bundles.h

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/* Copyright (c) 1995-2005 CEA
 *
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 *      4 place du General Leclerc
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 *
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 */
 
#ifndef AIMS_FIBERS_BUNDLES_H
#define AIMS_FIBERS_BUNDLES_H
 
#include <aims/curve/curve.h>
#include <aims/mesh/surface.h>
#include <aims/vector/vector.h>
#include <aims/resampling/motion.h>
#include <aims/io/motionR.h>
#include <aims/roi/roiIterator.h>
#include <graph/graph/graph.h>
#include <cartobase/smart/rcptr.h>
#include <cartobase/object/object.h>
#include <cartobase/object/property.h>
#include <fstream> 
#include <vector>
#include <map>
#include <string>
 
 
namespace aims
{
 
 
  //----------//
 //  Bundle  //
//----------//
 
class Bundle : public std::vector< aims::Polyline >
{
};
 
 
  //-----------//
 //  Bundles  //
//-----------//
 
class Bundles : public std::map< std::string, Bundle >
{
};
 
 
  //------------------------------------------------//
 //  Froward classes, smart pointers and typedefs  //
//------------------------------------------------//
 
class Bundle;
class BundleListener;
class BundleProducer;
 
typedef carto::rc_ptr<Bundle> RBundle;
typedef carto::rc_ptr<BundleListener> RBundleListener;
typedef carto::rc_ptr<BundleProducer> RBundleProducer;
 
typedef aims::Polyline::Point_t FiberPoint;
 
 
  //-------------//
 //  FiberInfo  //
//-------------//
 
class FiberInfo
{
public:
  
  inline FiberInfo();
  inline FiberInfo( int id );
  inline FiberInfo( int id, double weight );
  inline FiberInfo( const FiberInfo & fiber );
  inline int id() const;
  inline double weight() const;
  inline void setId( int id );
 
  inline FiberInfo & operator = ( const FiberInfo & fiber );
 
protected:
 
  int _id;
  double _weight;
};
 
 
  //--------------//
 //  BundleInfo  //
//--------------//
 
class BundleInfo
{
public:
  
  inline BundleInfo();
  inline BundleInfo( const std::string &name );
  inline BundleInfo( int id );
  inline BundleInfo( int id, const std::string &name );
  inline BundleInfo( const BundleInfo & bundle );
  inline int id() const;
  inline std::string name() const;
 
  inline BundleInfo & operator = ( const BundleInfo & bundle );
 
protected:
 
  int _id;
  std::string _name;
};
 
 
  //------------------//
 //  BundleListener  //
//------------------//
 
class BundleListener
{
protected:
 
  friend class BundleProducer;
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & ) ;
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                             const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                                const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                              const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
 
public:
  virtual ~BundleListener();
};
 
 
  //------------------//
 //  BundleProducer  //
//------------------//
 
class BundleProducer
{
public:
 
  void addBundleListener( BundleListener & );
 
protected:
  
  void startBundle( const BundleInfo & );
  void terminateBundle( const BundleInfo & );
  void startFiber( const BundleInfo &, const FiberInfo & );
  void terminateFiber( const BundleInfo &, const FiberInfo & );
  void addFiberPoint( const BundleInfo &, const FiberInfo &,
                      const FiberPoint & );
  void noMoreBundle();
 
private:
  
  typedef std::vector< BundleListener * > BundleListenerList;
  BundleListenerList _bundleListeners;
};
 
 
 
  //----------------//
 //  BundleWriter  //
//----------------//
 
// WARNING : This class should be a real writer in aimsdata but I prefer to
//           keep it here until the format is a bit more stable.
 
class BundleWriter : public virtual BundleListener, public carto::PropertySet
{
public:
 
  BundleWriter();
  void setFileString( const std::string &fileName );
  virtual ~BundleWriter();
 
  typedef std::vector< FiberPoint > FiberPoints;
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & );
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                     const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                        const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                      const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
  virtual void checkStreams();
  virtual void addFiber( const BundleProducer &, const BundleInfo &,
                         const FiberInfo &,  FiberPoint*, int &);
 
protected:
  int _ascii;
  std::string _fileName;
  carto::Object _header;
  std::ofstream _dataFile;
  int _firstFiberInBundle;
  int _writtenFibersCount;
  FiberPoints _fiberPoints;
};
 
 
 
  //----------------//
 //  BundleReader  //
//----------------//
 
// WARNING : This class should be a real writer in aimsdata but I prefer to
//           keep it here until the format is a bit more stable.
 
class BundleReader : public BundleProducer, public BundleListener
{
public:
 
