Neuron.cpp File Reference

#include "header.h"
#include "ElementValueFinfo.h"
#include "LookupElementValueFinfo.h"
#include "shell/Shell.h"
#include "shell/Wildcard.h"
#include "ReadCell.h"
#include "utility/Vec.h"
#include "SwcSegment.h"
#include "Spine.h"
#include "Neuron.h"
#include "basecode/global.h"
#include "muParser.h"

Include dependency graph for Neuron.cpp:

Go to the source code of this file.

Classes
class	nuParser

Functions
static void	addPos (unsigned int segIndex, unsigned int eIndex, double spacing, double minSpacing, double dendLength, vector< unsigned int > &seglistIndex, vector< unsigned int > &elistIndex, vector< double > &pos)
	Add entries into the pos vector for a given compartment i. More...
static vector< Id >	addSpine (Id parentCompt, Id spineProto, double pos, double angle, Vec &x, Vec &y, Vec &z, double size, unsigned int k)
static void	assignParam (Id obj, const string &field, double val, double len, double dia)
static void	assignSingleCompartmentParams (ObjId compt, double val, const string &field, double len, double dia)
static bool	buildFromProto (const string &name, const vector< ObjId > &elist, const vector< double > &val, vector< ObjId > &mech)
static double	coordSystem (Id soma, Id dend, Vec &x, Vec &y, Vec &z)
static void	doClassSpecificMessaging (Shell *shell, Id obj, ObjId compt)
Id	fillSegIndex (const vector< Id > &kids, map< Id, unsigned int > &segIndex)
static void	fillSegments (vector< SwcSegment > &segs, const map< Id, unsigned int > &segIndex, const vector< Id > &kids)
string	findArg (const vector< string > &line, const string &field)
static Id	getComptParent (Id id)
static void	makeAngleDistrib (const vector< ObjId > &elist, const vector< double > &val, vector< unsigned int > &elistIndex, vector< double > &theta, const vector< string > &line)
static void	makeSizeDistrib (const vector< ObjId > &elist, const vector< double > &val, vector< unsigned int > &elistIndex, vector< double > &size, const vector< string > &line)
bool	parseDistrib (vector< vector< string > > &lines, const vector< string > &distrib)
static void	reorientSpine (vector< Id > &spineCompts, vector< Vec > &coords, Vec &parentPos, double pos, double angle, Vec &x, Vec &y, Vec &z)
static void	setCompartmentParams (const vector< ObjId > &elist, const vector< double > &val, const string &field, const string &expr)
static void	setMechParams (const vector< ObjId > &mech, const vector< ObjId > &elist, const vector< double > &val, const string &field, const string &expr)
static void	traverseCumulativeDistance (SwcSegment &self, vector< SwcSegment > &segs, const vector< Id > &lookupId, double len, double L, double pSoma, double eSoma)
	Recursive function to fill in cumulative distances from soma. More...

Variables
static const Cinfo *	neuronCinfo = Neuron::initCinfo()

Function Documentation

static void addPos ( unsigned int  segIndex, unsigned int  eIndex, double  spacing, double  minSpacing, double  dendLength, vector< unsigned int > &  seglistIndex, vector< unsigned int > &  elistIndex, vector< double > &  pos  )

static

Add entries into the pos vector for a given compartment i.

Definition at line 1784 of file Neuron.cpp.

References moose::mtrand().

Referenced by Neuron::makeSpacingDistrib().

{
    if ( minSpacing < spacing * 0.1 && minSpacing < 1e-7 )
        minSpacing = spacing * 0.1;
    if ( minSpacing > spacing * 0.5 )
        minSpacing = spacing * 0.5;
    unsigned int n = 1 + dendLength / minSpacing;
    double dx = dendLength / n;
    for( unsigned int i = 0; i < n; ++i )
    {
        // Use global RNG.
        if ( moose::mtrand() < dx / spacing )
        {
            seglistIndex.push_back( segIndex );
            elistIndex.push_back( eIndex );
            pos.push_back( i * dx + dx*0.5 );
        }
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static vector< Id > addSpine ( Id  parentCompt, Id  spineProto, double  pos, double  angle, Vec &  x, Vec &  y, Vec &  z, double  size, unsigned int  k  )

static

Utility function to add a single spine to the given parent. Returns vector of added spine contents. parent is parent compartment for this spine. spineProto is just that. pos is position (in metres ) along parent compartment angle is angle (in radians) to rotate spine wrt x in plane xy. Size is size scaling factor, 1 leaves as is. x, y, z are unit vectors. Z is along the parent compt. We first shift the spine over so that it is offset by the parent compt diameter. We then need to reorient the spine which lies along (i,0,0) to lie along x. X is a unit vector so this is done simply by multiplying each coord of the spine by x. Finally we rotate the spine around the z axis by the specified angle k is index of this spine.

