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 CLITKEXTRACTLYMPHSTATIONSFILTER_H
20 #define CLITKEXTRACTLYMPHSTATIONSFILTER_H
23 #include "clitkFilterBase.h"
24 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
28 //--------------------------------------------------------------------
30 Try to extract the LymphStations part of a thorax CT.
31 Need a set of Anatomical Features (AFDB)
33 //--------------------------------------------------------------------
35 template <class TImageType>
36 class ITK_EXPORT ExtractLymphStationsFilter:
37 public virtual clitk::FilterBase,
38 public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
39 public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
43 /** Standard class typedefs. */
44 typedef itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > Superclass;
45 typedef ExtractLymphStationsFilter Self;
46 typedef itk::SmartPointer<Self> Pointer;
47 typedef itk::SmartPointer<const Self> ConstPointer;
49 /** Method for creation through the object factory. */
52 /** Run-time type information (and related methods). */
53 itkTypeMacro(ExtractLymphStationsFilter, ImageToImageFilter);
55 /** Some convenient typedefs. */
56 typedef TImageType ImageType;
57 typedef typename ImageType::ConstPointer ImageConstPointer;
58 typedef typename ImageType::Pointer ImagePointer;
59 typedef typename ImageType::RegionType ImageRegionType;
60 typedef typename ImageType::PixelType ImagePixelType;
61 typedef typename ImageType::SizeType ImageSizeType;
62 typedef typename ImageType::IndexType ImageIndexType;
63 typedef typename ImageType::PointType ImagePointType;
65 typedef uchar MaskImagePixelType;
66 typedef itk::Image<MaskImagePixelType, 3> MaskImageType;
67 typedef typename MaskImageType::Pointer MaskImagePointer;
68 typedef typename MaskImageType::RegionType MaskImageRegionType;
69 typedef typename MaskImageType::SizeType MaskImageSizeType;
70 typedef typename MaskImageType::IndexType MaskImageIndexType;
71 typedef typename MaskImageType::PointType MaskImagePointType;
73 typedef itk::Image<MaskImagePixelType, 2> MaskSliceType;
75 /** ImageDimension constants */
76 itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
79 itkGetConstMacro(BackgroundValue, MaskImagePixelType);
80 itkGetConstMacro(ForegroundValue, MaskImagePixelType);
81 itkSetMacro(BackgroundValue, MaskImagePixelType);
82 itkSetMacro(ForegroundValue, MaskImagePixelType);
85 itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
86 itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
87 itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
88 itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
89 itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
90 itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
91 itkSetMacro(FuzzyThresholdForS8, double);
92 itkGetConstMacro(FuzzyThresholdForS8, double);
95 itkSetMacro(FuzzyThreshold, double);
96 itkGetConstMacro(FuzzyThreshold, double);
97 itkSetMacro(Station7Filename, std::string);
98 itkGetConstMacro(Station7Filename, std::string);
101 ExtractLymphStationsFilter();
102 virtual ~ExtractLymphStationsFilter() {}
104 virtual void GenerateOutputInformation();
105 virtual void GenerateInputRequestedRegion();
106 virtual void GenerateData();
108 ImageConstPointer m_Input;
109 MaskImagePointer m_Mediastinum;
110 MaskImagePointer m_Working_Support;
111 std::map<std::string, MaskImagePointer> m_ListOfStations;
112 MaskImagePixelType m_BackgroundValue;
113 MaskImagePixelType m_ForegroundValue;
116 double m_DistanceMaxToAnteriorPartOfTheSpine;
117 double m_DiaphragmInferiorLimit;
119 double m_OriginOfRightMiddleLobeBronchusZ;
120 double m_FuzzyThresholdForS8;
121 MaskImagePointType m_EsophagusDiltationForAnt;
122 MaskImagePointType m_EsophagusDiltationForRight;
123 MaskImagePointer EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & eso);
124 void ExtractStation_8();
125 void ExtractStation_8_SI_Limits();
126 void ExtractStation_8_Post_Limits();
127 void ExtractStation_8_Ant_Limits();
128 void ExtractStation_8_LR_Limits();
129 void ExtractStation_8_LR_Limits_old();
132 void ExtractStation_7();
133 void ExtractStation_7_SI_Limits();
134 void ExtractStation_7_RL_Limits();
135 void ExtractStation_7_Posterior_Limits();
136 std::string m_Station7Filename;
137 MaskImagePointer m_working_trachea;
138 double m_FuzzyThreshold;
139 MaskImagePointer m_LeftBronchus;
140 MaskImagePointer m_RightBronchus;
141 MaskImagePointer m_Station7;
142 typedef std::vector<MaskImageType::PointType> ListOfPointsType;
143 ListOfPointsType m_RightMostInLeftBronchus;
144 ListOfPointsType m_AntMostInLeftBronchus;
145 ListOfPointsType m_PostMostInLeftBronchus;
146 ListOfPointsType m_LeftMostInRightBronchus;
147 ListOfPointsType m_AntMostInRightBronchus;
148 ListOfPointsType m_PostMostInRightBronchus;
150 void FindExtremaPointsInBronchus(MaskImagePointer input,
152 double distance_max_from_center_point,
153 ListOfPointsType & LR,
154 ListOfPointsType & Ant,
155 ListOfPointsType & Post);
157 void ExtractStation_4RL();
158 void ExtractStation_4RL_SI_Limits();
159 void ExtractStation_4RL_LR_Limits();
160 void ExtractStation_4RL_AP_Limits();
161 MaskImagePointer m_RightSupport;
162 MaskImagePointer m_LeftSupport;
165 ExtractLymphStationsFilter(const Self&); //purposely not implemented
166 void operator=(const Self&); //purposely not implemented
169 //--------------------------------------------------------------------
171 } // end namespace clitk
172 //--------------------------------------------------------------------
174 #ifndef ITK_MANUAL_INSTANTIATION
175 #include "clitkExtractLymphStationsFilter.txx"
176 #include "clitkExtractLymphStation_8.txx"
177 #include "clitkExtractLymphStation_7.txx"
178 #include "clitkExtractLymphStation_4RL.txx"