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_DEFAULT_IMAGE_TYPES(Dim);
  55 }
  56 //--------------------------------------------------------------------
  57
  58
  59 //--------------------------------------------------------------------
  60 template<class args_info_type>
  61 void FooImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
  62     mArgsInfo=a;
  63     SetIOVerbose(mArgsInfo.verbose_flag);
  64     if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  65
  66     if (mArgsInfo.input_given) {
  67         SetInputFilename(mArgsInfo.input_arg);
  68     }
  69     if (mArgsInfo.output_given) {
  70         SetOutputFilename(mArgsInfo.output_arg);
  71     }
  72 }
  73 //--------------------------------------------------------------------
  74
  75 //--------------------------------------------------------------------
  76 // Update with the number of dimensions and the pixeltype
  77 //--------------------------------------------------------------------
  78 template<class args_info_type>
  79 template<class InputImageType>
  80 void
  81 FooImageGenericFilter<args_info_type>::UpdateWithInputImageType()
  82 {
  83
  84     // Reading input
  85     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  86
  87     // Main filter
  88     typedef typename InputImageType::PixelType PixelType;
  89     typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
  90
  91     // Filter
  92     typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
  93     typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
  94     thresholdFilter->SetInput(input);
  95     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
  96
  97     if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
  98     if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
  99
 100     if (mArgsInfo.mode_arg == std::string("both")) {
 101         thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 102         thresholdFilter->Update();
 103
 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 clitkFooImageGenericFilter_txx