filters/clitkBinarizeImageGenericFilter.txx

   1 #ifndef clitkBinarizeImageGenericFilter_txx
   2 #define clitkBinarizeImageGenericFilter_txx
   3
   4 /* =================================================
   5  * @file   clitkBinarizeImageGenericFilter.txx
   6  * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
   7  * @date   29 june 2009
   8  *
   9  * @brief
  10  *
  11  ===================================================*/
  12
  13 // itk include
  14 #include "itkBinaryThresholdImageFilter.h"
  15 #include "itkMaskImageFilter.h"
  16 #include "itkMaskNegatedImageFilter.h"
  17
  18 namespace clitk
  19 {
  20
  21   //--------------------------------------------------------------------
  22   template<class args_info_type>
  23   BinarizeImageGenericFilter<args_info_type>::BinarizeImageGenericFilter():
  24     ImageToImageGenericFilter<Self>("Binarize") {
  25     //    InitializeImageType<2>();
  26     InitializeImageType<3>();
  27     //InitializeImageType<4>();
  28   }
  29   //--------------------------------------------------------------------
  30
  31
  32   //--------------------------------------------------------------------
  33   template<class args_info_type>
  34   template<unsigned int Dim>
  35   void BinarizeImageGenericFilter<args_info_type>::InitializeImageType() {
  36     //ADD_IMAGE_TYPE(Dim, char);
  37     ADD_IMAGE_TYPE(Dim, short);
  38     //ADD_IMAGE_TYPE(Dim, int);
  39     //ADD_IMAGE_TYPE(Dim, float);
  40   }
  41   //--------------------------------------------------------------------
  42
  43
  44   //--------------------------------------------------------------------
  45   template<class args_info_type>
  46   void BinarizeImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
  47     mArgsInfo=a;
  48     SetIOVerbose(mArgsInfo.verbose_flag);
  49
  50     if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  51
  52     if (mArgsInfo.input_given) {
  53       SetInputFilename(mArgsInfo.input_arg);
  54     }
  55     if (mArgsInfo.output_given) {
  56       SetOutputFilename(mArgsInfo.output_arg);
  57     }
  58   }
  59   //--------------------------------------------------------------------
  60
  61   //--------------------------------------------------------------------
  62   // Update with the number of dimensions and the pixeltype
  63   //--------------------------------------------------------------------
  64   template<class args_info_type>
  65   template<class InputImageType>
  66   void
  67   BinarizeImageGenericFilter<args_info_type>::UpdateWithInputImageType()
  68   {
  69
  70     // Reading input
  71     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  72
  73     // Main filter
  74     typedef typename InputImageType::PixelType PixelType;
  75     typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
  76
  77     // Filter
  78     typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
  79     typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
  80     thresholdFilter->SetInput(input);
  81     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
  82
  83     if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
  84     if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
  85
  86     DD(mArgsInfo.lower_given);
  87     DD(mArgsInfo.upper_given);
  88     DD(mArgsInfo.lower_arg);
  89     DD(mArgsInfo.upper_arg);
  90     DD(mArgsInfo.fg_arg);
  91     DD(mArgsInfo.bg_arg);
  92     DD(mArgsInfo.fg_given);
  93     DD(mArgsInfo.bg_given);
  94     DD(mArgsInfo.mode_arg);
  95
  96     /* Three modes :
  97        - FG -> only use FG value for pixel in the Foreground (or Inside), keep input values for outside
  98        - BG -> only use BG value for pixel in the Background (or Outside), keep input values for inside
  99        - both -> use FG and BG (real binary image)
 100     */
 101       if (mArgsInfo.mode_arg == std::string("both")) {
 102       thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 103       thresholdFilter->Update();
 104       typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
 105       this->template SetNextOutput<OutputImageType>(outputImage);
 106     }
 107     else {
 108       typename InputImageType::Pointer outputImage;
 109       thresholdFilter->SetOutsideValue(0);
 110       if (mArgsInfo.mode_arg == std::string("BG")) {
 111         typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
 112         typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 113         maskFilter->SetInput1(input);
 114         maskFilter->SetInput2(thresholdFilter->GetOutput());
 115         maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
 116         maskFilter->Update();
 117         outputImage = maskFilter->GetOutput();
 118       }
 119       else {
 120         typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
 121         typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 122         maskFilter->SetInput1(input);
 123         maskFilter->SetInput2(thresholdFilter->GetOutput());
 124         maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
 125         maskFilter->Update();
 126         outputImage = maskFilter->GetOutput();
 127       }
 128       // Write/Save results
 129       this->template SetNextOutput<InputImageType>(outputImage);
 130     }
 131   }
 132   //--------------------------------------------------------------------
 133
 134
 135 }//end clitk
 136
 137 #endif //#define clitkBinarizeImageGenericFilter_txx