NeuroNode.cpp File Reference

#include "header.h"
#include "SparseMatrix.h"
#include "Boundary.h"
#include "MeshEntry.h"
#include "VoxelJunction.h"
#include "ChemCompt.h"
#include "MeshCompt.h"
#include "CubeMesh.h"
#include "../utility/Vec.h"
#include "../utility/strutil.h"
#include "CylBase.h"
#include "NeuroNode.h"

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Functions
static bool	checkForSpine (unsigned int dendIndex, Id compt, vector< Id > &shaftId, vector< Id > &headId, vector< unsigned int > &spineParent)
void	diagnoseTree (const vector< NeuroNode > &tree, const vector< NeuroNode > &nodes)
static vector< Id >	findAllConnectedCompartments (Id compt)
bool	isPartOfDend (ObjId i)
void	reassignNodeIndices (vector< NeuroNode > &temp, const vector< unsigned int > &nodeToTempMap)
static void	sortByShaftIds (vector< Id > &shaftId, vector< Id > &headId, vector< unsigned int > &spineParent)
static void	spinyTraverse (unsigned int dendIndex, vector< Id > &dend, const unordered_map< Id, unsigned int > &dendMap, vector< int > &seen, unsigned int numSeen, vector< Id > &shaftId, vector< Id > &headId, vector< int > &dendParent, vector< unsigned int > &spineParent)

Function Documentation

static bool checkForSpine ( unsigned int  dendIndex, Id  compt, vector< Id > &  shaftId, vector< Id > &  headId, vector< unsigned int > &  spineParent  )

static

Definition at line 391 of file NeuroNode.cpp.

References Id::element(), findAllConnectedCompartments(), Element::getName(), and name.

Referenced by spinyTraverse().

{
    const string& name = compt.element()->getName();
    if ( name.find( "shaft" ) != string::npos ||
        name.find( "neck" ) != string::npos ) {
        spineParent.push_back( dendIndex );
        shaftId.push_back( compt );
        vector< Id > conn = findAllConnectedCompartments( compt );
        bool foundHead = false;
        for ( vector< Id >::iterator i =
                        conn.begin(); i != conn.end(); ++i ) {
            const string& n2 = i->element()->getName();
            if ( n2.find( "spine" ) != string::npos ||
                n2.find( "head" ) != string::npos ) {
                headId.push_back( *i );
                foundHead = true;
                break;
            }
        }
        if (!foundHead) {
            headId.push_back( Id() );
        }
        return true;
    }
    return false;
}

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void diagnoseTree	(	const vector< NeuroNode > &	tree,
		const vector< NeuroNode > &	nodes
	)

static func

Definition at line 298 of file NeuroNode.cpp.

References Id::path().

Referenced by NeuroNode::traverse().

{
    map< Id , const NeuroNode* > m;
    for ( vector< NeuroNode >::const_iterator
                    i = tree.begin(); i != tree.end(); ++i ) {
        m[ i->elecCompt() ] = &( *i );
    }
    unsigned int j = 0;
    for ( vector< NeuroNode >::const_iterator
                    i = nodes.begin(); i != nodes.end(); ++i ) {
        if ( m.find( i->elecCompt() ) == m.end() ) {
            Id pa;
            if ( i->parent() != ~0U && i->parent() < nodes.size() )
                pa = nodes[ i->parent() ].elecCompt();
            cout << "diagnoseTree:" << j++ << " " << i->elecCompt().path() <<
                    ",  pa = " << i->parent() << ", " << pa.path() << endl;
        }
    }
}

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static vector< Id > findAllConnectedCompartments ( Id  compt )

static

Finds all the compartments connected to current node, put them all into the return vector even if they may be 'parent' by the messaging. This is because this function has to be robust enough to sort this out

Definition at line 151 of file NeuroNode.cpp.

References axialOut, Element::cinfo(), cylinderOut(), distalOut(), Id::element(), Cinfo::find(), Cinfo::findFinfo(), Element::getNeighbors(), Cinfo::isA(), proximalOut(), raxialOut, and sumRaxialOut().

Referenced by checkForSpine(), NeuroNode::findConnectedCompartments(), and spinyTraverse().

{
    static const Finfo* axialOut = Cinfo::find( "CompartmentBase" )->findFinfo( "axialOut" );
    static const Finfo* raxialOut = Cinfo::find( "CompartmentBase" )->findFinfo( "raxialOut" );
    static const Finfo* distalOut = Cinfo::find( "SymCompartment" )->findFinfo( "distalOut" );
    static const Finfo* proximalOut = Cinfo::find( "SymCompartment" )->findFinfo( "proximalOut" );
    static const Finfo* cylinderOut = Cinfo::find( "SymCompartment" )->findFinfo( "cylinderOut" );
    static const Finfo* sumRaxialOut = Cinfo::find( "SymCompartment" )->findFinfo( "sumRaxialOut" );
    assert( axialOut );
    assert( raxialOut );
    assert( distalOut );
    assert( proximalOut );
    assert( cylinderOut );
    assert( sumRaxialOut );

