SynapseGroup (Simbrain API)

java.lang.Object
- org.simbrain.network.groups.Group
- - org.simbrain.network.groups.SynapseGroup

```
public class SynapseGroup
extends Group
```
A group of synapses. Must connect a source and target neuron group.

Author:

Zach Tosi

Field Summary

Fields
Modifier and Type	Field and Description
`static ConnectNeurons`	`DEFAULT_CONNECTION_MANAGER` All to All.
`static double`	`DEFAULT_EXCITATORY_RATIO` The default ratio (all excitatory) for all synapse groups.

Constructor Summary

Constructors
Constructor and Description
`SynapseGroup(NeuronGroup source, NeuronGroup target)` Creates a blank synapse group between a source and target neuron group using the default connection manager.
`SynapseGroup(NeuronGroup source, NeuronGroup target, ConnectNeurons connectionManager)` Creates a blank synapse group between a source and target neuron group.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addExcitatorySynapseUnsafe(Synapse synapse)` See: `addSynapseUnsafe(Synapse)`.
`void`	`addInhibitorySynapseUnsafe(Synapse synapse)` See: `addSynapseUnsafe(Synapse)`.
`void`	`addNewExcitatorySynapse(Synapse synapse)`
`void`	`addNewInhibitorySynapse(Synapse synapse)`
`void`	`addNewSynapse(Synapse synapse)` Adds a new synapse (one which is "blank") to the synapse group.
`void`	`addSynapseUnsafe(Synapse synapse)` Add a synapse to this synapse group adding it to the appropriate synapse set (excitatory or inhibitory if it's weight is above or below zero respecively).
`double`	`calculateExcitatoryRatio()` If a randomize operation changes the ratio of excitatory to inhibitory synapses, this method can be called to change the excitatoryRatio to reflect this value.
`<T> T`	`checkSynapses(ConnectionUtilities.SynapseParameterGetter<T> check, SimbrainConstants.Polarity polarity)` A generic method which takes in a functional interface and a polarity.
`void`	`clear()` Removes all synapses from this synapse group and the network.
`static SynapseGroup`	`createSynapseGroup(NeuronGroup source, NeuronGroup target)` Completely creates a synapse group between the two neuron groups with all default parameters.
`static SynapseGroup`	`createSynapseGroup(NeuronGroup source, NeuronGroup target, ConnectNeurons connectionManager)` Completely creates a synapse group with the desired parameters.
`static SynapseGroup`	`createSynapseGroup(NeuronGroup source, NeuronGroup target, ConnectNeurons connectionManager, double excitatoryRatio)` Completely creates a synapse group with the desired parameters.
`static SynapseGroup`	`createSynapseGroup(NeuronGroup source, NeuronGroup target, ConnectNeurons connectionManager, double excitatoryRatio, PolarizedRandomizer exciteRand, PolarizedRandomizer inhibRand)` Completely creates a synapse group with the desired parameters.
`static SynapseGroup`	`createSynapseGroup(NeuronGroup source, NeuronGroup target, double excitatoryRatio)` Completely creates a synapse group with the desired parameters.
`void`	`delete()` Perform necessary deletion cleanup.
`java.util.List<Synapse>`	`getAllSynapses()`
`ConnectNeurons`	`getConnectionManager()`
`java.lang.Integer`	`getDelay(SimbrainConstants.Polarity polarity)`
`Synapse`	`getExcitatoryPrototype()` Reveals the excitatory prototype synapse, allowing more detailed synapse values to be queried at the group level.
`PolarizedRandomizer`	`getExcitatoryRandomizer()`
`double`	`getExcitatoryRatioParameter()` Returns the excitatory ratio parameter.
`double`	`getExcitatoryRatioPrecise()`
`double[]`	`getExcitatoryStrengths()`
`java.util.Set<Synapse>`	`getExcitatorySynapses()`
`double`	`getIncrement(SimbrainConstants.Polarity polarity)`
`Synapse`	`getInhibitoryPrototype()` Reveals the inhibitory prototype synapse, allowing more detailed synapse values to be queried at the group level.
`PolarizedRandomizer`	`getInhibitoryRandomizer()`
`double[]`	`getInhibitoryStrengths()`
`java.util.Set<Synapse>`	`getInhibitorySynapses()`
`java.lang.String`	`getLearningRuleDescription(SimbrainConstants.Polarity polarity)`
`double`	`getLowerBound(SimbrainConstants.Polarity polarity)`
`double[][]`	`getNumericIndices()` A more compressed version of a weight matrix for cases where a weight matrix is needed, but may cause memory issues if fully instantiated.
`java.lang.Number[][]`	`getNumericIndices(ConnectionUtilities.SynapseParameterGetter<java.lang.Number> getter)` A more compressed version of a weight matrix for cases where a weight matrix is needed, but may cause memory issues if fully instantiated.
`long[]`	`getRowCompressedMatrixRepresentation()`
`NeuronGroup`	`getSourceNeuronGroup()`
`java.util.List<Neuron>`	`getSourceNeurons()` Return a list of source neurons associated with the synapses in this group.
`java.lang.String`	`getSpikeResponderDescription(SimbrainConstants.Polarity polarity)`
`NeuronGroup`	`getTargetNeuronGroup()`
`java.util.List<Neuron>`	`getTargetNeurons()` Return a list of target neurons associated with the synapses in this group.