  BundleReader( const std::string &fileName );
  virtual ~BundleReader();
 
  void read();
  virtual carto::Object readHeader();
  static std::set<std::string> supportedFormats();
  static std::set<std::string> formatExtensions(
    const std::string & format = "ALL" );
 
protected:
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & );
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                     const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                        const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                      const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
 
private:
 
  std::string _fileName;
};
 
 
  //----------------------//
 //  BundleFormatReader  //
//----------------------//
 
// WARNING : This class should be a real writer in aimsdata but I prefer to
//           keep it here until the format is a bit more stable.
 
class BundleFormatReader : public BundleProducer
{
public:
 
  BundleFormatReader();
  virtual ~BundleFormatReader();
 
  virtual void read() = 0;
  virtual carto::Object readHeader();
 
private:
 
  std::string _fileName;
};
 
 
class ConnectomistBundlesReader : public BundleFormatReader
{
public:
 
  ConnectomistBundlesReader( const std::string &fileName );
  virtual ~ConnectomistBundlesReader();
 
  virtual void read();
  virtual carto::Object readHeader();
 
private:
 
  std::string _fileName;
};
 
 
  //-----------------//
 //  BundleToGraph  //
//-----------------//
 
class BundleToGraph : public BundleListener, 
                      virtual public carto::PropertySet
{
public:
 
  BundleToGraph();
  BundleToGraph( Graph & );
  virtual ~BundleToGraph();
 
  inline const carto::rc_ptr< Graph > &getGraph() const;
 
protected:
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & );
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                     const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                        const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                      const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
  virtual void parametersValueChanged();
  void parameterChangedSlot( const carto::Object &, const std::string &,
                             const carto::Object & );
  void shuffleBundle();
 
  Graph *_meshResult;
  carto::rc_ptr< Graph > _rcptrMeshResult;
  float _minimumLength;
  float _width;
  int _numPointsInMeshSection;
  std::vector< Point2df > _section;
  std::vector<int>      _boundingbox_min;
  std::vector<int>      _boundingbox_max;
  bool _normalsAsFiberStartPos;
  Point3df _relatveFiberStartPos;
  bool _autoFiberStartPos;
 
  Vertex *_currentVertex;
  aims::Polyline _currentCurve;
  carto::rc_ptr< AimsSurfaceTriangle > _currentMesh;
  carto::rc_ptr< AimsTimeSurface<2,Void> > _currentLines;
  size_t _current_fibers_count;
};
 
 
 
  //-----------------------//
 //  BundleToGraphWriter  //
//-----------------------//
 
class BundleToGraphWriter : public BundleToGraph
{
public:
 
  inline virtual ~BundleToGraphWriter();
 
  void setFileString( const std::string & );
 
protected:
  
  virtual void noMoreBundle( const BundleProducer & );
 
private:
  
  std::string _fileName;
};
 
 
  //------------------//
 //  BundleROISplit  //
//------------------//
 
class BundleROISplit : public BundleProducer, public BundleListener
{
public:
 
  BundleROISplit( carto::rc_ptr< aims::RoiIterator > roiIterator,
                  bool keepOriginalBundle = false );
  virtual ~BundleROISplit();
 
protected:
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & );
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                     const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                        const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                      const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
 
private:
 
  carto::rc_ptr< aims::ROILabelMap > _roiLabelMap;
 
  typedef std::vector< FiberPoint > FiberPoints;
  typedef std::vector< FiberPoints > Fibers;
 
  std::map< std::string, std::map< std::pair<int,int>, Fibers > > 
    _result;
 
  int _currentLabel;
  int _lastLabel;
  FiberPoints _currentPoints;
  bool _keepOriginalBundle;
};
 
 
 
  //-------------------//
 //  BundleROISelect  //
//-------------------//
 
class BundleROISelect : public BundleProducer, public BundleListener
{
public:
 
  BundleROISelect( carto::rc_ptr< aims::RoiIterator > roiIterator,
                   const std::string &,
                   float defaultROIMinimumOverlap = 0 );
  virtual ~BundleROISelect();
 
protected:
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & );
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                     const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                        const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                      const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
 
private:
 
  carto::rc_ptr< aims::ROILabelMap > _roiLabelMap;
 
  typedef std::vector< FiberPoint > FiberPoints;
 
  std::vector< uint32_t > _crossedROI;
  FiberPoints _currentPoints;
  std::map< std::string, std::vector< FiberPoints > > _result;
 
  struct SelectionRule
  {
    std::string name;
    uint32_t min, max;
    std::vector< bool > mustBeCrossed;
  };
  std::vector< SelectionRule > _selectionRules;
  float _defaultROIMinimumOverlap;
};
 
 
 
  //----------------//
 //  BundleMotion  //
//----------------//
 
class BundleMotion : public BundleProducer, public BundleListener
{
public:
 
  BundleMotion( const std::string & );
  BundleMotion( const Motion & );
  virtual ~BundleMotion();
 
protected:
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & );
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                     const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                        const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                      const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
 
private:
 