Definition at line 1649 of file Neuron.cpp.

References Vec::a0(), Neutral::children(), Eref::data(), Shell::doAddMsg(), Shell::doCopy(), Shell::doDelete(), Shell::doMove(), Id::eref(), Field< A >::get(), Neutral::parent(), reorientSpine(), and SetGet2< A1, A2 >::set().

Referenced by Neuron::installSpines().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    Id parentObject = Neutral::parent( parentCompt );
    stringstream sstemp;
    sstemp << k;
    string kstr = sstemp.str();
    Id spine = shell->doCopy( spineProto, parentObject, "_spine" + kstr,
                              1, false, false );
    vector< Id > kids;
    Neutral::children( spine.eref(), kids );
    double x0 = Field< double >::get( parentCompt, "x0" );
    double y0 = Field< double >::get( parentCompt, "y0" );
    double z0 = Field< double >::get( parentCompt, "z0" );
    double parentRadius = Field< double >::get( parentCompt, "diameter" )/2;
    Vec ppos( x0, y0, z0 );
    // First, build the coordinates vector for the spine. Assume that its
    // major axis is along the unit vector [1,0,0].
    vector< Vec > coords;
    vector< Id > ret; // Filtered to make sure that it returns only compts
    for ( vector< Id >::iterator i = kids.begin(); i != kids.end(); ++i )
    {
        if ( i->element()->cinfo()->isA( "CompartmentBase" ) )
        {
            i->element()->setName( i->element()->getName() + kstr );
            x0 = Field< double >::get( *i, "x0" ) * size;
            y0 = Field< double >::get( *i, "y0" ) * size;
            z0 = Field< double >::get( *i, "z0" ) * size;
            coords.push_back( Vec( x0 + parentRadius, y0, z0 ) );
            double x = Field< double >::get( *i, "x" ) * size;
            double y = Field< double >::get( *i, "y" ) * size;
            double z = Field< double >::get( *i, "z" ) * size;
            double dia = Field< double >::get( *i, "diameter" ) * size;
            // Field< double >::set( *i, "diameter", dia );

            double len = sqrt(
                             (x-x0)*(x-x0) +
                             (y-y0)*(y-y0) +
                             (z-z0)*(z-z0) );
            SetGet2< double, double >::set( *i, "setGeomAndElec", len, dia );


            coords.push_back( Vec( x + parentRadius, y, z ) );
            // scaleSpineCompt( *i, size );
            shell->doMove( *i, parentObject );
            ret.push_back( *i );
        }
    }
    // Then, take the projection of this along the x vector passed in.
    for( vector< Vec >::iterator i = coords.begin(); i != coords.end(); ++i)
        *i = x * i->a0();
    shell->doDelete( spine ); // get rid of the holder for the spine copy.
    shell->doAddMsg( "Single", parentCompt, "axial", kids[0], "raxial" );
    reorientSpine( kids, coords, ppos, pos, angle, x, y, z );

    return ret;
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void assignParam ( Id  obj, const string &  field, double  val, double  len, double  dia  )

static

Definition at line 680 of file Neuron.cpp.

References Element::cinfo(), Id::element(), FaradayConst, Cinfo::isA(), PI, and Field< A >::set().

Referenced by setMechParams().

{
    if ( obj.element()->cinfo()->isA( "ChanBase" ) )
    {
        if ( field == "Gbar" )
        {
            if ( val > 0 )
                Field< double >::set( obj, "Gbar", val * len * dia * PI );
        }
        else if ( field == "Ek" )
        {
            Field< double >::set( obj, "Ek", val );
        }
    }
    else if ( obj.element()->cinfo()->isA( "CaConcBase" ) )
    {
        Field< double >::set( obj, "length", len );
        Field< double >::set( obj, "diameter", dia );
        // cout << "len, dia = " << len << ", " << dia << endl;
        if ( field == "CaBasal" || field == "tau" || field == "thick" ||
                field == "floor" || field == "ceiling" )
        {
            Field< double >::set( obj, field, val );
        }
        else if ( field == "B" )
        {
            // The system obeys dC/dt = B*I_Ca - C/tau
            // So B = arg/( vol * F ). Here the system provides vol and F,
            // so the arg is just a scale factor over this, typically
            // to be thought of in terms of buffering. Small B is more
            // buffering. This field is deprecated but used in legacy
            // GENESIS scripts.
            Field< double >::set( obj, "B", val /
                                  ( FaradayConst * len * dia * dia * PI / 4.0 ) );
        }
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void assignSingleCompartmentParams ( ObjId  compt, double  val, const string &  field, double  len, double  dia  )

static

Definition at line 719 of file Neuron.cpp.

References PI, and Field< A >::set().

Referenced by setCompartmentParams().

{
    if ( field == "initVm" || field == "INITVM" )
    {
        Field< double >::set( compt, "initVm", val );
        return;
    }
    if ( field == "Em" || field == "EM" )
    {
        Field< double >::set( compt, "Em", val );
        return;
    }
    if ( val > 0.0 )
    {
        if ( field == "Rm" || field == "Ra" || field == "Cm" )
        {
            Field< double >::set( compt, field, val );
        }
        else if ( field == "RM" )
        {
            Field< double >::set( compt, "Rm", val / ( len  * dia * PI ) );
        }
        else if ( field == "RA" )
        {
            Field< double >::set( compt, "Ra", val*len*4 / (dia*dia*PI) );
        }
        else if ( field == "CM" )
        {
            Field< double >::set( compt, "Cm", val * len * dia * PI );
        }
        else
        {
            cout << "Warning: setCompartmentParam: field '" << field <<
                 "' not found\n";
        }
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static bool buildFromProto ( const string &  name, const vector< ObjId > &  elist, const vector< double > &  val, vector< ObjId > &  mech  )

static

Definition at line 647 of file Neuron.cpp.

References Neutral::child(), Eref::data(), doClassSpecificMessaging(), Shell::doCopy(), Id::element(), Id::eref(), nuParser::EXPR, Element::getName(), and nuParser::numVal.

Referenced by Neuron::setChannelDistribution().

{
    Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
    Id proto( "/library/" + name );
    if ( proto == Id() )
    {
        cout << "Warning: Neuron::buildFromProto: proto '"
             << name << "' not found, skipping\n";
        return false;
    }
    mech.clear();
    mech.resize( elist.size() );
    for ( unsigned int i = 0; i < elist.size(); ++i )
    {
        unsigned int j = i * nuParser::numVal;
        if ( val[ j + nuParser::EXPR ] > 0 )
        {
            string name = proto.element()->getName();
            Id obj = Neutral::child( elist[i].eref(), name );
            if ( obj == Id() )   // Need to copy it in from proto.
            {
                obj = shell->doCopy( proto, elist[i], name, 1, false, false );
                doClassSpecificMessaging( shell, obj, elist[i] );
            }
            mech[i] = obj;
        }
    }
    return true;
}

Here is the call graph for this function:

Here is the caller graph for this function:

static double coordSystem ( Id  soma, Id  dend, Vec &  x, Vec &  y, Vec &  z  )

static

Utility function to return a coordinate system where z is the direction of a dendritic segment, x is the direction of spines outward from soma and perpendicular to z and y is the perpendicular to x and z.

Definition at line 1546 of file Neuron.cpp.

References Vec::a0(), Vec::a1(), Vec::a2(), Vec::crossProduct(), doubleEq(), EPSILON, Field< A >::get(), and Vec::length().

Referenced by Neuron::installSpines().

{
    static const double EPSILON = 1e-20;
    double x0 = Field< double >::get( dend, "x0" );
    double y0 = Field< double >::get( dend, "y0" );
    double z0 = Field< double >::get( dend, "z0" );
    double x1 = Field< double >::get( dend, "x" );
    double y1 = Field< double >::get( dend, "y" );
    double z1 = Field< double >::get( dend, "z" );

