filters/clitkFooImageGenericFilter.txx

   1 /*=========================================================================
   2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
   3
   4   Authors belong to:
   5   - University of LYON              http://www.universite-lyon.fr/
   6   - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   7   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
   8
   9   This software is distributed WITHOUT ANY WARRANTY; without even
  10   the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  11   PURPOSE.  See the copyright notices for more information.
  12
  13   It is distributed under dual licence
  14
  15   - BSD        See included LICENSE.txt file
  16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  17 ======================================================================-====*/
  18 #ifndef clitkFooImageGenericFilter_txx
  19 #define clitkFooImageGenericFilter_txx
  20
  21 /* =================================================
  22  * @file   clitkFooImageGenericFilter.txx
  23  * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
  24  * @date   29 june 2009
  25  *
  26  * @brief
  27  *
  28  ===================================================*/
  29
  30 // itk include
  31 #include "itkBinaryThresholdImageFilter.h"
  32 #include "itkMaskImageFilter.h"
  33 #include "itkMaskNegatedImageFilter.h"
  34 #include <clitkCommon.h>
  35
  36 namespace clitk
  37 {
  38
  39 //--------------------------------------------------------------------
  40 template<class args_info_type>
  41 FooImageGenericFilter<args_info_type>::FooImageGenericFilter():
  42         ImageToImageGenericFilter<Self>("FooImage") {
  43     InitializeImageType<2>();
  44     InitializeImageType<3>();
  45     InitializeImageType<4>();
  46 }
  47 //--------------------------------------------------------------------
  48
  49
  50 //--------------------------------------------------------------------
  51 template<class args_info_type>
  52 template<unsigned int Dim>
  53 void FooImageGenericFilter<args_info_type>::InitializeImageType() {
  54     ADD_IMAGE_TYPE(Dim, char);
  55     ADD_IMAGE_TYPE(Dim, uchar);
  56     ADD_IMAGE_TYPE(Dim, short);
  57     ADD_IMAGE_TYPE(Dim, ushort);
  58     ADD_IMAGE_TYPE(Dim, int);
  59     ADD_IMAGE_TYPE(Dim, float);
  60     ADD_IMAGE_TYPE(Dim, double);
  61 }
  62 //--------------------------------------------------------------------
  63
  64
  65 //--------------------------------------------------------------------
  66 template<class args_info_type>
  67 void FooImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
  68     mArgsInfo=a;
  69     SetIOVerbose(mArgsInfo.verbose_flag);
  70     if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  71
  72     if (mArgsInfo.input_given) {
  73         SetInputFilename(mArgsInfo.input_arg);
  74     }
  75     if (mArgsInfo.output_given) {
  76         SetOutputFilename(mArgsInfo.output_arg);
  77     }
  78 }
  79 //--------------------------------------------------------------------
  80
  81 //--------------------------------------------------------------------
  82 // Update with the number of dimensions and the pixeltype
  83 //--------------------------------------------------------------------
  84 template<class args_info_type>
  85 template<class InputImageType>
  86 void
  87 FooImageGenericFilter<args_info_type>::UpdateWithInputImageType()
  88 {
  89
  90     // Reading input
  91     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  92
  93     // Main filter
  94     typedef typename InputImageType::PixelType PixelType;
  95     typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
  96
  97     // Filter
  98     typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
  99     typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
 100     thresholdFilter->SetInput(input);
 101     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
 102
 103     if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
 104     if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
 105
 106     if (mArgsInfo.mode_arg == std::string("both")) {
 107         thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 108         thresholdFilter->Update();
 109
 110         typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
 111         this->template SetNextOutput<OutputImageType>(outputImage);
 112     }
 113     else {
 114         typename InputImageType::Pointer outputImage;
 115         thresholdFilter->SetOutsideValue(0);
 116         if (mArgsInfo.mode_arg == std::string("BG")) {
 117             typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
 118             typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 119             maskFilter->SetInput1(input);
 120             maskFilter->SetInput2(thresholdFilter->GetOutput());
 121             maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
 122             maskFilter->Update();
 123             outputImage = maskFilter->GetOutput();
 124         }
 125         else {
 126             typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
 127             typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 128             maskFilter->SetInput1(input);
 129             maskFilter->SetInput2(thresholdFilter->GetOutput());
 130             maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
 131             maskFilter->Update();
 132             outputImage = maskFilter->GetOutput();
 133         }
 134         // Write/Save results
 135         this->template SetNextOutput<InputImageType>(outputImage);
 136     }
 137 }
 138 //--------------------------------------------------------------------
 139
 140
 141 }//end clitk
 142
 143 #endif //#define clitkFooImageGenericFilter_txx