/*=========================================================================
  Program:   vv                     http://www.creatis.insa-lyon.fr/rio/vv

  Authors belong to: 
  - University of LYON              http://www.universite-lyon.fr/
  - Léon Bérard cancer center       http://www.centreleonberard.fr
  - CREATIS CNRS laboratory         http://www.creatis.insa-lyon.fr

  This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.  See the copyright notices for more information.

  It is distributed under dual licence

  - BSD        See included LICENSE.txt file
  - CeCILL-B   http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
  ===========================================================================**/

#ifndef CLITKEXTRACTAIRWAYTREEINFOSFILTER_H
#define CLITKEXTRACTAIRWAYTREEINFOSFILTER_H

// clitk 
#include "clitkFilterBase.h"
#include "clitkDecomposeAndReconstructImageFilter.h"
#include "clitkExplosionControlledThresholdConnectedImageFilter.h"
#include "clitkSegmentationUtils.h"
#include "clitkFilterWithAnatomicalFeatureDatabaseManagement.h"
#include "tree.hh"

// itk
#include "itkStatisticsImageFilter.h"

namespace clitk {
  
  //--------------------------------------------------------------------
  /*
    From a trachea binary image, compute the skeleton and track the
    path to find the carena.
  */
  //--------------------------------------------------------------------
  


  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;
    double weight;
    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 ITK_EXPORT ExtractAirwaysTreeInfoFilter: 
    public virtual clitk::FilterBase, 
    public clitk::FilterWithAnatomicalFeatureDatabaseManagement,
    public itk::ImageToImageFilter<TImageType, TImageType> 
  {
    
  public:
    /** Standard class typedefs. */
    typedef itk::ImageToImageFilter<TImageType, TImageType> Superclass;
    typedef ExtractAirwaysTreeInfoFilter         Self;
    typedef itk::SmartPointer<Self>             Pointer;
    typedef itk::SmartPointer<const Self>       ConstPointer;
    
    /** Method for creation through the object factory. */
    itkNewMacro(Self);  
    
    /** Run-time type information (and related methods). */
    itkTypeMacro(ExtractAirwaysTreeInfoFilter, ImageToImageFilter);
    FILTERBASE_INIT;

    /** Some convenient typedefs */
    typedef TImageType                       ImageType;
    typedef typename ImageType::ConstPointer ImageConstPointer;
    typedef typename ImageType::Pointer      ImagePointer;
    typedef typename ImageType::RegionType   ImageRegionType; 
    typedef typename ImageType::PixelType    ImagePixelType; 
    typedef typename ImageType::SizeType     ImageSizeType; 
    typedef typename ImageType::IndexType    ImageIndexType; 
    typedef typename ImageType::PointType    ImagePointType; 
        
    typedef Bifurcation BifurcationType;
    typedef ImageIndexType NodeType;
    typedef tree<NodeType> TreeType;
    typedef typename TreeType::iterator TreeIterator;

    itkStaticConstMacro(ImageDimension, unsigned int, ImageType::ImageDimension);
    typedef int InternalPixelType;
    typedef itk::Image<InternalPixelType, ImageType::ImageDimension> InternalImageType;
    typedef typename InternalImageType::Pointer                      InternalImagePointer;
    typedef typename InternalImageType::IndexType                    InternalIndexType;
    typedef LabelizeParameters<InternalPixelType>                    LabelParamType;

    // Data Structures for trees 
    struct FullTreeNodeType {
      ImageIndexType index;
      ImagePointType point;
      double weight;
    };
    struct StructuralTreeNodeType {
      ImageIndexType index;
      ImagePointType point;
      double weight;
    };
    typedef tree<FullTreeNodeType> FullTreeType;
    typedef tree<StructuralTreeNodeType> StructuralTreeType;
    FullTreeType mFullSkeletonTree; 
    StructuralTreeType mStructuralSkeletonTree;

    /** Connect inputs */
    void SetInput(const ImageType * image);

    // Background / Foreground
    itkGetConstMacro(BackgroundValue, ImagePixelType);
    itkGetConstMacro(ForegroundValue, ImagePixelType);
    
    // Get results
    itkGetConstMacro(FirstTracheaPoint, ImagePointType);
    itkGetConstMacro(CarinaPoint, ImagePointType);

  protected:
    ExtractAirwaysTreeInfoFilter();
    virtual ~ExtractAirwaysTreeInfoFilter() {}

    // Main members
    ImageConstPointer input;
    ImagePointer skeleton;
    ImagePointer working_input;

    // Global options
    itkSetMacro(BackgroundValue, ImagePixelType);
    itkSetMacro(ForegroundValue, ImagePixelType);
    ImagePixelType m_BackgroundValue;
    ImagePixelType m_ForegroundValue;

    // Results
    ImagePointType m_FirstTracheaPoint;
    ImagePointType m_CarinaPoint;
    
    virtual void GenerateOutputInformation();
    virtual void GenerateData();

    TreeType m_SkeletonTree;
    void TrackFromThisIndex2(ImageIndexType index, ImagePointer skeleton, 
			     ImagePixelType label, 
			     typename FullTreeType::iterator currentNode, 
                             typename StructuralTreeType::iterator currentSNode);
    void TrackFromThisIndex(std::vector<BifurcationType> & listOfBifurcations, 
                            ImagePointer skeleton, 
                            ImageIndexType index,
                            ImagePixelType label, 
			    TreeIterator currentNode);
  private:
    ExtractAirwaysTreeInfoFilter(const Self&); //purposely not implemented
    void operator=(const Self&); //purposely not implemented
    
  }; // end class
  //--------------------------------------------------------------------

} // end namespace clitk
//--------------------------------------------------------------------

#ifndef ITK_MANUAL_INSTANTIATION
#include "clitkExtractAirwaysTreeInfoFilter.txx"
#endif

#endif