Subnetwork (Simbrain API)

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

Direct Known Subclasses:

CompetitiveNetwork, EchoStateNetwork, FeedForward, Hopfield, SimpleRecurrentNetwork, SOMNetwork
```
public abstract class Subnetwork
extends Group
```
A collection of neuron groups and synapse groups which functions as a subnetwork within the main root network, with its own update rules.

Constructor Summary

Constructors
Constructor and Description

Subnetwork(Network net)
Create subnetwork group.

Constructors
Constructor and Description
`Subnetwork(Network net)` Create subnetwork group.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addAndLabelSynapseGroup(SynapseGroup synGrp)` Adds an already constructed synapse group to the subnetwork and provides it with an appropriate label.
`void`	`addNeuronGroup(NeuronGroup group)` Add a neuron group.
`void`	`addRowToTrainingSet()` If this subnetwork is trainable, then add the current activation of the "input" neuron group to the input data of the training set.
`void`	`addSynapseGroup(SynapseGroup group)` Add a synapse group.
`void`	`clearActivations()` Set all activations to 0.
`SynapseGroup`	`connectNeuronGroups(NeuronGroup source, NeuronGroup target)` Connects one group of neurons to another group of neurons using an All to All connection.
`SynapseGroup`	`connectNeuronGroups(NeuronGroup source, NeuronGroup target, ConnectNeurons connection)` Connects two groups of neurons according to some connection style.
`SynapseGroup`	`connectNeuronGroups(NeuronGroup source, NeuronGroup target, java.lang.String sourceLabel, java.lang.String targetLabel, ConnectNeurons connection)` Connects two groups of neurons according to some connection style, and allows for custom labels of the neuron groups within the weights label.
`void`	`delete()` Perform necessary deletion cleanup.
`boolean`	`displayNeuronGroups()`
`boolean`	`getEnabled()`
`java.util.List<Neuron>`	`getFlatNeuronList()` Return a "flat" list containing every neuron in every neuron group in this subnetwork.
`java.util.List<Synapse>`	`getFlatSynapseList()` Return a "flat" list containing every synapse in every synapse group in this subnetwork.
`int`	`getIndexOfNeuronGroup(NeuronGroup group)` Returns the index of a neuron group.
`java.lang.String`	`getLongDescription()` Get long description for info box, formmated in html.
`protected java.util.List<Neuron>`	`getModifiableNeuronList()` Returns a "flat" list containing every neuron in every neuron group in this subnetwork.
`NeuronGroup`	`getNeuronGroup()` Get the first neuron group in the list.
`NeuronGroup`	`getNeuronGroup(int index)` Get a neuron group by index.
`NeuronGroup`	`getNeuronGroupByLabel(java.lang.String label)` Find neuron group with a given label, or null if none found.
`int`	`getNeuronGroupCount()` Get number of neuron groups or "layers" in the list.
`java.util.List<NeuronGroup>`	`getNeuronGroupList()` Returns an unmodifiable version of the neuron group list.
`java.util.List<java.util.List<Neuron>>`	`getNeuronGroupsAsList()` Return neuron groups as a list.
`SynapseGroup`	`getSynapseGroup()` Get the first synapse group in the list.
`SynapseGroup`	`getSynapseGroup(int index)` Get a synapse group by index.
`SynapseGroup`	`getSynapseGroupByLabel(java.lang.String label)` Find synapse group with a given label, or null if none found.
`int`	`getSynapseGroupCount()` Get number of synapse groups in the list.
`java.util.List<SynapseGroup>`	`getSynapseGroupList()` Returns an unmodifiable version of the synapse group list.
`java.lang.String`	`getUpdateMethodDesecription()` Returns a description of this group's update method, which is displayed in the update manager panel.
`boolean`	`isEmpty()` Whether this group is empty or not.
`void`	`recursivelySetIds()` Set the id for this group.
`void`	`removeNeuronGroup(NeuronGroup neuronGroup)` Remove a neuron group.
`void`	`removeSynapseGroup(SynapseGroup synapseGroup)` Remove a synapse group.
`void`	`setDisplayNeuronGroups(boolean displayNeuronGroups)`
`void`	`setEnabled(boolean enabled)`
`int`	`size()`
`java.lang.String`	`toString()`
`void`	`update()` Update this group.

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

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

- Constructor Detail
  - Subnetwork
```
public Subnetwork(Network net)
```
    Create subnetwork group.
    
    Parameters:
    
    net - parent network.
- Method Detail
  - delete
```
public void delete()
```
    Description copied from class: Group
    
    Perform necessary deletion cleanup.
    
    Specified by:
    
    delete in class Group
  - isEmpty
```
public boolean isEmpty()
```
    Description copied from class: Group
    
    Whether this group is empty or not.
    
    Specified by:
    
    isEmpty in class Group
    
    Returns:
    
    true if the group is empty, false otherwise.
  - addSynapseGroup
```
public void addSynapseGroup(SynapseGroup group)
```
    Add a synapse group.
    
    Parameters:
    
    group - the synapse group to add
  - addNeuronGroup
```
public void addNeuronGroup(NeuronGroup group)
```
    Add a neuron group.
    
    Parameters:
    
    group - the neuron group to add
  - connectNeuronGroups
```
public SynapseGroup connectNeuronGroups(NeuronGroup source,
                                        NeuronGroup target)
```
    Connects one group of neurons to another group of neurons using an All to All connection.
    
    Parameters:
    
    source - the source group
    
    target - the target group
    
    Returns:
    
    the new neuron group
  - connectNeuronGroups
```
public SynapseGroup connectNeuronGroups(NeuronGroup source,
                                        NeuronGroup target,
                                        ConnectNeurons connection)
```
    Connects two groups of neurons according to some connection style.
    
