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://oncora1.lyon.fnclcc.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") {
43 InitializeImageType<2>();
44 InitializeImageType<3>();
45 InitializeImageType<4>();
47 //--------------------------------------------------------------------
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);
56 //--------------------------------------------------------------------
59 //--------------------------------------------------------------------
60 template<class args_info_type>
61 void FooImageGenericFilter<args_info_type>::SetArgsInfo(const args_info_type & a) {
63 SetIOVerbose(mArgsInfo.verbose_flag);
64 if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
66 if (mArgsInfo.input_given) {
67 SetInputFilename(mArgsInfo.input_arg);
69 if (mArgsInfo.output_given) {
70 SetOutputFilename(mArgsInfo.output_arg);
73 //--------------------------------------------------------------------
75 //--------------------------------------------------------------------
76 // Update with the number of dimensions and the pixeltype
77 //--------------------------------------------------------------------
78 template<class args_info_type>
79 template<class InputImageType>
81 FooImageGenericFilter<args_info_type>::UpdateWithInputImageType()
85 typename InputImageType::Pointer input = this->template GetInput<InputImageType>(0);
88 typedef typename InputImageType::PixelType PixelType;
89 typedef itk::Image<char, InputImageType::ImageDimension> OutputImageType;
92 typedef itk::BinaryThresholdImageFilter<InputImageType, OutputImageType> BinaryThresholdImageFilterType;
93 typename BinaryThresholdImageFilterType::Pointer thresholdFilter=BinaryThresholdImageFilterType::New();
94 thresholdFilter->SetInput(input);
95 thresholdFilter->SetInsideValue(mArgsInfo.fg_arg);
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));
100 if (mArgsInfo.mode_arg == std::string("both")) {
101 thresholdFilter->SetOutsideValue(mArgsInfo.bg_arg);
102 thresholdFilter->Update();
104 typename OutputImageType::Pointer outputImage = thresholdFilter->GetOutput();
105 this->template SetNextOutput<OutputImageType>(outputImage);
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();
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();
128 // Write/Save results
129 this->template SetNextOutput<InputImageType>(outputImage);
132 //--------------------------------------------------------------------
137 #endif //#define clitkFooImageGenericFilter_txx