org.simbrain.network.connections

Class Radial

java.lang.Object

org.simbrain.network.connections.Sparse

org.simbrain.network.connections.Radial

All Implemented Interfaces:

ConnectNeurons

public class Radial
extends Sparse

This connection type makes four types of distance-based connection probabilistically.

1. Excitatory to Excitatory (EE)
2. Excitatory to Inhibitory (EI)
3. Inhibitory to Inhibitory (II)
4. Inhibitory to Excitatory (IE)

In each case, the probability of a connection is more likely the closer two neurons of the relevant type are to each other. Probabilities of connection are given by an exponential probability distribution e^-( D(a, b) / (λ^2) ) where D is distance in pixels. Lambda controls the number of pixels over which to expect connections to be made. Any of the 4 constants for the 4 cases can be set to a value between 0 and 1. Set to 0, if you want no connections of that type to be made. Set to 1 to have it make the most connections possible given the exponential distribution.

Author:

Zach Tosi

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
class	Radial.DensityEstimator

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_DIST_CONST For neurons with no polarity.
static double	DEFAULT_EE_CONST
static double	DEFAULT_EI_CONST
static double	DEFAULT_IE_CONST
static double	DEFAULT_II_CONST
static double	DEFAULT_LAMBDA

Fields inherited from class org.simbrain.network.connections.Sparse

connectionDensity, DEFAULT_CONNECTION_DENSITY, DEFAULT_FF_PREF, DEFAULT_SELF_CONNECT_PREF, selfConnectionAllowed

Constructor Summary

Constructors

Constructor and Description
Radial() Default constructor
Radial(double lambda)
Radial(double distConst, double lambda)
Radial(double eeDistConst, double eiDistConst, double ieDistConst, double iiDistConst, double lambda)

Method Summary

Modifier and Type	Method and Description
void	connectNeurons(SynapseGroup synGroup) Apply connection to a synapse group using specified parameters.
static java.util.List<Synapse>	connectRadialNoPolarity(java.util.List<Neuron> source, java.util.List<Neuron> target, double distConst, double lambda, boolean loose)
static java.util.List<Synapse>	connectRadialPolarized(java.util.List<Neuron> source, java.util.List<Neuron> target, double eeDistConst, double eiDistConst, double ieDistConst, double iiDistConst, double distConst, double lambda, boolean loose)
double	getDistConst()
double	getEeDistConst()
double	getEiDistConst()
double	getIeDistConst()
double	getIiDistConst()
double	getLambda()
void	setDistConst(double distConst)
void	setEeDistConst(double eeDistConst)
void	setEiDistConst(double eiDistConst)
void	setIeDistConst(double ieDistConst)
void	setIiDistConst(double iiDistConst)
void	setLambda(double lambda)
java.lang.String	toString()

Methods inherited from class org.simbrain.network.connections.Sparse

addToSparsity, connectSparse, connectSparse, getConnectionDensity, getMaxPossibleConnections, getName, getSynapseGroup, isEqualizeEfferents, isPermitDensityEditing, isSelfConnectionAllowed, randShuffleK, removeToSparsity, setConnectionDensity, setEqualizeEfferents, setPermitDensityEditing, setSelfConnectionAllowed

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

DEFAULT_DIST_CONST

public static final double DEFAULT_DIST_CONST

For neurons with no polarity.

See Also:

Constant Field Values

DEFAULT_EE_CONST

public static final double DEFAULT_EE_CONST

See Also:

Constant Field Values

DEFAULT_EI_CONST

public static final double DEFAULT_EI_CONST

See Also:

Constant Field Values

DEFAULT_IE_CONST

public static final double DEFAULT_IE_CONST

See Also:

Constant Field Values

DEFAULT_II_CONST

public static final double DEFAULT_II_CONST

See Also:

Constant Field Values

DEFAULT_LAMBDA

public static final double DEFAULT_LAMBDA

See Also:

Constant Field Values

Constructor Detail

Radial

public Radial()

Default constructor

Radial

public Radial(double lambda)

Parameters:

lambda - average connection distance.

Radial

public Radial(double distConst,
              double lambda)

Parameters:

distConst - the connection constant for general connections. Used in cases where neurons have no explicit polarity.

lambda - average connection distance.

Radial

public Radial(double eeDistConst,
              double eiDistConst,
              double ieDistConst,
              double iiDistConst,
              double lambda)

Parameters:

eeDistConst - the connection constant for connections between 2 excitatoy neurons

eiDistConst - the connection constant for connection from an excitatory to an inhibitory neuron.

ieDistConst - the connectino constant for connection from an inhibitory to an excitatory neuron.

iiDistConst - the conneciton constant for connections between 2 inhibitory neurons.

lambda - average connection distance.

Method Detail

connectRadialPolarized

public static java.util.List<Synapse> connectRadialPolarized(java.util.List<Neuron> source,
                                                             java.util.List<Neuron> target,
                                                             double eeDistConst,
                                                             double eiDistConst,
                                                             double ieDistConst,
                                                             double iiDistConst,
                                                             double distConst,
                                                             double lambda,
                                                             boolean loose)

Parameters:

source - the source neurons.

target - the target neurons.

eeDistConst - the connection constant for connections between 2 excitatory neurons.

eiDistConst - the connection constant for connection from an excitatory to an inhibitory neuron.

ieDistConst - the connection constant for connection from an inhibitory to an excitatory neuron.

iiDistConst - the connection constant for connections between 2 inhibitory neurons.

distConst - the connection constant for general connections. Used in cases where neurons have no explicit polarity.

lambda - average connection distance.

loose -

Returns:

synapses

connectRadialNoPolarity

public static java.util.List<Synapse> connectRadialNoPolarity(java.util.List<Neuron> source,
                                                              java.util.List<Neuron> target,
                                                              double distConst,
                                                              double lambda,
                                                              boolean loose)

Parameters:

source - the source neurons

target - the target neurons

distConst - the connection constant for general connections. Used in cases where neurons have no explicit polarity.

lambda - average connection distance.

loose -

Returns:

array of synapses

connectNeurons

public void connectNeurons(SynapseGroup synGroup)

Apply connection to a synapse group using specified parameters. Specifically: Connects neurons based on a probability function related to their distance from one another, which exponentially decays with distance.

Specified by:

connectNeurons in interface ConnectNeurons

Overrides:

connectNeurons in class Sparse

Parameters:

synGroup - The synapse group that the connections this class will generate will be added to.

toString

public java.lang.String toString()

Overrides:

toString in class Sparse

getEeDistConst

public double getEeDistConst()

setEeDistConst

public void setEeDistConst(double eeDistConst)

getEiDistConst

public double getEiDistConst()

setEiDistConst

public void setEiDistConst(double eiDistConst)

getIeDistConst

public double getIeDistConst()

setIeDistConst

public void setIeDistConst(double ieDistConst)

getIiDistConst

public double getIiDistConst()

setIiDistConst

public void setIiDistConst(double iiDistConst)

getDistConst

public double getDistConst()

setDistConst

public void setDistConst(double distConst)

getLambda

public double getLambda()

setLambda

public void setLambda(double lambda)