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://www.centreleonberard.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.output_given) AddOutputFilename(mArgsInfo.output_arg);
58 if (mArgsInfo.outputTrachea_given) AddOutputFilename(mArgsInfo.outputTrachea_arg);
60 //--------------------------------------------------------------------
63 //--------------------------------------------------------------------
64 template<class ArgsInfoType>
65 template<class FilterType>
66 void clitk::ExtractLungGenericFilter<ArgsInfoType>::
67 SetOptionsFromArgsInfoToFilter(FilterType * f)
69 //f->SetVerboseFlag(mArgsInfo.verbose_flag);
70 f->SetVerboseOptionFlag(mArgsInfo.verboseOption_flag);
71 f->SetVerboseStepFlag(mArgsInfo.verboseStep_flag);
72 f->SetWriteStepFlag(mArgsInfo.writeStep_flag);
73 f->SetVerboseWarningFlag(!mArgsInfo.verboseWarningOff_flag);
74 f->SetVerboseMemoryFlag(mArgsInfo.verboseMemory_flag);
76 if (mArgsInfo.afdb_given)
77 f->SetAFDBFilename(mArgsInfo.afdb_arg);
78 f->SetOutputLungFilename(mArgsInfo.output_arg);
79 f->SetOutputTracheaFilename(mArgsInfo.outputTrachea_arg);
81 f->SetUpperThreshold(mArgsInfo.upper_arg);
82 f->SetLowerThreshold(mArgsInfo.lower_arg);
84 f->SetNumberOfSlicesToSkipBeforeSearchingSeed(mArgsInfo.skipslices_arg);
86 f->SetTracheaVolumeMustBeCheckedFlag(!mArgsInfo.doNotCheckTracheaVolume_flag);
87 f->SetVerboseRegionGrowingFlag(mArgsInfo.verboseRG_flag);
89 f->SetUpperThresholdForTrachea(mArgsInfo.upperThresholdForTrachea_arg);
90 f->SetMultiplierForTrachea(mArgsInfo.multiplierForTrachea_arg);
91 f->SetThresholdStepSizeForTrachea(mArgsInfo.thresholdStepSizeForTrachea_arg);
93 typename FilterType::InputImageIndexType s;
94 if (mArgsInfo.seed_given) {
95 ConvertOptionMacro(mArgsInfo.seed, s, 3, false);
99 f->SetMinimalComponentSize(mArgsInfo.minSize_arg);
100 f->SetNumberOfHistogramBins(mArgsInfo.bins_arg);
101 f->SetRadiusForTrachea(mArgsInfo.radius_arg);
103 f->SetOpenCloseFlag(mArgsInfo.openclose_flag);
104 f->SetOpenCloseRadius(mArgsInfo.opencloseRadius_arg);
105 f->SetAutoCrop(!mArgsInfo.noAutoCrop_flag);
107 if (mArgsInfo.doNotFillHoles_given)
108 f->SetFillHolesFlag(false);
110 f->SetFillHolesFlag(true);
112 //--------------------------------------------------------------------
115 //--------------------------------------------------------------------
116 // Update with the number of dimensions and the pixeltype
117 //--------------------------------------------------------------------
118 template<class ArgsInfoType>
119 template<class ImageType>
120 void clitk::ExtractLungGenericFilter<ArgsInfoType>::UpdateWithInputImageType()
122 // Mask & output image type
123 typedef itk::Image<uchar, ImageType::ImageDimension> MaskImageType;
126 typename ImageType::Pointer input = this->template GetInput<ImageType>(0);
129 typedef clitk::ExtractLungFilter<ImageType> FilterType;
130 typename FilterType::Pointer filter = FilterType::New();
132 // Set the filter (needed for example for threaded monitoring)
133 this->SetFilterBase(filter);
135 // Set global Options
136 filter->SetInput(input);
137 SetOptionsFromArgsInfoToFilter<FilterType>(filter);
142 // Write/Save results
143 typename MaskImageType::Pointer output = filter->GetOutput();
144 this->template SetNextOutput<MaskImageType>(output);
145 this->template SetNextOutput<typename FilterType::MaskImageType>(filter->GetTracheaImage());
147 //--------------------------------------------------------------------
149 #endif //#define CLITKEXTRACTLUNGSGENERICFILTER_TXX