mesh/NeuroNode.h

Go to the documentation of this file.

/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2012 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 _NEURO_NODE_H
#define _NEURO_NODE_H

class NeuroNode: public CylBase
{
    public:
        NeuroNode( const CylBase& cb, 
            unsigned int parent, const vector< unsigned int >& children,
            unsigned int startFid_, Id elecCompt,
            bool isSphere );
        NeuroNode( Id elecCompt );
        NeuroNode();


        unsigned int parent() const;
        unsigned int startFid() const;
        Id elecCompt() const;

        bool isDummyNode() const; // True if CylBase::numDivs is zero.
        bool isSphere() const;
        bool isStartNode() const; // True if startFid_ == 0
        const vector< unsigned int >& children() const;


        void addChild( unsigned int child );

        void clearChildren();

        void setParent( unsigned int parent );

        void setStartFid( unsigned int f );

        double calculateLength( const CylBase& parent );

        // A set of calls for safely generating a tree by traversing
        // compartment messages. Designed to be somewhat resilient, even
        // when given a badly set up neuron.

        void findConnectedCompartments( 
                            const map< Id, unsigned int >& nodeMap,
                            const vector< NeuroNode >& nodes );

        static unsigned int removeDisconnectedNodes( 
                        vector< NeuroNode >& nodes );

        static unsigned int findStartNode( 
                        const vector< NeuroNode >& nodes );

        static void traverse( 
                        vector< NeuroNode >& nodes, unsigned int start );

        void innerTraverse( 
                vector< NeuroNode >& tree, 
                const vector< NeuroNode >& nodes,
                vector< unsigned int >& seen
                ) const;

        static void buildTree( vector< NeuroNode >& nodes, 
                        vector< ObjId > elist );
        static void buildSpinyTree( 
                    vector< ObjId >& elist, vector< NeuroNode >& nodes,
                    vector< Id >& shaftId, vector< Id >& headId,
                    vector< unsigned int >& spineParent );
        void setParentAndChildren( unsigned int index, int dendParent,
                vector< NeuroNode >& nodes, 
                const map< Id, unsigned int >& dendMap );

        static void filterSpines( vector< NeuroNode >& nodes, 
                vector< Id >& shaftId, vector< Id >& headId,
                vector< unsigned int >& parent );
    private:
        unsigned int parent_; 

        vector< unsigned int >children_;

        unsigned int startFid_;


        Id elecCompt_; 

        bool isSphere_;

    // For spines we will also need a double to indicate position along
    // parent dendrite. 
    //
};

#endif  // _NEURO_NODE_H

---