    Vec temp( x1-x0, y1-y0, z1-z0 );
    double len = temp.length();
    z = Vec( temp.a0()/len, temp.a1()/len, temp.a2()/len );

    double sx0 = Field< double >::get( soma, "x0" );
    double sy0 = Field< double >::get( soma, "y0" );
    double sz0 = Field< double >::get( soma, "z0" );
    Vec temp2( x0 - sx0, y0-sy0, z0-sz0 );
    Vec y2 = temp.crossProduct( z );
    double ylen = y2.length();
    double ytemp = 1.0;
    while ( ylen < EPSILON )
    {
        Vec t( ytemp , sqrt( 2.0 ), 0.0 );
        y2 = t.crossProduct( z );
        ylen = y2.length();
        ytemp += 1.0;
    }
    y = Vec( y2.a0()/ylen, y2.a1()/ylen, y2.a2()/ylen );
    x = z.crossProduct( y );
    assert( doubleEq( x.length(), 1.0 ) );
    return len;
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void doClassSpecificMessaging ( Shell *  shell, Id  obj, ObjId  compt  )

static

Definition at line 619 of file Neuron.cpp.

References ReadCell::addChannelMessage(), ObjId::bad(), Neutral::child(), Element::cinfo(), Shell::doAddMsg(), Id::element(), Id::eref(), Element::getName(), Cinfo::isA(), Neutral::parent(), ObjId::path(), path, and wildcardFind().

Referenced by buildFromProto().

{
    if ( obj.element()->cinfo()->isA( "ChanBase" ) )
    {
        shell->doAddMsg( "Single", compt, "channel", obj, "channel" );
        // Add the message to the Ca pool if our obj has 'Ca' in its name.
        if ( obj.element()->getName().find( "Ca" ) != string::npos )
        {
            // Don't do it if we have the legacy GENESIS format
            if ( Neutral::child( obj.eref(), "addmsg1" ) == Id() )
            {
                vector< ObjId > elist;
                string path = Neutral::parent( obj ).path() + "/#[ISA=CaConcBase]";
                // cout << "OK2 to Add Ca Msg for " << path << endl;
                wildcardFind( path, elist );
                if ( elist.size() > 0 )
                {
                    // cout << "Added Ca Msg for " << obj.path() << ", name = " << obj.element()->getName() << endl;
                    ObjId mid = shell->doAddMsg(
                                    "single", obj, "IkOut", elist[0], "current" );
                    assert( !mid.bad());
                }
            }
        }
    }
    ReadCell::addChannelMessage( obj );
}

Here is the call graph for this function:

Here is the caller graph for this function:

Id fillSegIndex	(	const vector< Id > &	kids,
		map< Id, unsigned int > &	segIndex
	)

Definition at line 1241 of file Neuron.cpp.

References Element::cinfo(), Id::element(), Field< A >::get(), Element::getName(), and Cinfo::isA().

Referenced by Neuron::buildSegmentTree().

{
    Id soma;
    segIndex.clear();
    Id fatty;
    double maxDia = 0.0;
    unsigned int numKids = 0;
    for ( unsigned int i = 0; i < kids.size(); ++i )
    {
        const Id& k = kids[i];
        if ( k.element()->cinfo()->isA( "CompartmentBase" ) )
        {
            segIndex[ k ] = numKids++;
            const string& s = k.element()->getName();
            if ( s.find( "soma" ) != s.npos ||
                    s.find( "Soma" ) != s.npos ||
                    s.find( "SOMA" ) != s.npos )
            {
                soma = k;
            }
            double dia = Field< double >::get( k, "diameter" );
            if ( dia > maxDia )
            {
                maxDia = dia;
                fatty = k;
            }
        }
    }
    if ( soma != Id() )
        return soma;
    return fatty; // Fallback.
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void fillSegments ( vector< SwcSegment > &  segs, const map< Id, unsigned int > &  segIndex, const vector< Id > &  kids  )

static

Definition at line 1275 of file Neuron.cpp.

References Element::cinfo(), Id::element(), Field< A >::get(), getComptParent(), and Cinfo::isA().

Referenced by Neuron::buildSegmentTree().

