org.simbrain.network.connections

Class Sparse

java.lang.Object

org.simbrain.network.connections.Sparse

All Implemented Interfaces:

ConnectNeurons

Direct Known Subclasses:

Radial, RadialSimpleConstrainedKIn

public class Sparse
extends java.lang.Object
implements ConnectNeurons

A superclass for all connectors whose primary parameter is related to base connection density, taking no other major factors into account insofar as selecting which neurons should be connected goes.

Author:

Zach Tosi

Field Summary

Fields

Modifier and Type	Field and Description
protected double	connectionDensity Generally speaking the connectionDensity parameter represents a probability reflecting how many possible connections between a given source neuron and all available target neurons will actually be made.
static double	DEFAULT_CONNECTION_DENSITY The default sparsity (between 0 and 1).
static boolean	DEFAULT_FF_PREF Sets the default behavior concerning whether or not the number of efferents of each source neurons should be equalized.
static boolean	DEFAULT_SELF_CONNECT_PREF The default preference as to whether or not self connections are allowed.
protected boolean	selfConnectionAllowed Whether or not connections where the source and target are the same neuron are allowed.

Constructor Summary

Constructors

Constructor and Description
Sparse() Default constructor.
Sparse(double sparsity, boolean equalizeEfferents, boolean selfConnectionAllowed) Construct a sparse object from main arguments.

Method Summary

Modifier and Type	Method and Description
void	addToSparsity(double newSparsity)
void	connectNeurons(SynapseGroup synapseGroup) Apply connection to a synapse group using specified parameters.
java.util.List<Synapse>	connectSparse(java.util.List<Neuron> sourceNeurons, java.util.List<Neuron> targetNeurons) Connect source to target neurons using this instance of the sparse object's properties to set all parameters of the connections.
static java.util.List<Synapse>	connectSparse(java.util.List<Neuron> sourceNeurons, java.util.List<Neuron> targetNeurons, double sparsity, boolean selfConnectionAllowed, boolean equalizeEfferents, boolean looseSynapses) Connects two lists of neurons with synapses assigning connections between source and target neurons randomly in such a way that results in "sparsity" percentage of possible connections being created.
double	getConnectionDensity()
int	getMaxPossibleConnections()
static java.lang.String	getName() Returns a short name for this connection type, used in combo boxes.
SynapseGroup	getSynapseGroup()
boolean	isEqualizeEfferents()
boolean	isPermitDensityEditing()
boolean	isSelfConnectionAllowed()
static void	randShuffleK(java.util.ArrayList<java.lang.Integer> inds, int k, java.util.Random rand) Randomly shuffles k integers in a list.
void	removeToSparsity(double newSparsity)
void	setConnectionDensity(double connectionDensity) Set how dense the connections are between source and target neurons, generally speaking the connectionDensity parameter represents a probability reflecting how many possible connections between a given source neuron and all available target neurons will actually be made.
void	setEqualizeEfferents(boolean equalizeEfferents)
void	setPermitDensityEditing(boolean permitDensityEditing)
void	setSelfConnectionAllowed(boolean selfConnectionAllowed) Set whether or not self connections (connections where the source and target neuron are the same neuron) are allowed.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_SELF_CONNECT_PREF

public static boolean DEFAULT_SELF_CONNECT_PREF

The default preference as to whether or not self connections are allowed.

DEFAULT_FF_PREF

public static boolean DEFAULT_FF_PREF

Sets the default behavior concerning whether or not the number of efferents of each source neurons should be equalized.

DEFAULT_CONNECTION_DENSITY

public static double DEFAULT_CONNECTION_DENSITY

The default sparsity (between 0 and 1).

connectionDensity

protected double connectionDensity

Generally speaking the connectionDensity parameter represents a probability reflecting how many possible connections between a given source neuron and all available target neurons will actually be made.

selfConnectionAllowed

protected boolean selfConnectionAllowed

Whether or not connections where the source and target are the same neuron are allowed. Only applicable if the source and target neuron sets are the same.

