X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=segmentation%2FclitkExtractLungFilter.h;h=3183457dde0a6eb7ff06d445670cb132523a2ae8;hb=5668d4a49a5a6b68dc80fa28f0f82b54187cb70c;hp=781a885f67eca478cb989b347696eee61a67434b;hpb=c8d53d40ac8f5f83843193c51ac1787a8f38ee90;p=clitk.git

diff --git a/segmentation/clitkExtractLungFilter.h b/segmentation/clitkExtractLungFilter.h
index 781a885..3183457 100644
--- a/segmentation/clitkExtractLungFilter.h
+++ b/segmentation/clitkExtractLungFilter.h
@@ -24,6 +24,7 @@
 #include "clitkDecomposeAndReconstructImageFilter.h"
 #include "clitkExplosionControlledThresholdConnectedImageFilter.h"
 #include "clitkSegmentationUtils.h"
+#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
 
 // itk
 #include "itkStatisticsImageFilter.h"
@@ -54,15 +55,18 @@ namespace clitk {
   */
   //--------------------------------------------------------------------
   
-  template <class TInputImageType, class TMaskImageType>
+  //--------------------------------------------------------------------
+  template <class TImageType>
   class ITK_EXPORT ExtractLungFilter: 
-    public clitk::FilterBase, 
-    public itk::ImageToImageFilter<TInputImageType, TMaskImageType> 
+    public virtual clitk::FilterBase, 
+    public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
+    public itk::ImageToImageFilter<TImageType, itk::Image<uchar, TImageType::ImageDimension> > 
   {
     
   public:
     /** Standard class typedefs. */
-    typedef itk::ImageToImageFilter<TInputImageType, TMaskImageType> Superclass;
+    typedef itk::Image<uchar, TImageType::ImageDimension> MaskImageType;
+    typedef itk::ImageToImageFilter<TImageType, MaskImageType> Superclass;
     typedef ExtractLungFilter              Self;
     typedef itk::SmartPointer<Self>        Pointer;
     typedef itk::SmartPointer<const Self>  ConstPointer;
@@ -75,36 +79,45 @@ namespace clitk {
     FILTERBASE_INIT;
 
     /** Some convenient typedefs */
-    typedef TInputImageType                       InputImageType;
-    typedef typename InputImageType::ConstPointer InputImageConstPointer;
-    typedef typename InputImageType::Pointer      InputImagePointer;
-    typedef typename InputImageType::RegionType   InputImageRegionType; 
-    typedef typename InputImageType::PixelType    InputImagePixelType; 
-    typedef typename InputImageType::SizeType     InputImageSizeType; 
-    typedef typename InputImageType::IndexType    InputImageIndexType; 
+    typedef TImageType                       ImageType;
+    typedef typename ImageType::ConstPointer InputImageConstPointer;
+    typedef typename ImageType::Pointer      InputImagePointer;
+    typedef typename ImageType::RegionType   InputImageRegionType; 
+    typedef typename ImageType::PixelType    InputImagePixelType; 
+    typedef typename ImageType::SizeType     InputImageSizeType; 
+    typedef typename ImageType::IndexType    InputImageIndexType; 
+    typedef typename ImageType::PointType    InputImagePointType; 
         
-    typedef TMaskImageType                       MaskImageType;
     typedef typename MaskImageType::ConstPointer MaskImageConstPointer;
     typedef typename MaskImageType::Pointer      MaskImagePointer;
     typedef typename MaskImageType::RegionType   MaskImageRegionType; 
     typedef typename MaskImageType::PixelType    MaskImagePixelType; 
     typedef typename MaskImageType::SizeType     MaskImageSizeType; 
     typedef typename MaskImageType::IndexType    MaskImageIndexType; 
+    typedef typename MaskImageType::PointType    MaskImagePointType; 
 
-    itkStaticConstMacro(ImageDimension, unsigned int, InputImageType::ImageDimension);
+    itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
     typedef int InternalPixelType;
-    typedef itk::Image<InternalPixelType, InputImageType::ImageDimension> InternalImageType;
-    typedef typename InternalImageType::Pointer                           InternalImagePointer;
-    typedef typename InternalImageType::IndexType                         InternalIndexType;
-    typedef LabelizeParameters<InternalPixelType>                         LabelParamType;
+    typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
+    typedef typename InternalImageType::Pointer                      InternalImagePointer;
+    typedef typename InternalImageType::IndexType                    InternalIndexType;
+    typedef LabelizeParameters<InternalPixelType>                    LabelParamType;
     
     /** Connect inputs */
-    void SetInput(const InputImageType * image);
-    void SetInputPatientMask(MaskImageType * mask, MaskImagePixelType BG);
+    void SetInput(const ImageType * image);
     itkSetMacro(PatientMaskBackgroundValue, MaskImagePixelType);
     itkGetConstMacro(PatientMaskBackgroundValue, MaskImagePixelType);
     GGO_DefineOption(patientBG, SetPatientMaskBackgroundValue, MaskImagePixelType);
 