`java.lang.String`	`getUpdateMethodDesecription()` Returns a description of this group's update method, which is displayed in the update manager panel.
`double`	`getUpperBound(SimbrainConstants.Polarity polarity)`
`double[][]`	`getWeightMatrix()` For large, sparse synapse groups this will cause a heap overflow.
`double[]`	`getWeightVector()` Return weight strengths as a double vector.
`boolean`	`hasExcitatory()`
`boolean`	`hasInhibitory()`
`void`	`initializeSynapseVisibility()` Determine whether this synpasegroup should initially have its synapses displayed.
`boolean`	`isDisplaySynapses()`
`boolean`	`isEmpty()` Whether this group is empty or not.
`java.lang.Boolean`	`isEnabled(SimbrainConstants.Polarity polarity)`
`java.lang.Boolean`	`isFrozen(SimbrainConstants.Polarity polarity)`
`boolean`	`isRecurrent()` Check whether this synapse group connects a neuron group to itself.
`boolean`	`isUseFullRepOnSave()`
`boolean`	`isUseGroupLevelSettings()`
`void`	`makeConnections()` The "build" method which actually constructs the group in terms of populating it with synapses.
`void`	`postSaveReInit()` A post initialization which must be done if the user wants to save the network, but continue using the network after saving (since the saving process sets the synapse sets to null.
`void`	`postUnmarshallingInit()` Perform operations required after opening a synapse group.
`void`	`preAllocateSynapses(int expectedNumSynapses)` Pre-allocates, that is sets the initial capacity of the arraylist containing this synapse group's synapses.
`void`	`preSaveInit()` Perform operations required before saving a synapse group.
`void`	`preSaveInitFull()` The pre-save init to be used to save all relevant synapse parameters in the byte array.
`void`	`prune()` Removes all synapses with weight 0 from the group.
`void`	`randomizeConnectionWeights()` Randomizes all the synapses according to their corresponding randomizers.
`void`	`randomizeExcitatoryConnections()` Randomizes the weights of the excitatory connections in this group based on the parameters of `exciteRand`.
`void`	`randomizeInhibitoryConnections()` Randomizes the weights of the inhibitory connections in this group based on the parameters of `inhibRand`.
`Synapse`	`removeSynapse(Synapse toDelete)` Remove the provided synapse from the group, but not the network.
`void`	`revalidateSynapseSets()` If an algorithm (like training) extensively changes the polarity of the synapses in this group, it's impractical to check every time a change is made.
`void`	`saveToFileAsLinkedList()` See: `saveToFileAsLinkedList(String)` Uses the default name which is: label + date & time
`void`	`saveToFileAsLinkedList(java.lang.String filename)` Saves the synapse group to a file in linked list format which can be read by most graph analysis software, in particular as of 6/27/2015 the author is aware of both OSLOM and Infomap which can interpret the linked list format.
`void`	`saveToFileAsMatrix(java.lang.String filename)` Saves the weight matrix represented by this synapse group to a file.
`void`	`setAndConformToTemplate(Synapse template, SimbrainConstants.Polarity polarity)`
`void`	`setConnectionManager(ConnectNeurons connection)` Sets the connection manager for this synapse group once and only once.
`void`	`setDelay(int delay, SimbrainConstants.Polarity polarity)`
`void`	`setDisplaySynapses(boolean displaySynapses)`
`void`	`setEnabled(boolean enabled, SimbrainConstants.Polarity polarity)`
`void`	`setExcitatoryRandomizer(PolarizedRandomizer excitatoryRandomizer)`
`void`	`setExcitatoryRatio(double excitatoryRatio)` Changes the ratio of synapses in this group that are excitatory subject to two constraints: 1) If neurons in the source neuron group have their own polarity ratio, the desired excitatoryRatio may not be possible.
`void`	`setFrozen(boolean frozen, SimbrainConstants.Polarity polarity)`
`void`	`setIncrement(double increment, SimbrainConstants.Polarity polarity)`
`void`	`setInhibitoryRandomizer(PolarizedRandomizer inhibitoryRandomizer)`
`void`	`setLearningRule(SynapseUpdateRule sur, SimbrainConstants.Polarity polarity)`
`void`	`setLowerBound(double lowerBound, SimbrainConstants.Polarity polarity)`
`void`	`setRandomizers(PolarizedRandomizer excitatoryRandomizer, PolarizedRandomizer inhibitoryRandomizer)`
`void`	`setSpikeResponder(SpikeResponder spr, SimbrainConstants.Polarity polarity)`
`void`	`setStrength(double strength, SimbrainConstants.Polarity polarity)`
`<T> void`	`setSynapses(ConnectionUtilities.SynapseParameterSetter<T> set, T val, SimbrainConstants.Polarity polarity)` A generic method that takes in a functional interface, a value and a polarity.
`boolean`	`setSynapseStrength(Synapse synapse, double newWeight)` Sets the strength of a single synapse in the group specified as a parameter.
`void`	`setUpperBound(double upperBound, SimbrainConstants.Polarity polarity)`
`void`	`setUseFullRepOnSave(boolean useFullRepOnSave)`
`void`	`setUseGroupLevelSettings(boolean useGroupLevelSettings)`
`int`	`size()`
`java.lang.String`	`toString()`
`void`	`update()` Update group.

