pointer setBackgroundFilter = SetBackgroundFilterType::New();
  78     setBackgroundFilter->SetInput(input);
  79     setBackgroundFilter->SetInput2(mask);
  80     if(m_ArgsInfo.fg_flag)  setBackgroundFilter->SetForeground(m_ArgsInfo.fg_flag);
  81     if(m_ArgsInfo.maskValue_given)  setBackgroundFilter->SetMaskValue(m_ArgsInfo.maskValue_arg);
  82     if(m_ArgsInfo.outsideValue_given)  setBackgroundFilter->SetOutsideValue(m_ArgsInfo.outsideValue_arg);
  83     setBackgroundFilter->Update();
  84     typename InputImageType::Pointer output =setBackgroundFilter->GetOutput();
  85
  86     // Output
  87     typedef itk::ImageFileWriter<InputImageType> WriterType;
  88     typename WriterType::Pointer writer = WriterType::New();
  89     writer->SetFileName(m_ArgsInfo.output_arg);
  90     writer->SetInput(output);
  91     writer->Update();
  92
  93   }
  94
  95
  96 }//end clitk
  97
  98 #endif //#define clitkSetBackgroundGenericFilter_txx