#include "clitkFilterBase.h"
#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
+// vtk
+#include <vtkPolyData.h>
+
namespace clitk {
//--------------------------------------------------------------------
typedef typename MaskImageType::IndexType MaskImageIndexType;
typedef typename MaskImageType::PointType MaskImagePointType;
+ 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);
FILTERBASE_INIT;
- /** Main options (from ggo) */
- template <class ArgsInfoType>
- void SetArgsInfo(ArgsInfoType & argsinfo);
-
itkGetConstMacro(BackgroundValue, MaskImagePixelType);
itkGetConstMacro(ForegroundValue, MaskImagePixelType);
itkSetMacro(BackgroundValue, MaskImagePixelType);
itkSetMacro(ForegroundValue, MaskImagePixelType);
-
+
+ // Station 8
+ // itkSetMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
+ //itkGetConstMacro(DistanceMaxToAnteriorPartOfTheSpine, double);
+ itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
+ itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
+ itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
+ itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
+ itkSetMacro(InjectedThresholdForS8, double);
+ itkGetConstMacro(InjectedThresholdForS8, double);
+
// Station 7
- itkSetMacro(FuzzyThreshold, double);
- itkGetConstMacro(FuzzyThreshold, double);
- itkSetMacro(Station7Filename, std::string);
- itkGetConstMacro(Station7Filename, std::string);
+ 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);
+ itkGetConstMacro(ComputeStationsSupportsFlag, bool);
+ itkSetMacro(ComputeStationsSupportsFlag, bool);
+ itkBooleanMacro(ComputeStationsSupportsFlag);
protected:
ExtractLymphStationsFilter();
virtual void GenerateData();
ImageConstPointer m_Input;
- MaskImagePointer m_Support;
+ MaskImagePointer m_Mediastinum;
MaskImagePointer m_Working_Support;
- MaskImagePointer m_Output;
+ std::map<std::string, MaskImagePointer> m_ListOfStations;
+ std::map<std::string, MaskImagePointer> m_ListOfSupports;
MaskImagePixelType m_BackgroundValue;
- MaskImagePixelType m_ForegroundValue;
+ MaskImagePixelType m_ForegroundValue;
+ std::map<std::string, bool> m_ComputeStationMap;
+
+ bool CheckForStation(std::string station);
+ void Remove_Structures(std::string station, std::string s);
+
+ // Functions common to several stations
+ double FindCarina();
+ double FindApexOfTheChest();
+ double FindSuperiorBorderOfAorticArch();
+ double FindInferiorBorderOfAorticArch();
+ void FindLeftAndRightBronchi();
+ void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
+ MaskImagePointer FindAntPostVessels();
+ MaskImagePointer FindAntPostVessels2();
- // Common
- MaskImagePointer m_Trachea;
+ // Global parameters
+ typedef std::map<std::string, double> FuzzyThresholdByStructureType;
+ std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
+
+ // Station's supports
+ void ExtractStationSupports();
+ void Support_SupInf_S1RL();
+ void Support_LeftRight_S1R_S1L();
+ void Support_SupInf_S2R_S2L();
+ void Support_LeftRight_S2R_S2L();
+ void Support_SupInf_S4R_S4L();
+ void Support_LeftRight_S4R_S4L();
+ void Support_Post_S1S2S4();
+ void Support_S3P();
+ void Support_S3A();
+ void Support_S5();
+ void Support_S6();
+
+ MaskImagePointer LimitsWithTrachea(MaskImageType * input,
+ int extremaDirection, int lineDirection,
+ double offset, double maxSupPosition);
+ MaskImagePointer LimitsWithTrachea(MaskImageType * input,
+ int extremaDirection, int lineDirection,
+ double offset);
+
+ // Station 8
+ // double m_DistanceMaxToAnteriorPartOfTheSpine;
+ double m_DiaphragmInferiorLimit;
+ double m_OriginOfRightMiddleLobeBronchusZ;
+ double m_InjectedThresholdForS8;
+ MaskImagePointer m_Esophagus;
+ MaskImagePointType m_EsophagusDiltationForAnt;
+ MaskImagePointType m_EsophagusDiltationForRight;
+
+ void ExtractStation_8();
+ void ExtractStation_8_SetDefaultValues();
+ void ExtractStation_8_SI_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_Remove_Structures();
+
+ // Station 3P
+ void ExtractStation_3P();
+ void ExtractStation_3P_SetDefaultValues();
+ void ExtractStation_3P_LR_inf_Limits();
+ void ExtractStation_3P_LR_sup_Limits_2();
+ void ExtractStation_3P_Remove_Structures();
+ void ExtractStation_3P_LR_sup_Limits();
+
+ // Station 3A
+ void ExtractStation_3A();
+ void ExtractStation_3A_SetDefaultValues();
+ void ExtractStation_3A_AntPost_S5();
+ void ExtractStation_3A_AntPost_S6();
+ void ExtractStation_3A_AntPost_Superiorly();
+ void ExtractStation_3A_SI_Limits();
+ void ExtractStation_3A_Ant_Limits();
+ void ExtractStation_3A_Post_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 7
void ExtractStation_7();
+ void ExtractStation_7_SetDefaultValues();
void ExtractStation_7_SI_Limits();
- void ExtractStation_7_RL_Limits();
- void ExtractStation_7_Posterior_Limits();
- std::string m_Station7Filename;
- MaskImagePointer m_working_trachea;
- double m_FuzzyThreshold;
+ 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;
+ bool m_ComputeStationsSupportsFlag;
+ MaskImagePointer m_Working_Trachea;
MaskImagePointer m_LeftBronchus;
MaskImagePointer m_RightBronchus;
- MaskImagePointer m_Station7;
+ typedef std::vector<MaskImageType::PointType> ListOfPointsType;
+ ListOfPointsType m_RightMostInLeftBronchus;
+ ListOfPointsType m_AntMostInLeftBronchus;
+ ListOfPointsType m_PostMostInLeftBronchus;
+ ListOfPointsType m_LeftMostInRightBronchus;
+ ListOfPointsType m_AntMostInRightBronchus;
+ ListOfPointsType m_PostMostInRightBronchus;
+ void FindExtremaPointsInBronchus(MaskImagePointer input,
+ int direction,
+ double distance_max_from_center_point,
+ ListOfPointsType & LR,
+ ListOfPointsType & Ant,
+ ListOfPointsType & Post);
// Station 4RL
void ExtractStation_4RL();
void ExtractStation_4RL_SI_Limits();
void ExtractStation_4RL_LR_Limits();
- MaskImagePointer m_Station4RL;
+ void ExtractStation_4RL_AP_Limits();
+ MaskImagePointer m_RightSupport;
+ MaskImagePointer m_LeftSupport;
private:
ExtractLymphStationsFilter(const Self&); //purposely not implemented
#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"
#endif
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff