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, uchar);
  38     ADD_IMAGE_TYPE(Dim, short);
  39     ADD_IMAGE_TYPE(Dim, int);
  40     ADD_IMAGE_TYPE(Dim, float);
  41   }
  42   //--------------------------------------------------------------------
  43
  44
  45   //--------------------------------------------------------------------
  46   template<class args_info_type>
  47   void BinarizeImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
  48     mArgsInfo=a;
  49     SetIOVerbose(mArgsInfo.verbose_flag);
  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 // <<<<<<< clitkBinarizeImageGenericFilter.txx
  97 //     DD(mArgsInfo.useFG_flag);
  98 //     DD(mArgsInfo.useBG_flag);
  99
 100 //     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
 101
 102 //     // Keep BG value to 0 if maskFilterType is used after
 103 //     if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
 104 //       thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 105 //     }
 106 //     else {
 107 //       DD("0");
 108 //       thresholdFilter->SetOutsideValue(0);
 109 //     }
 110
 111 //     // thresholdFilter->Update();
 112
 113 //     // If no BG or no FG : new image, copy input with MaskImageFilter
 114 //     // If setFG -> FG BG have been changed
 115 //     if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
 116 // =======
 117     /* Three modes :
 118        - FG -> only use FG value for pixel in the Foreground (or Inside), keep input values for outside
 119        - BG -> only use BG value for pixel in the Background (or Outside), keep input values for inside
 120        - both -> use FG and BG (real binary image)
 121     */
 122       if (mArgsInfo.mode_arg == std::string("both")) {
 123       thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 124       thresholdFilter->Update();
 125       //>>>>>>> 1.5
 126       typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
 127       this->template SetNextOutput<OutputImageType>(outputImage);
 128     }
 129     else {
 130       typename InputImageType::Pointer outputImage;
 131       thresholdFilter->SetOutsideValue(0);
 132       if (mArgsInfo.mode_arg == std::string("BG")) {
 133         typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
 134         typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 135         maskFilter->SetInput1(input);
 136         maskFilter->SetInput2(thresholdFilter->GetOutput());
 137         maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
 138         maskFilter->Update();
 139         outputImage = maskFilter->GetOutput();
 140       }
 141       else {
 142         typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
 143         typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 144         maskFilter->SetInput1(input);
 145         maskFilter->SetInput2(thresholdFilter->GetOutput());
 146         maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
 147         maskFilter->Update();
 148         outputImage = maskFilter->GetOutput();
 149       }
 150       // Write/Save results
 151       this->template SetNextOutput<InputImageType>(outputImage);
 152     }
 153   }
 154   //--------------------------------------------------------------------
 155
 156
 157 }//end clitk
 158
 159 #endif //#define clitkBinarizeImageGenericFilter_txx