{
    segs.clear();
    for ( unsigned int i = 0; i < kids.size(); ++i )
    {
        const Id& k = kids[i];
        if ( k.element()->cinfo()->isA( "CompartmentBase" ) )
        {
            double x = Field< double >::get( k, "x" );
            double y = Field< double >::get( k, "y" );
            double z = Field< double >::get( k, "z" );
            double dia = Field< double >::get( k, "diameter" );
            Id pa = getComptParent( k );
            unsigned int paIndex = ~0U; // soma
            int comptType = 1; // soma
            if ( pa != Id() )
            {
                map< Id, unsigned int >::const_iterator
                j = segIndex.find( pa );
                if ( j != segIndex.end() )
                {
                    paIndex = j->second;
                    comptType = 3; // generic dendrite
                }
            }
            // cout << "Seg[" << i << "].xy = " << int(x*1e6) << " " << int(y*1e6) << endl;

            segs.push_back(
                SwcSegment( i, comptType, x, y, z, dia/2.0, paIndex ) );
        }
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

string findArg	(	const vector< string > &	line,
		const string &	field
	)

Definition at line 1716 of file Neuron.cpp.

Referenced by makeAngleDistrib(), makeSizeDistrib(), and Neuron::makeSpacingDistrib().

{
    // line has: proto path [field val]...
    assert( (line.size() % 2) != 1 );
    for ( unsigned int i = 2; i < line.size(); i+=2 )
        if ( line[i] == field )
            return line[i+1];
    string ret = "";
    if ( field == "spacing" )
    {
        ret = "1.0e-6";
    }
    else if ( field == "spacingDistrib" )
    {
        ret = "0";
    }
    else if ( field == "size" )
    {
        ret = "1";
    }
    else if ( field == "sizeDistrib" )
    {
        ret = "0";
    }
    else if ( field == "angle" )
    {
        ret = "0";
    }
    else if ( field == "angleDistrib" )
    {
        ret = "6.283185307";
    }
    else if ( field == "rotation" )
    {
        ret = "0";
    }
    else if ( field == "rotationDistrib" )
    {
        ret = "6.283185307"; // 2*PI
    }
    else if ( field == "shaftLen" )
    {
        ret = "1.0e-6";
    }
    else if ( field == "shaftDia" )
    {
        ret = "0.2e-6";
    }
    else if ( field == "headLen" )
    {
        ret = "0.5e-6";
    }
    else if ( field == "headDia" )
    {
        ret = "0.5e-6";
    }
    else if ( field == "theta" )
    {
        ret = "0";
    }
    else if ( field == "phi" )
    {
        ret = "1.5707963268"; // PI/2
    }
    return ret;
}

Here is the caller graph for this function:

static Id getComptParent ( Id  id )

static

Definition at line 1215 of file Neuron.cpp.

References Cinfo::find(), and Cinfo::findFinfo().

Referenced by fillSegments().

{
    // raxial points towards soma.
    static const Finfo* raxialFinfo =
        Cinfo::find( "Compartment" )->findFinfo( "raxialOut" );
    static const Finfo* proximalFinfo =
        Cinfo::find( "SymCompartment" )->findFinfo( "proximalOut" );

    if ( id.element()->cinfo()->isA( "CompartmentBase" ) )
    {
        vector< Id > ret;
        id.element()->getNeighbors( ret, raxialFinfo );
        if ( ret.size() == 1 )
            return ret[0];
        // If it didn't find an axial, maybe it is a symCompt
        if ( id.element()->cinfo()->isA( "SymCompartment" ) )
        {
            id.element()->getNeighbors( ret, proximalFinfo );
            if ( ret.size() == 1 )
                return ret[0];
        }
    }
    return Id();
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void makeAngleDistrib ( const vector< ObjId > &  elist, const vector< double > &  val, vector< unsigned int > &  elistIndex, vector< double > &  theta, const vector< string > &  line  )

static

Definition at line 1888 of file Neuron.cpp.

References nuParser::eval(), findArg(), moose::mtrand(), and nuParser::numVal.

Referenced by Neuron::installSpines().

{
    string angleExpr = findArg( line, "angle" );
    string angleDistribExpr = findArg( line, "angleDistrib" );
    // I won't bother with rotation and rotation distrb for now.
    // Easy to add, but on reflection they don't make sense.
    theta.clear();
    theta.resize( elistIndex.size(), 0.0 );

    try
    {
        nuParser angleParser( angleExpr );
        nuParser distribParser( angleDistribExpr );
        unsigned int lastIndex = ~0U;
        double angle = 0;
        double angleDistrib = 0;
        for ( unsigned int k = 0; k < elistIndex.size(); ++k )
        {
            unsigned int i = elistIndex[k];
            if ( i != lastIndex )
            {
                lastIndex = i;
                unsigned int j = i * nuParser::numVal;
                angle = angleParser.eval( val.begin() + j );
                angleDistrib = distribParser.eval( val.begin() + j);
            }

            // Use global RNG.
            if ( angleDistrib > 0 )
                theta[k] = angle + ( moose::mtrand() - 0.5 ) * angleDistrib;
            else
                theta[k] = angle;
        }
    }
    catch ( mu::Parser::exception_type& err )
    {
        cout << err.GetMsg() << endl;
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void makeSizeDistrib ( const vector< ObjId > &  elist, const vector< double > &  val, vector< unsigned int > &  elistIndex, vector< double > &  size, const vector< string > &  line  )

static

Definition at line 1932 of file Neuron.cpp.

