Synapse (Simbrain API)

java.lang.Object
- org.simbrain.network.core.Synapse

```
public class Synapse
extends java.lang.Object
```
Synapse objects represent "connections" between neurons, which learn (grow or weaken) based on various factors, including the activation level of connected neurons.

Author:

Jeff Yoshimi, Zach Tosi

Constructor Summary

Constructors
Constructor and Description
`Synapse(Network newParent, Neuron source, Neuron target, SynapseUpdateRule learningRule)` Construct a synapse using a source and target neuron, and a specified learning rule and parent network
`Synapse(Network newParent, Neuron source, Neuron target, SynapseUpdateRule learningRule, Synapse templateSynapse)` Construct a synapse using a source and target neuron, and a specified learning rule.
`Synapse(Network newParent, Synapse synapse)` Copy a synapse with a specified new parent.
`Synapse(Neuron source, Neuron target)` Construct a synapse using a source and target neuron, defaulting to ClampedSynapse and assuming the parent of the source neuron is the parent of this synapse.
`Synapse(Neuron source, Neuron target, double initialStrength)` Construct a synapse with a specified initial strength.
`Synapse(Neuron source, Neuron target, SynapseUpdateRule learningRule)` Construct a synapse using a source and target neuron, and a specified learning rule.
`Synapse(Neuron source, Neuron target, SynapseUpdateRule learningRule, Network parent)` Construct a synapse using a source and target neuron, and a specified learning rule.
`Synapse(Synapse s)` Copy constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`double`	`calcPSR()` For spiking source neurons, returns the spike-responder's value times the synapse strength.
`double`	`calcWeightedSum()` For non-spiking neurons returns the weighted sum, i.e.
`void`	`checkBounds()` If weight value is above or below its bounds set it to those bounds.
`double`	`clip(double value)` Utility function for use in learning rules.
`static Synapse`	`copyTemplateSynapse(Synapse s)` Makes a deep copy of a template synapse (one with no source or target).
`void`	`decay(double decayPercent)` Decay this synapse by the indicated percentage.
`void`	`decodeNumericByteArray(java.nio.ByteBuffer byteValues)`
`void`	`decrementWeight()` Decrement this weight by increment.
`void`	`forceSetStrength(double wt)`
`int`	`getDelay()`
`java.lang.String`	`getId()`
`double`	`getIncrement()`
`SynapseUpdateRule`	`getLearningRule()`
`double`	`getLowerBound()`
`Network`	`getNetwork()` Convenience method for getting a reference to the parent root network.
`byte[]`	`getNumericValuesAsByteArray()`
`SynapseGroup`	`getParentGroup()`
`Network`	`getParentNetwork()`
`double`	`getPsr()`
`static java.util.List<SynapseUpdateRule>`	`getRuleList(java.util.Collection<Synapse> synapseCollection)` A method which takes in a collection of synapses and returns a list of their update rules in the order in which they appear in the original collection, if that collection supports a consistent order.
`Neuron`	`getSource()`
`SpikeResponder`	`getSpikeResponder()`
`double`	`getStrength()`
`Synapse`	`getSymmetricSynapse()` Returns symmetric synapse if there is one, null otherwise.
`Neuron`	`getTarget()`
`static Synapse`	`getTemplateSynapse()` Returns a "template" synapse.
`static Synapse`	`getTemplateSynapse(SynapseUpdateRule rule)` Returns a template synapse with a specified learning rule.
`java.lang.String`	`getToolTipText()` Returns string for tool tip or short description.
`java.lang.String`	`getType()` The name of the learning rule of the synapse; it's "type".
`double`	`getUpperBound()`
`void`	`incrementWeight()` Increment this weight by increment.
`void`	`initSpikeResponder()` Set a default spike responder if the source neuron is a spiking neuron, else set the spikeResponder to null.
`Synapse`	`instantiateTemplateSynapse(Neuron source, Neuron target, Network parent)` A template synapse is a synapse that has no proper references, but is used for setting properties.
`boolean`	`isEnabled()` Whether this synapse is enabled or not.
`boolean`	`isFrozen()`
`void`	`postUnmarshallingInit()` Called after a synapse is de-serialized, to repopulate fan-in and fan-out lists.
`void`	`randomize()` Randomize this weight to a value between its upper and lower bounds.
`void`	`randomizeSymmetric()` Randomizes this synapse and sets the symmetric analogue to the same value.
`void`	`reinforce()` Increase the absolute value of this weight by increment amount.
`void`	`setDelay(int dly)` Delay manager.
`void`	`setEnabled(boolean enabled)` A better name than setSendWeightedInput.
`void`	`setFrozen(boolean frozen)`
`void`	`setId(java.lang.String id)`
`void`	`setIncrement(double d)` Sets the amount to increment neuron.
`void`	`setLearningRule(SynapseUpdateRule newLearningRule)` Change this synapse's learning rule.
`void`	`setLowerBound(double d)` Sets the lower synapse bound.
`void`	`setParentGroup(SynapseGroup parentGroup)`
`void`	`setPsr(double psr)`
`void`	`setSpikeResponder(SpikeResponder sr)`
`void`	`setStrength(double wt)` Sets the strength of the synapse.
`void`	`setUpperBound(double d)` Sets the upper synapse bound.
`java.lang.String`	`toString()`
`void`	`update()` Update this synapse using its current learning rule.
`void`	`weaken()` Decrease the absolute value of this weight by increment amount.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - Synapse
```
public Synapse(Neuron source,
               Neuron target)
```
    Construct a synapse using a source and target neuron, defaulting to ClampedSynapse and assuming the parent of the source neuron is the parent of this synapse.
    
