X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.h;h=4c7c669d964524b24e7cb7ec6c113340aaada037;hb=2300716104b55267692efc2c0e506b3c5c45df38;hp=e90abd4045c39fb277f6b4ca33c136469c020f09;hpb=e008d74b0ecdc4ca2eaae8c429901a78f9ef5c31;p=clitk.git diff --git a/segmentation/clitkExtractLymphStationsFilter.h b/segmentation/clitkExtractLymphStationsFilter.h index e90abd4..4c7c669 100644 --- a/segmentation/clitkExtractLymphStationsFilter.h +++ b/segmentation/clitkExtractLymphStationsFilter.h @@ -19,30 +19,33 @@ #ifndef CLITKEXTRACTLYMPHSTATIONSFILTER_H #define CLITKEXTRACTLYMPHSTATIONSFILTER_H +// clitk #include "clitkFilterBase.h" +#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h" + +// vtk +#include namespace clitk { //-------------------------------------------------------------------- /* Try to extract the LymphStations part of a thorax CT. - Inputs : - - Patient label image - - Lungs label image - - Bones label image + Need a set of Anatomical Features (AFDB) */ //-------------------------------------------------------------------- template class ITK_EXPORT ExtractLymphStationsFilter: - public clitk::FilterBase, - public itk::ImageToImageFilter + public virtual clitk::FilterBase, + public clitk::FilterWithAnatomicalFeatureDatabaseManagement, + public itk::ImageToImageFilter > { public: /** Standard class typedefs. */ - typedef itk::ImageToImageFilter Superclass; - typedef ExtractLymphStationsFilter Self; + typedef itk::ImageToImageFilter > Superclass; + typedef ExtractLymphStationsFilter Self; typedef itk::SmartPointer Pointer; typedef itk::SmartPointer ConstPointer; @@ -50,8 +53,7 @@ namespace clitk { itkNewMacro(Self); /** Run-time type information (and related methods). */ - itkTypeMacro(ExtractLymphStationsFilter, InPlaceImageFilter); - FILTERBASE_INIT; + itkTypeMacro(ExtractLymphStationsFilter, ImageToImageFilter); /** Some convenient typedefs. */ typedef TImageType ImageType; @@ -61,47 +63,57 @@ namespace clitk { typedef typename ImageType::PixelType ImagePixelType; typedef typename ImageType::SizeType ImageSizeType; typedef typename ImageType::IndexType ImageIndexType; + typedef typename ImageType::PointType ImagePointType; - /** Connect inputs */ - void SetInputMediastinumLabelImage(const TImageType * image, ImagePixelType bg=0); - void SetInputTracheaLabelImage(const TImageType * image, ImagePixelType bg=0); - - /** ImageDimension constants */ - itkStaticConstMacro(ImageDimension, unsigned int, TImageType::ImageDimension); - - // Set all options at a time - template - void SetArgsInfo(ArgsInfoType arg); - - // Background / Foreground - itkSetMacro(BackgroundValueMediastinum, ImagePixelType); - itkGetConstMacro(BackgroundValueMediastinum, ImagePixelType); - //GGO_DefineOption(MediastinumBG, SetBackgroundValueMediastinum, ImagePixelType); - - itkSetMacro(BackgroundValueTrachea, ImagePixelType); - itkGetConstMacro(BackgroundValueTrachea, ImagePixelType); - //GGO_DefineOption(TracheaBG, SetBackgroundValueTrachea, ImagePixelType); - - itkGetConstMacro(BackgroundValue, ImagePixelType); - itkGetConstMacro(ForegroundValue, ImagePixelType); + typedef uchar MaskImagePixelType; + typedef itk::Image MaskImageType; + typedef typename MaskImageType::Pointer MaskImagePointer; + typedef typename MaskImageType::RegionType MaskImageRegionType; + typedef typename MaskImageType::SizeType MaskImageSizeType; + typedef typename MaskImageType::IndexType MaskImageIndexType; + typedef typename MaskImageType::PointType MaskImagePointType; - itkSetMacro(CarenaZPositionInMM, double); - itkGetConstMacro(CarenaZPositionInMM, double); - GGO_DefineOption(carenaZposition, SetCarenaZPositionInMM, double); + typedef