References nuParser::eval(), findArg(), moose::mtrand(), and nuParser::numVal.

Referenced by Neuron::installSpines().

{
    string sizeExpr = findArg( line, "size" );
    string sizeDistribExpr = findArg( line, "sizeDistrib" );
    size.clear();
    size.resize( elistIndex.size(), 0.0 );

    try
    {
        nuParser sizeParser( sizeExpr );
        nuParser distribParser( sizeDistribExpr );
        unsigned int lastIndex = ~0U;
        double sz = 1.0;
        double sizeDistrib = 0;
        for ( unsigned int k = 0; k < elistIndex.size(); ++k )
        {
            unsigned int i = elistIndex[k];
            if ( i != lastIndex )
            {
                lastIndex = i;
                unsigned int j = i * nuParser::numVal;
                sz = sizeParser.eval( val.begin() + j );
                sizeDistrib = distribParser.eval( val.begin() + j);
            }

            // Use global RNG.
            if ( sizeDistrib > 0 )
                size[k] = sz + ( moose::mtrand() - 0.5 ) * sizeDistrib;
            else
                size[k] = sz;
        }
    }
    catch ( mu::Parser::exception_type& err )
    {
        cout << err.GetMsg() << endl;
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

bool parseDistrib	(	vector< vector< string > > &	lines,
		const vector< string > &	distrib
	)

Definition at line 587 of file Neuron.cpp.

Referenced by Neuron::setChannelDistribution(), Neuron::setPassiveDistribution(), and Neuron::setSpineDistribution().

{
    lines.clear();
    vector< string > temp;
    for ( unsigned int i = 0; i < distrib.size(); ++i )
    {
        if ( distrib[i] == "" )
        {
            if ( temp.size() < 4 )
            {
                cout << "Warning: Neuron::parseDistrib: <4 args: " <<
                     temp.size() << endl;
                return false;
            }
            if ( temp.size() % 2 == 1 )
            {
                cout << "Warning: Neuron::parseDistrib: : odd # of args:"
                     << temp.size() << endl;
                return false;
            }
            lines.push_back( temp );
            temp.clear();
        }
        else
        {
            temp.push_back( distrib[i] );
        }
    }
    return true;
}

Here is the caller graph for this function:

static void reorientSpine ( vector< Id > &  spineCompts, vector< Vec > &  coords, Vec &  parentPos, double  pos, double  angle, Vec &  x, Vec &  y, Vec &  z  )

static

Utility function to change coords of spine so as to reorient it.

Definition at line 1583 of file Neuron.cpp.

References Vec::a0(), Vec::a1(), Vec::a2(), and Field< A >::set().

Referenced by addSpine().

{
    double c = cos( angle );
    double s = sin( angle );
    double omc = 1.0 - c;

    Vec rot0(       z.a0()*z.a0()*omc + c,
                    z.a1()*z.a0()*omc - z.a2()*s ,
                    z.a2()*z.a0()*omc + z.a1()*s );

    Vec rot1(       z.a0()*z.a1()*omc + z.a2()*s,
                    z.a1()*z.a1()*omc + c,
                    z.a2()*z.a1()*omc - z.a0()*s );

    Vec rot2(       z.a0()*z.a2()*omc - z.a1()*s,
                    z.a1()*z.a2()*omc + z.a0()*s,
                    z.a2()*z.a2()*omc + c );

    Vec translation = z * pos + parentPos;
    // Vec translation = parentPos;
    vector< Vec > ret( coords.size() );
    for ( unsigned int i = 0; i < coords.size(); ++i )
    {
        ret[i] = Vec(   rot0.dotProduct( coords[i] ) + translation.a0(),
                        rot1.dotProduct( coords[i] ) + translation.a1(),
                        rot2.dotProduct( coords[i] ) + translation.a2() );

