add lib dependence to some tools

[clitk.git] / segmentation / clitkExtractLungFilter.h

diff --git a/segmentation/clitkExtractLungFilter.h b/segmentation/clitkExtractLungFilter.h
index cf94b07f73e023d660c0a927aa7054f610d3b5ae..3183457dde0a6eb7ff06d445670cb132523a2ae8 100644 (file)
--- a/segmentation/clitkExtractLungFilter.h
+++ b/segmentation/clitkExtractLungFilter.h
@@ -25,11 +25,9 @@
 #include "clitkExplosionControlledThresholdConnectedImageFilter.h"
 #include "clitkSegmentationUtils.h"
 #include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
-#include "tree.hh"
 
 // itk
 #include "itkStatisticsImageFilter.h"
-#include "itkTreeContainer.h"
 
 namespace clitk {
   
@@ -57,45 +55,18 @@ namespace clitk {
   */
   //--------------------------------------------------------------------
   
-
-  //--------------------------------------------------------------------
-
-class Bifurcation
-{
-public:
-  typedef itk::Index<3> IndexType;
-  typedef itk::Point<double, 3> PointType;
-  typedef double PixelType;
-  Bifurcation(IndexType _index, PixelType _l, PixelType _l1, PixelType _l2) {
-    index = _index;
-    _l = l;
-    _l1 = l1;
-    _l2 = l2;
-  }
-  IndexType index;
-  PointType point;
-  PixelType l;
-  PixelType l1;
-  PixelType l2;
-  typedef itk::Index<3> NodeType;
-  typedef tree<NodeType> TreeType;
-  typedef TreeType::iterator TreeIterator;
-  TreeIterator treeIter;
-};
   //--------------------------------------------------------------------
-
-
-  //--------------------------------------------------------------------
-  template <class TImageType, class TMaskImageType>
+  template <class TImageType>
   class ITK_EXPORT ExtractLungFilter: 
     public virtual clitk::FilterBase, 
     public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
-    public itk::ImageToImageFilter<TImageType, TMaskImageType> 
+    public itk::ImageToImageFilter<TImageType, itk::Image<uchar, TImageType::ImageDimension> > 
   {
     
   public:
     /** Standard class typedefs. */
-    typedef itk::ImageToImageFilter<TImageType, 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;
@@ -117,7 +88,6 @@ public:
     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; 
@@ -133,18 +103,21 @@ public:
     typedef typename InternalImageType::IndexType                    InternalIndexType;
     typedef LabelizeParameters<InternalPixelType>                    LabelParamType;
     
-    typedef Bifurcation BifurcationType;
-    typedef MaskImageIndexType NodeType;
-    typedef tree<NodeType> TreeType;
-    typedef typename TreeType::iterator TreeIterator;
-
     /** Connect inputs */
     void SetInput(const ImageType * image);
-    void SetInputPatientMask(MaskImageType * mask, MaskImagePixelType BG);
     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);
@@ -216,15 +189,21 @@ public:
     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);
 
-    // Bronchial bifurcations
-    itkSetMacro(FindBronchialBifurcations, bool);
-    itkGetConstMacro(FindBronchialBifurcations, bool);
-    itkBooleanMacro(FindBronchialBifurcations);
+    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();
@@ -234,6 +213,8 @@ public:
     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;
@@ -270,21 +251,18 @@ public:
     LabelParamType* m_LabelizeParameters3;
 
     // Step 5
-    //     bool m_FinalOpenClose;    
-    bool m_FindBronchialBifurcations;
-    
-    virtual void GenerateOutputInformation();
-    virtual void GenerateData();
+    bool m_OpenClose;    
+    int m_OpenCloseRadius;
 
-    TreeType m_SkeletonTree;
-
-    void TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations, 
-                            MaskImagePointer skeleton, 
-                            MaskImageIndexType index,
-                            MaskImagePixelType label, 
-                           TreeIterator currentNode);
-        
+    // 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();