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 #include <tiff.h>
  36
  37 namespace clitk
  38 {
  39
  40 //--------------------------------------------------------------------
  41 template<class args_info_type>
  42 FooImageGenericFilter<args_info_type>::FooImageGenericFilter():
  43         ImageToImageGenericFilter<Self>("FooImage") {
  44     InitializeImageType<2>();
  45     InitializeImageType<3>();
  46     InitializeImageType<4>();
  47 }
  48 //--------------------------------------------------------------------
  49
  50
  51 //--------------------------------------------------------------------
  52 template<class args_info_type>
  53 template<unsigned int Dim>
  54 void FooImageGenericFilter<args_info_type>::InitializeImageType() {
  55     ADD_IMAGE_TYPE(Dim, char);
  56     ADD_IMAGE_TYPE(Dim, uchar);
  57     ADD_IMAGE_TYPE(Dim, short);
  58     ADD_IMAGE_TYPE(Dim, ushort);
  59     ADD_IMAGE_TYPE(Dim, int);
  60     ADD_IMAGE_TYPE(Dim, float);
  61     ADD_IMAGE_TYPE(Dim, double);
  62 }
  63 //--------------------------------------------------------------------
  64
  65
  66 //--------------------------------------------------------------------
  67 template<class args_info_type>
  68 void FooImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
  69     mArgsInfo=a;
  70     SetIOVerbose(mArgsInfo.verbose_flag);
  71     if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  72
  73     if (mArgsInfo.input_given) {
  74         SetInputFilename(mArgsInfo.input_arg);
  75     }
  76     if (mArgsInfo.output_given) {
  77         SetOutputFilename(mArgsInfo.output_arg);
  78     }
  79 }
  80 //--------------------------------------------------------------------
  81
  82 //--------------------------------------------------------------------
  83 // Update with the number of dimensions and the pixeltype
  84 //--------------------------------------------------------------------
  85 template<class args_info_type>
  86 template<class InputImageType>
  87 void
  88 FooImageGenericFilter<args_info_type>::UpdateWithInputImageType()
  89 {
  90
  91     // Reading input
  92     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  93
  94     // Main filter
  95     typedef typename InputImageType::PixelType PixelType;
  96     typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
  97
  98     // Filter
  99     typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
 100     typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
 101     thresholdFilter->SetInput(input);
 102     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
 103
 104     if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
 105     if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
 106
 107     if (mArgsInfo.mode_arg == std::string("both")) {
 108         thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 109         thresholdFilter->Update();
 110
 111         typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
 112         this->template SetNextOutput<OutputImageType>(outputImage);
 113     }
 114     else {
 115         typename InputImageType::Pointer outputImage;
 116         thresholdFilter->SetOutsideValue(0);
 117         if (mArgsInfo.mode_arg == std::string("BG")) {
 118             typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
 119             typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 120             maskFilter->SetInput1(input);
 121             maskFilter->SetInput2(thresholdFilter->GetOutput());
 122             maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
 123             maskFilter->Update();
 124             outputImage = maskFilter->GetOutput();
 125         }
 126         else {
 127             typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
 128             typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 129             maskFilter->SetInput1(input);
 130             maskFilter->SetInput2(thresholdFilter->GetOutput());
 131             maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
 132             maskFilter->Update();
 133             outputImage = maskFilter->GetOutput();
 134         }
 135         // Write/Save results
 136         this->template SetNextOutput<InputImageType>(outputImage);
 137     }
 138 }
 139 //--------------------------------------------------------------------
 140
 141
 142 }//end clitk
 143
 144 #endif //#define clitkFooImageGenericFilter_txx