Methods inherited from class org.simbrain.network.groups.Group
getId, getLabel, getParentGroup, getParentNetwork, getStateInfo, hasParentGroup, isMarkedForDeletion, isTopLevelGroup, recursivelySetIds, setId, setLabel, setMarkedForDeletion, setParentGroup, setStateInfo

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

- Field Detail
  - DEFAULT_EXCITATORY_RATIO
```
public static final double DEFAULT_EXCITATORY_RATIO
```
    The default ratio (all excitatory) for all synapse groups.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_CONNECTION_MANAGER
```
public static final ConnectNeurons DEFAULT_CONNECTION_MANAGER
```
    All to All.
- Constructor Detail
  - SynapseGroup
```
public SynapseGroup(NeuronGroup source,
                    NeuronGroup target)
```
    Creates a blank synapse group between a source and target neuron group using the default connection manager. Until makeConnections() is called this group will be empty and will not be added to the source or target neuron groups' respective outgoing and incoming synapse group sets.
    
    Parameters:
    
    source - the source neuron group.
    
    target - the target neuron group.
  - SynapseGroup
```
public SynapseGroup(NeuronGroup source,
                    NeuronGroup target,
                    ConnectNeurons connectionManager)
```
    Creates a blank synapse group between a source and target neuron group. Until makeConnections() is called this group will be empty and will not be added to the source or target neuron groups' respective outgoing and incoming synapse group sets.
    
    Parameters:
    
    source - source neuron group
    
    target - target neuron group
    
    connectionManager - a connection object which builds this group
- Method Detail
  - createSynapseGroup
```
public static SynapseGroup createSynapseGroup(NeuronGroup source,
                                              NeuronGroup target)
```
    Completely creates a synapse group between the two neuron groups with all default parameters. This method creates the individual connections.
    
    Parameters:
    
    source - the source neuron group.
    
    target - the target neuron group.
    
    Returns:
    
    a synapse group with all default values connecting the source and target neuron groups.
  - createSynapseGroup
```
public static SynapseGroup createSynapseGroup(NeuronGroup source,
                                              NeuronGroup target,
                                              double excitatoryRatio)
```
    Completely creates a synapse group with the desired parameters. That is the connections (individual synapses) are created along with the group.
    
    Parameters:
    
    source - the source neuron group.
    
    target - the target neuron group. neurons in the group are connected
    
    excitatoryRatio - the ratio of excitatory to inhibitory synapses [0, 1].
    
    Returns:
    
    a synapse group with the above parameters.
  - createSynapseGroup
```
public static SynapseGroup createSynapseGroup(NeuronGroup source,
                                              NeuronGroup target,
                                              ConnectNeurons connectionManager)
```
    Completely creates a synapse group with the desired parameters. That is the connections (individual synapses) are created along with the group.
    
    Parameters:
    
    source - the source neuron group.
    
    target - the target neuron group.
    
    connectionManager - the connection manager used to establish which
    
    Returns:
    
    a synapse group with the above parameters.
  - createSynapseGroup
```
public static SynapseGroup createSynapseGroup(NeuronGroup source,
                                              NeuronGroup target,
                                              ConnectNeurons connectionManager,
                                              double excitatoryRatio)
```
    Completely creates a synapse group with the desired parameters. That is the connections (individual synapses) are created along with the group.
    
