With ITK 5, add itkReadRawBytesAfterSwappingMacro and itkWriteRawBytesAfterSwappingMacro

[clitk.git] / segmentation / clitkExtractLungFilter.h

diff --git a/segmentation/clitkExtractLungFilter.h b/segmentation/clitkExtractLungFilter.h
index 50d553ae41ce9c130d9ba7acfde941354f3d1fd6..6c50b1c2d96c85e3c9b8485d970d9ad6e0a261b3 100644 (file)
--- a/segmentation/clitkExtractLungFilter.h
+++ b/segmentation/clitkExtractLungFilter.h
@@ -142,6 +142,9 @@ namespace clitk {
 
     void SetLabelizeParameters1(LabelParamType * a) { m_LabelizeParameters1 = a; }
     itkGetConstMacro(LabelizeParameters1, LabelParamType*);
+    
+    itkSetMacro(TracheaSeedAlgorithm, int);
+    itkGetConstMacro(TracheaSeedAlgorithm, int);
 
     // Step 2 options FindTrachea
     itkSetMacro(UpperThresholdForTrachea, InputImagePixelType);
@@ -153,7 +156,16 @@ namespace clitk {
     itkSetMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
     itkGetConstMacro(ThresholdStepSizeForTrachea, InputImagePixelType);
 
-    void AddSeed(InternalIndexType s);
+    // options FindTrachea2
+    itkSetMacro(NumSlices, int);
+    itkGetConstMacro(NumSlices, int);
+    itkSetMacro(MaxElongation, double);
+    itkGetConstMacro(MaxElongation, double);
+    itkSetMacro(SeedPreProcessingThreshold, int);
+    itkGetConstMacro(SeedPreProcessingThreshold, int);
+
+    void AddSeedInPixels(InternalIndexType s);
+    void AddSeed(InputImagePointType s);
     std::vector<InternalIndexType> & GetSeeds() { return  m_Seeds; }
 
     itkSetMacro(TracheaVolumeMustBeCheckedFlag, bool);
@@ -164,6 +176,10 @@ namespace clitk {
     itkGetConstMacro(VerboseRegionGrowingFlag, bool);
     itkBooleanMacro(VerboseRegionGrowingFlag);    
 
+    itkSetMacro(RemoveSmallLabelBeforeSeparationFlag, bool);
+    itkGetConstMacro(RemoveSmallLabelBeforeSeparationFlag, bool);
+    itkBooleanMacro(RemoveSmallLabelBeforeSeparationFlag);    
+
     // Step 3 options ExtractLung
     itkSetMacro(NumberOfHistogramBins, int);
     itkGetConstMacro(NumberOfHistogramBins, int);
@@ -191,6 +207,16 @@ namespace clitk {
     itkGetConstMacro(FillHolesFlag, bool);
     itkBooleanMacro(FillHolesFlag);
 
+    // Separate lungs
+    itkSetMacro(SeparateLungsFlag, bool);
+    itkGetConstMacro(SeparateLungsFlag, bool);
+    itkBooleanMacro(SeparateLungsFlag);
+
+    // Step Auto Crop
+    itkSetMacro(AutoCrop, bool);
+    itkGetConstMacro(AutoCrop, bool);
+    itkBooleanMacro(AutoCrop);
+    
   protected:
     ExtractLungFilter();
     virtual ~ExtractLungFilter() {}
@@ -212,6 +238,8 @@ namespace clitk {
     MaskImagePixelType m_BackgroundValue;
     MaskImagePixelType m_ForegroundValue;
     int m_MinimalComponentSize;
+    bool m_AutoCrop;
+    bool m_RemoveSmallLabelBeforeSeparationFlag;
 
     // Step 1
     InputImagePixelType m_UpperThreshold;
@@ -220,13 +248,18 @@ namespace clitk {
     LabelParamType* m_LabelizeParameters1;
 
     // Step 2
+    int m_TracheaSeedAlgorithm;
     InputImagePixelType m_UpperThresholdForTrachea;
     InputImagePixelType m_ThresholdStepSizeForTrachea;
     double m_MultiplierForTrachea;
     std::vector<InternalIndexType> m_Seeds;
+    std::vector<InputImagePointType> m_SeedsInMM;
     int m_NumberOfSlicesToSkipBeforeSearchingSeed;
     bool m_TracheaVolumeMustBeCheckedFlag;
     bool m_VerboseRegionGrowingFlag;
+    int m_NumSlices;
+    double m_MaxElongation;
+    int m_SeedPreProcessingThreshold;
 
     // Step 3
     int m_NumberOfHistogramBins;
@@ -244,6 +277,8 @@ namespace clitk {
     bool m_FillHolesFlag;    
     InputImageSizeType m_FillHolesDirections;
 
+    bool m_SeparateLungsFlag;
+    
     // Main functions
     virtual void GenerateOutputInformation();
     virtual void GenerateInputRequestedRegion();
@@ -251,6 +286,7 @@ namespace clitk {
     
     // Functions for trachea extraction
     bool SearchForTracheaSeed(int skip);
+    bool SearchForTracheaSeed2(int numberOfSlices);
     void SearchForTrachea();
     void TracheaRegionGrowing();
     double ComputeTracheaVolume();