+    // Output filename  (for AFBD)
+    itkSetMacro(OutputLungFilename, std::string);
+    itkGetMacro(OutputLungFilename, std::string);
+    GGO_DefineOption(output, SetOutputLungFilename, std::string);
+
+    itkSetMacro(OutputTracheaFilename, std::string);
+    itkGetMacro(OutputTracheaFilename, std::string);
+    GGO_DefineOption(outputTrachea, SetOutputTracheaFilename, std::string);
+
     // Set all options at a time
     template<class ArgsInfoType>
       void SetArgsInfo(ArgsInfoType arg);
@@ -126,6 +139,10 @@ namespace clitk {
     itkGetConstMacro(UpperThreshold, InputImagePixelType);
     GGO_DefineOption(upper, SetUpperThreshold, InputImagePixelType);
 
+    itkSetMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int);
+    itkGetConstMacro(NumberOfSlicesToSkipBeforeSearchingSeed, int);
+    GGO_DefineOption(skipslices, SetNumberOfSlicesToSkipBeforeSearchingSeed, int);
+    
     itkSetMacro(LowerThreshold, InputImagePixelType);
     itkGetConstMacro(LowerThreshold, InputImagePixelType);
     itkSetMacro(UseLowerThreshold, bool);
@@ -152,7 +169,7 @@ namespace clitk {
 
     void AddSeed(InternalIndexType s);
     std::vector<InternalIndexType> & GetSeeds() { return  m_Seeds; }
-    GGO_DefineOption_Vector(seed, AddSeed, InternalIndexType, InputImageType::ImageDimension, true);
+    GGO_DefineOption_Vector(seed, AddSeed, InternalIndexType, ImageType::ImageDimension, true);
 
     // Step 3 options ExtractLung
     itkSetMacro(NumberOfHistogramBins, int);
@@ -172,17 +189,38 @@ namespace clitk {
     itkGetConstMacro(LabelizeParameters3, LabelParamType*);
     GGO_DefineOption_LabelParam(3, SetLabelizeParameters3, LabelParamType);
 
-    // Step 5 options LungSeparation
-    //     itkSetMacro(FinalOpenClose, bool);
-    //     itkGetConstMacro(FinalOpenClose, bool);
-    //     itkBooleanMacro(FinalOpenClose);
+    // Step 5 final openclose
+    itkSetMacro(OpenClose, bool);
+    itkGetConstMacro(OpenClose, bool);
+    itkBooleanMacro(OpenClose);
+    GGO_DefineOption_Flag(openclose, SetOpenClose);
 
- //    virtual void Update();
+    itkSetMacro(OpenCloseRadius, int);
+    itkGetConstMacro(OpenCloseRadius, int);
+    GGO_DefineOption(opencloseRadius, SetOpenCloseRadius, int);
+    
+    // Step 6 fill holes
+    itkSetMacro(FillHoles, bool);
+    itkGetConstMacro(FillHoles, bool);
+    itkBooleanMacro(FillHoles);
+    GGO_DefineOption_Flag(doNotFillHoles, SetFillHoles);
 
   protected:
     ExtractLungFilter();
     virtual ~ExtractLungFilter() {}
-    
+
+    // Main members
+    InputImageConstPointer input;
+    MaskImageConstPointer patient;
+    InputImagePointer working_input;
+    std::string m_OutputLungFilename;
+    std::string m_OutputTracheaFilename;
+    typename InternalImageType::Pointer working_image;  
+    typename InternalImageType::Pointer trachea_tmp;
+    MaskImagePointer trachea;
+    MaskImagePointer output;
+    unsigned int m_MaxSeedNumber;
+
     // Global options
     itkSetMacro(BackgroundValue, MaskImagePixelType);
     itkSetMacro(ForegroundValue, MaskImagePixelType);
@@ -202,6 +240,7 @@ namespace clitk {
     InputImagePixelType m_ThresholdStepSizeForTrachea;
     double m_MultiplierForTrachea;
     std::vector<InternalIndexType> m_Seeds;
+    int m_NumberOfSlicesToSkipBeforeSearchingSeed;
 
     // Step 3
     int m_NumberOfHistogramBins;
@@ -212,24 +251,23 @@ namespace clitk {
     LabelParamType* m_LabelizeParameters3;
 
     // Step 5
-    //     bool m_FinalOpenClose;
-    
+    bool m_OpenClose;    
+    int m_OpenCloseRadius;
+
+    // Step 6
+    bool m_FillHoles;    
+    InputImageSizeType m_FillHolesDirections;
+
+    // Main functions
     virtual void GenerateOutputInformation();
     virtual void GenerateData();
+    
+    // Functions for trachea extraction
+    bool SearchForTracheaSeed(int skip);
+    void SearchForTrachea();
+    void TracheaRegionGrowing();
+    double ComputeTracheaVolume();
 
-    // Steps
-    void RemoveAir();
-    void FindTrachea();
-    void ExtractLung();
-    void RemoveTrachea();
-    void LungSeparation();
-    InputImageConstPointer input;
-    MaskImageConstPointer patient;
-    InputImagePointer working_input;
-    typename InternalImageType::Pointer working_image;  
-    typename InternalImageType::Pointer trachea_tmp;
-    MaskImagePointer trachea;
-        
   private:
     ExtractLungFilter(const Self&); //purposely not implemented
     void operator=(const Self&); //purposely not implemented