    Parameters:
    
    source - source neuron
    
    target - target neuron
  - Synapse
```
public Synapse(Neuron source,
               Neuron target,
               double initialStrength)
```
    Construct a synapse with a specified initial strength.
    
    Parameters:
    
    source - source neuron
    
    target - target neuron
    
    initialStrength - initial strength for synapse
  - Synapse
```
public Synapse(Network newParent,
               Neuron source,
               Neuron target,
               SynapseUpdateRule learningRule)
```
    Construct a synapse using a source and target neuron, and a specified learning rule and parent network
    
    Parameters:
    
    newParent - new parent network for this synapse.
    
    source - source neuron
    
    target - target neuron
    
    learningRule - update rule for this synapse
  - Synapse
```
public Synapse(Neuron source,
               Neuron target,
               SynapseUpdateRule learningRule)
```
    Construct a synapse using a source and target neuron, and a specified learning rule. Assumes the parent network is the same as the parent network of the provided source neuron.
    
    Parameters:
    
    source - source neuron
    
    target - target neuron
    
    learningRule - update rule for this synapse
  - Synapse
```
public Synapse(Network newParent,
               Neuron source,
               Neuron target,
               SynapseUpdateRule learningRule,
               Synapse templateSynapse)
```
    Construct a synapse using a source and target neuron, and a specified learning rule. Assumes the parent network is the same as the parent network of the provided source neuron.
    
    Parameters:
    
    newParent - new parent network for this synapse. Used when copying and pasting to new network.
    
    source - source neuron
    
    target - target neuron
    
    learningRule - update rule for this synapse
    
    templateSynapse - synapse with parameters to copy
  - Synapse
```
public Synapse(Neuron source,
               Neuron target,
               SynapseUpdateRule learningRule,
               Network parent)
```
    Construct a synapse using a source and target neuron, and a specified learning rule.
    
    Parameters:
    
    source - source neuron
    
    target - target neuron
    
    learningRule - update rule for this synapse
    
    parent - parent network for this synapse.
  - Synapse
```
public Synapse(Network newParent,
               Synapse synapse)
```
    Copy a synapse with a specified new parent.
    
    Parameters:
    
    newParent - new parent network
    
    synapse - synapse to copy
  - Synapse
```
public Synapse(Synapse s)
```
    Copy constructor.
    
    Parameters:
    
    s - Synapse to used as a template for constructing a new synapse.
- Method Detail
  - copyTemplateSynapse
```
public static Synapse copyTemplateSynapse(Synapse s)
```
    Makes a deep copy of a template synapse (one with no source or target).
    
    Parameters:
    
    s - the synapse to copy
    
    Returns:
    
    a new synapse with all the same variable valueas as the original
  - initSpikeResponder
```
public void initSpikeResponder()
```
    Set a default spike responder if the source neuron is a spiking neuron, else set the spikeResponder to null.
  - update
```
public void update()
```
    Update this synapse using its current learning rule.
  - calcPSR
```
public double calcPSR()
```
    For spiking source neurons, returns the spike-responder's value times the synapse strength. For non-spiking neurons, returns the pre-synaptic activation times the synapse strength.
    