    Parameters:
    
    source - the source neuron group.
    
    target - the target neuron group.
    
    connectionManager - the connection manager used to establish which
    
    excitatoryRatio - the ratio of excitatory to inhibitory synapses [0, 1].
    
    Returns:
    
    a synapse group with the above parameters.
  - createSynapseGroup
```
public static SynapseGroup createSynapseGroup(NeuronGroup source,
                                              NeuronGroup target,
                                              ConnectNeurons connectionManager,
                                              double excitatoryRatio,
                                              PolarizedRandomizer exciteRand,
                                              PolarizedRandomizer inhibRand)
```
    Completely creates a synapse group with the desired parameters. That is the connections (individual synapses) are created along with the group.
    
    Parameters:
    
    source - the source neuron group.
    
    target - the target neuron group.
    
    connectionManager - the connection manager used to establish which
    
    excitatoryRatio - the ratio of excitatory to inhibitory synapses [0, 1].
    
    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.
    
    Returns:
    
    a synapse group with the above parameters.
  - makeConnections
```
public void makeConnections()
```
    The "build" method which actually constructs the group in terms of populating it with synapses. If called on a synapse group which has already been made (i.e. already has synapses populating it) those synapses will be destroyed and the current connection manager and parameters used to create new connections. This method adds the current synapse group the the source neuron group's outgoing synapse set and the target neuron group's incoming synapse set.
  - preAllocateSynapses
```
public void preAllocateSynapses(int expectedNumSynapses)
                         throws java.lang.IllegalStateException
```
    Pre-allocates, that is sets the initial capacity of the arraylist containing this synapse group's synapses. This allows expectedNumber of synapses to be added to this synapse group without the synapse list having to perform any operations related to expanding the list size.
    
    Parameters:
    
    expectedNumSynapses - the number of synapses the connection manager predicts will be created.
    
    Throws:
    
    java.lang.IllegalStateException - if the synapse group has already been initialized.
  - revalidateSynapseSets
```
public void revalidateSynapseSets()
```
    If an algorithm (like training) extensively changes the polarity of the synapses in this group, it's impractical to check every time a change is made. Thus after the bulk of the algorithm is completed this method can be called to sort synapses into their appropriate sets.
  - update
```
public void update()
```
    Update group. Override for special updating. Recommended that overrides call super.update() some time during the custom update.
    
    Specified by:
    
    update in class Group
  - size
```
public int size()
```
    Specified by:
    
    size in class Group
    
    Returns:
    
    the number of synapses/neurons in this group as applicable to the group type
  - isEmpty
```
public boolean isEmpty()
```
    Whether this group is empty or not.
    
    Specified by:
    
    isEmpty in class Group
    
    Returns:
    
    true if the group is empty, false otherwise.
  - delete
```
public void delete()
```
    Perform necessary deletion cleanup.
    
    Specified by:
    
    delete in class Group
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class Group
  - getUpdateMethodDesecription
```
public java.lang.String getUpdateMethodDesecription()
```
    Returns a description of this group's update method, which is displayed in the update manager panel.
    
    Specified by:
    
    getUpdateMethodDesecription in class Group
    
    Returns:
    
    a description of the update method.
  - initializeSynapseVisibility
```
public void initializeSynapseVisibility()
```
    Determine whether this synpasegroup should initially have its synapses displayed. For isolated synapse groups check its number of synapses. If the maximum number of possible connections exceeds a the network's synapse visibility threshold, then individual synapses will not be displayed.
  - setDisplaySynapses
```
public void setDisplaySynapses(boolean displaySynapses)
```
    Parameters:
    
    displaySynapses - the displaySynapses to set
  - isDisplaySynapses
```
public boolean isDisplaySynapses()
```
    Returns:
    
    the displaySynapses
  - removeSynapse
```
public Synapse removeSynapse(Synapse toDelete)
```
    Remove the provided synapse from the group, but not the network.
    
    Parameters:
    
    toDelete - the synapse to delete
    
    Returns:
    
    the deleted synapse
  - prune
```
public void prune()
```
    Removes all synapses with weight 0 from the group.
  - clear
```
public void clear()
```
    Removes all synapses from this synapse group and the network. Deletes all synapses in this group.
  - addNewSynapse
```
public void addNewSynapse(Synapse synapse)
```
    Adds a new synapse (one which is "blank") to the synapse group. This is the preferred method to use for adding synapses to the synapse group over addSynapseUnsafe(Synapse) because it makes the added synapse conform to the global parameters of this synapse group.
    
