#define CLITKEXTRACTLYMPHSTATIONSFILTER_H
// clitk
-#include "clitkFilterBase.h"
-#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
+#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.
template <class TImageType>
class ITK_EXPORT ExtractLymphStationsFilter:
- public virtual clitk::FilterBase,
- public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
- public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
+ public clitk::StructuresExtractionFilter<TImageType>
{
public:
/** Standard class typedefs. */
- typedef itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > Superclass;
+ typedef clitk::StructuresExtractionFilter<TImageType> Superclass;
typedef ExtractLymphStationsFilter Self;
typedef itk::SmartPointer<Self> Pointer;
typedef itk::SmartPointer<const Self> ConstPointer;
/** ImageDimension constants */
itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
FILTERBASE_INIT;
-
+
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);
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);
+ 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 GenerateInputRequestedRegion();
virtual void GenerateData();
+ // 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;
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 FindInferiorBorderOfAorticArch();
void FindLeftAndRightBronchi();
void FindLineForS7S8Separation(MaskImagePointType & A, MaskImagePointType & B);
- MaskImagePointer FindAntPostVessels();
+ 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_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,
MaskImagePointer LimitsWithTrachea(MaskImageType * input,
int extremaDirection, int lineDirection,
double offset);
-
// Station 8
- // double m_DistanceMaxToAnteriorPartOfTheSpine;
double m_DiaphragmInferiorLimit;
double m_OriginOfRightMiddleLobeBronchusZ;
double m_InjectedThresholdForS8;
// Station 3A
void ExtractStation_3A();
void ExtractStation_3A_SetDefaultValues();
- void ExtractStation_3A_AntPost_S5();
- void ExtractStation_3A_AntPost_S6();
+ 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();
-
- 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();
+ 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_ComputeStationsSupportsFlag;
+ bool m_ForceSupportsFlag;
+ bool m_CheckSupportFlag;
MaskImagePointer m_Working_Trachea;
MaskImagePointer m_LeftBronchus;
MaskImagePointer m_RightBronchus;
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
#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"
+#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