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 CLITKEXTRACTLUNGSGENERICFILTER_TXX
20 #define CLITKEXTRACTLUNGSGENERICFILTER_TXX
22 #include "clitkImageCommon.h"
24 //--------------------------------------------------------------------
25 template<class ArgsInfoType>
26 clitk::ExtractLungGenericFilter<ArgsInfoType>::ExtractLungGenericFilter():
27 ImageToImageGenericFilter<Self>("ExtractLung")
29 this->SetFilterBase(NULL);
31 cmdline_parser_clitkExtractLung_init(&mArgsInfo);
32 InitializeImageType<3>();
34 //--------------------------------------------------------------------
37 //--------------------------------------------------------------------
38 template<class ArgsInfoType>
39 template<unsigned int Dim>
40 void clitk::ExtractLungGenericFilter<ArgsInfoType>::InitializeImageType()
42 ADD_IMAGE_TYPE(Dim, short);
43 // ADD_IMAGE_TYPE(Dim, int);
44 // ADD_IMAGE_TYPE(Dim, float);
46 //--------------------------------------------------------------------
49 //--------------------------------------------------------------------
50 template<class ArgsInfoType>
51 void clitk::ExtractLungGenericFilter<ArgsInfoType>::SetArgsInfo(const ArgsInfoType & a)
54 SetIOVerbose(mArgsInfo.verbose_flag);
55 if (mArgsInfo.imagetypes_flag) this->PrintAvailableImageTypes();
56 if (mArgsInfo.input_given) AddInputFilename(mArgsInfo.input_arg);
57 if (mArgsInfo.patient_given) AddInputFilename(mArgsInfo.patient_arg);
58 if (mArgsInfo.output_given) AddOutputFilename(mArgsInfo.output_arg);
59 if (mArgsInfo.outputTrachea_given) AddOutputFilename(mArgsInfo.outputTrachea_arg);
61 //--------------------------------------------------------------------
64 //--------------------------------------------------------------------
65 // Update with the number of dimensions and the pixeltype
66 //--------------------------------------------------------------------
67 template<class ArgsInfoType>
68 template<class ImageType>
69 void clitk::ExtractLungGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
71 // Mask & output image type
72 typedef itk::Image<uchar, ImageType::ImageDimension> OutputImageType;
73 typedef itk::Image<uchar, ImageType::ImageDimension> MaskImageType;
76 typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
77 typename MaskImageType::Pointer patient = this->template GetInput<MaskImageType>(1);
80 typedef clitk::ExtractLungFilter<ImageType, MaskImageType> FilterType;
81 typename FilterType::Pointer filter = FilterType::New();
83 // Set the filter (needed for example for threaded monitoring)
84 this->SetFilterBase(filter);
87 filter->SetStopOnError(this->GetStopOnError());
88 filter->SetArgsInfo(mArgsInfo);
89 filter->SetInput(input);
90 filter->SetInputPatientMask(patient, mArgsInfo.patientBG_arg);
96 if (filter->HasError()) {
97 SetLastError(filter->GetLastError());
102 // Write/Save results
103 typename OutputImageType::Pointer output = filter->GetOutput();
104 this->template SetNextOutput<OutputImageType>(output);
105 this->template SetNextOutput<typename FilterType::MaskImageType>(filter->GetTracheaImage());
107 //--------------------------------------------------------------------
109 #endif //#define CLITKEXTRACTLUNGSGENERICFILTER_TXX