itk::Image 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; - itkSetMacro(MiddleLobeBronchusZPositionInMM, double); - itkGetConstMacro(MiddleLobeBronchusZPositionInMM, double); - GGO_DefineOption(middleLobeBronchusZposition, SetMiddleLobeBronchusZPositionInMM, double); - - itkSetMacro(IntermediateSpacing, double); - itkGetConstMacro(IntermediateSpacing, double); - GGO_DefineOption(spacing, SetIntermediateSpacing, double); + /** ImageDimension constants */ + itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension); + FILTERBASE_INIT; + + itkGetConstMacro(BackgroundValue, MaskImagePixelType); + itkGetConstMacro(ForegroundValue, MaskImagePixelType); + itkSetMacro(BackgroundValue, MaskImagePixelType); + itkSetMacro(ForegroundValue, MaskImagePixelType); - itkSetMacro(FuzzyThreshold1, double); - itkGetConstMacro(FuzzyThreshold1, double); - GGO_DefineOption(fuzzy1, SetFuzzyThreshold1, double); + // 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 + 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); + void SetThreshold(std::string station, std::string tag, double value); + double GetThreshold(std::string station, std::string tag); + itkGetConstMacro(ComputeStationsSupportsFlag, bool); + itkSetMacro(ComputeStationsSupportsFlag, bool); + itkBooleanMacro(ComputeStationsSupportsFlag); protected: ExtractLymphStationsFilter(); @@ -110,26 +122,140 @@ namespace clitk { virtual void GenerateOutputInformation(); virtual void GenerateInputRequestedRegion(); virtual void GenerateData(); - - itkSetMacro(BackgroundValue, ImagePixelType); - itkSetMacro(ForegroundValue, ImagePixelType); - - ImageConstPointer m_mediastinum; - ImageConstPointer m_trachea; - ImagePointer m_working_image; - ImagePointer m_working_trachea; - ImagePointer m_output; - - ImagePixelType m_BackgroundValueMediastinum; - ImagePixelType m_BackgroundValueTrachea; - ImagePixelType m_BackgroundValue; - ImagePixelType m_ForegroundValue; - - double m_CarenaZPositionInMM; - double m_MiddleLobeBronchusZPositionInMM; - double m_IntermediateSpacing; - double m_FuzzyThreshold1; + ImageConstPointer m_Input; + MaskImagePointer m_Mediastinum; + MaskImagePointer m_Working_Support; + std::map m_ListOfStations; + std::map m_ListOfSupports; + MaskImagePixelType m_BackgroundValue; + MaskImagePixelType m_ForegroundValue; + std::map 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(); + + // Global parameters + typedef std::map FuzzyThresholdByStructureType; + std::map m_FuzzyThreshold; + typedef std::map ThresholdByStructureType; + std::map m_Threshold; + + // 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_Remove_Structures(); + void ExtractStation_3A_PostToBones(); + + // 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 Build3DMeshFrom2DContour(const std::vector & points); + + // Station 7 + void ExtractStation_7(); + void ExtractStation_7_SetDefaultValues(); + void ExtractStation_7_SI_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; + bool m_ComputeStationsSupportsFlag; + MaskImagePointer m_Working_Trachea; + MaskImagePointer m_LeftBronchus; + MaskImagePointer m_RightBronchus; + typedef std::vector 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(); + void ExtractStation_4RL_AP_Limits(); + MaskImagePointer m_RightSupport; + MaskImagePointer m_LeftSupport; + private: ExtractLymphStationsFilter(const Self&); //purposely not implemented void operator=(const Self&); //purposely not implemented @@ -142,6 +268,13 @@ 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" #endif #endif