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);
73 f->SetDistanceMaxToAnteriorPartOfTheSpine(mArgsInfo.maxAntSpine_arg);
74 f->SetFuzzyThreshold("8", "Esophagus", mArgsInfo.tS8_Esophagus_arg);
75 f->SetInjectedThresholdForS8(mArgsInfo.injectedThresholdForS8_arg);
77 // Check multiple options for radius dilatation
79 typename FilterType::MaskImagePointType p;
80 SetMultipleOptionMacro(mArgsInfo, esophagusDilatation, 3, p);
81 default ? = set before
84 typename FilterType::MaskImagePointType p;
85 p[0] = 7; p[1] = 5; p[2] = 0; // default value
86 if (mArgsInfo.esophagusDilatationForAnt_given == 3) {
87 for(uint i=0; i<3; i++)
88 p[i] = mArgsInfo.esophagusDilatationForAnt_arg[i];
91 if (mArgsInfo.esophagusDilatationForAnt_given == 1) {
92 for(uint i=0; i<3; i++)
93 p[i] = mArgsInfo.esophagusDilatationForAnt_arg[0];
96 f->SetEsophagusDiltationForAnt(p);
98 p[0] = 5; p[1] = 10; p[2] = 1; // default value
99 if (mArgsInfo.esophagusDilatationForRight_given == 3) {
100 for(uint i=0; i<3; i++)
101 p[i] = mArgsInfo.esophagusDilatationForRight_arg[i];
104 if (mArgsInfo.esophagusDilatationForRight_given == 1) {
105 for(uint i=0; i<3; i++)
106 p[i] = mArgsInfo.esophagusDilatationForRight_arg[0];
109 f->SetEsophagusDiltationForRight(p);
111 for(uint i=0; i<mArgsInfo.station_given; i++)
112 f->AddComputeStation(mArgsInfo.station_arg[i]);
115 f->SetFuzzyThreshold("7", "Bronchi", mArgsInfo.tS7_Bronchi_arg);
116 f->SetFuzzyThreshold("7", "LeftSuperiorPulmonaryVein", mArgsInfo.tS7_LeftSuperiorPulmonaryVein_arg);
117 f->SetFuzzyThreshold("7", "RightSuperiorPulmonaryVein", mArgsInfo.tS7_RightSuperiorPulmonaryVein_arg);
118 f->SetFuzzyThreshold("7", "RightPulmonaryArtery", mArgsInfo.tS7_RightPulmonaryArtery_arg);
119 f->SetFuzzyThreshold("7", "LeftPulmonaryArtery", mArgsInfo.tS7_LeftPulmonaryArtery_arg);
120 f->SetFuzzyThreshold("7", "SVC", mArgsInfo.tS7_SVC_arg);
123 f->SetFuzzyThreshold("3A", "Sternum", mArgsInfo.tS3A_Sternum_arg);
124 f->SetFuzzyThreshold("3A", "SubclavianArtery", mArgsInfo.tS3A_SubclavianArtery_arg);
127 f->SetFuzzyThreshold("2RL", "CommonCarotidArtery", mArgsInfo.tS2RL_CommonCarotidArtery_arg);
128 f->SetFuzzyThreshold("2RL", "BrachioCephalicTrunk", mArgsInfo.tS2RL_BrachioCephalicTrunk_arg);
129 f->SetFuzzyThreshold("2RL", "BrachioCephalicVein", mArgsInfo.tS2RL_BrachioCephalicVein_arg);
130 f->SetFuzzyThreshold("2RL", "Aorta", mArgsInfo.tS2RL_Aorta_arg);
131 f->SetFuzzyThreshold("2RL", "SubclavianArteryLeft", mArgsInfo.tS2RL_SubclavianArteryLeft_arg);
132 f->SetFuzzyThreshold("2RL", "SubclavianArteryRight", mArgsInfo.tS2RL_SubclavianArteryRight_arg);
134 //--------------------------------------------------------------------
137 //--------------------------------------------------------------------
138 // Update with the number of dimensions and the pixeltype
139 //--------------------------------------------------------------------
140 template<class ArgsInfoType>
141 template<class ImageType>
142 void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
145 typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
148 typedef clitk::ExtractLymphStationsFilter<ImageType> FilterType;
149 typename FilterType::Pointer filter = FilterType::New();
151 // Set global Options
152 filter->SetInput(input);
153 SetOptionsFromArgsInfoToFilter<FilterType>(filter);
158 // Write/Save results
159 typedef uchar MaskImagePixelType;
160 typedef itk::Image<MaskImagePixelType, 3> OutputImageType;
161 typename OutputImageType::Pointer output = filter->GetOutput();
162 this->template SetNextOutput<OutputImageType>(output);
164 //--------------------------------------------------------------------
166 #endif //#define CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX