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     // Check option
  74     if (!mArgsInfo.useFG_flag && !mArgsInfo.useBG_flag) {
  75       // Do nothing !!
  76       std::cerr << "Warning : FG and BG are not used ! Do nothing." << std::endl;
  77       this->template SetNextOutput<InputImageType>(input);
  78       return;
  79     }
  80
  81     // Main filter
  82     typedef typename InputImageType::PixelType PixelType;
  83     typedef itk::Image<int, InputImageType::ImageDimension> OutputImageType;
  84
  85     // Filter
  86     typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
  87     typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
  88     thresholdFilter->SetInput(input);
  89
  90     /*    if (mArgsInfo.useFG_flag && !mArgsInfo.useBG_flag) {
  91       DD("inverse");
  92       // double fg = mArgsInfo.fg_arg;
  93       //mArgsInfo.fg_arg = mArgsInfo.bg_arg;
  94       // mArgsInfo.bg_arg = fg;
  95        //   bool lo = mArgsInfo.lower_given;
  96        //mArgsInfo.lower_given = mArgsInfo.upper_given;
  97        //mArgsInfo.upper_given = lo;
  98        }*/
  99
 100     if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
 101     if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
 102
 103     DD(mArgsInfo.lower_given);
 104     DD(mArgsInfo.upper_given);
 105     DD(mArgsInfo.lower_arg);
 106     DD(mArgsInfo.upper_arg);
 107
 108     DD(mArgsInfo.fg_arg);
 109     DD(mArgsInfo.bg_arg);
 110     DD(mArgsInfo.fg_given);
 111     DD(mArgsInfo.bg_given);
 112
 113     DD(mArgsInfo.useFG_flag);
 114     DD(mArgsInfo.useBG_flag);
 115
 116     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
 117     thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 118
 119     thresholdFilter->Update();
 120
 121     // If no BG or no FG : new image, copy input with MaskImageFilter
 122     // If setFG -> FG BG have been changed
 123     if (mArgsInfo.useBG_flag && mArgsInfo.useFG_flag) {
 124       typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
 125       // Write/Save results
 126       this->template SetNextOutput<OutputImageType>(outputImage);
 127     }
 128     else {
 129       typename InputImageType::Pointer outputImage;
 130       if (mArgsInfo.useBG_flag) {
 131         DD("use 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->Update();
 137         maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
 138         outputImage = maskFilter->GetOutput();
 139       }
 140       else {
 141         DD("use FG");
 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