    Returns:
    
    the post-synaptic response as determined by a spike responder.
  - calcWeightedSum
```
public double calcWeightedSum()
```
    For non-spiking neurons returns the weighted sum, i.e. the activation of the pre-synaptic (source) neuron multiplied by the strength of this synapse.
    
    Returns:
    
    the post synaptic response calculated as a simple weighted sum
  - getType
```
public java.lang.String getType()
```
    The name of the learning rule of the synapse; it's "type". Used via reflection for consistency checking in the gui. (Open multiple synapses and if they are of the different types the dialog is different).
    
    Returns:
    
    the name of the class of this network.
  - getSource
```
public Neuron getSource()
```
    Returns:
    
    Source neuron to which the synapse is attached.
  - getTarget
```
public Neuron getTarget()
```
    Returns:
    
    Target neuron to which the synapse is attached.
  - getStrength
```
public final double getStrength()
```
    Returns:
    
    Strength of synapse.
  - setStrength
```
public void setStrength(double wt)
```
    Sets the strength of the synapse.
    
    Parameters:
    
    wt - Strength value
  - forceSetStrength
```
public void forceSetStrength(double wt)
```
    Parameters:
    
    wt - the value to set the strength of the synapse to
  - getUpperBound
```
public double getUpperBound()
```
    Returns:
    
    Upper synapse bound.
  - setUpperBound
```
public void setUpperBound(double d)
```
    Sets the upper synapse bound.
    
    Parameters:
    
    d - bound
  - getLowerBound
```
public double getLowerBound()
```
    Returns:
    
    Lower synapse bound.
  - setLowerBound
```
public void setLowerBound(double d)
```
    Sets the lower synapse bound.
    
    Parameters:
    
    d - bound
  - getIncrement
```
public double getIncrement()
```
    Returns:
    
    Amount to increment neuron.
  - setIncrement
```
public void setIncrement(double d)
```
    Sets the amount to increment neuron.
    
    Parameters:
    
    d - Increment amount
  - incrementWeight
```
public void incrementWeight()
```
    Increment this weight by increment.
  - decrementWeight
```
public void decrementWeight()
```
    Decrement this weight by increment.
  - reinforce
```
public void reinforce()
```
    Increase the absolute value of this weight by increment amount.
  - weaken
```
public void weaken()
```
    Decrease the absolute value of this weight by increment amount.
  - randomizeSymmetric
```
public void randomizeSymmetric()
```
    Randomizes this synapse and sets the symmetric analogue to the same value. A bit of a hack, since it it is used on a collection a bunch of redundancy could happen.
  - getToolTipText
```
public java.lang.String getToolTipText()
```
    Returns string for tool tip or short description.
    
    Returns:
    
    tool tip text
  - getSymmetricSynapse
```
public Synapse getSymmetricSynapse()
```
    Returns symmetric synapse if there is one, null otherwise.
    
    Returns:
    
    the symmetric synapse, if any.
  - randomize
```
public void randomize()
```
    Randomize this weight to a value between its upper and lower bounds.
  - checkBounds
```
public void checkBounds()
```
    If weight value is above or below its bounds set it to those bounds.
  - clip
```
public double clip(double value)
```
    Utility function for use in learning rules. If value is above or below the bounds of this synapse set it to those bounds.
    
    Parameters:
    
    value - Value to be checked
    
    Returns:
    
    Evaluated value
  - getId
```
public java.lang.String getId()
```
    Returns:
    
    Returns the id.
  - setId
```
public void setId(java.lang.String id)
```
    Parameters:
    
    id - The id to set.
  - getSpikeResponder
```
public SpikeResponder getSpikeResponder()
```
    Returns:
    
    Returns the spikeResponder.
  - setSpikeResponder
```
public void setSpikeResponder(SpikeResponder sr)
```
    Parameters:
    
    sr - The spikeResponder to set.
  - setDelay
```
public void setDelay(int dly)
```
    Delay manager.
    
    Parameters:
    
    dly - Amount of delay
  - getDelay
```
public int getDelay()
```
    Returns:
    
    Current amount of delay.
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object
  - getParentNetwork
```
public Network getParentNetwork()
```
    Returns:
    
    Returns the parent.
  - setEnabled
```
public void setEnabled(boolean enabled)
```
    A better name than setSendWeightedInput. Forwarding to setSendWeightedInput for now. Possibly change name for 3.0. have not done so yet so as note to break a bunch of simulations.
    
