#include <Neuron.h>

Collaboration diagram for Neuron:

Public Member Functions
void	buildElist (const Eref &e, const vector< string > &line, vector< ObjId > &elist, vector< double > &val)

void	buildSegmentTree (const Eref &e)
	Fills up vector of segments. First entry is soma. More...

void	evalExprForElist (const vector< ObjId > &elist, const string &expn, vector< double > &val) const

vector< string >	getChannelDistribution (const Eref &e) const

double	getCM () const

double	getCompartmentLengthInLambdas () const

vector< ObjId >	getCompartments () const

vector< double >	getElecDistFromSoma () const

double	getEm () const

vector< ObjId >	getExprElist (const Eref &e, string line) const

vector< double >	getExprVal (const Eref &e, string line) const

vector< double >	getGeomDistFromSoma () const

unsigned int	getNumBranches () const

unsigned int	getNumCompartments () const

unsigned int	getNumSpines () const

ObjId	getParentCompartmentOfSpine (const Eref &e, ObjId compt) const

vector< string >	getPassiveDistribution (const Eref &e) const

vector< double >	getPathDistFromSoma () const

double	getPhi () const

double	getRA () const

double	getRM () const

string	getSourceFile () const

vector< string >	getSpineDistribution (const Eref &e) const

vector< ObjId >	getSpineIdsFromCompartmentIds (const Eref &e, vector< ObjId > compt) const

vector< ObjId >	getSpinesFromExpression (const Eref &e, string line) const

vector< ObjId >	getSpinesOnCompartment (const Eref &e, ObjId compt) const

double	getTheta () const

void	installMechanism (const string &name, const vector< ObjId > &elist, const vector< double > &val, const vector< string > &line)

void	installSpines (const vector< ObjId > &elist, const vector< double > &val, const vector< string > &line)

Spine *	lookupSpine (unsigned int index)

void	makeSpacingDistrib (const vector< ObjId > &elist, const vector< double > &val, vector< unsigned int > &seglistIndex, vector< unsigned int > &elistIndex, vector< double > &pos, const vector< string > &line) const

	Neuron ()

	Neuron (const Neuron &other)

void	parseMechSpec (const Eref &e)

void	scaleBufAndRates (unsigned int spineNum, double lenScale, double diaScale) const

void	scaleHeadDiffusion (unsigned int spineNum, double len, double dia) const
	Scale the diffusion parameters due to a change in the head dimensions. More...

void	scaleShaftDiffusion (unsigned int spineNum, double len, double dia) const
	Scale the diffusion parameters due to a change in the shaft dimensions. More...

void	setChannelDistribution (const Eref &e, vector< string > v)

void	setCM (double v)

void	setCompartmentLengthInLambdas (double v)

void	setEm (double v)

void	setNumSpines (unsigned int num)

void	setPassiveDistribution (const Eref &e, vector< string > v)

void	setPhi (double v)

void	setRA (double v)

void	setRM (double v)

void	setSourceFile (string v)

void	setSpineAndPsdDsolve (Id spineDsolve, Id psdDsolve)

void	setSpineAndPsdMesh (Id spineMesh, Id psdMesh)
	Fills up vector of segments. First entry is soma. More...

void	setSpineDistribution (const Eref &e, vector< string > v)

void	setTheta (double v)

const vector< Id > &	spineIds (unsigned int index) const

void	updateSegmentLengths ()

Static Public Member Functions
static const Cinfo *	initCinfo ()

Private Attributes
vector< vector< Id > >	allSpinesPerCompt_
	Id of each compt in each spine. More...

vector< SwcBranch >	branches_

vector< string >	channelDistribution_

double	CM_

double	compartmentLengthInLambdas_

double	Em_

Id	headDsolve_

double	maxG_

double	maxL_

double	maxP_

vector< string >	passiveDistribution_

double	phi_

Id	psdDsolve_
	Id of the Dsolve for the head compt. More...

vector< Id >	psdStoich_
	Id of stoich associated with each PSD. Typically all the same. More...

double	RA_

double	RM_

vector< Id >	segId_

map< Id, unsigned int >	segIndex_
	Map to look up Seg index from Id of associated compt. More...

vector< SwcSegment >	segs_
	Id of compartment in each Seg entry, below. More...

Id	soma_

string	sourceFile_

vector< string >	spineDistribution_

Spine	spineEntry_
	Id of the Dsolve for the PSD compt. More...

vector< unsigned int >	spineParentSegIndex_
	Look up seg index of parent compartment, from index of spine. More...

vector< vector< Id > >	spines_

vector< Id >	spineStoich_
	Id of stoich associated with each spine. Typically all the same. More...

vector< unsigned int >	spineToMeshOrdering_
	looks up spine/psd mesh index from FieldIndex of selected spine. More...

double	theta_

Detailed Description

The Neuron class to hold the Compartment class elements.

Definition at line 18 of file Neuron.h.

Constructor & Destructor Documentation

Neuron::Neuron ( )

Definition at line 542 of file Neuron.cpp.

     :
     RM_( 1.0 ),
     RA_( 1.0 ),
     CM_( 0.01 ),
     Em_( -0.065 ),
     theta_( 0.0 ),
     phi_( 0.0 ),
     maxP_( 0.0 ),
     maxG_( 0.0 ),
     maxL_( 0.0 ),
     sourceFile_( "" ),
     compartmentLengthInLambdas_( 0.2 ),
     spineEntry_( this )
 {
     ;
 }

Neuron::Neuron ( const Neuron & other )

Definition at line 562 of file Neuron.cpp.

     :
     RM_( other.RM_ ),
     RA_( other.RA_ ),
     CM_( other.CM_ ),
     Em_( other.Em_ ),
     theta_( other.theta_ ),
     phi_( other.phi_ ),
     maxP_( other.maxP_ ),
     maxG_( other.maxG_ ),
     maxL_( other.maxL_ ),
     sourceFile_( other.sourceFile_ ),
     compartmentLengthInLambdas_(other.compartmentLengthInLambdas_),
     channelDistribution_( other.channelDistribution_ ),
     passiveDistribution_( other.passiveDistribution_ ),
     spineDistribution_( other.spineDistribution_ ),
     spineEntry_( this )
 {
     ;
 }

Member Function Documentation

void Neuron::buildElist	(	const Eref &	e,
		const vector< string > &	line,
		vector< ObjId > &	elist,
		vector< double > &	val
	)

Definition at line 1116 of file Neuron.cpp.

References Eref::data(), Id::eref(), evalExprForElist(), Shell::getCwe(), Eref::objId(), path, Shell::setCwe(), and wildcardFind().

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

 {
     Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
     const string& path = line[1];
     const string& expr = line[3];
     ObjId oldCwe = shell->getCwe();
     shell->setCwe( e.objId() );
     wildcardFind( path, elist );
     sort( elist.begin(), elist.end() );
     shell->setCwe( oldCwe );
     evalExprForElist( elist, expr, val );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::buildSegmentTree ( const Eref & e )

Fills up vector of segments. First entry is soma.

Definition at line 1362 of file Neuron.cpp.

References Neutral::children(), fillSegIndex(), fillSegments(), Eref::id(), Id::path(), segId_, segIndex_, segs_, soma_, and updateSegmentLengths().

Referenced by initCinfo().

 {
     vector< Id > kids;
     Neutral::children( e, kids );
     sort( kids.begin(), kids.end() );
 
     soma_ = fillSegIndex( kids, segIndex_ );
     if ( kids.size() == 0 || soma_ == Id() )
     {
         cout << "Error: Neuron::buildSegmentTree( " << e.id().path() <<
              " ): \n        Valid neuronal model not found.\n";
         return;
     }
     fillSegments( segs_, segIndex_, kids );
     int numPa = 0;
     for ( unsigned int i = 0; i < segs_.size(); ++i )
     {
         if ( segs_[i].parent() == ~0U )
         {
             numPa++;
         }
         else
         {
             segs_[ segs_[i].parent() ].addChild( i );
         }
     }
     for ( unsigned int i = 0; i < segs_.size(); ++i )
     {
         segs_[i].figureOutType();
     }
 
     if ( numPa != 1 )
     {
         cout << "Warning: Neuron.cpp: buildTree: numPa = " << numPa << endl;
     }
     segId_.clear();
     segId_.resize( segIndex_.size(), Id() );
     for ( map< Id, unsigned int >::const_iterator
             i = segIndex_.begin(); i != segIndex_.end(); ++i )
     {
         assert( i->second < segId_.size() );
         segId_[ i->second ] = i->first;
     }
     updateSegmentLengths();
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::evalExprForElist	(	const vector< ObjId > &	elist,
		const string &	expn,
		vector< double > &	val
	)		const

Evaluates expn for every CompartmentBase entry in elist. Pushes value, length and dia for each elist entry into the 'val' vector.

Definition at line 1478 of file Neuron.cpp.

References nuParser::DIA, nuParser::EL, nuParser::eval(), nuParser::EXPR, nuParser::G, Field< A >::get(), nuParser::LEN, nuParser::MAXG, maxG_, nuParser::MAXL, maxL_, nuParser::MAXP, maxP_, nuParser::numVal, nuParser::OLDVAL, nuParser::P, segIndex_, segs_, nuParser::X, nuParser::Y, and nuParser::Z.

Referenced by buildElist(), getExprElist(), and getExprVal().

 {
     val.clear();
     val.resize( elist.size() * nuParser::numVal );
     // Build the function
     double len = 0; // Length of compt in metres
     double dia = 0; // Diameter of compt in metres
     unsigned int valIndex = 0;
     try
     {
         nuParser parser( expn );
 
         // Go through the elist checking for the channels. If not there,
         // build them.
         for ( vector< ObjId >::const_iterator
                 i = elist.begin(); i != elist.end(); ++i )
         {
             if ( i->element()->cinfo()->isA( "CompartmentBase" ) )
             {
                 map< Id, unsigned int >:: const_iterator j =
                     segIndex_.find( *i );
                 if ( j != segIndex_.end() )
                 {
                     dia = Field< double >::get( *i, "diameter" );
                     len = Field< double >::get( *i, "length" );
                     assert( j->second < segs_.size() );
                     val[valIndex + nuParser::P] =
                         segs_[j->second].getPathDistFromSoma();
                     val[valIndex + nuParser::G] =
                         segs_[j->second].getGeomDistFromSoma();
                     val[valIndex + nuParser::EL] =
                         segs_[j->second].getElecDistFromSoma();
                     val[valIndex + nuParser::LEN] = len;
                     val[valIndex + nuParser::DIA] = dia;
                     val[valIndex + nuParser::MAXP] = maxP_;
                     val[valIndex + nuParser::MAXG] = maxG_;
                     val[valIndex + nuParser::MAXL] = maxL_;
                     val[valIndex + nuParser::X] = segs_[j->second].vec().a0();
                     val[valIndex + nuParser::Y] = segs_[j->second].vec().a1();
                     val[valIndex + nuParser::Z] = segs_[j->second].vec().a2();
                     // Can't assign oldVal on first arg
                     val[valIndex + nuParser::OLDVAL] = 0.0;
 
                     val[valIndex + nuParser::EXPR] = parser.eval(
                                                          val.begin() + valIndex );
                 }
             }
             valIndex += nuParser::numVal;
         }
     }
     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:

vector< string > Neuron::getChannelDistribution ( const Eref & e ) const

Definition at line 1158 of file Neuron.cpp.

References channelDistribution_.

Referenced by initCinfo().

 {
     return channelDistribution_;
 }

Here is the caller graph for this function:

double Neuron::getCM ( ) const

Definition at line 845 of file Neuron.cpp.

References CM_.

Referenced by initCinfo().

 {
     return CM_;
 }

Here is the caller graph for this function:

double Neuron::getCompartmentLengthInLambdas ( ) const

Definition at line 899 of file Neuron.cpp.

References compartmentLengthInLambdas_.

Referenced by initCinfo().

 {
     return compartmentLengthInLambdas_;
 }

Here is the caller graph for this function:

vector< ObjId > Neuron::getCompartments ( ) const

Definition at line 945 of file Neuron.cpp.

References segId_.

Referenced by initCinfo().

 {
     vector< ObjId > ret( segId_.size() );
     for ( unsigned int i = 0; i < segId_.size(); ++i )
         ret[i] = segId_[i];
     return ret;
 }

Here is the caller graph for this function:

vector< double > Neuron::getElecDistFromSoma ( ) const

Definition at line 937 of file Neuron.cpp.

References segs_.

Referenced by initCinfo().

 {
     vector< double > ret( segs_.size(), 0.0 );
     for ( unsigned int i = 0; i < segs_.size(); ++i )
         ret[i] = segs_[i].getElecDistFromSoma();
     return ret;
 }

Here is the caller graph for this function:

double Neuron::getEm ( ) const

Definition at line 855 of file Neuron.cpp.

References Em_.

Referenced by initCinfo().

 {
     return Em_;
 }

Here is the caller graph for this function:

vector< ObjId > Neuron::getExprElist	(	const Eref &	e,
		string	line
	)		const

Digest the path and the math expression to obtain an elist of compartments that satisfy both criteria. The argument 'line' has path followed by the math expression, separated by a space.

Definition at line 959 of file Neuron.cpp.

References Eref::data(), Id::eref(), evalExprForElist(), Shell::getCwe(), nuParser::numVal, Eref::objId(), path, Shell::setCwe(), and wildcardFind().

Referenced by getSpinesFromExpression(), and initCinfo().

 {
     Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
     vector< ObjId > ret;
     vector< ObjId > elist;
     vector< double > val;
     unsigned long pos = line.find_first_of( " \t" );
     string path = line.substr( 0, pos );
     string expr = line.substr( pos );
     ObjId oldCwe = shell->getCwe();
     shell->setCwe( e.objId() );
     wildcardFind( path, elist );
     shell->setCwe( oldCwe );
     if ( elist.size() == 0 )
         return ret;
     evalExprForElist( elist, expr, val );
     ret.reserve( elist.size() );
     for ( unsigned int i = 0; i < elist.size(); ++i )
     {
         if ( val[i * nuParser::numVal] > 0 )
             ret.push_back( elist[i] );
     }
     return ret;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

vector< double > Neuron::getExprVal	(	const Eref &	e,
		string	line
	)		const

Digest the path and the math expression to obtain all the values pertaining to the elements in the path. There are nuParser::numVal * elist.size() entries. The argument 'line' has path followed by the math expression, separated by a space.

Definition at line 991 of file Neuron.cpp.

References Eref::data(), Id::eref(), evalExprForElist(), Shell::getCwe(), Eref::objId(), path, Shell::setCwe(), and wildcardFind().

Referenced by initCinfo().

 {
     Shell* shell = reinterpret_cast< Shell* >( Id().eref().data() );
     vector< ObjId > elist;
     vector< double > val;
     unsigned long pos = line.find_first_of( " \t" );
     string path = line.substr( 0, pos );
     string expr = line.substr( pos );
     ObjId oldCwe = shell->getCwe();
     shell->setCwe( e.objId() );
     wildcardFind( path, elist );
     shell->setCwe( oldCwe );
     if ( elist.size() == 0 )
         return val;
     evalExprForElist( elist, expr, val );
     return val;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

vector< double > Neuron::getGeomDistFromSoma ( ) const

Definition at line 929 of file Neuron.cpp.

References segs_.

Referenced by initCinfo().

