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 "clitkStructuresExtractionFilter.h"
26 #include <vtkPolyData.h>
30 //--------------------------------------------------------------------
32 Try to extract the LymphStations part of a thorax CT.
33 Need a set of Anatomical Features (AFDB)
35 //--------------------------------------------------------------------
37 template <class TImageType>
38 class ITK_EXPORT ExtractLymphStationsFilter:
39 public clitk::StructuresExtractionFilter<TImageType>
43 /** Standard class typedefs. */
44 typedef clitk::StructuresExtractionFilter<TImageType> 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;
74 typedef typename MaskSliceType::Pointer MaskSlicePointer;
75 typedef typename MaskSliceType::PointType MaskSlicePointType;
76 typedef typename MaskSliceType::RegionType MaskSliceRegionType;
77 typedef typename MaskSliceType::SizeType MaskSliceSizeType;
78 typedef typename MaskSliceType::IndexType MaskSliceIndexType;
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(EsophagusDiltationForAnt, MaskImagePointType);
91 itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
92 itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
93 itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
94 itkSetMacro(InjectedThresholdForS8, double);
95 itkGetConstMacro(InjectedThresholdForS8, double);
98 itkGetConstMacro(S7_UseMostInferiorPartOnlyFlag, bool);
99 itkSetMacro(S7_UseMostInferiorPartOnlyFlag, bool);
100 itkBooleanMacro(S7_UseMostInferiorPartOnlyFlag);
103 bool GetComputeStation(std::string s);
104 void AddComputeStation(std::string station) ;
105 void SetFuzzyThreshold(std::string station, std::string tag, double value);
106 double GetFuzzyThreshold(std::string station, std::string tag);
107 void SetThreshold(std::string station, std::string tag, double value);
108 double GetThreshold(std::string station, std::string tag);
109 itkGetConstMacro(ComputeStationsSupportsFlag, bool);
110 itkSetMacro(ComputeStationsSupportsFlag, bool);
111 itkBooleanMacro(ComputeStationsSupportsFlag);
114 ExtractLymphStationsFilter();
115 virtual ~ExtractLymphStationsFilter() {}
117 virtual void GenerateOutputInformation();
118 virtual void GenerateInputRequestedRegion();
119 virtual void GenerateData();
121 // To avoid repeat "this->"
122 AnatomicalFeatureDatabase * GetAFDB() { return clitk::FilterWithAnatomicalFeatureDatabaseManagement::GetAFDB(); }
123 void WriteAFDB() { clitk::FilterWithAnatomicalFeatureDatabaseManagement::WriteAFDB(); }
124 void LoadAFDB() { clitk::FilterWithAnatomicalFeatureDatabaseManagement::LoadAFDB(); }
125 void StartNewStep(std::string s) { clitk::FilterBase::StartNewStep(s); }
126 void StartSubStep() { clitk::FilterBase::StartSubStep(); }
127 template<class TInternalImageType>
128 void StopCurrentStep(typename TInternalImageType::Pointer p, std::string txt="") { clitk::FilterBase::StopCurrentStep<TInternalImageType>(p, txt); }
129 void StopCurrentStep() {clitk::FilterBase::StopCurrentStep(); }
130 void StopSubStep() {clitk::FilterBase::StopSubStep(); }
132 ImageConstPointer m_Input;
133 MaskImagePointer m_Mediastinum;
134 MaskImagePointer m_Working_Support;
135 std::map<std::string, MaskImagePointer> m_ListOfStations;
136 std::map<std::string, MaskImagePointer> m_ListOfSupports;
137 MaskImagePixelType m_BackgroundValue;
138 MaskImagePixelType m_ForegroundValue;
139 std::map<std::string, bool> m_ComputeStationMap;
141 bool CheckForStation(std::string station);
142 void Remove_Structures(std::string station, std::string s);
144 // Functions common to several stations
146 double FindApexOfTheChest();
147 double FindSuperiorBorderOfAorticArch();
148 double FindInferiorBorderOfAorticArch();
149 void FindLeftAndRightBronchi();
150 void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
151 MaskImagePointer FindAntPostVesselsOLD();
152 MaskImagePointer FindAntPostVessels2();
155 typedef std::map<std::string, double> FuzzyThresholdByStructureType;
156 std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
157 typedef std::map<std::string, double> ThresholdByStructureType;
158 std::map<std::string, ThresholdByStructureType> m_Threshold;
160 // Station's supports
161 void ExtractStationSupports();
162 void Support_SupInf_S1RL();
163 void Support_LeftRight_S1R_S1L();
164 void Support_SupInf_S2R_S2L();
