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, uint16);
  61     ADD_IMAGE_TYPE(Dim, float);
  62     ADD_IMAGE_TYPE(Dim, double);
  63 }
  64 //--------------------------------------------------------------------
  65
  66
  67 //--------------------------------------------------------------------
  68 template<class args_info_type>
  69 void FooImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
  70     mArgsInfo=a;
  71     SetIOVerbose(mArgsInfo.verbose_flag);
  72     if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
  73
  74     if (mArgsInfo.input_given) {
  75         SetInputFilename(mArgsInfo.input_arg);
  76     }
  77     if (mArgsInfo.output_given) {
  78         SetOutputFilename(mArgsInfo.output_arg);
  79     }
  80 }
  81 //--------------------------------------------------------------------
  82
  83 //--------------------------------------------------------------------
  84 // Update with the number of dimensions and the pixeltype
  85 //--------------------------------------------------------------------
  86 template<class args_info_type>
  87 template<class InputImageType>
  88 void
  89 FooImageGenericFilter<args_info_type>::UpdateWithInputImageType()
  90 {
  91
  92     // Reading input
  93     typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
  94
  95     // Main filter
  96     typedef typename InputImageType::PixelType PixelType;
  97     typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
  98
  99     // Filter
 100     typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
 101     typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
 102     thresholdFilter->SetInput(input);
 103     thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
 104
 105     if (mArgsInfo.lower_given) thresholdFilter->SetLowerThreshold(static_cast<PixelType>(mArgsInfo.lower_arg));
 106     if (mArgsInfo.upper_given) thresholdFilter->SetUpperThreshold(static_cast<PixelType>(mArgsInfo.upper_arg));
 107
 108     if (mArgsInfo.mode_arg == std::string("both")) {
 109         thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
 110         thresholdFilter->Update();
 111
 112         typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
 113         this->template SetNextOutput<OutputImageType>(outputImage);
 114     }
 115     else {
 116         typename InputImageType::Pointer outputImage;
 117         thresholdFilter->SetOutsideValue(0);
 118         if (mArgsInfo.mode_arg == std::string("BG")) {
 119             typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
 120             typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 121             maskFilter->SetInput1(input);
 122             maskFilter->SetInput2(thresholdFilter->GetOutput());
 123             maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
 124             maskFilter->Update();
 125             outputImage = maskFilter->GetOutput();
 126         }
 127         else {
 128             typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
 129             typename maskFilterType::Pointer maskFilter = maskFilterType::New();
 130             maskFilter->SetInput1(input);
 131             maskFilter->SetInput2(thresholdFilter->GetOutput());
 132             maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
 133             maskFilter->Update();
 134             outputImage = maskFilter->GetOutput();
 135         }
 136         // Write/Save results
 137         this->template SetNextOutput<InputImageType>(outputImage);
 138     }
 139 }
 140 //--------------------------------------------------------------------
 141
 142
 143 }//end clitk
 144
 145 #endif //#define clitkFooImageGenericFilter_txx