 {
     vector< double > ret( segs_.size(), 0.0 );
     for ( unsigned int i = 0; i < segs_.size(); ++i )
         ret[i] = segs_[i].getGeomDistFromSoma();
     return ret;
 }

Here is the caller graph for this function:

unsigned int Neuron::getNumBranches ( ) const

Definition at line 916 of file Neuron.cpp.

References branches_.

Referenced by initCinfo().

 {
     return branches_.size();
 }

Here is the caller graph for this function:

unsigned int Neuron::getNumCompartments ( ) const

Definition at line 904 of file Neuron.cpp.

References segId_.

Referenced by initCinfo().

 {
     return segId_.size();
 }

Here is the caller graph for this function:

unsigned int Neuron::getNumSpines ( ) const

Definition at line 2039 of file Neuron.cpp.

References spines_.

Referenced by initCinfo().

 {
     return spines_.size();
 }

Here is the caller graph for this function:

ObjId Neuron::getParentCompartmentOfSpine	(	const Eref &	e,
		ObjId	compt
	)		const

Definition at line 1066 of file Neuron.cpp.

References allSpinesPerCompt_, ObjId::id, and segId_.

Referenced by initCinfo().

 {
     for ( unsigned int comptIndex = 0; comptIndex < allSpinesPerCompt_.size(); ++comptIndex )
     {
         const vector< Id >& v = allSpinesPerCompt_[comptIndex];
         for ( unsigned int j = 0; j < v.size(); j++ )
             if ( v[j] == compt.id )
                 return segId_[ comptIndex ];
     }
     return ObjId();
 }

Here is the caller graph for this function:

vector< string > Neuron::getPassiveDistribution ( const Eref & e ) const

Definition at line 1183 of file Neuron.cpp.

References passiveDistribution_.

Referenced by initCinfo().

 {
     return passiveDistribution_;
 }

Here is the caller graph for this function:

vector< double > Neuron::getPathDistFromSoma ( ) const

Definition at line 921 of file Neuron.cpp.

References segs_.

Referenced by initCinfo().

 {
     vector< double > ret( segs_.size(), 0.0 );
     for ( unsigned int i = 0; i < segs_.size(); ++i )
         ret[i] = segs_[i].getPathDistFromSoma();
     return ret;
 }

Here is the caller graph for this function:

double Neuron::getPhi ( ) const

Definition at line 877 of file Neuron.cpp.

References phi_.

Referenced by initCinfo().

 {
     return phi_;
 }

Here is the caller graph for this function:

double Neuron::getRA ( ) const

Definition at line 833 of file Neuron.cpp.

References RA_.

Referenced by initCinfo().

 {
     return RA_;
 }

Here is the caller graph for this function:

double Neuron::getRM ( ) const

Definition at line 821 of file Neuron.cpp.

References RM_.

Referenced by initCinfo().

 {
     return RM_;
 }

Here is the caller graph for this function:

string Neuron::getSourceFile ( ) const

Definition at line 889 of file Neuron.cpp.

References sourceFile_.

Referenced by initCinfo().

 {
     return sourceFile_;
 }

Here is the caller graph for this function:

vector< string > Neuron::getSpineDistribution ( const Eref & e ) const

Definition at line 1205 of file Neuron.cpp.

References spineDistribution_.

Referenced by initCinfo().

 {
     return spineDistribution_;
 }

Here is the caller graph for this function:

vector< ObjId > Neuron::getSpineIdsFromCompartmentIds	(	const Eref &	e,
		vector< ObjId >	compt
	)		const

Definition at line 1079 of file Neuron.cpp.

References Eref::dataIndex(), Eref::id(), lookupSpine(), spines_, and Id::value().

Referenced by initCinfo().

 {
     vector< ObjId > ret;
     map< Id, unsigned int > lookupSpine;
     Id spineBase = Id( e.id().value() + 1 );
     for ( unsigned int i = 0; i < spines_.size(); ++i )
     {
         for ( vector< Id >::const_iterator j = spines_[i].begin(); j != spines_[i].end(); ++j )
         {
             lookupSpine[ *j ] = i;
         }
     }
     // cout << "################## " << lookupSpine.size() << endl;
     for ( map< Id, unsigned int >::const_iterator k = lookupSpine.begin(); k != lookupSpine.end(); ++k )
     {
         // cout << "spine[" << k->second << "] has " << k->first.element()->getName() << endl;
         // cout << "spine[" << k->second << "] has " << k->first << endl;
 
     }
     for ( vector< ObjId >::const_iterator j = compt.begin(); j != compt.end(); ++j )
     {
         // cout << "compt: " << *j << " " << j->element()->getName() << endl;
         map< Id, unsigned int >::const_iterator k = lookupSpine.find( j->id );
         if ( k != lookupSpine.end() )
         {
             ret.push_back( ObjId( spineBase, e.dataIndex(), k->second ) );
             // cout << "spine[" << k->second << "] has " << j->element()->getName() << endl;
         }
         else
         {
             ret.push_back( ObjId() );
         }
     }
     return ret;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

vector< ObjId > Neuron::getSpinesFromExpression	(	const Eref &	e,
		string	line
	)		const

Definition at line 1009 of file Neuron.cpp.

References allSpinesPerCompt_, getExprElist(), matchBeforeBrace(), path, segId_, and segIndex_.

Referenced by initCinfo().

 {
     unsigned long pos = line.find_first_of( " \t" );
     string path = line.substr( 0, pos );
     string expr = line.substr( pos );
 
     // Look for all compartments that fit the expression.
     vector< ObjId > temp = getExprElist( e, "# " + expr );
     // indexed by segIndex, includes all compts in all spines.
     /*
     vector< vector< Id > > allSpinesPerCompt( segId_.size() );
     for ( unsigned int i = 0; i < spines_.size(); ++i ) {
         assert( allSpinesPerCompt.size() > spineParentSegIndex_[i] );
         vector< Id >& s = allSpinesPerCompt[ spineParentSegIndex_[i] ];
         s.insert( s.end(), spines_[i].begin(), spines_[i].end() );
     }
     */
     vector< ObjId >ret;
     if ( allSpinesPerCompt_.size() == 0 )
         return ret;
     for ( vector< ObjId >::iterator
             i = temp.begin(); i != temp.end(); ++i )
     {
         map< Id, unsigned int >::const_iterator si =
             segIndex_.find( i->id );
         assert( si != segIndex_.end() );
         assert( si->second < segId_.size() );
         if ( allSpinesPerCompt_.size() > si->second )
         {
             const vector< Id >& s = allSpinesPerCompt_[ si->second ];
             for ( vector< Id >::const_iterator j = s.begin(); j != s.end(); ++j )
             {
                 if ( matchBeforeBrace( *j, path ) )
                     ret.push_back( *j );
             }
         }
     }
     return ret;
 }

Here is the call graph for this function:

Here is the caller graph for this function:

vector< ObjId > Neuron::getSpinesOnCompartment	(	const Eref &	e,
		ObjId	compt
	)		const

Definition at line 1050 of file Neuron.cpp.

References allSpinesPerCompt_, ObjId::id, and segIndex_.

Referenced by initCinfo().

 {
     vector< ObjId > ret;
     map< Id, unsigned int >::const_iterator pos =
         segIndex_.find( compt.id );
     if ( pos != segIndex_.end() )
     {
         assert( pos->second < allSpinesPerCompt_.size() );
         const vector< Id >& spines = allSpinesPerCompt_[pos->second];
         for ( unsigned int i = 0; i < spines.size(); ++i )
             ret.push_back( spines[i] );
     }
     return ret;
 }

Here is the caller graph for this function:

double Neuron::getTheta ( ) const

Definition at line 866 of file Neuron.cpp.

References theta_.

Referenced by initCinfo().

 {
     return theta_;
 }

Here is the caller graph for this function:

const Cinfo * Neuron::initCinfo ( )

static

Initializes the class info.

Definition at line 106 of file Neuron.cpp.

