mesh/SpineMesh.h

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/**********************************************************************
** This program is part of 'MOOSE', the
** Messaging Object Oriented Simulation Environment.
**           Copyright (C) 2013 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 _SPINE_MESH_H
#define _SPINE_MESH_H

class SpineMesh: public MeshCompt
{
    public: 
        SpineMesh();
        SpineMesh( const SpineMesh& other );
        ~SpineMesh();
//      SpineMesh& operator=( const SpineMesh& other );
        //  Utility func

        void updateCoords();

        // Field assignment stuff

        vector< unsigned int > getParentVoxel() const;
        vector< unsigned int > getNeuronVoxel() const;

        vector< Id > getElecComptMap() const;

        vector< unsigned int > getStartVoxelInCompt() const;
        vector< unsigned int > getEndVoxelInCompt() const;

        // FieldElement assignment stuff for MeshEntries

        unsigned int getMeshType( unsigned int fid ) const;
        unsigned int getMeshDimensions( unsigned int fid ) const;
        double getMeshEntryVolume( unsigned int fid ) const;
        void setMeshEntryVolume( unsigned int fid, double volume );
        vector< double > getCoordinates( unsigned int fid ) const;
        vector< double > getDiffusionArea( unsigned int fid ) const;
        vector< double > getDiffusionScaling( unsigned int fid ) const;
        double extendedMeshEntryVolume( unsigned int fid ) const;


        unsigned int innerGetNumEntries() const;
        void innerSetNumEntries( unsigned int n );

        unsigned int innerGetDimensions() const;

        double vGetEntireVolume() const;

        bool vSetVolumeNotRates( double volume );
        
        // Dest funcs

        void innerBuildDefaultMesh( const Eref& e,
            double volume, unsigned int numEntries );

        /*
        void innerHandleRequestMeshStats(
            const Eref& e,
            const SrcFinfo2< unsigned int, vector< double > >*
                meshStatsFinfo
        );
            */

        void innerHandleNodeInfo(
            const Eref& e, 
            unsigned int numNodes, unsigned int numThreads );

        void handleSpineList(
            const Eref& e,
            vector< Id > shaft, vector< Id > head, 
            vector< unsigned int > parentVoxel );

        void transmitChange( const Eref& e );

        void buildStencil();

        // inherited virtual funcs for Boundary
        
        void matchMeshEntries( const ChemCompt* other, 
            vector< VoxelJunction > & ret ) const;

        void matchNeuroMeshEntries( const ChemCompt* other, 
            vector< VoxelJunction > & ret ) const;

        void matchCubeMeshEntries( const ChemCompt* other, 
            vector< VoxelJunction > & ret ) const;

        void matchSpineMeshEntries( const ChemCompt* other, 
            vector< VoxelJunction > & ret ) const;

        double nearest( double x, double y, double z, 
                        unsigned int& index ) const;
    
        void indexToSpace( unsigned int index, 
                        double& x, double& y, double& z ) const;
        
        const vector< double >& vGetVoxelVolume() const;
        const vector< double >& vGetVoxelMidpoint() const;
        const vector< double >& getVoxelArea() const;
        const vector< double >& getVoxelLength() const;
        // Utility function for tests
        const vector< SpineEntry >& spines() const;
        static const Cinfo* initCinfo();

    private:
        vector< SpineEntry > spines_;

        double surfaceGranularity_;

        vector< double > vs_;

        vector< double > area_;
        
        vector< double > length_;
};


#endif  // _SPINE_MESH_H

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