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1 /*=========================================================================
2   Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv
3
4   Authors belong to: 
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
8
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.
12
13   It is distributed under dual licence
14
15   - BSD        See included LICENSE.txt file
16   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
17   ======================================================================-====*/
18
19 #ifndef CLITKEXTRACTLYMPHSTATIONSFILTER_H
20 #define CLITKEXTRACTLYMPHSTATIONSFILTER_H
21
22 // clitk
23 #include "clitkFilterBase.h"
24 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
25
26 namespace clitk {
27   
28   //--------------------------------------------------------------------
29   /*
30     Try to extract the LymphStations part of a thorax CT.
31     Need a set of Anatomical Features (AFDB)
32   */
33   //--------------------------------------------------------------------
34   
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> >
40   {
41
42   public:
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;
48     
49     /** Method for creation through the object factory. */
50     itkNewMacro(Self);
51     
52     /** Run-time type information (and related methods). */
53     itkTypeMacro(ExtractLymphStationsFilter, ImageToImageFilter);
54
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; 
64         
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; 
72
73     typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
74
75     /** ImageDimension constants */
76     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
77     FILTERBASE_INIT;
78    
79     itkGetConstMacro(BackgroundValue, MaskImagePixelType);
80     itkGetConstMacro(ForegroundValue, MaskImagePixelType);
81     itkSetMacro(BackgroundValue, MaskImagePixelType);
82     itkSetMacro(ForegroundValue, MaskImagePixelType);
83
84     // Station 8
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);
93
94     // Station 7
95     itkSetMacro(FuzzyThreshold, double);
96     itkGetConstMacro(FuzzyThreshold, double);
97     itkSetMacro(Station7Filename, std::string);
98     itkGetConstMacro(Station7Filename, std::string);
99     
100     bool GetComputeStation(std::string s);
101     void AddComputeStation(std::string station) ;
102
103   protected:
104     ExtractLymphStationsFilter();
105     virtual ~ExtractLymphStationsFilter() {}
106     
107     virtual void GenerateOutputInformation();
108     virtual void GenerateInputRequestedRegion();
109     virtual void GenerateData();
110     
111     ImageConstPointer  m_Input;
112     MaskImagePointer   m_Mediastinum;
113     MaskImagePointer   m_Working_Support;
114     std::map<std::string, MaskImagePointer> m_ListOfStations;
115     MaskImagePixelType m_BackgroundValue;
116     MaskImagePixelType m_ForegroundValue;
117     std::map<std::string, bool> m_ComputeStationMap;
118
119     bool CheckForStation(std::string station);
120
121     // Station 8
122     double m_DistanceMaxToAnteriorPartOfTheSpine;
123     double m_DiaphragmInferiorLimit;
124     double m_CarinaZ;
125     double m_OriginOfRightMiddleLobeBronchusZ;
126     double m_FuzzyThresholdForS8;
127     MaskImagePointType m_EsophagusDiltationForAnt;
128     MaskImagePointType m_EsophagusDiltationForRight;
129     MaskImagePointer EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & eso);
130     void ExtractStation_8();
131     void ExtractStation_8_SetDefaultValues();
132     void ExtractStation_8_SI_Limits();
133     void ExtractStation_8_Post_Limits();
134     void ExtractStation_8_Ant_Limits();
135     void ExtractStation_8_LR_Limits();
136     void ExtractStation_8_LR_Limits_old();
137     
138     // Station 3P
139     void ExtractStation_3P();
140     void ExtractStation_3P_SetDefaultValues();
141     void ExtractStation_3P_SI_Limits();
142  
143     // Station 7
144     void ExtractStation_7();
145     void ExtractStation_7_SI_Limits();
146     void ExtractStation_7_RL_Limits();
147     void ExtractStation_7_Posterior_Limits();   
148     std::string      m_Station7Filename;
149     MaskImagePointer m_working_trachea;
150     double           m_FuzzyThreshold;
151     MaskImagePointer m_LeftBronchus;
152     MaskImagePointer m_RightBronchus;
153     MaskImagePointer m_Station7;
154     typedef std::vector<MaskImageType::PointType> ListOfPointsType;
155     ListOfPointsType  m_RightMostInLeftBronchus;
156     ListOfPointsType  m_AntMostInLeftBronchus;
157     ListOfPointsType  m_PostMostInLeftBronchus;
158     ListOfPointsType  m_LeftMostInRightBronchus;
159     ListOfPointsType  m_AntMostInRightBronchus;
160     ListOfPointsType  m_PostMostInRightBronchus;
161
162     void FindExtremaPointsInBronchus(MaskImagePointer input, 
163                                      int direction,
164                                      double distance_max_from_center_point, 
165                                      ListOfPointsType & LR, 
166                                      ListOfPointsType & Ant, 
167                                      ListOfPointsType & Post);
168     // Station 4RL
169     void ExtractStation_4RL();
170     void ExtractStation_4RL_SI_Limits();
171     void ExtractStation_4RL_LR_Limits();
172     void ExtractStation_4RL_AP_Limits();
173     MaskImagePointer m_RightSupport;
174     MaskImagePointer m_LeftSupport;
175
176   private:
177     ExtractLymphStationsFilter(const Self&); //purposely not implemented
178     void operator=(const Self&); //purposely not implemented
179     
180   }; // end class
181   //--------------------------------------------------------------------
182
183 } // end namespace clitk
184 //--------------------------------------------------------------------
185
186 #ifndef ITK_MANUAL_INSTANTIATION
187 #include "clitkExtractLymphStationsFilter.txx"
188 #include "clitkExtractLymphStation_8.txx"
189 #include "clitkExtractLymphStation_3P.txx"
190 #include "clitkExtractLymphStation_7.txx"
191 #include "clitkExtractLymphStation_4RL.txx"
192 #endif
193
194 #endif