biophysics/Neuron.h

Go to the documentation of this file.

/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment,
** also known as GENESIS 3 base code.
**           copyright (C) 2003-2006 Upinder S. Bhalla. and NCBS
** It is made available under the terms of the
** GNU Lesser General Public License version 2.1
** See the file COPYING.LIB for the full notice.
**********************************************************************/

#ifndef _NEURON_H
#define _NEURON_H

class Neuron
{
    public:
        Neuron();
        Neuron( const Neuron& other );
        void setRM( double v );
        double getRM() const;
        void setRA( double v );
        double getRA() const;
        void setCM( double v );
        double getCM() const;
        void setEm( double v );
        double getEm() const;
        void setTheta( double v );
        double getTheta() const;
        void setPhi( double v );
        double getPhi() const;
        void setSourceFile( string v );
        string getSourceFile() const;
        void setCompartmentLengthInLambdas( double v );
        double getCompartmentLengthInLambdas() const;
        unsigned int getNumCompartments() const;
        unsigned int getNumBranches() const;
        vector< double> getPathDistFromSoma() const;
        vector< double> getGeomDistFromSoma() const;
        vector< double> getElecDistFromSoma() const;
        vector< ObjId > getCompartments() const;
        vector< ObjId > getExprElist( const Eref& e, string line ) const;
        vector< double > getExprVal( const Eref& e, string line ) const;
        vector< ObjId > getSpinesFromExpression( 
                            const Eref& e, string line ) const;
        void setChannelDistribution( const Eref& e, vector< string > v );
        vector< string > getChannelDistribution( const Eref& e ) const;
        void setPassiveDistribution( const Eref& e, vector< string > v );
        vector< string > getPassiveDistribution( const Eref& e ) const;
        void setSpineDistribution( const Eref& e, vector< string > v );
        vector< string > getSpineDistribution( const Eref& e ) const;

        void buildSegmentTree( const Eref& e );
        void setSpineAndPsdMesh( Id spineMesh, Id psdMesh );
        void setSpineAndPsdDsolve( Id spineDsolve, Id psdDsolve );

        // MechSpec set
        void updateSegmentLengths();
        void installSpines( const vector< ObjId >& elist,
            const vector< double >& val, const vector< string >& line );
        void makeSpacingDistrib( 
            const vector< ObjId >& elist, const vector< double >& val,
            vector< unsigned int >& seglistIndex, 
            vector< unsigned int >& elistIndex, 
            vector< double >& pos,
            const vector< string >& line ) const;
        void parseMechSpec( const Eref& e );
        void installMechanism(  const string& name,
            const vector< ObjId >& elist, const vector< double >& val,
            const vector< string >& line );
        void buildElist(
                const Eref& e,
                const vector< string >& line, vector< ObjId >& elist,
                vector< double >& val );

        void evalExprForElist( const vector< ObjId >& elist,
            const string& expn, vector< double >& val ) const;

        // Interface for Spine class, used mostly in resizing spines.
        Spine* lookupSpine( unsigned int index );
        void setNumSpines( unsigned int num );
        unsigned int getNumSpines() const;

        const vector< Id >& spineIds( unsigned int index ) const;
        void scaleBufAndRates( unsigned int spineNum, 
                double lenScale, double diaScale ) const;
        void scaleShaftDiffusion( unsigned int spineNum, 
                        double len, double dia) const;
        void scaleHeadDiffusion( unsigned int spineNum, 
                        double len, double dia) const;

        static const Cinfo* initCinfo();
    private:
        double RM_;
        double RA_;
        double CM_;
        double Em_;
        double theta_;
        double phi_;
        double maxP_; // Maximum value of path dist from soma for this cell
        double maxG_; // Maximum value of geom dist from soma for this cell
        double maxL_; // Maximum value of elec dist from soma for this cell
        Id soma_;
        string sourceFile_;
        double compartmentLengthInLambdas_;
        vector< string > channelDistribution_;
        vector< string > passiveDistribution_;
        vector< string > spineDistribution_;

        map< Id, unsigned int > segIndex_; 
        vector< unsigned int > spineParentSegIndex_; 
        vector< vector< Id > > spines_; 

        vector< Id > spineStoich_; 
        vector< Id > psdStoich_; 
        vector< unsigned int > spineToMeshOrdering_;

        Id headDsolve_; 
        Id psdDsolve_; 
        // looks up spine/psd Dsolve::DiffJunction::VoxelJunction index 
        //from FieldIndex of selected spine.
        // Turns out this is the same as spineToMeshOrdering.
        //vector< unsigned int > spineToVoxelJunctionOrdering_;

        Spine spineEntry_; 

        vector< Id > segId_; 
        vector< SwcSegment > segs_;
        vector< SwcBranch > branches_;

};

// 

#endif // 

---