1 /*=========================================================================
2 Program: vv http://www.creatis.insa-lyon.fr/rio/vv
5 - University of LYON http://www.universite-lyon.fr/
6 - Léon Bérard cancer center http://www.centreleonberard.fr
7 - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
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.
13 It is distributed under dual licence
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
21 /* =================================================
22 * @file clitkFooImageGenericFilter.txx
23 * @author Jef Vandemeulebroucke <jef@creatis.insa-lyon.fr>
28 ===================================================*/
31 #include "itkBinaryThresholdImageFilter.h"
32 #include "itkMaskImageFilter.h"
33 #include "itkMaskNegatedImageFilter.h"
34 #include <clitkCommon.h>
39 //--------------------------------------------------------------------
40 template<class args_info_type>
41 FooImageGenericFilter<args_info_type>::FooImageGenericFilter():
42 ImageToImageGenericFilter<Self>("FooImage")
44 InitializeImageType<2>();
45 InitializeImageType<3>();
46 InitializeImageType<4>();
48 //--------------------------------------------------------------------
51 //--------------------------------------------------------------------
52 template<class args_info_type>
53 template<unsigned int Dim>
54 void FooImageGenericFilter<args_info_type>::InitializeImageType()
56 ADD_DEFAULT_IMAGE_TYPES(Dim);
58 //--------------------------------------------------------------------
61 //--------------------------------------------------------------------
62 template<class args_info_type>
63 void FooImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a)
66 SetIOVerbose(mArgsInfo.verbose_flag);
67 if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
69 if (mArgsInfo.input_given) {
70 SetInputFilename(mArgsInfo.input_arg);
72 if (mArgsInfo.output_given) {
73 SetOutputFilename(mArgsInfo.output_arg);
76 //--------------------------------------------------------------------
78 //--------------------------------------------------------------------
79 // Update with the number of dimensions and the pixeltype
80 //--------------------------------------------------------------------
81 template<class args_info_type>
82 template<class InputImageType>
84 FooImageGenericFilter<args_info_type>::UpdateWithInputImageType()
88 typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
91 typedef typename InputImageType::PixelType PixelType;
92 typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
95 typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
96 typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
97 thresholdFilter->SetInput(input);
98 thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
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));
103 if (mArgsInfo.mode_arg == std::string("both")) {
104 thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
105 thresholdFilter->Update();
107 typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
108 this->template SetNextOutput<OutputImageType>(outputImage);
110 typename InputImageType::Pointer outputImage;
111 thresholdFilter->SetOutsideValue(0);
112 if (mArgsInfo.mode_arg == std::string("BG")) {
113 typedef itk::MaskImageFilter<InputImageType,OutputImageType> maskFilterType;
114 typename maskFilterType::Pointer maskFilter = maskFilterType::New();
115 maskFilter->SetInput1(input);
116 maskFilter->SetInput2(thresholdFilter->GetOutput());
117 maskFilter->SetOutsideValue(mArgsInfo.bg_arg);
118 maskFilter->Update();
119 outputImage = maskFilter->GetOutput();
121 typedef itk::MaskNegatedImageFilter<InputImageType,OutputImageType> maskFilterType;
122 typename maskFilterType::Pointer maskFilter = maskFilterType::New();
123 maskFilter->SetInput1(input);
124 maskFilter->SetInput2(thresholdFilter->GetOutput());
125 maskFilter->SetOutsideValue(mArgsInfo.fg_arg);
126 maskFilter->Update();
127 outputImage = maskFilter->GetOutput();
129 // Write/Save results
130 this->template SetNextOutput<InputImageType>(outputImage);
133 //--------------------------------------------------------------------
138 #endif //#define clitkFooImageGenericFilter_txx