X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLymphStationsFilter.h;h=5fb011b64646cd3633dce2f5ec1cb4578ec125b9;hb=d30d301ddbebb5f290f8d9c0104dc6448ea531e1;hp=e6b11a753f4630e33788b71e201f2c9745566e1c;hpb=2d513dbdb78fe0a0e2c3980eea894699f3496192;p=clitk.git

diff --git a/segmentation/clitkExtractLymphStationsFilter.h b/segmentation/clitkExtractLymphStationsFilter.h
index e6b11a7..5fb011b 100644
--- a/segmentation/clitkExtractLymphStationsFilter.h
+++ b/segmentation/clitkExtractLymphStationsFilter.h
@@ -19,29 +19,29 @@
 #ifndef CLITKEXTRACTLYMPHSTATIONSFILTER_H
 #define CLITKEXTRACTLYMPHSTATIONSFILTER_H
 
+// clitk
 #include "clitkFilterBase.h"
+#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
 
 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 TImageType>
   class ITK_EXPORT ExtractLymphStationsFilter: 
-    public clitk::FilterBase, 
-    public itk::ImageToImageFilter<TImageType, TImageType> 
+    public virtual clitk::FilterBase, 
+    public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
+    public itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> >
   {
 
   public:
     /** Standard class typedefs. */
-    typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
+    typedef itk::ImageToImageFilter<TImageType, itk::Image<uchar, 3> > Superclass;
     typedef ExtractLymphStationsFilter          Self;
     typedef itk::SmartPointer<Self>             Pointer;
     typedef itk::SmartPointer<const Self>       ConstPointer;
@@ -50,8 +50,7 @@ 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 +60,42 @@ 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<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);
-
-    itkGetConstMacro(BackgroundValue, ImagePixelType);
-    itkGetConstMacro(ForegroundValue, ImagePixelType);
-
-    itkSetMacro(CarenaZPositionInMM, double);
-    itkGetConstMacro(CarenaZPositionInMM, double);
-    GGO_DefineOption(carenaZposition, SetCarenaZPositionInMM, 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);
+    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; 
 
+    typedef itk::Image<MaskImagePixelType, 2>    MaskSliceType;
 
+    /** 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);
+    itkGetConstMacro(EsophagusDiltationForRight, MaskImagePointType);
+    itkSetMacro(FuzzyThresholdForS8, double);
+    itkGetConstMacro(FuzzyThresholdForS8, double);
+
+    // Station 7
+    itkSetMacro(FuzzyThreshold, double);
+    itkGetConstMacro(FuzzyThreshold, double);
+    itkSetMacro(Station7Filename, std::string);
+    itkGetConstMacro(Station7Filename, std::string);
 
   protected:
     ExtractLymphStationsFilter();
@@ -110,26 +104,61 @@ 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<std::string, MaskImagePointer> m_ListOfStations;
+    MaskImagePixelType m_BackgroundValue;
+    MaskImagePixelType m_ForegroundValue;    
+
+    // Station 8
+    double m_DistanceMaxToAnteriorPartOfTheSpine;
+    double m_DiaphragmInferiorLimit;
+    double m_CarinaZ;
+    double m_OriginOfRightMiddleLobeBronchusZ;
+    double m_FuzzyThresholdForS8;
+    MaskImagePointType m_EsophagusDiltationForAnt;
+    MaskImagePointType m_EsophagusDiltationForRight;
+    MaskImagePointer EnlargeEsophagusDilatationRadiusInferiorly(MaskImagePointer & eso);
+    void ExtractStation_8();
+    void ExtractStation_8_SI_Limits();
+    void ExtractStation_8_AP_Limits();
+    void ExtractStation_8_LR_Limits();
+ 
+    // Station 7
+    void ExtractStation_7();
+    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;
+    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();
+    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 +171,9 @@ namespace clitk {
 
 #ifndef ITK_MANUAL_INSTANTIATION
 #include "clitkExtractLymphStationsFilter.txx"
+#include "clitkExtractLymphStation_8.txx"
+#include "clitkExtractLymphStation_7.txx"
+#include "clitkExtractLymphStation_4RL.txx"
 #endif
 
 #endif