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 ======================================================================-====*/
19 #ifndef CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
20 #define CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX
22 #include "clitkImageCommon.h"
24 //--------------------------------------------------------------------
25 template<class ArgsInfoType>
26 clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::ExtractLymphStationsGenericFilter():
27 ImageToImageGenericFilter<Self>("ExtractLymphStations")
30 cmdline_parser_clitkExtractLymphStations_init(&mArgsInfo);
31 InitializeImageType<3>(); // Only for 3D images
33 //--------------------------------------------------------------------
36 //--------------------------------------------------------------------
37 template<class ArgsInfoType>
38 template<unsigned int Dim>
39 void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::InitializeImageType()
41 ADD_IMAGE_TYPE(Dim, short); // Can add float later
43 //--------------------------------------------------------------------
46 //--------------------------------------------------------------------
47 template<class ArgsInfoType>
48 void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
51 SetIOVerbose(mArgsInfo.verbose_flag);
52 if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
53 if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
54 if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
56 //--------------------------------------------------------------------
59 //--------------------------------------------------------------------
60 template<class ArgsInfoType>
61 template<class FilterType>
63 clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::
64 SetOptionsFromArgsInfoToFilter(FilterType * f)
66 f->SetVerboseOptionFlag(mArgsInfo.verbose_flag);
67 f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
68 f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
69 f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
70 f->SetAFDBFilename(mArgsInfo.afdb_arg);
72 f->SetComputeStationsSupportsFlag(!mArgsInfo.nosupport_flag);
75 //f->SetDistanceMaxToAnteriorPartOfTheSpine(mArgsInfo.S8_maxAntSpine_arg);
76 f->SetFuzzyThreshold("8", "Esophagus", mArgsInfo.S8_ft_Esophagus_arg);
77 // f->SetInjectedThresholdForS8(mArgsInfo.tS8_injectedThreshold_arg);
79 // Check multiple options for radius dilatation
81 typename FilterType::MaskImagePointType p;
82 SetMultipleOptionMacro(mArgsInfo, esophagusDilatation, 3, p);
83 default ? = set before
86 typename FilterType::MaskImagePointType p;
87 p[0] = 7; p[1] = 5; p[2] = 0; // default value
88 if (mArgsInfo.S8_esophagusDilatationForAnt_given == 3) {
89 for(uint i=0; i<3; i++)
90 p[i] = mArgsInfo.S8_esophagusDilatationForAnt_arg[i];
93 if (mArgsInfo.S8_esophagusDilatationForAnt_given == 1) {
94 for(uint i=0; i<3; i++)
95 p[i] = mArgsInfo.S8_esophagusDilatationForAnt_arg[0];
98 f->SetEsophagusDiltationForAnt(p);
100 p[0] = 5; p[1] = 10; p[2] = 1; // default value
101 if (mArgsInfo.S8_esophagusDilatationForRight_given == 3) {
102 for(uint i=0; i<3; i++)
103 p[i] = mArgsInfo.S8_esophagusDilatationForRight_arg[i];
106 if (mArgsInfo.S8_esophagusDilatationForRight_given == 1) {
107 for(uint i=0; i<3; i++)
108 p[i] = mArgsInfo.S8_esophagusDilatationForRight_arg[0];
111 f->SetEsophagusDiltationForRight(p);
113 for(uint i=0; i<mArgsInfo.station_given; i++)
114 f->AddComputeStation(mArgsInfo.station_arg[i]);
117 f->SetFuzzyThreshold("3A", "SVC", mArgsInfo.S3A_ft_SVC_arg);
118 f->SetFuzzyThreshold("3A", "Bones", mArgsInfo.S3A_ft_Bones_arg);
119 f->SetThreshold("3A", "Bones", mArgsInfo.S3A_t_Bones_arg);
120 f->SetFuzzyThreshold("3A", "Aorta", mArgsInfo.S3A_ft_Aorta_arg);
121 f->SetFuzzyThreshold("3A", "SubclavianArtery", mArgsInfo.S3A_ft_SubclavianArtery_arg);
124 f->SetFuzzyThreshold("7", "Bronchi", mArgsInfo.S7_ft_Bronchi_arg);
125 f->SetFuzzyThreshold("7", "LeftSuperiorPulmonaryVein", mArgsInfo.S7_ft_LeftSuperiorPulmonaryVein_arg);
126 f->SetFuzzyThreshold("7", "RightSuperiorPulmonaryVein", mArgsInfo.S7_ft_RightSuperiorPulmonaryVein_arg);
127 f->SetFuzzyThreshold("7", "RightPulmonaryArtery", mArgsInfo.S7_ft_RightPulmonaryArtery_arg);
128 f->SetFuzzyThreshold("7", "LeftPulmonaryArtery", mArgsInfo.S7_ft_LeftPulmonaryArtery_arg);
129 f->SetFuzzyThreshold("7", "SVC", mArgsInfo.S7_ft_SVC_arg);
130 f->SetS7_UseMostInferiorPartOnlyFlag(mArgsInfo.S7_UseMostInferiorPartOnly_flag);
133 f->SetFuzzyThreshold("2RL", "CommonCarotidArtery", mArgsInfo.S2RL_ft_CommonCarotidArtery_arg);
134 f->SetFuzzyThreshold("2RL", "BrachioCephalicTrunk", mArgsInfo.S2RL_ft_BrachioCephalicTrunk_arg);
135 f->SetFuzzyThreshold("2RL", "BrachioCephalicVein", mArgsInfo.S2RL_ft_BrachioCephalicVein_arg);
136 f->SetFuzzyThreshold("2RL", "Aorta", mArgsInfo.S2RL_ft_Aorta_arg);
137 f->SetFuzzyThreshold("2RL", "SubclavianArteryLeft", mArgsInfo.S2RL_ft_SubclavianArteryLeft_arg);
138 f->SetFuzzyThreshold("2RL", "SubclavianArteryRight", mArgsInfo.S2RL_ft_SubclavianArteryRight_arg);
140 //--------------------------------------------------------------------
143 //--------------------------------------------------------------------
144 // Update with the number of dimensions and the pixeltype
145 //--------------------------------------------------------------------
146 template<class ArgsInfoType>
147 template<class ImageType>
148 void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
151 typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
154 typedef clitk::ExtractLymphStationsFilter<ImageType> FilterType;
155 typename FilterType::Pointer filter = FilterType::New();
157 // Set global Options
158 filter->SetInput(input);
159 SetOptionsFromArgsInfoToFilter<FilterType>(filter);
164 // Write/Save results
165 typedef uchar MaskImagePixelType;
166 typedef itk::Image<MaskImagePixelType, 3> OutputImageType;
167 typename OutputImageType::Pointer output = filter->GetOutput();
168 this->template SetNextOutput<OutputImageType>(output);
170 //--------------------------------------------------------------------
172 #endif //#define CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX