#ifndef CLITKEXTRACTLYMPHSTATIONSFILTER_H
#define CLITKEXTRACTLYMPHSTATIONSFILTER_H
-#include "clitkFilterBase.h"
+// clitk
+#include "clitkStructuresExtractionFilter.h"
+#include "clitkLabelImageOverlapMeasureFilter.h"
+
+// vtk
+#include <vtkPolyData.h>
namespace clitk {
+ class SupportLimitsType {
+ public:
+ std::string station_limit;
+ std::string station;
+ std::string structure_limit;
+ std::string structure;
+ double offset;
+ void Read(istream & is) {
+ is >> station_limit;
+ is >> station;
+ is >> structure_limit;
+ is >> structure;
+ std::string s;
+ is >> s;
+ offset = atof(s.c_str());
+ }
+ };
+
//--------------------------------------------------------------------
/*
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 TImageType>
class ITK_EXPORT ExtractLymphStationsFilter:
- public clitk::FilterBase,
- public itk::ImageToImageFilter<TImageType, TImageType>
+ public clitk::StructuresExtractionFilter<TImageType>
{
public:
/** Standard class typedefs. */
- typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
+ typedef clitk::StructuresExtractionFilter<TImageType> Superclass;
typedef ExtractLymphStationsFilter Self;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
itkNewMacro(Self);
/** Run-time type information (and related methods). */
- itkTypeMacro(ExtractLymphStationsFilter, InPlaceImageFilter);
- FILTERBASE_INIT;
+ itkTypeMacro(ExtractLymphStationsFilter, ImageToImageFilter);
/** Some convenient typedefs. */
typedef TImageType ImageType;
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<class ArgsInfoType>
- 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);
+ typedef uchar MaskImagePixelType;
+ typedef itk::Image<MaskImagePixelType, 3> 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;
- itkGetConstMacro(BackgroundValue, ImagePixelType);
- itkGetConstMacro(ForegroundValue, ImagePixelType);
+ 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;
- itkSetMacro(CarenaZPositionInMM, double);
- itkGetConstMacro(CarenaZPositionInMM, double);
- GGO_DefineOption(carenaZposition, SetCarenaZPositionInMM, double);
+ /** ImageDimension constants */
+ itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
+ FILTERBASE_INIT;
+
+ itkGetConstMacro(BackgroundValue, MaskImagePixelType);
+ itkGetConstMacro(ForegroundValue, MaskImagePixelType);
+ itkSetMacro(BackgroundValue, MaskImagePixelType);
+ itkSetMacro(ForegroundValue, MaskImagePixelType);
- itkSetMacro(MiddleLobeBronchusZPositionInMM, double);
- itkGetConstMacro(MiddleLobeBronchusZPositionInMM, double);
- GGO_DefineOption(middleLobeBronchusZposition, SetMiddleLobeBronchusZPositionInMM, double);
+ // Station 8
+ itkSetMacro(EsophagusDiltationForAnt, MaskImagePointType);
+ itkGetConstMacro(EsophagusDiltationForAnt, MaskImagePointType);
+ itkSetMacro(EsophagusDiltationForRight, MaskImagePointType);
+ itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
+ itkSetMacro(InjectedThresholdForS8, double);
+ itkGetConstMacro(InjectedThresholdForS8, double);
- itkSetMacro(IntermediateSpacing, double);
- itkGetConstMacro(IntermediateSpacing, double);
- GGO_DefineOption(spacing, SetIntermediateSpacing, double);
+ // Station 7
+ itkGetConstMacro(S7_UseMostInferiorPartOnlyFlag, bool);
+ itkSetMacro(S7_UseMostInferiorPartOnlyFlag, bool);
+ itkBooleanMacro(S7_UseMostInferiorPartOnlyFlag);
- itkSetMacro(FuzzyThreshold1, double);
- itkGetConstMacro(FuzzyThreshold1, double);
- GGO_DefineOption(fuzzy1, SetFuzzyThreshold1, double);
+ // 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(ForceSupportsFlag, bool);
+ itkSetMacro(ForceSupportsFlag, bool);
+ itkBooleanMacro(ForceSupportsFlag);
+ itkGetConstMacro(CheckSupportFlag, bool);
+ itkSetMacro(CheckSupportFlag, bool);
+ itkBooleanMacro(CheckSupportFlag);
+ itkGetConstMacro(SupportLimitsFilename, std::string);
+ itkSetMacro(SupportLimitsFilename, std::string);
protected:
ExtractLymphStationsFilter();
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;
+ // To avoid repeat "this->"
+ AnatomicalFeatureDatabase * GetAFDB() { return clitk::FilterWithAnatomicalFeatureDatabaseManagement::GetAFDB(); }
+ void WriteAFDB() { clitk::FilterWithAnatomicalFeatureDatabaseManagement::WriteAFDB(); }
+ void LoadAFDB() { clitk::FilterWithAnatomicalFeatureDatabaseManagement::LoadAFDB(); }
+ void StartNewStep(std::string s) { clitk::FilterBase::StartNewStep(s); }
+ void StartSubStep() { clitk::FilterBase::StartSubStep(); }
+ template<class TInternalImageType>
+ void StopCurrentStep(typename TInternalImageType::Pointer p, std::string txt="") { clitk::FilterBase::StopCurrentStep<TInternalImageType>(p, txt); }
+ void StopCurrentStep() {clitk::FilterBase::StopCurrentStep(); }
+ void StopSubStep() {clitk::FilterBase::StopSubStep(); }
+
+ ImageConstPointer m_Input;
+ 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;
+ std::string m_SupportLimitsFilename;
+ std::vector<SupportLimitsType> m_ListOfSupportLimits;
+
+ bool CheckForStation(std::string station);
+ void Remove_Structures(std::string station, std::string s);
+ void WriteImageSupport(std::string support);
+ void WriteImageStation(std::string station);
+ void ComputeOverlapWithRef(std::string station);
+ void Support_SI_Limit(const std::string station_limit, const std::string station,
+ const std::string structure_limit, const std::string structure,
+ const double offset);
+ void ReadSupportLimits(std::string filename);
+
+ // Functions common to several stations
+ double FindCarina();
+ double FindApexOfTheChest();
+ double FindSuperiorBorderOfAorticArch();
+ double FindInferiorBorderOfAorticArch();
+ void FindLeftAndRightBronchi();
+ void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
+ MaskImagePointer FindAntPostVesselsOLD();
+ MaskImagePointer FindAntPostVessels2();
+
+ // Global parameters
+ typedef std::map<std::string, double> FuzzyThresholdByStructureType;
+ std::map<std::string, FuzzyThresholdByStructureType> m_FuzzyThreshold;
+ typedef std::map<std::string, double> ThresholdByStructureType;
+ std::map<std::string, ThresholdByStructureType> m_Threshold;
+
+ // Station's supports
+ void ExtractStationSupports();
+ void Support_LeftRight_S1R_S1L();
+ void Support_LeftRight_S2R_S2L();
+ void Support_LeftRight_S4R_S4L();
+ void Support_Post_S1S2S4();
+
+ 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_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_Post_Left_Limits_With_Aorta_S5_Support();
+ void ExtractStation_3A_Post_Limits_With_Dilated_Aorta_S6_Support();
+ void ExtractStation_3A_AntPost_Superiorly();
+ void ExtractStation_3A_Remove_Structures();
+
+ // Station 2RL
+ void ExtractStation_2RL();
+ void ExtractStation_2RL_SetDefaultValues();
+ void ExtractStation_2RL_Ant_Limits(std::string s);
+ void ExtractStation_2RL_Remove_Structures(std::string s);
+ void ExtractStation_2RL_Cut_BrachioCephalicVein_superiorly_when_it_split();
+ vtkSmartPointer<vtkPolyData> Build3DMeshFrom2DContour(const std::vector<ImagePointType> & points);
+
+ // Station 1RL
+ void ExtractStation_1RL();
+ void ExtractStation_1RL_SetDefaultValues();
+ void ExtractStation_1RL_Ant_Limits();
+ void ExtractStation_1RL_Post_Limits();
+
+ // Station 4RL
+ void ExtractStation_4RL_SetDefaultValues();
+ void ExtractStation_4L();
+ void ExtractStation_4R();
+ void ExtractStation_S4L_S5_Limits_Aorta_LeftPulmonaryArtery(int KeepPoint);
+
+ // Station 5
+ void ExtractStation_5_SetDefaultValues();
+ void ExtractStation_5();
+ void ExtractStation_5_Limits_AscendingAorta_Ant();
+
+ // Station 6
+ void ExtractStation_6_SetDefaultValues();
+ void ExtractStation_6();
+
+
+ // 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_ForceSupportsFlag;
+ bool m_CheckSupportFlag;
+ MaskImagePointer m_Working_Trachea;
+ MaskImagePointer m_LeftBronchus;
+ MaskImagePointer m_RightBronchus;
+ 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);
private:
ExtractLymphStationsFilter(const Self&); //purposely not implemented
void operator=(const Self&); //purposely not implemented
#ifndef ITK_MANUAL_INSTANTIATION
#include "clitkExtractLymphStationsFilter.txx"
+#include "clitkExtractLymphStation_Supports.txx"
+#include "clitkExtractLymphStation_3P.txx"
+#include "clitkExtractLymphStation_2RL.txx"
+#include "clitkExtractLymphStation_3A.txx"
+#include "clitkExtractLymphStation_4RL.txx"
+#include "clitkExtractLymphStation_1RL.txx"
+#include "clitkExtractLymphStation_5.txx"
+#include "clitkExtractLymphStation_6.txx"
+
+#include "clitkExtractLymphStation_8.txx"
+#include "clitkExtractLymphStation_7.txx"
#endif
#endif
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff