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);
71 f->SetDistanceMaxToAnteriorPartOfTheSpine(mArgsInfo.maxAntSpine_arg);
72 f->SetFuzzyThresholdForS8(mArgsInfo.fuzzyThresholdForS8_arg);
74 // Check multiple options for radius dilatation
76 typename FilterType::MaskImagePointType p;
77 SetMultipleOptionMacro(mArgsInfo, esophagusDilatation, 3, p);
78 default ? = set before
81 typename FilterType::MaskImagePointType p;
82 p[0] = 7; p[1] = 5; p[2] = 0; // default value
83 if (mArgsInfo.esophagusDilatationForAnt_given == 3) {
84 for(uint i=0; i<3; i++)
85 p[i] = mArgsInfo.esophagusDilatationForAnt_arg[i];
88 if (mArgsInfo.esophagusDilatationForAnt_given == 1) {
89 for(uint i=0; i<3; i++)
90 p[i] = mArgsInfo.esophagusDilatationForAnt_arg[0];
93 f->SetEsophagusDiltationForAnt(p);
95 p[0] = 5; p[1] = 10; p[2] = 1; // default value
96 if (mArgsInfo.esophagusDilatationForRight_given == 3) {
97 for(uint i=0; i<3; i++)
98 p[i] = mArgsInfo.esophagusDilatationForRight_arg[i];
101 if (mArgsInfo.esophagusDilatationForRight_given == 1) {
102 for(uint i=0; i<3; i++)
103 p[i] = mArgsInfo.esophagusDilatationForRight_arg[0];
106 f->SetEsophagusDiltationForRight(p);
108 //--------------------------------------------------------------------
111 //--------------------------------------------------------------------
112 // Update with the number of dimensions and the pixeltype
113 //--------------------------------------------------------------------
114 template<class ArgsInfoType>
115 template<class ImageType>
116 void clitk::ExtractLymphStationsGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
119 typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
122 typedef clitk::ExtractLymphStationsFilter<ImageType> FilterType;
123 typename FilterType::Pointer filter = FilterType::New();
125 // Set global Options
126 filter->SetInput(input);
127 SetOptionsFromArgsInfoToFilter<FilterType>(filter);
132 // Write/Save results
133 typedef uchar MaskImagePixelType;
134 typedef itk::Image<MaskImagePixelType, 3> OutputImageType;
135 typename OutputImageType::Pointer output = filter->GetOutput();
136 this->template SetNextOutput<OutputImageType>(output);
138 //--------------------------------------------------------------------
140 #endif //#define CLITKEXTRACTLYMPHSTATIONSSGENERICFILTER_TXX