    Parameters:
    
    enabled - true if enabled, false otherwise.
  - isEnabled
```
public boolean isEnabled()
```
    Whether this synapse is enabled or not.
    
    Returns:
    
    true if enabled, false otherwise.
  - getNetwork
```
public Network getNetwork()
```
    Convenience method for getting a reference to the parent root network.
    
    Returns:
    
    reference to root network.
  - getLearningRule
```
public SynapseUpdateRule getLearningRule()
```
    Returns:
    
    the learningRule
  - setLearningRule
```
public void setLearningRule(SynapseUpdateRule newLearningRule)
```
    Change this synapse's learning rule.
    
    Parameters:
    
    newLearningRule - the learningRule to set
  - getTemplateSynapse
```
public static Synapse getTemplateSynapse()
```
    Returns a "template" synapse.
    
    Returns:
    
    the template synapse.
    
    See Also:
    
    instantiateTemplateSynapse
  - getTemplateSynapse
```
public static Synapse getTemplateSynapse(SynapseUpdateRule rule)
```
    Returns a template synapse with a specified learning rule.
    
    Parameters:
    
    rule - the learning rule.
    
    Returns:
    
    the template synapse
    
    See Also:
    
    instantiateTemplateSynapse
  - getRuleList
```
public static java.util.List<SynapseUpdateRule> getRuleList(java.util.Collection<Synapse> synapseCollection)
```
    A method which takes in a collection of synapses and returns a list of their update rules in the order in which they appear in the original collection, if that collection supports a consistent order.
    
    Parameters:
    
    synapseCollection - The collection of synapses whose update rules we want to query.
    
    Returns:
    
    Returns a list of synapse update rules associated with the group of synapses
  - instantiateTemplateSynapse
```
public Synapse instantiateTemplateSynapse(Neuron source,
                                          Neuron target,
                                          Network parent)
```
    A template synapse is a synapse that has no proper references, but is used for setting properties. When the user is ready to instantiate it, they call this method to give the proper references.
    
    Parameters:
    
    source - source neuron
    
    target - target neuron
    
    parent - parent network
    
    Returns:
    
    a new synapse with these references and the base synapse's properties
  - getParentGroup
```
public SynapseGroup getParentGroup()
```
    Returns:
    
    the parentGroup
  - setParentGroup
```
public void setParentGroup(SynapseGroup parentGroup)
```
    Parameters:
    
    parentGroup - the parentGroup to set
  - decay
```
public void decay(double decayPercent)
```
    Decay this synapse by the indicated percentage. E.g. .5 cuts the strength in half.
    
    Parameters:
    
    decayPercent - decay percent
  - isFrozen
```
public boolean isFrozen()
```
    Returns:
    
    if the synapse's strength is frozen
  - setFrozen
```
public void setFrozen(boolean frozen)
```
    Parameters:
    
    frozen - sets whether or not this synapses strength will be frozen
  - getPsr
```
public double getPsr()
```
    Returns:
    
    the post-synaptic response
  - setPsr
```
public void setPsr(double psr)
```
    Parameters:
    
    psr - set the post-synaptic response
  - getNumericValuesAsByteArray
```
public byte[] getNumericValuesAsByteArray()
```
  - decodeNumericByteArray
```
public void decodeNumericByteArray(java.nio.ByteBuffer byteValues)
```
  - postUnmarshallingInit
```
public void postUnmarshallingInit()
```
    Called after a synapse is de-serialized, to repopulate fan-in and fan-out lists.

Class Synapse

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

Synapse

Synapse

Synapse

Synapse

Synapse

Synapse

Synapse

Synapse

Method Detail

copyTemplateSynapse

initSpikeResponder

update

calcPSR

calcWeightedSum

getType

getSource

getTarget

getStrength

setStrength

forceSetStrength

getUpperBound

setUpperBound

getLowerBound

setLowerBound

getIncrement

setIncrement

incrementWeight

decrementWeight

reinforce

weaken

randomizeSymmetric

getToolTipText

getSymmetricSynapse

randomize

checkBounds

clip

getId

setId

getSpikeResponder

setSpikeResponder

setDelay

getDelay

toString

getParentNetwork

setEnabled

isEnabled

getNetwork

getLearningRule

setLearningRule

getTemplateSynapse

getTemplateSynapse

getRuleList

instantiateTemplateSynapse

getParentGroup

setParentGroup

decay

isFrozen

setFrozen

getPsr

setPsr

getNumericValuesAsByteArray

decodeNumericByteArray

postUnmarshallingInit