References buildSegmentTree(), getChannelDistribution(), getCM(), getCompartmentLengthInLambdas(), getCompartments(), getElecDistFromSoma(), getEm(), getExprElist(), getExprVal(), getGeomDistFromSoma(), getNumBranches(), getNumCompartments(), getNumSpines(), getParentCompartmentOfSpine(), getPassiveDistribution(), getPathDistFromSoma(), getPhi(), getRA(), getRM(), getSourceFile(), getSpineDistribution(), getSpineIdsFromCompartmentIds(), getSpinesFromExpression(), getSpinesOnCompartment(), getTheta(), Spine::initCinfo(), Neutral::initCinfo(), lookupSpine(), neuronCinfo, setChannelDistribution(), setCM(), setCompartmentLengthInLambdas(), setEm(), setNumSpines(), setPassiveDistribution(), setPhi(), setRA(), setRM(), setSourceFile(), setSpineAndPsdDsolve(), setSpineAndPsdMesh(), setSpineDistribution(), and setTheta().

 {
     // ValueFinfos
     static ValueFinfo< Neuron, double > RM( "RM",
                                             "Membrane resistivity, in ohm.m^2. Default value is 1.0.",
                                             &Neuron::setRM,
                                             &Neuron::getRM
                                           );
     static ValueFinfo< Neuron, double > RA( "RA",
                                             "Axial resistivity of cytoplasm, in ohm.m. Default value is 1.0.",
                                             &Neuron::setRA,
                                             &Neuron::getRA
                                           );
     static ValueFinfo< Neuron, double > CM( "CM",
                                             "Membrane Capacitance, in F/m^2. Default value is 0.01",
                                             &Neuron::setCM,
                                             &Neuron::getCM
                                           );
     static ValueFinfo< Neuron, double > Em( "Em",
                                             "Resting membrane potential of compartments, in Volts. "
                                             "Default value is -0.065.",
                                             &Neuron::setEm,
                                             &Neuron::getEm
                                           );
     static ValueFinfo< Neuron, double > theta( "theta",
             "Angle to rotate cell geometry, around long axis of neuron. "
             "Think Longitude. Units are radians. "
             "Default value is zero, which means no rotation. ",
             &Neuron::setTheta,
             &Neuron::getTheta
                                              );
     static ValueFinfo< Neuron, double > phi( "phi",
             "Angle to rotate cell geometry, around elevation of neuron. "
             "Think Latitude. Units are radians. "
             "Default value is zero, which means no rotation. ",
             &Neuron::setPhi,
             &Neuron::getPhi
                                            );
 
     static ValueFinfo< Neuron, string > sourceFile( "sourceFile",
             "Name of source file from which to load a model. "
             "Accepts swc and dotp formats at present. "
             "Both these formats require that the appropriate channel "
             "definitions should have been loaded into /library. ",
             &Neuron::setSourceFile,
             &Neuron::getSourceFile
                                                   );
 
     static ValueFinfo< Neuron, double > compartmentLengthInLambdas(
         "compartmentLengthInLambdas",
         "Units: meters (SI). \n"
         "Electrotonic length to use for the largest compartment in the "
         "model. Used to define subdivision of branches into compartments. "
         "For example, if we set *compartmentLengthInLambdas*  to 0.1, "
         "and *lambda* (electrotonic length) is 250 microns, then it "
         "sets the compartment length to 25 microns. Thus a dendritic "
         "branch of 500 microns is subdivided into 20 commpartments. "
         "If the branch is shorter than *compartmentLengthInLambdas*, "
         "then it is not subdivided. "
         "If *compartmentLengthInLambdas* is set to 0 then the original "
         "compartmental structure of the model is preserved. "
         " Note that this routine does NOT merge branches, even if "
         "*compartmentLengthInLambdas* is bigger than the branch. "
         "While all this subdivision is being done, the Neuron class "
         "preserves as detailed a geometry as it can, so it can rebuild "
         "the more detailed version if needed. "
         "Default value of *compartmentLengthInLambdas* is 0. ",
         &Neuron::setCompartmentLengthInLambdas,
         &Neuron::getCompartmentLengthInLambdas
     );
 
     static ElementValueFinfo< Neuron, vector< string > >
     channelDistribution(
         "channelDistribution",
         "Specification for distribution of channels, CaConcens and "
         "any other model components that are defined as prototypes and "
         "have to be placed on the electrical compartments.\n"
         "Arguments: proto path field expr [field expr]...\n"
         " Each entry is terminated with an empty string. "
         "The prototype is any object created in */library*, "
         "If a channel matching the prototype name already exists, then "
         "all subsequent operations are applied to the extant channel and "
         "a new one is not created. "
         "The paired arguments are as follows: \n"
         "The *field* argument specifies the name of the parameter "
         "that is to be assigned by the expression.\n"
         "The *expression* argument is a mathematical expression in "
         "the muparser framework, which permits most operations including "
         "trig and transcendental ones. Of course it also handles simple "
         "numerical values like 1.0, 1e-10 and so on. "
         "Available arguments for muParser are:\n"
         " p, g, L, len, dia, maxP, maxG, maxL \n"
         "   p: path distance from soma, measured along dendrite, in metres.\n"
         "   g: geometrical distance from soma, in metres.\n"
         "   L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
         "   len: length of compartment, in metres.\n"
         "   dia: for diameter of compartment, in metres.\n"
         "   maxP: Maximum value of *p* for this neuron. \n"
         "   maxG: Maximum value of *g* for this neuron. \n"
         "   maxL: Maximum value of *L* for this neuron.\n"
         "The expression for the first field must evaluate to > 0 "
         "for the channel to be installed. For example, for "
         "channels, if Field == Gbar, and func( r, L, len, dia) < 0, \n"
         "then the channel is not installed. This feature is typically "
         "used with the sign() or Heaviside H() function to limit range: "
         "for example: H(1 - L) will only put channels closer than "
         "one length constant from the soma, and zero elsewhere. \n"
         "Available fields are: \n"
         "Channels: Gbar (install), Ek \n"
         "CaConcen: shellDia (install), shellFrac (install), tau, min\n"
         "Unless otherwise noted, all fields are scaled appropriately by "
         "the dimensions of their compartment. Thus the channel "
         "maximal conductance Gbar is automatically scaled by the area "
         "of the compartment, and the user does not need to insert this "
         "scaling into the calculations.\n"
         "All parameters are expressed in SI units. Conductance, for "
         "example, is Siemens/sq metre. "
         "\n\n"
         "Some example function forms might be for a channel Gbar: \n"
         " p < 10e-6 ? 400 : 0.0 \n"
         "       equivalently, \n"
         " H(10e-6 - p) * 400 \n"
         "       equivalently, \n"
         " ( sign(10e-6 - p) + 1) * 200 \n"
         "Each of these forms instruct the function to "
         "set channel Gbar to 400 S/m^2 only within 10 microns path "
         "distance of soma\n"
         "\n"
         " L < 1.0 ? 100 * exp( -L ) : 0.0 \n"
         " ->Set channel Gbar to an exponentially falling function of "
         "electrotonic distance from soma, provided L is under "
         "1.0 lambdas. \n",
         &Neuron::setChannelDistribution,
         &Neuron::getChannelDistribution
     );
 
