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     if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  50
  51     if (mArgsInfo.input_given) {
  52       SetInputFilename(mArgsInfo.input_arg);
  53     }
  54     if (mArgsInfo.output_given) {
  55       SetOutputFilename(mArgsInfo.output_arg);
  56     }
  57   }
  58   //--------------------------------------------------------------------
  59
  60   //--------------------------------------------------------------------
  61   // Update with the number of dimensions and the pixeltype
  62   //--------------------------------------------------------------------
  63   template<class args_info_type>
  64   template<class InputImageType>
  65   void
  66   BinarizeImageGenericFilter<args_info_type>::UpdateWithInputImageType()
  67   {
  68
  69     // Reading input
  70     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  71
  72     // Main filter
  73     typedef typename InputImageType::PixelType PixelType;
  74     typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
  75
  76     // Filter
  77     typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
  78     typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
  79     thresholdFilter->SetInput(input);
  80     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
  81
  82     if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
  83     if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
  84
  85     // DD(mArgsInfo.lower_given);
  86     // DD(mArgsInfo.upper_given);
  87     // DD(mArgsInfo.lower_arg);
  88     // DD(mArgsInfo.upper_arg);
  89     // DD(mArgsInfo.fg_arg);
  90     // DD(mArgsInfo.bg_arg);
  91     // DD(mArgsInfo.fg_given);
  92     // DD(mArgsInfo.bg_given);
  93     // DD(mArgsInfo.mode_arg);
  94
  95 // <<<<<<< clitkBinarizeImageGenericFilter.txx
  96 //     DD(mArgsInfo.useFG_flag);
  97 //     DD(mArgsInfo.useBG_flag);
  98
  99 //     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
 100
 101 //     // Keep BG value to 0 if maskFilterType is used after
 102 //     if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
 103 //       thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 104 //     }
 105 //     else {
 106 //       DD("0");
 107 //       thresholdFilter->SetOutsideValue(0);
 108 //     }
 109
 110 //     // thresholdFilter->Update();
 111
 112 //     // If no BG or no FG : new image, copy input with MaskImageFilter
 113 //     // If setFG -> FG BG have been changed
 114 //     if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
 115 // =======
 116     /* Three modes :
 117        - FG -> only use FG value for pixel in the Foreground (or Inside), keep input values for outside
 118        - BG -> only use BG value for pixel in the Background (or Outside), keep input values for inside
 119        - both -> use FG and BG (real binary image)
 120     */
 121       if (mArgsInfo.mode_arg == std::string("both")) {
 122       thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 123       thresholdFilter->Update();
 124       //>>>>>>> 1.5
 125       typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
 126       this->template SetNextOutput<OutputImageType>(outputImage);
 127     }
 128     else {
 129       typename InputImageType::Pointer outputImage;
 130       thresholdFilter->SetOutsideValue(0);
 131       if (mArgsInfo.mode_arg == std::string("BG")) {
 132         typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
 133         typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 134         maskFilter->SetInput1(input);
 135         maskFilter->SetInput2(thresholdFilter->GetOutput());
 136         maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
 137         maskFilter->Update();
 138         outputImage = maskFilter->GetOutput();
 139       }
 140       else {
 141         typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
 142         typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 143         maskFilter->SetInput1(input);
 144         maskFilter->SetInput2(thresholdFilter->GetOutput());
 145         maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
 146         maskFilter->Update();
 147         outputImage = maskFilter->GetOutput();
 148       }
 149       // Write/Save results
 150       this->template SetNextOutput<InputImageType>(outputImage);
 151     }
 152   }
 153   //--------------------------------------------------------------------
 154
 155
 156 }//end clitk
 157
 158 #endif //#define clitkBinarizeImageGenericFilter_txx