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;
79 typedef typename MaskSliceType::RegionType MaskSliceRegionType;
80 typedef typename MaskSliceType::SizeType MaskSliceSizeType;
81 typedef typename MaskSliceType::IndexType MaskSliceIndexType;
83 /** ImageDimension constants */
84 itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
87 itkGetConstMacro(BackgroundValue, MaskImagePixelType);
88 itkGetConstMacro(ForegroundValue, MaskImagePixelType);
89 itkSetMacro(BackgroundValue, MaskImagePixelType);
90 itkSetMacro(ForegroundValue, MaskImagePixelType);
93 // itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
94 //itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
95 itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
96 itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
97 itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
98 itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
99 itkSetMacro(InjectedThresholdForS8, double);
100 itkGetConstMacro(InjectedThresholdForS8, double);
103 itkGetConstMacro(S7_UseMostInferiorPartOnlyFlag, bool);
104 itkSetMacro(S7_UseMostInferiorPartOnlyFlag, bool);
105 itkBooleanMacro(S7_UseMostInferiorPartOnlyFlag);
108 bool GetComputeStation(std::string s);
109 void AddComputeStation(std::string station) ;
110 void SetFuzzyThreshold(std::string station, std::string tag, double value);
111 double GetFuzzyThreshold(std::string station, std::string tag);
114 ExtractLymphStationsFilter();
115 virtual ~ExtractLymphStationsFilter() {}
117 virtual void GenerateOutputInformation();
118 virtual void GenerateInputRequestedRegion();
119 virtual void GenerateData();
121 ImageConstPointer m_Input;
122 MaskImagePointer m_Mediastinum;
123 MaskImagePointer m_Working_Support;
124 std::map<std::string, MaskImagePointer> m_ListOfStations;
125 std::map<std::string, MaskImagePointer> m_ListOfSupports;
126 MaskImagePixelType m_BackgroundValue;
127 MaskImagePixelType m_ForegroundValue;
128 std::map<std::string, bool> m_ComputeStationMap;
130 bool CheckForStation(std::string station);
131 void Remove_Structures(std::string station, std::string s);
133 // Functions common to several stations
134 void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
135 double FindCarinaSlicePosition();
136 void FindLeftAndRightBronchi();
139 typedef std::map<std::string, double> FuzzyThresholdByStructureType;
140 std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
142 // Station's supports
143 void ExtractStationSupports();
146 // double m_DistanceMaxToAnteriorPartOfTheSpine;
147 double m_DiaphragmInferiorLimit;
149 double m_OriginOfRightMiddleLobeBronchusZ;
150 double m_InjectedThresholdForS8;
151 MaskImagePointer m_Esophagus;
152 MaskImagePointType m_EsophagusDiltationForAnt;
153 MaskImagePointType m_EsophagusDiltationForRight;
155 void ExtractStation_8();
156 void ExtractStation_8_SetDefaultValues();
157 void ExtractStation_8_SI_Limits();
158 void ExtractStation_8_Ant_Limits();
159 void ExtractStation_8_Left_Sup_Limits();
160 void ExtractStation_8_Left_Inf_Limits();
161 void ExtractStation_8_Single_CCL_Limits();
162 void ExtractStation_8_Remove_Structures();
165 void ExtractStation_3P();
166 void ExtractStation_3P_SetDefaultValues();
167 void ExtractStation_3P_SI_Limits();
168 void ExtractStation_3P_Remove_Structures();
169 void ExtractStation_3P_Ant_Limits();
170 void ExtractStation_3P_Post_Limits();
171 void ExtractStation_3P_LR_sup_Limits();
172 void ExtractStation_3P_LR_sup_Limits_2();
173 void ExtractStation_3P_LR_inf_Limits();
176 void ExtractStation_2RL();
177 void ExtractStation_2RL_SetDefaultValues();
178 void ExtractStation_2RL_SI_Limits();
179 void ExtractStation_2RL_Ant_Limits();
180 void ExtractStation_2RL_Ant_Limits2();
181 void ExtractStation_2RL_Post_Limits();
182 void ExtractStation_2RL_LR_Limits();
183 void ExtractStation_2RL_Remove_Structures();
184 void ExtractStation_2RL_SeparateRL();
185 vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
188 void ExtractStation_3A();
189 void ExtractStation_3A_SetDefaultValues();
190 void ExtractStation_3A_SI_Limits();
191 void ExtractStation_3A_Ant_Limits();
192 void ExtractStation_3A_Post_Limits();
195 void ExtractStation_7();
196 void ExtractStation_7_SetDefaultValues();
197 void ExtractStation_7_SI_Limits();
198 void ExtractStation_7_RL_Interior_Limits();
201 void ExtractStation_7_RL_Limits_OLD();
202 void ExtractStation_7_Posterior_Limits();
203 void ExtractStation_7_Remove_Structures();
204 bool m_S7_UseMostInferiorPartOnlyFlag;
205 MaskImagePointer m_Working_Trachea;
206 MaskImagePointer m_LeftBronchus;
207 MaskImagePointer m_RightBronchus;
208 typedef std::vector<MaskImageType::PointType> ListOfPointsType;
209 ListOfPointsType m_RightMostInLeftBronchus;
210 ListOfPointsType m_AntMostInLeftBronchus;
211 ListOfPointsType m_PostMostInLeftBronchus;
212 ListOfPointsType m_LeftMostInRightBronchus;
213 ListOfPointsType m_AntMostInRightBronchus;
214 ListOfPointsType m_PostMostInRightBronchus;
216 void FindExtremaPointsInBronchus(MaskImagePointer input,
218 double distance_max_from_center_point,
219 ListOfPointsType & LR,
220 ListOfPointsType & Ant,
221 ListOfPointsType & Post);
223 void ExtractStation_4RL();
224 void ExtractStation_4RL_SI_Limits();
225 void ExtractStation_4RL_LR_Limits();
226 void ExtractStation_4RL_AP_Limits();
227 MaskImagePointer m_RightSupport;
228 MaskImagePointer m_LeftSupport;
231 ExtractLymphStationsFilter(const Self&); //purposely not implemented
232 void operator=(const Self&); //purposely not implemented
235 //--------------------------------------------------------------------
237 } // end namespace clitk
238 //--------------------------------------------------------------------
240 #ifndef ITK_MANUAL_INSTANTIATION
241 #include "clitkExtractLymphStationsFilter.txx"
242 #include "clitkExtractLymphStation_Supports.txx"
243 #include "clitkExtractLymphStation_8.txx"
244 #include "clitkExtractLymphStation_3P.txx"
245 #include "clitkExtractLymphStation_2RL.txx"
246 #include "clitkExtractLymphStation_3A.txx"
247 #include "clitkExtractLymphStation_7.txx"
248 #include "clitkExtractLymphStation_4RL.txx"