X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.h;h=dd99c5fd4f8eced90f38eef544e1929417ddd802;hb=607ef9091246c288b0a1333e87d3d31ce7ee5cd7;hp=6f81423fe20cbcfdfc14921839faa48c8c631add;hpb=573d80d0f7a17607d2ee883c21c940c0ba020282;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsFilter.h b/segmentation/clitkExtractLymphStationsFilter.h
index 6f81423..dd99c5f 100644
--- a/segmentation/clitkExtractLymphStationsFilter.h
+++ b/segmentation/clitkExtractLymphStationsFilter.h
@@ -3,7 +3,7 @@
 
   Authors belong to: 
   - University of LYON              http://www.universite-lyon.fr/
-  - Léon Bérard cancer center       http://www.centreleonberard.fr
+  - Léon Bérard cancer center       http://oncora1.lyon.fnclcc.fr
   - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr
 
   This software is distributed WITHOUT ANY WARRANTY; without even
@@ -14,7 +14,7 @@
 
   - BSD        See included LICENSE.txt file
   - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
-  ===========================================================================**/
+  ======================================================================-====*/
 
 #ifndef CLITKEXTRACTLYMPHSTATIONSFILTER_H
 #define CLITKEXTRACTLYMPHSTATIONSFILTER_H
@@ -23,6 +23,9 @@
 #include "clitkFilterBase.h"
 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
 
+// vtk
+#include <vtkPolyData.h>
+
 namespace clitk {
   
   //--------------------------------------------------------------------
@@ -72,6 +75,10 @@ namespace clitk {
 
     typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
     typedef typename MaskSliceType::Pointer      MaskSlicePointer;
+    typedef typename MaskSliceType::PointType    MaskSlicePointType;
+    typedef typename MaskSliceType::RegionType   MaskSliceRegionType; 
+    typedef typename MaskSliceType::SizeType     MaskSliceSizeType; 
+    typedef typename MaskSliceType::IndexType    MaskSliceIndexType; 
 
     /** ImageDimension constants */
     itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
@@ -83,25 +90,25 @@ namespace clitk {
     itkSetMacro(ForegroundValue, MaskImagePixelType);
 
     // Station 8
-    itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
-    itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
+    // itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
+    //itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
     itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
     itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
     itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
     itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
-    itkSetMacro(FuzzyThresholdForS8, double);
-    itkGetConstMacro(FuzzyThresholdForS8, double);
-
     itkSetMacro(InjectedThresholdForS8, double);
     itkGetConstMacro(InjectedThresholdForS8, double);
 
     // Station 7
-    void SetFuzzyThresholdForS7(std::string tag, double value);
-    double GetFuzzyThresholdForS7(std::string tag);
+    itkGetConstMacro(S7_UseMostInferiorPartOnlyFlag, bool);
+    itkSetMacro(S7_UseMostInferiorPartOnlyFlag, bool);
+    itkBooleanMacro(S7_UseMostInferiorPartOnlyFlag);
 
     // All stations
     bool GetComputeStation(std::string s);
     void AddComputeStation(std::string station) ;
+    void SetFuzzyThreshold(std::string station, std::string tag, double value);
+    double GetFuzzyThreshold(std::string station, std::string tag);
 
   protected:
     ExtractLymphStationsFilter();
@@ -115,39 +122,45 @@ namespace clitk {
     MaskImagePointer   m_Mediastinum;
     MaskImagePointer   m_Working_Support;
     std::map<std::string, MaskImagePointer> m_ListOfStations;
+    std::map<std::string, MaskImagePointer> m_ListOfSupports;
     MaskImagePixelType m_BackgroundValue;
     MaskImagePixelType m_ForegroundValue;
     std::map<std::string, bool> m_ComputeStationMap;
 
     bool CheckForStation(std::string station);
-    void Remove_Structures(std::string s);
+    void Remove_Structures(std::string station, std::string s);
+
+    // Functions common to several stations
+    void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
+    double FindCarinaSlicePosition();
+    void FindLeftAndRightBronchi();
+
+    // Global parameters
+    typedef std::map<std::string, double> FuzzyThresholdByStructureType;
+    std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;    
+
+    // Station's supports
+    void ExtractStationSupports();
 
