org.simbrain.network.connections

Class ConnectionUtilities

java.lang.Object

org.simbrain.network.connections.ConnectionUtilities

public class ConnectionUtilities
extends java.lang.Object

A set of static utility functions/interfaces/etc for manipulating synapses. Usually, for manipulating loose synapses since most changes to Synapses in a synapse group should be done through the synapse group, but there are counter-examples. TODO: Make synapse group use more of these functions.

Author:

Zach Tosi

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static interface	ConnectionUtilities.SynapseParameterGetter<T> A functional interface that is intended to check/return the value of some parameter(s) of a(some) synapse(s).
static interface	ConnectionUtilities.SynapseParameterSetter<T> A functional interface that is intended to be used to set some parameter of the synapse to the specified value.

Field Summary

Fields

Modifier and Type	Field and Description
static double	DEFAULT_EXCITATORY_STRENGTH The default excitatory strength.
static double	DEFAULT_INHIBITORY_STRENGTH The default inhibitory strength.

Constructor Summary

Constructors

Constructor and Description
ConnectionUtilities()

Method Summary

Modifier and Type	Method and Description
static void	applyLearningRules(SynapseUpdateRule exciteRule, SynapseUpdateRule inhibRule, java.util.List<Synapse> synapses)
static void	conformToTemplates(java.util.Collection<Synapse> synapses, Synapse exTemplateSynapse, Synapse inTemplateSynapse) Makes the synapses in the given collection conform to the parameters of the given template synapses, which are essentially information ferries.
static java.util.ArrayList<Synapse>	getExcitatorySynapses(java.util.Collection<Synapse> synapses)
static java.util.ArrayList<Synapse>	getInhibitorySynapses(java.util.Collection<Synapse> synapses)
static void	polarizeSynapses(java.util.Collection<Synapse> synapses, double excitatoryRatio) Changes all the synapses in a given collection such that excitatoryRatio of them are excitatory and 1 - excitatoryRatio of them are inhibitory, assigning default strengths respectively to each.
static void	randomizeAndPolarizeSynapses(java.util.Collection<Synapse> synapses, double excitatoryRatio) Randomize and polarize synapses using default excitatory and inhibitory polarizers (uniform 0 to 1).
static void	randomizeAndPolarizeSynapses(java.util.Collection<Synapse> synapses, PolarizedRandomizer exciteRand, PolarizedRandomizer inhibRand, double excitatoryRatio) Randomizes a collection of synapses based on excitatory and inhibitory (polarized appropriately) randomizers, which cannot be the same randomizer.
static void	randomizeExcitatorySynapses(java.util.Collection<Synapse> synapses, PolarizedRandomizer exciteRand) Randomizes the excitatory synapses in the given list of synapses using the given excitatory randomizer.
static void	randomizeExcitatorySynapsesUnsafe(java.util.Collection<Synapse> synapses, PolarizedRandomizer exciteRand) Randomizes the given synapses using the given excitatory randomizer without checking first to make sure that the given synapses or their source neurons are not inhibitory.
static void	randomizeInhibitorySynapses(java.util.Collection<Synapse> synapses, PolarizedRandomizer inhibRand) Randomizes the inhibitory synapses in the given list of synapses using the given inhibitory randomizer.
static void	randomizeInhibitorySynapsesUnsafe(java.util.Collection<Synapse> synapses, PolarizedRandomizer inhibRand) Randomizes the given synapses using the given inhibitory randomizer without checking first to make sure that the given synapses or their source neurons are not excitatory.
static void	randomizeSynapses(java.util.Collection<Synapse> synapses, PolarizedRandomizer exciteRand, PolarizedRandomizer inhibRand)
static boolean	testRecurrence(java.util.List<Neuron> sourceNeurons, java.util.List<Neuron> targetNeurons) Tests whether or not these connections are recurrent, that is, whether or not the neurons in the source list are the same as those in the target list.

Methods inherited from class java.lang.Object

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

Field Detail

DEFAULT_EXCITATORY_STRENGTH

public static final double DEFAULT_EXCITATORY_STRENGTH

The default excitatory strength.

See Also:

Constant Field Values

DEFAULT_INHIBITORY_STRENGTH

public static final double DEFAULT_INHIBITORY_STRENGTH

The default inhibitory strength.

See Also:

Constant Field Values

Constructor Detail

ConnectionUtilities

public ConnectionUtilities()

Method Detail

randomizeAndPolarizeSynapses

public static void randomizeAndPolarizeSynapses(java.util.Collection<Synapse> synapses,
                                                PolarizedRandomizer exciteRand,
                                                PolarizedRandomizer inhibRand,
                                                double excitatoryRatio)
                                         throws java.lang.IllegalArgumentException

Randomizes a collection of synapses based on excitatory and inhibitory (polarized appropriately) randomizers, which cannot be the same randomizer. This method will always attempt to maintain the ratio of excitatory synapses specified. However if some of the source neurons are themselves polarized, this may not always be possible. In such a case, this method will get as close as possible to the desired ratio. This, however is not recommended. If the source neurons to these synapses are themselves, by and large, polarized, this method can be, but should NOT be used. Null values for either PolarizedRandomizer is permitted. Synapses are assigned default strengths based on their polarity depending on which randomizers are null.