    Parameters:
    
    synapse - the blank synapse to be added and assigned new values based on the parameters of this group.
  - addNewExcitatorySynapse
```
public void addNewExcitatorySynapse(Synapse synapse)
```
    Parameters:
    
    synapse - the blank excitatory synapse which will be added to the group and have its parameters set based on the parameters of this group.
  - addNewInhibitorySynapse
```
public void addNewInhibitorySynapse(Synapse synapse)
```
    Parameters:
    
    synapse - the blank inhibitory synapse which will be added to the group and have its parameters set based on the parameters of this group.
  - addSynapseUnsafe
```
public void addSynapseUnsafe(Synapse synapse)
```
    Add a synapse to this synapse group adding it to the appropriate synapse set (excitatory or inhibitory if it's weight is above or below zero respecively). Using this method is NOT RECOMMENDED under most circumstances. This is because no checks are performed on the synapse to ensure that it can sensibly be added to this group. The synapse can also have parameters which will make the global parameters of the synapse group no longer accurately apply to the whole group. This is not as problematic as say not connecting neurons which are in this synapse group's source and/or target neuron groups, but it does undermine the purpose of having synapse groups. Possible Use Case: When it is known beforehand that the synapse(s) being added all conform to the parameters of this synapse group.
    
    Parameters:
    
    synapse - synapse to add
  - addExcitatorySynapseUnsafe
```
public void addExcitatorySynapseUnsafe(Synapse synapse)
```
    See: addSynapseUnsafe(Synapse). Same but specific to excitatory synapses. This is even less safe however because an inhibitory synapse could potentially be added to the excitatory set.
    
    Parameters:
    
    synapse - the synapse to add.
  - addInhibitorySynapseUnsafe
```
public void addInhibitorySynapseUnsafe(Synapse synapse)
```
    See: addSynapseUnsafe(Synapse). Same but specific to inhibitory synapses. This is even less safe however because an excitatory synapse could potentially be added to the inhibitory set.
    
    Parameters:
    
    synapse - the synapse to add.
  - setExcitatoryRatio
```
public void setExcitatoryRatio(double excitatoryRatio)
                        throws java.lang.IllegalArgumentException
```
    Changes the ratio of synapses in this group that are excitatory subject to two constraints: 1) If neurons in the source neuron group have their own polarity ratio, the desired excitatoryRatio may not be possible. In this case, this class will NOT add or remove synapses to achieve this number. If not all source neurons are polarized, however this class will attempt to get as close as possible to the desired excitatoryRatio. 2) Changes in weights performed to achieve the desired excitatoryRatio will result from sign changes to synapses. The absolute value of synapse strengths will not be changed.
    
    Parameters:
    
    excitatoryRatio - the ratio of synapses which will be made excitatory, value must be in the range [0, 1]
    
    Throws:
    
    java.lang.IllegalArgumentException - if the ratio is not on [0, 1].
  - getExcitatoryRatioParameter
```
public double getExcitatoryRatioParameter()
```
    Returns the excitatory ratio parameter. For the actual value use getExcitatoryRatioPrecise().
    
    Returns:
    
    the ration of excitatory synapses in this group
  - getExcitatoryRatioPrecise
```
public double getExcitatoryRatioPrecise()
```
    Returns:
    
    the actual excitatory ratio measured as the number of excitatory synapses divided by the total.
  - getAllSynapses
```
public java.util.List<Synapse> getAllSynapses()
```
    Returns:
    
    a flat list representation of all the synapses in this synapse group. This list is a defensive copy.
  - getExcitatorySynapses
```
public java.util.Set<Synapse> getExcitatorySynapses()
```
    Returns:
    
    the set of excitatory synapses
  - getInhibitorySynapses
```
public java.util.Set<Synapse> getInhibitorySynapses()
```
    Returns:
    
    the set of inhibitory synapses
  - getWeightVector
```
public double[] getWeightVector()
```
    Return weight strengths as a double vector.
    
    Returns:
    
    weights
  - getInhibitoryStrengths
```
public double[] getInhibitoryStrengths()
```
    Returns:
    
    the strengths of all the inhibitory synapses as a double array
  - getExcitatoryStrengths
```
public double[] getExcitatoryStrengths()
```
    Returns:
    
    the strengths of all the excitatory synapses as a double array
  - getWeightMatrix
```
public double[][] getWeightMatrix()
```
    For large, sparse synapse groups this will cause a heap overflow. Use getRowCompressedMatrixRepresentation() instead.
    