Constructor Detail

Sparse

public Sparse()

Default constructor.

Sparse

public Sparse(double sparsity,
              boolean equalizeEfferents,
              boolean selfConnectionAllowed)

Construct a sparse object from main arguments. Used in scripts.

Parameters:

sparsity - sparsity level

equalizeEfferents - whether to equalize efferents

selfConnectionAllowed - whether self-connections should be allowed.

Method Detail

connectSparse

public java.util.List<Synapse> connectSparse(java.util.List<Neuron> sourceNeurons,
                                             java.util.List<Neuron> targetNeurons)

Connect source to target neurons using this instance of the sparse object's properties to set all parameters of the connections.

Parameters:

sourceNeurons - the source neurons

targetNeurons - the target neurons

Returns:

the newly creates synapses connecting source to target

connectSparse

public static java.util.List<Synapse> connectSparse(java.util.List<Neuron> sourceNeurons,
                                                    java.util.List<Neuron> targetNeurons,
                                                    double sparsity,
                                                    boolean selfConnectionAllowed,
                                                    boolean equalizeEfferents,
                                                    boolean looseSynapses)

Connects two lists of neurons with synapses assigning connections between source and target neurons randomly in such a way that results in "sparsity" percentage of possible connections being created.

Parameters:

sourceNeurons - source neurons

targetNeurons - target neurons

sparsity - sparsity of connection

selfConnectionAllowed - whether to allow self-connections

equalizeEfferents - whether or not the number of efferents of each source neurons should be equalized.

looseSynapses - are these loose synapses

Returns:

the new synapses

connectNeurons

public void connectNeurons(SynapseGroup synapseGroup)

Description copied from interface: ConnectNeurons

Apply connection to a synapse group using specified parameters.

Specified by:

connectNeurons in interface ConnectNeurons

Parameters:

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

randShuffleK

public static void randShuffleK(java.util.ArrayList<java.lang.Integer> inds,
                                int k,
                                java.util.Random rand)

Randomly shuffles k integers in a list. The first k elements are randomly swapped with other elements in the list. This method will alter the list passed to it, so situations where this would be undesirable should pass this method a copy.

Parameters:

inds - a list of integers. This methods WILL shuffle inds, so pass a copy unless inds being shuffled is not a problem.

k - how many elements will be shuffled

rand - a random number generator

removeToSparsity

public void removeToSparsity(double newSparsity)

Parameters:

newSparsity - new sparsity connection

addToSparsity

public void addToSparsity(double newSparsity)

Parameters:

newSparsity - new sparsity connection

getMaxPossibleConnections

public int getMaxPossibleConnections()

isEqualizeEfferents

public boolean isEqualizeEfferents()

setEqualizeEfferents

public void setEqualizeEfferents(boolean equalizeEfferents)

isPermitDensityEditing

public boolean isPermitDensityEditing()

setPermitDensityEditing

public void setPermitDensityEditing(boolean permitDensityEditing)

getConnectionDensity

public double getConnectionDensity()

setConnectionDensity

public void setConnectionDensity(double connectionDensity)

Set how dense the connections are between source and target neurons, generally speaking the connectionDensity parameter represents a probability reflecting how many possible connections between a given source neuron and all available target neurons will actually be made.

Parameters:

connectionDensity -

isSelfConnectionAllowed

public boolean isSelfConnectionAllowed()

Returns:

whether or not self connections (connections where the source and target neuron are the same neuron) are allowed.

setSelfConnectionAllowed

public void setSelfConnectionAllowed(boolean selfConnectionAllowed)

Set whether or not self connections (connections where the source and target neuron are the same neuron) are allowed.

Parameters:

selfConnectionAllowed - Connections are allowed to connect to themselves.

getSynapseGroup

public SynapseGroup getSynapseGroup()

Returns:

the synapse group tied to this sparse object.

getName

public static java.lang.String getName()

Returns a short name for this connection type, used in combo boxes.

Returns:

the name for this connection type

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object