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"
27 #include <vtkPolyData.h>
31 //--------------------------------------------------------------------
33 Try to extract the LymphStations part of a thorax CT.
34 Need a set of Anatomical Features (AFDB)
36 //--------------------------------------------------------------------
38 template <class TImageType>
39 class ITK_EXPORT ExtractLymphStationsFilter:
40 public virtual clitk::FilterBase,
41 public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
42 public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
46 /** Standard class typedefs. */
47 typedef itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > Superclass;
48 typedef ExtractLymphStationsFilter Self;
49 typedef itk::SmartPointer<Self> Pointer;
50 typedef itk::SmartPointer<const Self> ConstPointer;
52 /** Method for creation through the object factory. */
55 /** Run-time type information (and related methods). */
56 itkTypeMacro(ExtractLymphStationsFilter, ImageToImageFilter);
58 /** Some convenient typedefs. */
59 typedef TImageType ImageType;
60 typedef typename ImageType::ConstPointer ImageConstPointer;
61 typedef typename ImageType::Pointer ImagePointer;
62 typedef typename ImageType::RegionType ImageRegionType;
63 typedef typename ImageType::PixelType ImagePixelType;
64 typedef typename ImageType::SizeType ImageSizeType;
65 typedef typename ImageType::IndexType ImageIndexType;
66 typedef typename ImageType::PointType ImagePointType;
68 typedef uchar MaskImagePixelType;
69 typedef itk::Image<MaskImagePixelType, 3> MaskImageType;
70 typedef typename MaskImageType::Pointer MaskImagePointer;
71 typedef typename MaskImageType::RegionType MaskImageRegionType;
72 typedef typename MaskImageType::SizeType MaskImageSizeType;
73 typedef typename MaskImageType::IndexType MaskImageIndexType;
74 typedef typename MaskImageType::PointType MaskImagePointType;
76 typedef itk::Image<MaskImagePixelType, 2> MaskSliceType;
77 typedef typename MaskSliceType::Pointer MaskSlicePointer;
78 typedef typename MaskSliceType::PointType MaskSlicePointType;
80 /** ImageDimension constants */
81 itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
84 itkGetConstMacro(BackgroundValue, MaskImagePixelType);
85 itkGetConstMacro(ForegroundValue, MaskImagePixelType);
86 itkSetMacro(BackgroundValue, MaskImagePixelType);
87 itkSetMacro(ForegroundValue, MaskImagePixelType);
90 itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
91 itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
92 itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
93 itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
94 itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
95 itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
96 itkSetMacro(InjectedThresholdForS8, double);
97 itkGetConstMacro(InjectedThresholdForS8, double);
102 bool GetComputeStation(std::string s);
103 void AddComputeStation(std::string station) ;
104 void SetFuzzyThreshold(std::string station, std::string tag, double value);
105 double GetFuzzyThreshold(std::string station, std::string tag);
108 ExtractLymphStationsFilter();
109 virtual ~ExtractLymphStationsFilter() {}
111 virtual void GenerateOutputInformation();
112 virtual void GenerateInputRequestedRegion();
113 virtual void GenerateData();
115 ImageConstPointer m_Input;
116 MaskImagePointer m_Mediastinum;
117 MaskImagePointer m_Working_Support;
118 std::map<std::string, MaskImagePointer> m_ListOfStations;
119 MaskImagePixelType m_BackgroundValue;
120 MaskImagePixelType m_ForegroundValue;
121 std::map<std::string, bool> m_ComputeStationMap;
123 bool CheckForStation(std::string station);
124 void Remove_Structures(std::string station, std::string s);
127 typedef std::map<std::string, double> FuzzyThresholdByStructureType;
128 std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