     static ElementValueFinfo< Neuron, vector< string > >
     passiveDistribution(
         "passiveDistribution",
         "Specification for distribution of passive properties of cell.\n"
         "Arguments: . path field expr [field expr]...\n"
         "Note that the arguments list starts with a period. "
         " Each entry is terminated with an empty string. "
         "The paired arguments are as follows: \n"
         "The *field* argument specifies the name of the parameter "
         "that is to be assigned by the expression.\n"
         "The *expression* argument is a mathematical expression in "
         "the muparser framework, which permits most operations including "
         "trig and transcendental ones. Of course it also handles simple "
         "numerical values like 1.0, 1e-10 and so on. "
         "Available arguments for muParser are:\n"
         " p, g, L, len, dia, maxP, maxG, maxL \n"
         "   p: path distance from soma, measured along dendrite, in metres.\n"
         "   g: geometrical distance from soma, in metres.\n"
         "   L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
         "   len: length of compartment, in metres.\n"
         "   dia: for diameter of compartment, in metres.\n"
         "   maxP: Maximum value of *p* for this neuron. \n"
         "   maxG: Maximum value of *g* for this neuron. \n"
         "   maxL: Maximum value of *L* for this neuron.\n"
         "Available fields are: \n"
         "RM, RA, CM, Rm, Ra, Cm, Em, initVm \n"
         "The first three fields are scaled appropriately by "
         "the dimensions of their compartment. Thus the membrane "
         "resistivity RM (ohms.m^2) is automatically scaled by the area "
         "of the compartment, and the user does not need to insert this "
         "scaling into the calculations to compute Rm."
         "Using the Rm field lets the user directly assign the "
         "membrane resistance (in ohms), presumably using len and dia.\n"
         "Similarly, RA (ohms.m) and CM (Farads/m^2) are specific units "
         "and the actual values for each compartment are assigned by "
         "scaling by length and diameter. Ra (ohms) and Cm (Farads) "
         "require explicit evaluation of the expression. "
         "All parameters are expressed in SI units. Conductance, for "
         "example, is Siemens/sq metre.\n"
         "Note that time these calculations do NOT currently include spines\n",
         &Neuron::setPassiveDistribution,
         &Neuron::getPassiveDistribution
     );
 
     static ElementValueFinfo< Neuron, vector< string > >spineDistribution(
         "spineDistribution",
         "Specification for distribution of spines on dendrite. \n"
         "Arguments: proto path spacing expr [field expr]...\n"
         " Each entry is terminated with an empty string. "
         "The *prototype* is any spine object created in */library*, \n"
         "The *path* is the wildcard path of compartments on which to "
         "place the spine.\n"
         "The *spacing* is the spacing of spines, in metres. \n"
         "The *expression* argument is a mathematical expression in "
         "the muparser framework, which permits most operations including "
         "trig and transcendental ones. Of course it also handles simple "
         "numerical values like 1.0, 1e-10 and so on. "
         "The paired arguments are as follows: \n"
         "The *field* argument specifies the name of the parameter "
         "that is to be assigned by the expression.\n"
         "The *expression* argument is a mathematical expression as above. "
         "Available arguments for muParser are:\n"
         " p, g, L, len, dia, maxP, maxG, maxL \n"
         "   p: path distance from soma, measured along dendrite, in metres.\n"
         "   g: geometrical distance from soma, in metres.\n"
         "   L: electrotonic distance (# of lambdas) from soma, along dend. No units.\n"
         "   len: length of compartment, in metres.\n"
         "   dia: for diameter of compartment, in metres.\n"
         "   maxP: Maximum value of *p* for this neuron. \n"
         "   maxG: Maximum value of *g* for this neuron. \n"
         "   maxL: Maximum value of *L* for this neuron.\n"
         "The expression for the *spacing* field must evaluate to > 0 for "
         "the spine to be installed. For example, if the expresssion is\n"
         "       H(1 - L) \n"
         "then the systemwill only put spines closer than "
         "one length constant from the soma, and zero elsewhere. \n"
         "Available spine parameters are: \n"
         "spacing, minSpacing, size, sizeDistrib "
         "angle, angleDistrib \n",
         &Neuron::setSpineDistribution,
         &Neuron::getSpineDistribution
     );
 
 
     static ReadOnlyValueFinfo< Neuron, unsigned int > numCompartments(
         "numCompartments",
         "Number of electrical compartments in model. ",
         &Neuron::getNumCompartments
     );
 
     static ReadOnlyValueFinfo< Neuron, unsigned int > numSpines(
         "numSpines",
         "Number of dendritic spines in model. ",
         &Neuron::getNumSpines
     );
 
     static ReadOnlyValueFinfo< Neuron, unsigned int > numBranches(
         "numBranches",
         "Number of branches in dendrites. ",
         &Neuron::getNumBranches
     );
 
     static ReadOnlyValueFinfo< Neuron, vector< double > > pathDistFromSoma(
         "pathDistanceFromSoma",
         "geometrical path distance of each segment from soma, measured by "
         "threading along the dendrite.",
         &Neuron::getPathDistFromSoma
     );
 
     static ReadOnlyValueFinfo< Neuron, vector< double > > geomDistFromSoma(
         "geometricalDistanceFromSoma",
         "geometrical distance of each segment from soma.",
         &Neuron::getGeomDistFromSoma
     );
 
     static ReadOnlyValueFinfo< Neuron, vector< double > > elecDistFromSoma(
         "electrotonicDistanceFromSoma",
         "geometrical distance of each segment from soma, as measured along "
         "the dendrite.",
         &Neuron::getElecDistFromSoma
     );
     static ReadOnlyValueFinfo< Neuron, vector< ObjId > > compartments(
         "compartments",
         "Vector of ObjIds of electrical compartments. Order matches order "
         "of segments, and also matches the order of the electrotonic and "
         "geometricalDistanceFromSoma vectors. ",
         &Neuron::getCompartments
     );
 
     static ReadOnlyLookupElementValueFinfo< Neuron, string, vector< ObjId > >
     compartmentsFromExpression(
         "compartmentsFromExpression",
         "Vector of ObjIds of electrical compartments that match the "
         "'path expression' pair in the argument string.",
         &Neuron::getExprElist
     );
 
     static ReadOnlyLookupElementValueFinfo< Neuron, string, vector< double > >
     valuesFromExpression(
         "valuesFromExpression",
         "Vector of values computed for each electrical compartment that "
         "matches the 'path expression' pair in the argument string."
         "This has 13 times the number of entries as # of compartments."
         "For each compartment the entries are: \n"
         "val, p, g, L, len, dia, maxP, maxG, maxL, x, y, z, 0",
         &Neuron::getExprVal
     );
 
     static ReadOnlyLookupElementValueFinfo< Neuron, string, vector< ObjId > >
     spinesFromExpression(
         "spinesFromExpression",
         //"Vector of ObjIds of spines/heads sitting on the electrical "
         //"compartments that match the 'path expression' pair in the "
         //"argument string.",
         "Vector of ObjIds of compartments comprising spines/heads "
         "that match the 'path expression' pair in the "
         "argument string.",
         &Neuron::getSpinesFromExpression
     );
 
     static ReadOnlyLookupElementValueFinfo< Neuron, ObjId,vector< ObjId > >
     spinesOnCompartment(
         "spinesOnCompartment",
         "Vector of ObjIds of spines shafts/heads sitting on the specified "
         "electrical compartment. If each spine has a shaft and a head,"
         "and there are 10 spines on the compartment, there will be 20 "
         "entries in the returned vector, ordered "
         "shaft0, head0, shaft1, head1, ... ",
         &Neuron::getSpinesOnCompartment
     );
 
     static ReadOnlyLookupElementValueFinfo< Neuron, ObjId, ObjId >
     parentCompartmentOfSpine(
         "parentCompartmentOfSpine",
         "Returns parent compartment of specified spine compartment."
         "Both the spine head or its shaft will return the same parent.",
         &Neuron::getParentCompartmentOfSpine
     );
 
     static ReadOnlyLookupElementValueFinfo< Neuron, vector< ObjId >, vector< ObjId > >
     spineIdsFromCompartmentIds(
         "spineIdsFromCompartmentIds",
         "Vector of ObjIds of spine entries (FieldElements on this Neuron, "
         "used for scaling) that map to the the specified "
         "electrical compartments. If a bad compartment Id is given, the"
         "corresponding spine entry is the root Id.",
         &Neuron::getSpineIdsFromCompartmentIds
     );
 