Parameters:

exciteRand - the randomizer to be used to determine the weights of excitatory synapses.

inhibRand - the randomizer to be used to determine the weights of inhibitory synapses.

excitatoryRatio - the ration of excitatory to inhibitory synapses.

synapses - the synapses to modify

Throws:

java.lang.IllegalArgumentException

randomizeAndPolarizeSynapses

public static void randomizeAndPolarizeSynapses(java.util.Collection<Synapse> synapses,
                                                double excitatoryRatio)

Randomize and polarize synapses using default excitatory and inhibitory polarizers (uniform 0 to 1). See randomizeAndPolarizeSynapses(Collection, PolarizedRandomizer, PolarizedRandomizer, double)

Parameters:

synapses - the synapses to modify

excitatoryRatio - the ration of excitatory to inhibitory synapses.

randomizeSynapses

public static void randomizeSynapses(java.util.Collection<Synapse> synapses,
                                     PolarizedRandomizer exciteRand,
                                     PolarizedRandomizer inhibRand)

Parameters:

synapses - the synapses to modify

exciteRand - the randomizer to be used to determine the weights of excitatory synapses.

inhibRand - the randomizer to be used to determine the weights of inhibitory synapses.

randomizeExcitatorySynapses

public static void randomizeExcitatorySynapses(java.util.Collection<Synapse> synapses,
                                               PolarizedRandomizer exciteRand)

Randomizes the excitatory synapses in the given list of synapses using the given excitatory randomizer.

Parameters:

synapses - the synapses to modify

exciteRand - the randomizer to be used to determine the weights of excitatory synapses.

randomizeExcitatorySynapsesUnsafe

public static void randomizeExcitatorySynapsesUnsafe(java.util.Collection<Synapse> synapses,
                                                     PolarizedRandomizer exciteRand)

Randomizes the given synapses using the given excitatory randomizer without checking first to make sure that the given synapses or their source neurons are not inhibitory. Used for speed when the polarity of the synapses in the list is known ahead of time.

Parameters:

synapses - the synapses to modify

exciteRand - the randomizer to be used to determine the weights of excitatory synapses.

randomizeInhibitorySynapses

public static void randomizeInhibitorySynapses(java.util.Collection<Synapse> synapses,
                                               PolarizedRandomizer inhibRand)

Randomizes the inhibitory synapses in the given list of synapses using the given inhibitory randomizer.

Parameters:

synapses - the synapses to modify

inhibRand - the randomizer to be used to determine the weights of inhibitory synapses.

randomizeInhibitorySynapsesUnsafe

public static void randomizeInhibitorySynapsesUnsafe(java.util.Collection<Synapse> synapses,
                                                     PolarizedRandomizer inhibRand)

Randomizes the given synapses using the given inhibitory randomizer without checking first to make sure that the given synapses or their source neurons are not excitatory. Used for speed when the polarity of the synapses in the list is known ahead of time.

Parameters:

synapses - the synapses to modify

inhibRand - the randomizer to be used to determine the weights of inhibitory synapses.

getExcitatorySynapses

public static java.util.ArrayList<Synapse> getExcitatorySynapses(java.util.Collection<Synapse> synapses)

Parameters:

synapses - the synapses to modify

Returns:

excitatory synapses

getInhibitorySynapses

public static java.util.ArrayList<Synapse> getInhibitorySynapses(java.util.Collection<Synapse> synapses)

Parameters:

synapses - the synapses to modify

Returns:

inhibitory synapses

polarizeSynapses

public static void polarizeSynapses(java.util.Collection<Synapse> synapses,
                                    double excitatoryRatio)

Changes all the synapses in a given collection such that excitatoryRatio of them are excitatory and 1 - excitatoryRatio of them are inhibitory, assigning default strengths respectively to each. This method will attempt to maintain the requested excitatoryRatio even if some or all of the source neurons are themselves polarized. In such cases the polarity of the Neurons efferent synapses will not be overridden. Though it may not be possible to obtain the desired excitatoryRatio in this case, this method will get as close as possible.

Parameters:

synapses - the synapses to polarize

excitatoryRatio - the ration of excitatory synapses (1 for all exctitatory)

conformToTemplates

public static void conformToTemplates(java.util.Collection<Synapse> synapses,
                                      Synapse exTemplateSynapse,
                                      Synapse inTemplateSynapse)

Makes the synapses in the given collection conform to the parameters of the given template synapses, which are essentially information ferries. Throws an exception if the template synapses do not match the appropriate polarities implied by their names.

Parameters:

synapses - the synpases to modify

exTemplateSynapse - temporary set containing all excitatory synapses

inTemplateSynapse - temporary set containing all inhibitory synapses

testRecurrence

public static boolean testRecurrence(java.util.List<Neuron> sourceNeurons,
                                     java.util.List<Neuron> targetNeurons)

Tests whether or not these connections are recurrent, that is, whether or not the neurons in the source list are the same as those in the target list.

Parameters:

sourceNeurons - the starting neurons

targetNeurons - the targeted neurons

Returns:

true or false: whether or not these connections are recurrent.

applyLearningRules

public static void applyLearningRules(SynapseUpdateRule exciteRule,
                                      SynapseUpdateRule inhibRule,
                                      java.util.List<Synapse> synapses)

Parameters:

exciteRule -

inhibRule -

synapses -