165 void Support_LeftRight_S2R_S2L();
166 void Support_SupInf_S4R_S4L();
167 void Support_LeftRight_S4R_S4L();
168 void Support_Post_S1S2S4();
174 MaskImagePointer LimitsWithTrachea(MaskImageType * input,
175 int extremaDirection, int lineDirection,
176 double offset, double maxSupPosition);
177 MaskImagePointer LimitsWithTrachea(MaskImageType * input,
178 int extremaDirection, int lineDirection,
181 double m_DiaphragmInferiorLimit;
182 double m_OriginOfRightMiddleLobeBronchusZ;
183 double m_InjectedThresholdForS8;
184 MaskImagePointer m_Esophagus;
185 MaskImagePointType m_EsophagusDiltationForAnt;
186 MaskImagePointType m_EsophagusDiltationForRight;
188 void ExtractStation_8();
189 void ExtractStation_8_SetDefaultValues();
190 void ExtractStation_8_SI_Limits();
191 void ExtractStation_8_Ant_Limits();
192 void ExtractStation_8_Left_Sup_Limits();
193 void ExtractStation_8_Left_Inf_Limits();
194 void ExtractStation_8_Single_CCL_Limits();
195 void ExtractStation_8_Remove_Structures();
198 void ExtractStation_3P();
199 void ExtractStation_3P_SetDefaultValues();
200 void ExtractStation_3P_LR_inf_Limits();
201 void ExtractStation_3P_LR_sup_Limits_2();
202 void ExtractStation_3P_Remove_Structures();
203 void ExtractStation_3P_LR_sup_Limits();
206 void ExtractStation_3A();
207 void ExtractStation_3A_SetDefaultValues();
208 void ExtractStation_3A_Post_Left_Limits_With_Aorta_S5_Support();
209 void ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support();
210 void ExtractStation_3A_AntPost_Superiorly();
211 void ExtractStation_3A_Remove_Structures();
214 void ExtractStation_2RL();
215 void ExtractStation_2RL_SetDefaultValues();
216 void ExtractStation_2RL_Ant_Limits(std::string s);
217 void ExtractStation_2RL_Remove_Structures(std::string s);
218 void ExtractStation_2RL_Cut_BrachioCephalicVein_superiorly_when_it_split();
219 vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
222 void ExtractStation_1RL();
223 void ExtractStation_1RL_SetDefaultValues();
224 void ExtractStation_1RL_Ant_Limits();
225 void ExtractStation_1RL_Post_Limits();
228 void ExtractStation_4RL_SetDefaultValues();
229 void ExtractStation_4RL();
230 void ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(int KeepPoint);
233 void ExtractStation_5_SetDefaultValues();
234 void ExtractStation_5();
235 void ExtractStation_5_Limits_AscendingAorta_Ant();
238 void ExtractStation_6_SetDefaultValues();
239 void ExtractStation_6();
243 void ExtractStation_7();
244 void ExtractStation_7_SetDefaultValues();
245 void ExtractStation_7_SI_Limits();
246 void ExtractStation_7_RL_Interior_Limits();
248 void ExtractStation_7_RL_Limits_OLD();
249 void ExtractStation_7_Posterior_Limits();
250 void ExtractStation_7_Remove_Structures();
251 bool m_S7_UseMostInferiorPartOnlyFlag;
252 bool m_ComputeStationsSupportsFlag;
253 MaskImagePointer m_Working_Trachea;
254 MaskImagePointer m_LeftBronchus;
255 MaskImagePointer m_RightBronchus;
256 typedef std::vector<MaskImageType::PointType> ListOfPointsType;
257 ListOfPointsType m_RightMostInLeftBronchus;
258 ListOfPointsType m_AntMostInLeftBronchus;
259 ListOfPointsType m_PostMostInLeftBronchus;
260 ListOfPointsType m_LeftMostInRightBronchus;
261 ListOfPointsType m_AntMostInRightBronchus;
262 ListOfPointsType m_PostMostInRightBronchus;
264 void FindExtremaPointsInBronchus(MaskImagePointer input,
266 double distance_max_from_center_point,
267 ListOfPointsType & LR,
268 ListOfPointsType & Ant,
269 ListOfPointsType & Post);
271 ExtractLymphStationsFilter(const Self&); //purposely not implemented
272 void operator=(const Self&); //purposely not implemented
275 //--------------------------------------------------------------------
277 } // end namespace clitk
278 //--------------------------------------------------------------------
280 #ifndef ITK_MANUAL_INSTANTIATION
281 #include "clitkExtractLymphStationsFilter.txx"
282 #include "clitkExtractLymphStation_Supports.txx"
283 #include "clitkExtractLymphStation_3P.txx"
284 #include "clitkExtractLymphStation_2RL.txx"
285 #include "clitkExtractLymphStation_3A.txx"
286 #include "clitkExtractLymphStation_4RL.txx"
287 #include "clitkExtractLymphStation_1RL.txx"
288 #include "clitkExtractLymphStation_5.txx"
289 #include "clitkExtractLymphStation_6.txx"
291 #include "clitkExtractLymphStation_8.txx"
292 #include "clitkExtractLymphStation_7.txx"