     // DestFinfos
     static DestFinfo buildSegmentTree( "buildSegmentTree",
                                        "Build the reference segment tree structure using the child "
                                        "compartments of the current Neuron. Fills in all the coords and "
                                        "length constant information into the segments, for later use "
                                        "when we build reduced compartment trees and channel "
                                        "distributions. Should only be called once, since subsequent use "
                                        "on a reduced model will lose the original full cell geometry. ",
                                        new EpFunc0< Neuron >( &Neuron::buildSegmentTree )
                                      );
     static DestFinfo setSpineAndPsdMesh( "setSpineAndPsdMesh",
                                          "Assigns the spine and psd mesh to the Neuron. This is used "
                                          "to build up a mapping from Spine entries on the Neuron to "
                                          "chem spines and PSDs, so that volume change operations from "
                                          "the Spine can propagate to the chem systems.",
                                          new OpFunc2< Neuron, Id, Id >( &Neuron::setSpineAndPsdMesh )
                                        );
     static DestFinfo setSpineAndPsdDsolve( "setSpineAndPsdDsolve",
                                            "Assigns the Dsolves used by spine and PSD to the Neuron. "
                                            "This is used "
                                            "to handle the rescaling of diffusion rates when spines are "
                                            "resized. ",
                                            new OpFunc2< Neuron, Id, Id >( &Neuron::setSpineAndPsdDsolve )
                                          );
 
     /*
     static DestFinfo rotateInSpace( "rotateInSpace",
         theta, phi
     static DestFinfo transformInSpace( "transformInSpace",
         transfMatrix(4x4)
     static DestFinfo saveAsNeuroML( "saveAsNeuroML", fname )
     static DestFinfo saveAsDotP( "saveAsDotP", fname )
     static DestFinfo saveAsSwc( "saveAsSwc", fname )
     */
     // FieldElement
     static FieldElementFinfo< Neuron, Spine > spineFinfo(
         "spine",
         "Field Element for spines. Used to handle dynamic "
         "geometry changes in spines. ",
         Spine::initCinfo(),
         &Neuron::lookupSpine,
         &Neuron::setNumSpines,
         &Neuron::getNumSpines,
         false
     );
 
     static Finfo* neuronFinfos[] =
     {
         &RM,                        // ValueFinfo
         &RA,                        // ValueFinfo
         &CM,                        // ValueFinfo
         &Em,                        // ValueFinfo
         &theta,                     // ValueFinfo
         &phi,                       // ValueFinfo
         &sourceFile,                // ValueFinfo
         &compartmentLengthInLambdas,    // ValueFinfo
         &numCompartments,           // ReadOnlyValueFinfo
         &numSpines,                 // ReadOnlyValueFinfo
         &numBranches,               // ReadOnlyValueFinfo
         &pathDistFromSoma,          // ReadOnlyValueFinfo
         &geomDistFromSoma,          // ReadOnlyValueFinfo
         &elecDistFromSoma,          // ReadOnlyValueFinfo
         &compartments,              // ReadOnlyValueFinfo
         &channelDistribution,       // ValueFinfo
         &passiveDistribution,       // ValueFinfo
         &spineDistribution,         // ValueFinfo
         // &mechSpec,               // ValueFinfo
         // &spineSpecification,     // ValueFinfo
         &compartmentsFromExpression,    // ReadOnlyLookupValueFinfo
         &valuesFromExpression,      // ReadOnlyLookupValueFinfo
         &spinesFromExpression,      // ReadOnlyLookupValueFinfo
         &spinesOnCompartment,       // ReadOnlyLookupValueFinfo
         &parentCompartmentOfSpine,  // ReadOnlyLookupValueFinfo
         &spineIdsFromCompartmentIds,    // ReadOnlyLookupValueFinfo
         &buildSegmentTree,          // DestFinfo
         &setSpineAndPsdMesh,        // DestFinfo
         &setSpineAndPsdDsolve,      // DestFinfo
         &spineFinfo,                // FieldElementFinfo
     };
     static string doc[] =
     {
         "Name", "Neuron",
         "Author", "C H Chaitanya, Upi Bhalla",
         "Description", "Neuron - Manager for neurons. "
         "Handles high-level specification of distribution of "
         "spines, channels and passive properties. Also manages "
         "spine resizing through a Spine FieldElement. ",
     };
     static Dinfo<Neuron> dinfo;
     static Cinfo neuronCinfo(
         "Neuron",
         Neutral::initCinfo(),
         neuronFinfos, sizeof( neuronFinfos ) / sizeof( Finfo* ),
         &dinfo,
         doc,
         sizeof(doc)/sizeof(string)
     );
 
     return &neuronCinfo;
 }

Here is the call graph for this function:

void Neuron::installMechanism	(	const string &	name,
		const vector< ObjId > &	elist,
		const vector< double > &	val,
		const vector< string > &	line
	)

void Neuron::installSpines	(	const vector< ObjId > &	elist,
		const vector< double > &	val,
		const vector< string > &	line
	)

Now fill in allSpinesPerCompt_ vector. First clear it out.

Definition at line 1974 of file Neuron.cpp.

References addSpine(), allSpinesPerCompt_, coordSystem(), makeAngleDistrib(), makeSizeDistrib(), makeSpacingDistrib(), psdStoich_, segId_, soma_, spineParentSegIndex_, spines_, spineStoich_, and spineToMeshOrdering_.

Referenced by setSpineDistribution().

 {
     Id spineProto( "/library/spine" );
 
     if ( spineProto == Id() )
     {
         cout << "Warning: Neuron::installSpines: Unable to find prototype spine: /library/spine\n";
         return;
     }
     // Look up elist index from pos index, since there may be many
     // spines on each segment.
     vector< unsigned int > elistIndex;
     vector< double > pos; // spacing of the new spines along compt.
     vector< double > theta; // Angle of spines
     vector< double > size; // Size scaling of spines
     pos.reserve( elist.size() );
     elistIndex.reserve( elist.size() );
 
     makeSpacingDistrib( elist, val,
                         spineParentSegIndex_, elistIndex, pos, line);
     makeAngleDistrib( elist, val, elistIndex, theta, line );
     makeSizeDistrib( elist, val, elistIndex, size, line );
     for ( unsigned int k = 0; k < spineParentSegIndex_.size(); ++k )
     {
         unsigned int i = spineParentSegIndex_[k];
         Vec x, y, z;
         coordSystem( soma_, segId_[i], x, y, z );
         spines_.push_back(
             addSpine( segId_[i], spineProto, pos[k], theta[k],
                       x, y, z, size[k], k )
         );
     }
     spineToMeshOrdering_.clear();
     spineToMeshOrdering_.resize( spines_.size(), 0 );
     spineStoich_.clear();
     spineStoich_.resize( spines_.size() );
     psdStoich_.clear();
     psdStoich_.resize( spines_.size() );
 
     allSpinesPerCompt_.clear();
     allSpinesPerCompt_.resize(segId_.size() );
     for ( unsigned int i = 0; i < spines_.size(); ++i )
     {
         assert( allSpinesPerCompt_.size() > spineParentSegIndex_[i] );
         vector< Id >& s = allSpinesPerCompt_[ spineParentSegIndex_[i] ];
         s.insert( s.end(), spines_[i].begin(), spines_[i].end() );
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

Spine * Neuron::lookupSpine ( unsigned int index )

Definition at line 2028 of file Neuron.cpp.

References spineEntry_.

Referenced by getSpineIdsFromCompartmentIds(), and initCinfo().

 {
     return &spineEntry_;
 }

Here is the caller graph for this function:

void Neuron::makeSpacingDistrib	(	const vector< ObjId > &	elist,
		const vector< double > &	val,
		vector< unsigned int > &	seglistIndex,
		vector< unsigned int > &	elistIndex,
		vector< double > &	pos,
		const vector< string > &	line
	)		const

Definition at line 1841 of file Neuron.cpp.