131 double m_DistanceMaxToAnteriorPartOfTheSpine;
132 double m_DiaphragmInferiorLimit;
134 double m_OriginOfRightMiddleLobeBronchusZ;
135 double m_InjectedThresholdForS8;
136 MaskImagePointer m_Esophagus;
137 MaskImagePointType m_EsophagusDiltationForAnt;
138 MaskImagePointType m_EsophagusDiltationForRight;
139 MaskImagePointer EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & eso);
140 void ExtractStation_8();
141 void ExtractStation_8_SetDefaultValues();
142 void ExtractStation_8_SI_Limits();
143 void ExtractStation_8_Post_Limits();
144 void ExtractStation_8_Ant_Sup_Limits();
145 void ExtractStation_8_Ant_Inf_Limits();
146 void ExtractStation_8_Ant_Injected_Limits();
147 void ExtractStation_8_LR_1_Limits();
148 void ExtractStation_8_LR_2_Limits();
149 void ExtractStation_8_Single_CCL_Limits();
150 void ExtractStation_8_LR_Limits();
151 void ExtractStation_8_Remove_Structures();
152 void ExtractStation_8_LR_Limits_old();
153 void ExtractStation_8_LR_Limits_old2();
156 void ExtractStation_3P();
157 void ExtractStation_3P_SetDefaultValues();
158 void ExtractStation_3P_SI_Limits();
159 void ExtractStation_3P_Remove_Structures();
160 void ExtractStation_3P_Ant_Limits();
161 void ExtractStation_3P_Post_Limits();
162 void ExtractStation_3P_LR_sup_Limits();
163 void ExtractStation_3P_LR_sup_Limits_2();
164 void ExtractStation_3P_LR_inf_Limits();
167 void ExtractStation_2RL();
168 void ExtractStation_2RL_SetDefaultValues();
169 void ExtractStation_2RL_SI_Limits();
170 void ExtractStation_2RL_Ant_Limits();
171 void ExtractStation_2RL_Ant_Limits2();
172 void ExtractStation_2RL_Post_Limits();
173 void ExtractStation_2RL_LR_Limits();
174 void ExtractStation_2RL_Remove_Structures();
175 void ExtractStation_2RL_SeparateRL();
176 vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
179 void ExtractStation_3A();
180 void ExtractStation_3A_SetDefaultValues();
181 void ExtractStation_3A_SI_Limits();
182 void ExtractStation_3A_Ant_Limits();
183 void ExtractStation_3A_Post_Limits();
186 void ExtractStation_7();
187 void ExtractStation_7_SetDefaultValues();
188 void ExtractStation_7_SI_Limits();
189 void ExtractStation_7_RL_Limits();
190 void ExtractStation_7_Posterior_Limits();
191 void ExtractStation_7_Remove_Structures();
192 MaskImagePointer m_Working_Trachea;
193 MaskImagePointer m_LeftBronchus;
194 MaskImagePointer m_RightBronchus;
195 typedef std::vector<MaskImageType::PointType> ListOfPointsType;
196 ListOfPointsType m_RightMostInLeftBronchus;
197 ListOfPointsType m_AntMostInLeftBronchus;
198 ListOfPointsType m_PostMostInLeftBronchus;
199 ListOfPointsType m_LeftMostInRightBronchus;
200 ListOfPointsType m_AntMostInRightBronchus;
201 ListOfPointsType m_PostMostInRightBronchus;
203 void FindExtremaPointsInBronchus(MaskImagePointer input,
205 double distance_max_from_center_point,
206 ListOfPointsType & LR,
207 ListOfPointsType & Ant,
208 ListOfPointsType & Post);
210 void ExtractStation_4RL();
211 void ExtractStation_4RL_SI_Limits();
212 void ExtractStation_4RL_LR_Limits();
213 void ExtractStation_4RL_AP_Limits();
214 MaskImagePointer m_RightSupport;
215 MaskImagePointer m_LeftSupport;
218 ExtractLymphStationsFilter(const Self&); //purposely not implemented
219 void operator=(const Self&); //purposely not implemented
222 //--------------------------------------------------------------------
224 } // end namespace clitk
225 //--------------------------------------------------------------------
227 #ifndef ITK_MANUAL_INSTANTIATION
228 #include "clitkExtractLymphStationsFilter.txx"
229 #include "clitkExtractLymphStation_8.txx"
230 #include "clitkExtractLymphStation_3P.txx"
231 #include "clitkExtractLymphStation_2RL.txx"
232 #include "clitkExtractLymphStation_3A.txx"
233 #include "clitkExtractLymphStation_7.txx"
234 #include "clitkExtractLymphStation_4RL.txx"