    Returns:
    
    a representation of the synapse strengths in this synapse group as a weight matrix between two activation vectors (neuron groups).
  - getNumericIndices
```
public double[][] getNumericIndices()
```
    A more compressed version of a weight matrix for cases where a weight matrix is needed, but may cause memory issues if fully instantiated. Eg, for very sparse synapse groups between very large neuron groups.
    
    Returns:
    
    a 2D array with a number of rows equal to the total number of synapses and a number of columns equal to 3. Each row contains the the source index number, the target index number, and the strength in that order. This array is then sorted by source index then target index. Ex: 1 2 .9 0 3 5.3 0 1 -.1 Becomes: 0 1 -.1 0 3 5.3 1 2 .9
  - getNumericIndices
```
public java.lang.Number[][] getNumericIndices(ConnectionUtilities.SynapseParameterGetter<java.lang.Number> getter)
```
    A more compressed version of a weight matrix for cases where a weight matrix is needed, but may cause memory issues if fully instantiated. Eg, for very sparse synapse groups between very large neuron groups.
    
    Returns:
    
    a 2D array with a number of rows equal to the total number of synapses and a number of columns equal to 3. Each row contains the the source index number, the target index number, and the strength in that order. This array is then sorted by source index then target index. Ex: 1 2 .9 0 3 5.3 0 1 -.1 Becomes: 0 1 -.1 0 3 5.3 1 2 .9
  - getRowCompressedMatrixRepresentation
```
public long[] getRowCompressedMatrixRepresentation()
```
    Returns:
    
    a row compressed representation of the weight matrix derived from this synapse group. All values are stored as longs, and row changes are denoted by -1.
  - saveToFileAsLinkedList
```
public void saveToFileAsLinkedList(java.lang.String filename)
```
    Saves the synapse group to a file in linked list format which can be read by most graph analysis software, in particular as of 6/27/2015 the author is aware of both OSLOM and Infomap which can interpret the linked list format. Format is as follows: source index target index weight By default ".dat" is appended to the given filename since .dat is the standard extension for linked lists.
    
    Parameters:
    
    filename - the name to be given to the file
  - saveToFileAsLinkedList
```
public void saveToFileAsLinkedList()
```
    See: saveToFileAsLinkedList(String) Uses the default name which is: label + date & time
  - saveToFileAsMatrix
```
public void saveToFileAsMatrix(java.lang.String filename)
                        throws java.lang.OutOfMemoryError
```
    Saves the weight matrix represented by this synapse group to a file.
    
    Parameters:
    
    filename - the name of the file to be used
    
    Throws:
    
    java.lang.OutOfMemoryError - if getWeightMatrix() causes an out of memory error for being to large.
  - setSynapseStrength
```
public boolean setSynapseStrength(Synapse synapse,
                                  double newWeight)
```
    Sets the strength of a single synapse in the group specified as a parameter. If the synapse does not exist in this group returns false. If the this makes the synapse change polarity it will be removed from its current set and added to the appropriate set.
    
    Parameters:
    
    synapse - sets the strength of an individual synapse in the group
    
    newWeight - the new weight to set it to
    
    Returns:
    
    true if this group contained the specified synapse, and false if it did not and thus failed to set the strength value.
  - randomizeConnectionWeights
```
public void randomizeConnectionWeights()
```
    Randomizes all the synapses according to their corresponding randomizers. randomizeExcitatoryConnections(), randomizeInhibitoryConnections()
  - randomizeExcitatoryConnections
```
public void randomizeExcitatoryConnections()
```
    Randomizes the weights of the excitatory connections in this group based on the parameters of exciteRand. Assumes that all synapses in exSynapseSet are--in fact--excitatory. If some action on the synapses may have corrupted that assumption call revalidateSynapseSets() first.
  - randomizeInhibitoryConnections
```
public void randomizeInhibitoryConnections()
```
    Randomizes the weights of the inhibitory connections in this group based on the parameters of inhibRand. Assumes that all synapses in inSynapseSet are--in fact--inhibitory. If some action on the synapses may have corrupted that assumption call revalidateSynapseSets() first.
  - setConnectionManager
```
public void setConnectionManager(ConnectNeurons connection)
```
    Sets the connection manager for this synapse group once and only once. Subsequent attempts to modify the connection manager will fail, as changing the connection manager amounts to (and should be implemented as) creating an entirely new synapse group.
    
