mesh/NeuroMesh.h

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/**********************************************************************
** 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_MESH_H
#define _NEURO_MESH_H

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

        void updateCoords();

        // Field assignment stuff

        void setSubTreePath( const Eref& e, string path );
        string getSubTreePath( const Eref& e ) const;

        void setSubTree( const Eref& e, vector< ObjId > compartments );
        vector< ObjId > getSubTree( const Eref& e ) const;

        void transmitSpineInfo( const Eref& e );


        void setSeparateSpines( bool v );
        bool getSeparateSpines() const;

        unsigned int getNumSegments() const;
        unsigned int getNumDiffCompts() const;

        void setDiffLength( double v );
        double getDiffLength() const;

        void setGeometryPolicy( string v );
        string getGeometryPolicy() const;

        unsigned int innerGetDimensions() const;

        vector< Id > getElecComptList() const;
        vector< Id > getElecComptMap() const;
        vector< unsigned int > getStartVoxelInCompt() const;
        vector< unsigned int > getEndVoxelInCompt() const;
        vector< int > getSpineVoxelOnDendVoxel() const;
        vector< unsigned int > getDendVoxelsOnCompartment( ObjId compt ) const;
        vector< unsigned int > getSpineVoxelsOnCompartment( ObjId compt ) const;

        vector< unsigned int > getParentVoxel() const;
        const vector< double >& vGetVoxelVolume() const;
        const vector< double >& vGetVoxelMidpoint() const;
        const vector< double >& getVoxelArea() const;
        const vector< double >& getVoxelLength() 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;
        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 );

        double vGetEntireVolume() const;

        bool vSetVolumeNotRates( double volume );
        
        // Dest funcs

        void innerBuildDefaultMesh( const Eref& e,
            double size, 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 transmitChange( const Eref& e, double oldVol );

        double getAdx( unsigned int curr, unsigned int& parentFid ) const;

        void buildStencil();

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

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

        void matchNeuroMeshEntries( 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;
        

        // Utility functions for building tree.

        void insertSingleDummy( unsigned int parent, unsigned int self,
               double x, double y, double z );

        void insertDummyNodes();

        Id putSomaAtStart( Id origSoma, unsigned int maxDiaIndex );

        void buildNodeTree( const map< Id, unsigned int >& comptMap );

        bool filterSpines( Id compt );
        void updateShaftParents();

        // Utility functions for testing
        // const Stencil* getStencil() const;
        const vector< NeuroNode >& getNodes() const;

        static const Cinfo* initCinfo();

    private:
        vector< NeuroNode > nodes_;

        string subTreePath_;

        vector< unsigned int > nodeIndex_;

        vector< double > vs_;

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

        // double size_; /// Total Volume
        double diffLength_; 

        bool separateSpines_; 

        string geometryPolicy_;

        double surfaceGranularity_;

        vector< Id > shaft_; 
        vector< Id > head_; 
        vector< unsigned int > parent_; 

        vector< unsigned int > parentVoxel_; 
};


#endif  // _NEURO_MESH_H

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