References addPos(), nuParser::eval(), nuParser::EXPR, findArg(), nuParser::numVal, segIndex_, and segs_.

Referenced by installSpines().

 {
     string distribExpr = findArg( line, "spacingDistrib"  );
     pos.resize( 0 );
     elistIndex.resize( 0 );
 
     try
     {
         nuParser parser( distribExpr );
 
         for ( unsigned int i = 0; i < elist.size(); ++i )
         {
             unsigned int j = i * nuParser::numVal;
             if ( val[ j + nuParser::EXPR ] > 0 )
             {
                 double spacing = val[ j + nuParser::EXPR ];
                 double spacingDistrib = parser.eval( val.begin() + j );
                 if ( spacingDistrib > spacing || spacingDistrib < 0 )
                 {
                     cout << "Warning: Neuron::makeSpacingDistrib: " <<
                          "0 < " << spacingDistrib << " < " << spacing <<
                          " fails on " << elist[i].path() << ". Using 0.\n";
                     spacingDistrib = 0.0;
                 }
                 map< Id, unsigned int>::const_iterator
                 lookupDend = segIndex_.find( elist[i] );
                 if ( lookupDend != segIndex_.end() )
                 {
                     double dendLength = segs_[lookupDend->second].length();
                     addPos( lookupDend->second, i,
                             spacing, spacingDistrib, dendLength,
                             seglistIndex, elistIndex, pos );
                 }
             }
         }
     }
     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:

void Neuron::parseMechSpec ( const Eref & e )

void Neuron::scaleBufAndRates	(	unsigned int	spineNum,
		double	lenScale,
		double	diaScale
	)		const

Definition at line 2055 of file Neuron.cpp.

References doubleEq(), psdStoich_, SetGet2< A1, A2 >::set(), spineStoich_, and spineToMeshOrdering_.

Referenced by Spine::setHeadDiameter(), Spine::setHeadLength(), and Spine::setHeadVolume().

 {
     double volScale = lenScale * diaScale * diaScale;
     if ( doubleEq( volScale, 1.0 ) )
         return;
     if ( spineStoich_.size() == 0 )
         // Perhaps no chem stuff in model, but user could have forgotten
         // to assign psd and spine meshes.
         return;
 
     if ( spineNum > spineStoich_.size() )
     {
         cout << "Error: Neuron::scaleBufAndRates: spineNum too big: " <<
              spineNum << " >= " << spineStoich_.size() << endl;
         return;
     }
     Id ss = spineStoich_[ spineNum ];
     if ( ss == Id() )
     {
         // The chem system for the spine may not have been defined.
         // Later figure out how to deal with cases where there is a psd
         // but no spine.
         return;
     }
     Id ps = psdStoich_[ spineNum ];
     if ( ps == Id() )
     {
         // The chem system for the spine may not have been defined.
         return;
     }
     SetGet2< unsigned int, double >::set( ss, "scaleBufsAndRates",
                                           spineToMeshOrdering_[spineNum], volScale );
     volScale = diaScale * diaScale;
     SetGet2< unsigned int, double >::set( ps, "scaleBufsAndRates",
                                           spineToMeshOrdering_[spineNum], volScale );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::scaleHeadDiffusion	(	unsigned int	spineNum,
		double	len,
		double	dia
	)		const

Scale the diffusion parameters due to a change in the head dimensions.

Definition at line 2106 of file Neuron.cpp.

References Field< A >::get(), headDsolve_, PI, psdDsolve_, SetGet2< A1, A2 >::set(), LookupField< L, A >::set(), and spineToMeshOrdering_.

Referenced by Spine::setHeadDiameter(), Spine::setHeadLength(), and Spine::setHeadVolume().

 {
     double vol = len * dia * dia * PI * 0.25;
     // Note that the diffusion scale for the PSD uses half the length
     // of the head compartment. I'm explicitly putting this in below.
     double diffScale = dia * dia * 0.25 * PI / (len/2.0);
     unsigned int meshIndex = spineToMeshOrdering_[ spineNum ];
     Id headCompt = Field< Id >::get( headDsolve_, "compartment" );
     LookupField< unsigned int, double >::set( headCompt, "oneVoxelVolume",
             meshIndex, vol );
     Id psdCompt = Field< Id >::get( psdDsolve_, "compartment" );
     double thick = Field< double >::get( psdCompt, "thickness" );
     double psdVol = thick * dia * dia * PI * 0.25;
     LookupField< unsigned int, double >::set( psdCompt, "oneVoxelVolume",
             meshIndex, psdVol );
     SetGet2< unsigned int, double >::set(
         headDsolve_, "setDiffVol1", meshIndex, vol );
     SetGet2< unsigned int, double >::set(
         psdDsolve_, "setDiffVol2", meshIndex, vol );
     SetGet2< unsigned int, double >::set(
         psdDsolve_, "setDiffVol1", meshIndex, psdVol );
     SetGet2< unsigned int, double >::set(
         psdDsolve_, "setDiffScale", meshIndex, diffScale );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::scaleShaftDiffusion	(	unsigned int	spineNum,
		double	len,
		double	dia
	)		const

Scale the diffusion parameters due to a change in the shaft dimensions.

Definition at line 2094 of file Neuron.cpp.

References headDsolve_, PI, SetGet2< A1, A2 >::set(), and spineToMeshOrdering_.

Referenced by Spine::setShaftDiameter(), and Spine::setShaftLength().

 {
     double diffScale = dia * dia * 0.25 * PI / len;
     SetGet2< unsigned int, double >::set(
         // Note that the buildNeuroMeshJunctions function is called
         // on the dendDsolve with the args smdsolve, pmdsolve.
         headDsolve_, "setDiffScale",
         spineToMeshOrdering_[ spineNum ], diffScale );
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::setChannelDistribution	(	const Eref &	e,
		vector< string >	v
	)

Definition at line 1132 of file Neuron.cpp.

References buildElist(), buildFromProto(), channelDistribution_, parseDistrib(), and setMechParams().

Referenced by initCinfo().

 {
     // Here we should clear the extant channels, if any.
     vector< vector< string > > lines;
     if ( parseDistrib( lines, v ) )
     {
         channelDistribution_ = v;
         for ( unsigned int i = 0; i < lines.size(); ++i )
         {
             vector< string >& temp = lines[i];
             vector< ObjId > elist;
             vector< double > val;
             buildElist( e, temp, elist, val );
 
             vector< ObjId > mech( elist.size() );
             if ( buildFromProto( temp[0], elist, val, mech ) )
             {
                 for ( unsigned int j = 2; j < temp.size(); j += 2 )
                 {
                     setMechParams( mech, elist, val, temp[j], temp[j+1] );
                 }
             }
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::setCM ( double v )

Definition at line 838 of file Neuron.cpp.

References CM_.

Referenced by initCinfo().

 {
     if ( v > 0.0 )
         CM_ = v;
     else
         cout << "Warning:: Neuron::setCM: value must be +ve, is " << v << endl;
 }

Here is the caller graph for this function:

void Neuron::setCompartmentLengthInLambdas ( double v )

Definition at line 895 of file Neuron.cpp.

References compartmentLengthInLambdas_.

Referenced by initCinfo().

 {
     compartmentLengthInLambdas_ = v;
 }

Here is the caller graph for this function:

void Neuron::setEm ( double v )

Definition at line 851 of file Neuron.cpp.

References Em_.

Referenced by initCinfo().

 {
     Em_ = v;
 }

Here is the caller graph for this function:

void Neuron::setNumSpines ( unsigned int num )

Ignore it. the number of spines is set when we build the tree.

Definition at line 2033 of file Neuron.cpp.