     // Station 8
-    double m_DistanceMaxToAnteriorPartOfTheSpine;
+    // double m_DistanceMaxToAnteriorPartOfTheSpine;
     double m_DiaphragmInferiorLimit;
     double m_CarinaZ;
     double m_OriginOfRightMiddleLobeBronchusZ;
-    double m_FuzzyThresholdForS8;
     double m_InjectedThresholdForS8;
     MaskImagePointer m_Esophagus;
     MaskImagePointType m_EsophagusDiltationForAnt;
     MaskImagePointType m_EsophagusDiltationForRight;
-    MaskImagePointer EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & eso);
+
     void ExtractStation_8();
     void ExtractStation_8_SetDefaultValues();
     void ExtractStation_8_SI_Limits();
-    void ExtractStation_8_Post_Limits();
-    void ExtractStation_8_Ant_Sup_Limits();
-    void ExtractStation_8_Ant_Inf_Limits();
-    void ExtractStation_8_Ant_Injected_Limits();
-    void ExtractStation_8_LR_1_Limits();
-    void ExtractStation_8_LR_2_Limits();
+    void ExtractStation_8_Ant_Limits();
+    void ExtractStation_8_Left_Sup_Limits();
+    void ExtractStation_8_Left_Inf_Limits();
     void ExtractStation_8_Single_CCL_Limits();
-    void ExtractStation_8_LR_Limits();
     void ExtractStation_8_Remove_Structures();
-    void ExtractStation_8_LR_Limits_old();
-    void ExtractStation_8_LR_Limits_old2();
-    
+
     // Station 3P
     void ExtractStation_3P();
     void ExtractStation_3P_SetDefaultValues();
@@ -159,21 +172,37 @@ namespace clitk {
     void ExtractStation_3P_LR_sup_Limits_2();
     void ExtractStation_3P_LR_inf_Limits();
 
+    // Station 2RL
+    void ExtractStation_2RL();
+    void ExtractStation_2RL_SetDefaultValues();
+    void ExtractStation_2RL_SI_Limits();
+    void ExtractStation_2RL_Ant_Limits();
+    void ExtractStation_2RL_Ant_Limits2();
+    void ExtractStation_2RL_Post_Limits();
+    void ExtractStation_2RL_LR_Limits();
+    void ExtractStation_2RL_Remove_Structures();
+    void ExtractStation_2RL_SeparateRL();
+    vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
+
     // Station 3A
     void ExtractStation_3A();
     void ExtractStation_3A_SetDefaultValues();
     void ExtractStation_3A_SI_Limits();
     void ExtractStation_3A_Ant_Limits();
+    void ExtractStation_3A_Post_Limits();
 
     // Station 7
     void ExtractStation_7();
     void ExtractStation_7_SetDefaultValues();
     void ExtractStation_7_SI_Limits();
-    void ExtractStation_7_RL_Limits();
+    void ExtractStation_7_RL_Interior_Limits();
+
+
+    void ExtractStation_7_RL_Limits_OLD();
     void ExtractStation_7_Posterior_Limits();   
     void ExtractStation_7_Remove_Structures();
+    bool m_S7_UseMostInferiorPartOnlyFlag;
     MaskImagePointer m_Working_Trachea;
-    std::map<std::string, double> m_FuzzyThresholdForS7;
     MaskImagePointer m_LeftBronchus;
     MaskImagePointer m_RightBronchus;
     typedef std::vector<MaskImageType::PointType> ListOfPointsType;
@@ -210,8 +239,10 @@ namespace clitk {
 
 #ifndef ITK_MANUAL_INSTANTIATION
 #include "clitkExtractLymphStationsFilter.txx"
+#include "clitkExtractLymphStation_Supports.txx"
 #include "clitkExtractLymphStation_8.txx"
 #include "clitkExtractLymphStation_3P.txx"
+#include "clitkExtractLymphStation_2RL.txx"
 #include "clitkExtractLymphStation_3A.txx"
 #include "clitkExtractLymphStation_7.txx"
 #include "clitkExtractLymphStation_4RL.txx"