    Parameters:
    
    connection - the connection manager to be used by this synapse group for making synaptic connections.
  - getConnectionManager
```
public ConnectNeurons getConnectionManager()
```
    Returns:
    
    the connection manager for this synapse group.
  - setExcitatoryRandomizer
```
public void setExcitatoryRandomizer(PolarizedRandomizer excitatoryRandomizer)
```
    Parameters:
    
    excitatoryRandomizer - the randomizer to be used to determine the weights of excitatory synapses.
  - setInhibitoryRandomizer
```
public void setInhibitoryRandomizer(PolarizedRandomizer inhibitoryRandomizer)
```
    Parameters:
    
    inhibitoryRandomizer - the randomizer to be used to determine the weights of inbihitory synapses.
  - setRandomizers
```
public void setRandomizers(PolarizedRandomizer excitatoryRandomizer,
                           PolarizedRandomizer inhibitoryRandomizer)
```
    Parameters:
    
    excitatoryRandomizer -
    
    inhibitoryRandomizer -
  - getExcitatoryRandomizer
```
public PolarizedRandomizer getExcitatoryRandomizer()
```
    Returns:
  - getInhibitoryRandomizer
```
public PolarizedRandomizer getInhibitoryRandomizer()
```
    Returns:
  - calculateExcitatoryRatio
```
public double calculateExcitatoryRatio()
```
    If a randomize operation changes the ratio of excitatory to inhibitory synapses, this method can be called to change the excitatoryRatio to reflect this value. This happens rarely, and generally speaking is not recommended outside prototyping.
    
    Returns:
    
    the ratio of synapses in this group that are excitatory.
  - isRecurrent
```
public boolean isRecurrent()
```
    Check whether this synapse group connects a neuron group to itself.
    
    Returns:
    
    true if this connects a neuron group to itself, false otherwise.
  - getSourceNeurons
```
public java.util.List<Neuron> getSourceNeurons()
```
    Return a list of source neurons associated with the synapses in this group.
    
    Returns:
    
    the source neuron list.
  - getTargetNeurons
```
public java.util.List<Neuron> getTargetNeurons()
```
    Return a list of target neurons associated with the synapses in this group.
    
    Returns:
    
    the target neuron list.
  - hasExcitatory
```
public boolean hasExcitatory()
```
  - hasInhibitory
```
public boolean hasInhibitory()
```
  - getSourceNeuronGroup
```
public NeuronGroup getSourceNeuronGroup()
```
    Returns:
    
    the sourceNeuronGroup
  - getTargetNeuronGroup
```
public NeuronGroup getTargetNeuronGroup()
```
    Returns:
    
    the targetNeuronGroup
  - getExcitatoryPrototype
```
public Synapse getExcitatoryPrototype()
```
    Reveals the excitatory prototype synapse, allowing more detailed synapse values to be queried at the group level. To use a prototype to change many values call #setAndConformToTemplate(Synapse, Polarity)
    
    Returns:
    
    the prototype synapse
  - getInhibitoryPrototype
```
public Synapse getInhibitoryPrototype()
```
    Reveals the inhibitory prototype synapse, allowing more detailed synapse values to be queried at the group level. To use a prototype to change many values call #setAndConformToTemplate(Synapse, Polarity)
    
    Returns:
    
    the prototype synapse
  - isUseGroupLevelSettings
```
public boolean isUseGroupLevelSettings()
```
    Returns:
    
    whether or not the synapse group is using group-level properties Homogeneous within synapse type (excitatory/inhibitory) for faster indexing and optimized updating.
  - setUseGroupLevelSettings
```
public void setUseGroupLevelSettings(boolean useGroupLevelSettings)
```
    Parameters:
    
    useGroupLevelSettings -
  - setAndConformToTemplate
```
public void setAndConformToTemplate(Synapse template,
                                    SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    template - the set synapse template
    
    polarity -
  - setDelay
```
public void setDelay(int delay,
                     SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    delay - the set delay
    
    polarity -
  - setEnabled
```
public void setEnabled(boolean enabled,
                       SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    enabled -
    
    polarity -
  - setFrozen
```
public void setFrozen(boolean frozen,
                      SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    frozen -
    
    polarity -
  - setIncrement
```
public void setIncrement(double increment,
                         SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    increment -
    
    polarity -
  - setLearningRule
```
public void setLearningRule(SynapseUpdateRule sur,
                            SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    sur -
    
    polarity -
  - setLowerBound
```
public void setLowerBound(double lowerBound,
                          SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    lowerBound -
    
    polarity -
  - setSpikeResponder
```
public void setSpikeResponder(SpikeResponder spr,
                              SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    spr -
    
    polarity -
  - setStrength
```
public void setStrength(double strength,
                        SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    strength -
    
    polarity -
  - setUpperBound
```
public void setUpperBound(double upperBound,
                          SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    upperBound -
    
    polarity -
  - getDelay
```
public java.lang.Integer getDelay(SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    polarity -
    
    Returns:
  - isEnabled
```
public java.lang.Boolean isEnabled(SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    polarity -
    