Referenced by initCinfo().

 {
     ;
 }

Here is the caller graph for this function:

void Neuron::setPassiveDistribution	(	const Eref &	e,
		vector< string >	v
	)

Definition at line 1163 of file Neuron.cpp.

References buildElist(), parseDistrib(), passiveDistribution_, and setCompartmentParams().

Referenced by initCinfo().

 {
     vector< vector< string > > lines;
     if ( parseDistrib( lines, v ) )
     {
         passiveDistribution_ = v;
         for ( unsigned int i = 0; i < lines.size(); ++i )
         {
             vector< string >& temp = lines[i];
             vector< ObjId > elist;
             vector< double > val;
             buildElist( e, temp, elist, val );
             for ( unsigned int j = 2; j < temp.size(); j += 2 )
             {
                 setCompartmentParams( elist, val, temp[j], temp[j+1] );
             }
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::setPhi ( double v )

Definition at line 872 of file Neuron.cpp.

References phi_.

Referenced by initCinfo().

 {
     phi_ = v;
     // Do stuff here for rotating it.
 }

Here is the caller graph for this function:

void Neuron::setRA ( double v )

Definition at line 826 of file Neuron.cpp.

References RA_.

Referenced by initCinfo().

 {
     if ( v > 0.0 )
         RA_ = v;
     else
         cout << "Warning:: Neuron::setRA: value must be +ve, is " << v << endl;
 }

Here is the caller graph for this function:

void Neuron::setRM ( double v )

Definition at line 814 of file Neuron.cpp.

References RM_.

Referenced by initCinfo().

 {
     if ( v > 0.0 )
         RM_ = v;
     else
         cout << "Warning:: Neuron::setRM: value must be +ve, is " << v << endl;
 }

Here is the caller graph for this function:

void Neuron::setSourceFile ( string v )

Definition at line 883 of file Neuron.cpp.

References sourceFile_.

Referenced by initCinfo().

 {
     sourceFile_ = v;
     // Stuff here for loading it.
 }

Here is the caller graph for this function:

void Neuron::setSpineAndPsdDsolve	(	Id	spineDsolve,
		Id	psdDsolve
	)

Definition at line 1462 of file Neuron.cpp.

References headDsolve_, and psdDsolve_.

Referenced by initCinfo().

 {
     headDsolve_ = spineDsolve;
     psdDsolve_ = psdDsolve;
 }

Here is the caller graph for this function:

void Neuron::setSpineAndPsdMesh	(	Id	spineMesh,
		Id	psdMesh
	)

Fills up vector of segments. First entry is soma.

Definition at line 1410 of file Neuron.cpp.

References Neutral::child(), Element::cinfo(), Id::element(), Id::eref(), Cinfo::isA(), Id::path(), psdStoich_, spines_, spineStoich_, and spineToMeshOrdering_.

Referenced by initCinfo().

 {
     if ( !spineMesh.element()->cinfo()->isA( "SpineMesh" ) )
     {
         cout << "Error: Neuron::setSpineAndPsdMesh: '" <<
              spineMesh.path() << "' is not a SpineMesh\n";
         return;
     }
     if ( !psdMesh.element()->cinfo()->isA( "PsdMesh" ) )
     {
         cout << "Error: Neuron::setSpineAndPsdMesh: '" <<
              psdMesh.path() << "' is not a PsdMesh\n";
         return;
     }
     Id spineStoich = Neutral::child( spineMesh.eref(), "stoich" );
     Id psdStoich = Neutral::child( psdMesh.eref(), "stoich" );
     if ( spineStoich == Id() || psdStoich == Id() )
     {
         cout << "Error: Neuron::setSpineAndPsdMesh: Stoich child not found\n";
         return;
     }
 
     vector< Id > spineList = Field< vector< Id > >::get(
                                  spineMesh, "elecComptList" );
     vector< Id > psdList = Field< vector< Id > >::get(
                                psdMesh, "elecComptList" );
     assert( spineList.size()== psdList.size() );
     map< Id, unsigned int > spineMap; // spineMap[ SpineOnNeuron ] = index
     for ( unsigned int i = 0; i < spines_.size(); ++i )
     {
         assert( spines_[i].size() > 1 );
         spineMap[ spines_[i][1] ] = i;
     }
     // We don't want to clear this because we can use a single vector
     // to overlay a number of spine meshes, since each will be a distinct
     // subset of the full list of spines. None is used twice.
     // spineToMeshOrdering_.clear();
     for( unsigned int i = 0; i < spineList.size(); ++i )
     {
         map< Id, unsigned int >::iterator j = spineMap.find( spineList[i]);
         if ( j == spineMap.end() )
         {
             cout << "Error: Neuron::setSpineAndPsdMesh: spine '" <<
                  spineList[i].path() << "' not found on Neuron\n";
             return;
         }
         spineToMeshOrdering_[ j->second ] = i;
         spineStoich_[ j->second ] = spineStoich;
         psdStoich_[ j->second ] = psdStoich;
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::setSpineDistribution	(	const Eref &	e,
		vector< string >	v
	)

Definition at line 1188 of file Neuron.cpp.

References buildElist(), installSpines(), parseDistrib(), and spineDistribution_.

Referenced by initCinfo().

 {
     // Here we should clear the extant spines, if any.
     vector< vector< string > > lines;
     if ( parseDistrib( lines, v ) )
     {
         spineDistribution_ = v;
         for ( unsigned int i = 0; i < lines.size(); ++i )
         {
             vector< ObjId > elist;
             vector< double > val;
             buildElist( e, lines[i], elist, val );
             installSpines( elist, val, lines[i] );
         }
     }
 }

Here is the call graph for this function:

Here is the caller graph for this function:

void Neuron::setTheta ( double v )

Definition at line 861 of file Neuron.cpp.

References theta_.

Referenced by initCinfo().

 {
     theta_ = v;
     // Do stuff here for rotating it.
 }

Here is the caller graph for this function:

const vector< Id > & Neuron::spineIds ( unsigned int index ) const

Definition at line 2047 of file Neuron.cpp.

References spines_.

Referenced by Spine::getHeadDiameter(), Spine::getHeadLength(), Spine::getShaftDiameter(), Spine::getShaftLength(), Spine::setHeadDiameter(), Spine::setHeadLength(), Spine::setHeadVolume(), Spine::setShaftDiameter(), and Spine::setShaftLength().

 {
     static vector< Id > fail;
     if ( index < spines_.size() )
         return spines_[index];
     return fail;
 }

Here is the caller graph for this function:

void Neuron::updateSegmentLengths ( )

Definition at line 1333 of file Neuron.cpp.

References Field< A >::get(), maxG_, maxL_, maxP_, segId_, segs_, soma_, and traverseCumulativeDistance().

Referenced by buildSegmentTree().

 {
     double len = Field< double >::get( soma_, "length" );
     double dia = Field< double >::get( soma_, "diameter" );
     if ( len < dia )
         len = dia;
     double Rm = Field< double >::get( soma_, "Rm" );
     double Ra = Field< double >::get( soma_, "Ra" );
     double L = sqrt( Ra / Rm );
 
     for ( unsigned int i = 0; i < segs_.size(); ++i )
     {
         segs_[i].setGeometricalDistanceFromSoma( segs_[0] );
     }
 
     traverseCumulativeDistance( segs_[0], segs_, segId_, len, L, 0, 0 );
     maxL_ = maxG_ = maxP_ = 0.0;
     for ( unsigned int i = 0; i < segs_.size(); ++i )
     {
         double p = segs_[i].getPathDistFromSoma();
         if ( maxP_ < p ) maxP_ = p;
         double g = segs_[i].getGeomDistFromSoma();
         if ( maxG_ < g ) maxG_ = g;
         double L = segs_[i].getElecDistFromSoma();
         if ( maxL_ < L ) maxL_ = L;
     }
 }