marExperiment.h

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/*=========================================================================

  Program:   wxMaracas
  Module:    $RCSfile: marExperiment.h,v $
  Language:  C++
  Date:      $Date: 2009/05/14 13:55:07 $
  Version:   $Revision: 1.1 $

  Copyright: (c) 2002, 2003
  License:
  
     This software is distributed WITHOUT ANY WARRANTY; without even 
     the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
     PURPOSE.  See the above copyright notice for more information.

=========================================================================*/
#ifndef __MAR__KERNEL__EXPERIMENT__HXX__
#define __MAR__KERNEL__EXPERIMENT__HXX__

#include <vector>
#include "volume.hxx"
#include "marAxis.h"
#include "marDynData.h"
#include "GestionBifurcations.h"

class MAR_KERNEL_EXPORT marExperiment : public marObject
{

public:

  marExperiment( marParameters* p = NULL );
  ~marExperiment( );

  wxString& getDescription( ) { return( _description ); };
  void setDescription( wxString& d )    { _description = d; };

  marDynData* getDynData( )     { return( _dynData ); };

  void getVOI( int* voi ) { memcpy( voi, _voi, sizeof( int ) * 6 ); };
  void setVOI( int* voi ) { memcpy( _voi, voi, sizeof( int ) * 6 ); };

  void initExperiment( kVolume* volume );

  void setStartPoint( int* sp )
  {
    setStartPoint( sp[ 0 ], sp[ 1 ], sp[ 2 ] );
  }

  void setStartPoint( int sx, int sy, int sz );
  void extractVascularTree( int sens = 1, double *vit=NULL, int cleanLevel=0 );
  void DeleteAxis ( unsigned int index );

//  marContour* generateContour( int slice, int x, int y, std::vector< double* >* points);
  vtkPolyData* generateContour( int slice, int x, int y, std::vector< double* >* points);

  void applyChangeResolution( );

  int getNumberOfAxes( )
  {
    return( _axes.size( ) - 1 );
  };

  marAxis* getAxis( int i = -1 ) 
  { 
    return( _axes[ i + 1 ] ); 
  };

  void appendAxis( marAxis* ax )
  {
    _axes.push_back( ax );
    _axes[ 0 ] = ax;
  }

  void setAxis( int i )
  {
    _axes[ 0 ] = _axes[ i + 1 ];
  }

  int   getQuantStart( )  { return _axes[0]->getStartQuant( );};
  int   getQuantFinish( ) { return _axes[0]->getFinishQuant( );};
  void  backQuant( );

  void prepareQuantification( );

  marContour*           getContour( int i )                     { return(_axes[0]->getContour           ( i ,  _dynData->getVolume( )  ));      };
  vtkImageData*         getSliceImage( int i )          { return(_axes[0]->getSliceImage        ( i ,  _dynData->getVolume( )  ));      };
  vtkProbeFilter*       get3DSlice( int i )                     { return(_axes[0]->get3DSlice           ( i ,  _dynData->getVolume( )  ));      };
  vtkPoints*            get3Dcontour( int i )           { return(_axes[0]->get3Dcontour         ( i ,  _dynData->getVolume( )  ));      };
  vtkPolyData*          get2Dcontour( int i )           { return(_axes[0]->get2Dcontour         ( i ,  _dynData->getVolume( )  ));      };
  vtkPoints*            get2DDiameterMin( int i )       { return(_axes[0]->get2DDiameterMin     ( i ,  _dynData->getVolume( )  ));      };
  vtkPoints*            get2DDiameterMax( int i )       { return(_axes[0]->get2DDiameterMax     ( i ,  _dynData->getVolume( )  ));      };
  double                        getTotalLength()                        { return _axes[0]->getTotalLength() * _dynData->getActualVoxel() ;              };
  double                        getSubAxisLength()                      { return _axes[0]->getSubAxisLength() * _dynData->getActualVoxel();             };
  double                        getReferenceArea()                      { return _axes[0]->getReferenceArea( _dynData->getVolume( ));                   };
  double                        getReferenceAverDiam()          { return _axes[0]->getReferenceAverDiam( _dynData->getVolume( ));               };

  double                        getAverageArea(int pIni, int pEnd) {return _axes[0]->getAverageArea(pIni,pEnd, _dynData->getVolume( ) );                };
  int                           getNumberOfSlices( )            { return _axes[0]->getNumberOfContours();                                                               };

  void calculateAxesSignal( );
  void prepareContourImages( );

  void ClearContours();
  void RegenerateAxis();
  void RegenerateSignal();
  void RecalculateAxis();

  //General methods.
  void reset( );
  void copyFrom( const marObject& from );

  //Persistence methods.
  bool save( std::ofstream& os );
  bool load( std::ifstream& is );

private:

  wxString _description;
  marDynData* _dynData;
  int _voi[ 6 ];
  int _startPoint[ 3 ];

  std::vector< marAxis* > _axes;
};

#endif // __MAR__KERNEL__EXPERIMENT__HXX__