X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.h;h=dd99c5fd4f8eced90f38eef544e1929417ddd802;hb=ae30683c11f6666246f2d9bcac250baacc28aa33;hp=6db26a222b138ee0c3fe4cdf24da968631a8f15b;hpb=df08bfa3c4c20736f7194764643e7104eed63be9;p=clitk.git diff --git a/segmentation/clitkExtractLymphStationsFilter.h b/segmentation/clitkExtractLymphStationsFilter.h index 6db26a2..dd99c5f 100644 --- a/segmentation/clitkExtractLymphStationsFilter.h +++ b/segmentation/clitkExtractLymphStationsFilter.h @@ -23,15 +23,15 @@ #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) */ //-------------------------------------------------------------------- @@ -39,12 +39,12 @@ namespace clitk { class ITK_EXPORT ExtractLymphStationsFilter: public virtual clitk::FilterBase, public clitk::FilterWithAnatomicalFeatureDatabaseManagement, - public itk::ImageToImageFilter + public itk::ImageToImageFilter > { public: /** Standard class typedefs. */ - typedef itk::ImageToImageFilter Superclass; + typedef itk::ImageToImageFilter > Superclass; typedef ExtractLymphStationsFilter Self; typedef itk::SmartPointer Pointer; typedef itk::SmartPointer ConstPointer; @@ -53,8 +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; @@ -66,46 +65,51 @@ namespace clitk { 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); + 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; + + 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; - // Set all options at a time - template - void SetArgsInfo(ArgsInfoType arg); + /** ImageDimension constants */ + itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension); + FILTERBASE_INIT; - // 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); + 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 + 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); - //itkSetMacro(CarinaZPositionInMM, double); - void SetCarinaZPositionInMM(double d) { m_CarinaZPositionInMM = d; Modified(); m_CarinaZPositionInMMIsSet = true; } - itkGetConstMacro(CarinaZPositionInMM, double); - GGO_DefineOption(carenaZposition, SetCarinaZPositionInMM, double); - - itkSetMacro(MiddleLobeBronchusZPositionInMM, double); - itkGetConstMacro(MiddleLobeBronchusZPositionInMM, double); - GGO_DefineOption(middleLobeBronchusZposition, SetMiddleLobeBronchusZPositionInMM, double); - - itkSetMacro(IntermediateSpacing, double); - itkGetConstMacro(IntermediateSpacing, double); - GGO_DefineOption(spacing, SetIntermediateSpacing, double); - - itkSetMacro(FuzzyThreshold1, double); - itkGetConstMacro(FuzzyThreshold1, double); - GGO_DefineOption(fuzzy1, SetFuzzyThreshold1, double); - protected: ExtractLymphStationsFilter(); virtual ~ExtractLymphStationsFilter() {} @@ -113,27 +117,116 @@ 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_CarinaZPositionInMM; - bool m_CarinaZPositionInMMIsSet; - 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 + void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B); + double FindCarinaSlicePosition(); + void FindLeftAndRightBronchi(); + + // Global parameters + typedef std::map FuzzyThresholdByStructureType; + std::map m_FuzzyThreshold; + + // Station's supports + void ExtractStationSupports(); + + // Station 8 + // double m_DistanceMaxToAnteriorPartOfTheSpine; + double m_DiaphragmInferiorLimit; + double m_CarinaZ; + 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_SI_Limits(); + void ExtractStation_3P_Remove_Structures(); + void ExtractStation_3P_Ant_Limits(); + void ExtractStation_3P_Post_Limits(); + void ExtractStation_3P_LR_sup_Limits(); + 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 Build3DMeshFrom2DContour(const std::vector & 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_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; + 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 @@ -146,6 +239,13 @@ 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