    Returns:
  - isFrozen
```
public java.lang.Boolean isFrozen(SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    polarity -
    
    Returns:
  - getIncrement
```
public double getIncrement(SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    polarity -
    
    Returns:
  - getLearningRuleDescription
```
public java.lang.String getLearningRuleDescription(SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    polarity -
    
    Returns:
  - getLowerBound
```
public double getLowerBound(SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    polarity -
    
    Returns:
  - getSpikeResponderDescription
```
public java.lang.String getSpikeResponderDescription(SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    polarity -
    
    Returns:
  - getUpperBound
```
public double getUpperBound(SimbrainConstants.Polarity polarity)
```
    Parameters:
    
    polarity -
    
    Returns:
  - checkSynapses
```
public <T> T checkSynapses(ConnectionUtilities.SynapseParameterGetter<T> check,
                           SimbrainConstants.Polarity polarity)
```
    A generic method which takes in a functional interface and a polarity. It then performs that function on every synapse in the set(s) corresponding to the polarity parameter and returns a result matching the type specified by the passed function.
    
    Type Parameters:
    
    T -
    
    Parameters:
    
    check -
    
    polarity -
    
    Returns:
  - setSynapses
```
public <T> void setSynapses(ConnectionUtilities.SynapseParameterSetter<T> set,
                            T val,
                            SimbrainConstants.Polarity polarity)
```
    A generic method that takes in a functional interface, a value and a polarity. The functional interface takes in a synapse and a value and the calling method specifies which parameter of synapse the function sets the value to. This method then performs that function (setting some synapse parameter) on all the synapses in the set(s) corresponding to the specified polarity.
    
    Type Parameters:
    
    T -
    
    Parameters:
    
    set -
    
    val -
    
    polarity -
  - isUseFullRepOnSave
```
public boolean isUseFullRepOnSave()
```
  - setUseFullRepOnSave
```
public void setUseFullRepOnSave(boolean useFullRepOnSave)
```
  - preSaveInit
```
public void preSaveInit()
```
    Perform operations required before saving a synapse group.
  - preSaveInitFull
```
public void preSaveInitFull()
```
    The pre-save init to be used to save all relevant synapse parameters in the byte array.
  - postSaveReInit
```
public void postSaveReInit()
```
    A post initialization which must be done if the user wants to save the network, but continue using the network after saving (since the saving process sets the synapse sets to null.
  - postUnmarshallingInit
```
public void postUnmarshallingInit()
```
    Perform operations required after opening a synapse group.

Class SynapseGroup

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.simbrain.network.groups.Group

Methods inherited from class java.lang.Object

Field Detail

DEFAULT_EXCITATORY_RATIO

DEFAULT_CONNECTION_MANAGER

Constructor Detail

SynapseGroup

SynapseGroup

Method Detail

createSynapseGroup

createSynapseGroup

createSynapseGroup

createSynapseGroup

createSynapseGroup

makeConnections

preAllocateSynapses

revalidateSynapseSets

update

size

isEmpty

delete

toString

getUpdateMethodDesecription

initializeSynapseVisibility

setDisplaySynapses

isDisplaySynapses

removeSynapse

prune

clear

addNewSynapse

addNewExcitatorySynapse

addNewInhibitorySynapse

addSynapseUnsafe

addExcitatorySynapseUnsafe

addInhibitorySynapseUnsafe

setExcitatoryRatio

getExcitatoryRatioParameter

getExcitatoryRatioPrecise

getAllSynapses

getExcitatorySynapses

getInhibitorySynapses

getWeightVector

getInhibitoryStrengths

getExcitatoryStrengths

getWeightMatrix

getNumericIndices

getNumericIndices

getRowCompressedMatrixRepresentation

saveToFileAsLinkedList

saveToFileAsLinkedList

saveToFileAsMatrix

setSynapseStrength

randomizeConnectionWeights

randomizeExcitatoryConnections

randomizeInhibitoryConnections

setConnectionManager

getConnectionManager

setExcitatoryRandomizer

setInhibitoryRandomizer

setRandomizers

getExcitatoryRandomizer

getInhibitoryRandomizer

calculateExcitatoryRatio

isRecurrent

getSourceNeurons

getTargetNeurons

hasExcitatory

hasInhibitory

getSourceNeuronGroup

getTargetNeuronGroup

getExcitatoryPrototype

getInhibitoryPrototype

isUseGroupLevelSettings

setUseGroupLevelSettings

setAndConformToTemplate

setDelay