    const Cinfo* cinfo = compt.element()->cinfo();
    vector< Id > all;
    if ( cinfo->isA( "SymCompartment" ) ) { // Check derived first.
        vector< Id > ret;
        compt.element()->getNeighbors( ret, distalOut );
        all.insert( all.end(), ret.begin(), ret.end() );
        compt.element()->getNeighbors( ret, proximalOut );
        all.insert( all.end(), ret.begin(), ret.end() );
        compt.element()->getNeighbors( ret, cylinderOut );
        all.insert( all.end(), ret.begin(), ret.end() );
        compt.element()->getNeighbors( ret, sumRaxialOut );
        all.insert( all.end(), ret.begin(), ret.end() );
    }
    // In addition, check if the bog standard messaging applies.
    assert( cinfo->isA( "CompartmentBase" ) );
    vector< Id > ret;
    compt.element()->getNeighbors( ret, axialOut );
    all.insert( all.end(), ret.begin(), ret.end() );
    compt.element()->getNeighbors( ret, raxialOut );
    all.insert( all.end(), ret.begin(), ret.end() );

    sort( all.begin(), all.end() );
    all.erase( unique( all.begin(), all.end() ), all.end() ); //@#$%&* C++
    // Now we have a list of all compartments connected to the current one.
    return all;
}

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bool isPartOfDend

(

ObjId

i

)

Definition at line 376 of file NeuroNode.cpp.

References Element::cinfo(), ObjId::element(), Element::getName(), Cinfo::isA(), and name.

Referenced by NeuroNode::buildSpinyTree().

{
    if ( i.element()->cinfo()->isA( "CompartmentBase" ) ) {
        string name = i.element()->getName();
        if ( name.find( "shaft" ) == string::npos &&
            name.find( "neck" ) == string::npos &&
            name.find( "spine" ) == string::npos &&
            name.find( "head" ) == string::npos )
        {
            return true;
        }
    }
    return false;
}

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void reassignNodeIndices	(	vector< NeuroNode > &	temp,
		const vector< unsigned int > &	nodeToTempMap
	)

Definition at line 591 of file NeuroNode.cpp.

Referenced by NeuroNode::filterSpines().

{
    for ( vector< NeuroNode >::iterator
            i = temp.begin(); i != temp.end(); ++i ) {
        unsigned int pa = i->parent();
        if ( pa != ~0U ) {
            assert( nodeToTempMap[ pa ] != ~0U );
            i->setParent( nodeToTempMap[ pa ] );
        }

        vector< unsigned int > kids = i->children();
        i->clearChildren();
        for ( unsigned int j = 0; j < kids.size(); ++j ) {
            unsigned int newKid = nodeToTempMap[ kids[j] ];
            if ( newKid != ~0U ) // Some may be spine shafts, no longer here
                i->addChild( newKid );
        }
    }
}

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static void sortByShaftIds ( vector< Id > &  shaftId, vector< Id > &  headId, vector< unsigned int > &  spineParent  )

static

Definition at line 457 of file NeuroNode.cpp.

Referenced by NeuroNode::buildSpinyTree().

{
    size_t sortedIndex(0);
    vector<int> y(shaftId.size());
    generate(begin(y), end(y), [&]{ return sortedIndex++; });
    sort(  begin(y), end(y),
        [&](int i1, int i2) { return shaftId[i1] < shaftId[i2]; } );

    assert( sortedIndex == shaftId.size() );
    assert( sortedIndex == headId.size() );
    assert( sortedIndex == spineParent.size() );

    auto a = shaftId;
    auto b = headId;
    auto c = spineParent;
    for ( size_t i = 0; i < sortedIndex; ++i) {
        shaftId[i] = a[y[i]];
        headId[i] = b[y[i]];
        spineParent[i] = c[y[i]];
    }
}

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static void spinyTraverse ( unsigned int  dendIndex, vector< Id > &  dend, const unordered_map< Id, unsigned int > &  dendMap, vector< int > &  seen, unsigned int  numSeen, vector< Id > &  shaftId, vector< Id > &  headId, vector< int > &  dendParent, vector< unsigned int > &  spineParent  )

static

spinyTraverse goes takes current dend entry and finds everything connected to it, recursively. Paints the 'seen' entries with the latest index for the number seen so we keep track of which subgroup the dend set belongs to. This does a depth-first recursive traverse. Looks for spines on every dend compt found.

Definition at line 429 of file NeuroNode.cpp.

References checkForSpine(), and findAllConnectedCompartments().

Referenced by NeuroNode::buildSpinyTree().

{
    vector< Id > conn = findAllConnectedCompartments( dend[dendIndex] );
    seen[ dendIndex ] = numSeen;
    for ( vector< Id >::iterator i = conn.begin(); i != conn.end(); ++i ) {
        unordered_map< Id, unsigned int >::const_iterator idLookup =
                dendMap.find( *i );
        if ( idLookup != dendMap.end() ) {
            if ( !seen[ idLookup->second ] ) {
                dendParent[ idLookup->second ] = dendIndex;
                spinyTraverse( idLookup->second, dend, dendMap,
                    seen, numSeen,
                    shaftId, headId, dendParent, spineParent );
            }
        } else {
            checkForSpine( dendIndex, *i, shaftId, headId, spineParent );
        }
    }
}

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