    }
    assert( spineCompts.size() * 2 == ret.size() );

    for ( unsigned int i = 0; i < spineCompts.size(); ++i )
    {
        unsigned int j = 2 * i;
        Field< double >::set( spineCompts[i], "x0", ret[j].a0() );
        Field< double >::set( spineCompts[i], "y0", ret[j].a1() );
        Field< double >::set( spineCompts[i], "z0", ret[j].a2() );
        // cout << "(" << ret[j].a0() << ", " << ret[j].a1() << ", " << ret[j].a2() << ")";
        j = j + 1;
        Field< double >::set( spineCompts[i], "x", ret[j].a0() );
        Field< double >::set( spineCompts[i], "y", ret[j].a1() );
        Field< double >::set( spineCompts[i], "z", ret[j].a2() );
        // cout << "(" << ret[j].a0() << ", " << ret[j].a1() << ", " << ret[j].a2() << ")\n";
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void setCompartmentParams ( const vector< ObjId > &  elist, const vector< double > &  val, const string &  field, const string &  expr  )

static

Definition at line 758 of file Neuron.cpp.

References assignSingleCompartmentParams(), nuParser::DIA, nuParser::eval(), nuParser::EXPR, nuParser::LEN, and nuParser::numVal.

Referenced by Neuron::setPassiveDistribution().

{
    try
    {
        nuParser parser( expr );
        for ( unsigned int i = 0; i < elist.size(); ++i )
        {
            unsigned int j = i * nuParser::numVal;
            if ( val[ j + nuParser::EXPR ] > 0 )
            {
                double len = val[j + nuParser::LEN ];
                double dia = val[j + nuParser::DIA ];
                double x = parser.eval( val.begin() + j );
                assignSingleCompartmentParams( elist[i],
                                               x, field, len, dia );
            }
        }
    }
    catch ( mu::Parser::exception_type& err )
    {
        cout << err.GetMsg() << endl;
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void setMechParams ( const vector< ObjId > &  mech, const vector< ObjId > &  elist, const vector< double > &  val, const string &  field, const string &  expr  )

static

Definition at line 784 of file Neuron.cpp.

References assignParam(), nuParser::DIA, nuParser::eval(), nuParser::EXPR, nuParser::LEN, and nuParser::numVal.

Referenced by Neuron::setChannelDistribution().

{
    try
    {
        nuParser parser ( expr );
        for ( unsigned int i = 0; i < elist.size(); ++i )
        {
            unsigned int j = i * nuParser::numVal;
            if ( val[ j + nuParser::EXPR ] > 0 )
            {
                double len = val[j + nuParser::LEN ];
                double dia = val[j + nuParser::DIA ];
                double x = parser.eval( val.begin() + j );
                assignParam( mech[i], field, x, len, dia );
            }
        }
    }
    catch ( mu::Parser::exception_type& err )
    {
        cout << err.GetMsg() << endl;
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

static void traverseCumulativeDistance ( SwcSegment &  self, vector< SwcSegment > &  segs, const vector< Id > &  lookupId, double  len, double  L, double  pSoma, double  eSoma  )

static

Recursive function to fill in cumulative distances from soma.

Definition at line 1311 of file Neuron.cpp.

References SwcSegment::distance(), and Field< A >::get().

Referenced by Neuron::updateSegmentLengths().

{
    self.setCumulativeDistance( len, L, pSoma, eSoma );
    for ( unsigned int i = 0; i < self.kids().size(); ++i )
    {
        SwcSegment& kid = segs[ self.kids()[i] ];
        double segmentLength = kid.distance( self );
        double p = pSoma + segmentLength;
        Id kidId = lookupId[ self.kids()[i] ];
        double Rm = Field< double >::get( kidId, "Rm" );
        double Ra = Field< double >::get( kidId, "Ra" );
        // Note that sqrt( Rm/Ra ) = lambda/length = 1/L.
        double electrotonicLength = sqrt( Ra / Rm );
        double e = eSoma + electrotonicLength;
        traverseCumulativeDistance( kid, segs, lookupId,
                                    segmentLength, electrotonicLength, p, e );
    }
}

Here is the call graph for this function:

Here is the caller graph for this function:

Variable Documentation

const Cinfo* neuronCinfo = Neuron::initCinfo()

static

Definition at line 539 of file Neuron.cpp.

Referenced by Neuron::initCinfo().