  Motion _motion;
};
 
 
  //------------------//
 //  CurveSelection  //
//------------------//
 
class CurveSelection : public BundleProducer, public BundleListener
{
public:
 
  CurveSelection( const double &minimumLength );
  virtual ~CurveSelection();
 
protected:
 
  typedef std::vector< FiberPoint > FiberPoints;
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & );
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                     const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                        const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                      const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
 
private:
 
  double _minimumLength;
  double _currentLength;
  FiberPoints _currentPoints;
};
 
 
  //--------------------//
 //  CurveOrientation  //
//--------------------//
 
class CurveOrientation : public BundleProducer, public BundleListener
{
public:
 
  CurveOrientation();
  virtual ~CurveOrientation();
 
protected:
 
  typedef std::vector< FiberPoint > FiberPoints;
 
  virtual void bundleStarted( const BundleProducer &, const BundleInfo & );
  virtual void bundleTerminated( const BundleProducer &, const BundleInfo & );
  virtual void fiberStarted( const BundleProducer &, const BundleInfo &,
                     const FiberInfo & );
  virtual void fiberTerminated( const BundleProducer &, const BundleInfo &,
                        const FiberInfo & );
  virtual void newFiberPoint( const BundleProducer &, const BundleInfo &,
                      const FiberInfo &, const FiberPoint & );
  virtual void noMoreBundle( const BundleProducer & );
 
private:
 
  FiberPoint _beginSum;
  aims::Polyline::Scalar_t _count;
  FiberPoints _currentPoints;
};
 
 
 
 
  //-------------//
 //  FiberInfo  //
//-------------//
 
//-----------------------------------------------------------------------------
inline FiberInfo::FiberInfo()
  : _id( 0 ), _weight( 1.0 )
{}
 
 
//-----------------------------------------------------------------------------
inline FiberInfo::FiberInfo( int id ) :
  _id( id ), _weight( 1.0 )
{}
 
 
//-----------------------------------------------------------------------------
inline FiberInfo::FiberInfo( int id, double weight ) :
  _id( id ), _weight( weight )
{}
 
 
//-----------------------------------------------------------------------------
inline FiberInfo::FiberInfo( const FiberInfo & fiber )
  : _id( fiber.id() ), _weight( fiber.weight() )
{}
 
 
//-----------------------------------------------------------------------------
inline int FiberInfo::id() const 
{ 
  return _id;
}
 
//-----------------------------------------------------------------------------
inline double FiberInfo::weight() const
{ 
  return _weight;
}
 
//-----------------------------------------------------------------------------
inline void FiberInfo::setId( int id )
{
  _id = id;
}
 
//-----------------------------------------------------------------------------
inline FiberInfo & FiberInfo::operator = ( const FiberInfo & fiber )
{
  _id = fiber.id();
  _weight = fiber.weight();
 
  return *this;
}
 
 
  //--------------//
 //  BundleInfo  //
//--------------//
 
//-----------------------------------------------------------------------------
inline BundleInfo::BundleInfo()
{}
 
 
//-----------------------------------------------------------------------------
inline BundleInfo::BundleInfo( const std::string &name ) :
  _name( name )
{}
 
 
//-----------------------------------------------------------------------------
inline BundleInfo::BundleInfo( int id ) :
  _id( id ) 
{}
 
 
//-----------------------------------------------------------------------------
inline BundleInfo::BundleInfo( int id, const std::string &name ) :
  _id( id ), _name( name ) 
{}
 
 
//-----------------------------------------------------------------------------
inline BundleInfo::BundleInfo( const BundleInfo & bundle ) :
  _id( bundle.id() ), _name( bundle.name() )
{}
 
 
//-----------------------------------------------------------------------------
inline std::string BundleInfo::name() const 
{ 
  return _name; 
}
 
 
//-----------------------------------------------------------------------------
inline int BundleInfo::id() const 
{ 
  return _id; 
}
 
//-----------------------------------------------------------------------------
inline BundleInfo & BundleInfo::operator = ( const BundleInfo & bundle )
{
  _id = bundle.id();
  _name = bundle.name();
 
  return *this;
}
 
  //-----------------//
 //  BundleToGraph  //
//-----------------//
 
//-----------------------------------------------------------------------------
inline const carto::rc_ptr< Graph > &BundleToGraph::getGraph() const
{
  return _rcptrMeshResult;
}
 
 
  //-----------------------//
 //  BundleToGraphWriter  //
//-----------------------//
 
//-----------------------------------------------------------------------------
inline BundleToGraphWriter::~BundleToGraphWriter()
{
}
 
} // namespace comist
 
#endif // ifndef AIMS_FIBERS_BUNDLES_H