    Parameters:
    
    source - the source group
    
    target - the target group
    
    connection - the type of connection desired between the two groups
    
    Returns:
    
    the new group
  - connectNeuronGroups
```
public SynapseGroup connectNeuronGroups(NeuronGroup source,
                                        NeuronGroup target,
                                        java.lang.String sourceLabel,
                                        java.lang.String targetLabel,
                                        ConnectNeurons connection)
```
    Connects two groups of neurons according to some connection style, and allows for custom labels of the neuron groups within the weights label.
    
    Parameters:
    
    source - the source group
    
    target - the target group
    
    sourceLabel - the name of the source group in the weights label
    
    targetLabel - the name of the target group in the weights label
    
    connection - the type of connection desired between the two groups
    
    Returns:
    
    the new group
  - addAndLabelSynapseGroup
```
public void addAndLabelSynapseGroup(SynapseGroup synGrp)
```
    Adds an already constructed synapse group to the subnetwork and provides it with an appropriate label.
    
    Parameters:
    
    synGrp - group to add
  - removeNeuronGroup
```
public void removeNeuronGroup(NeuronGroup neuronGroup)
```
    Remove a neuron group.
    
    Parameters:
    
    neuronGroup - group to remove
  - removeSynapseGroup
```
public void removeSynapseGroup(SynapseGroup synapseGroup)
```
    Remove a synapse group.
    
    Parameters:
    
    synapseGroup - group to remove
  - getNeuronGroup
```
public NeuronGroup getNeuronGroup(int index)
```
    Get a neuron group by index.
    
    Parameters:
    
    index - which neuron group to get
    
    Returns:
    
    the neuron group.
  - getNeuronGroupByLabel
```
public NeuronGroup getNeuronGroupByLabel(java.lang.String label)
```
    Find neuron group with a given label, or null if none found.
    
    Parameters:
    
    label - label to search for.
    
    Returns:
    
    neurongroup with that label found, null otherwise
  - getSynapseGroupByLabel
```
public SynapseGroup getSynapseGroupByLabel(java.lang.String label)
```
    Find synapse group with a given label, or null if none found.
    
    Parameters:
    
    label - label to search for.
    
    Returns:
    
    synapsegroup with that label found, null otherwise
  - getNeuronGroup
```
public NeuronGroup getNeuronGroup()
```
    Get the first neuron group in the list. Convenience method when there is just one neuron group.
    
    Returns:
    
    the neuron group.
  - getNeuronGroupCount
```
public int getNeuronGroupCount()
```
    Get number of neuron groups or "layers" in the list.
    
    Returns:
    
    number of neuron groups.
  - getNeuronGroupList
```
public java.util.List<NeuronGroup> getNeuronGroupList()
```
    Returns an unmodifiable version of the neuron group list.
    
    Returns:
    
    the neuron group list.
  - getNeuronGroupsAsList
```
public java.util.List<java.util.List<Neuron>> getNeuronGroupsAsList()
```
    Return neuron groups as a list. Used in backprop trainer.
    
    Returns:
    
    layers list
  - getIndexOfNeuronGroup
```
public int getIndexOfNeuronGroup(NeuronGroup group)
```
    Returns the index of a neuron group.
    
    Parameters:
    
    group - the group being queried.
    
    Returns:
    
    the index of the group in the list.
  - getSynapseGroup
```
public SynapseGroup getSynapseGroup(int index)
```
    Get a synapse group by index.
    
    Parameters:
    
    index - which synapse group to get
    
    Returns:
    
    the synapse group.
  - getSynapseGroup
```
public SynapseGroup getSynapseGroup()
```
    Get the first synapse group in the list. Convenience method when there is just one synapse group.
    
    Returns:
    
    the synapse group.
  - getSynapseGroupCount
```
public int getSynapseGroupCount()
```
    Get number of synapse groups in the list.
    
    Returns:
    
    number of synapse groups.
  - getSynapseGroupList
```
public java.util.List<SynapseGroup> getSynapseGroupList()
```
    Returns an unmodifiable version of the synapse group list.
    
    Returns:
    
    the synapse group list.
  - getFlatNeuronList
```
public java.util.List<Neuron> getFlatNeuronList()
```
    Return a "flat" list containing every neuron in every neuron group in this subnetwork.
    
    Returns:
    
    the flat neuron list.
  - getModifiableNeuronList
```
protected java.util.List<Neuron> getModifiableNeuronList()
```
    Returns a "flat" list containing every neuron in every neuron group in this subnetwork. This list is modifiable, but this method is protected... use with care.
    
    Returns:
    
    flat neuron list
  - getFlatSynapseList
```
public java.util.List<Synapse> getFlatSynapseList()
```
    Return a "flat" list containing every synapse in every synapse group in this subnetwork.
    
    Returns:
    
    the flat synapse list.
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class Group
  - size
```
public int size()
```
    Specified by:
    
    size in class Group
    
    Returns:
    
    the number of synapses and neurons in this subnetwork.
  - getLongDescription
```
public java.lang.String getLongDescription()
```
    Get long description for info box, formmated in html. Override for more detailed description.
    
    Returns:
    
    the long description.
  - getEnabled
```
public boolean getEnabled()
```
    Returns:
  - setEnabled
```
public void setEnabled(boolean enabled)
```
    Parameters:
    
    enabled -
  - update
```
public void update()
```
    Description copied from class: Group
    
    Update this group.
    
    Specified by:
    
    update in class Group
  - displayNeuronGroups
```
public boolean displayNeuronGroups()
```
    Returns:
    
    the displayNeuronGroups
  - setDisplayNeuronGroups
```
public void setDisplayNeuronGroups(boolean displayNeuronGroups)
```
    Parameters:
    
    displayNeuronGroups - the displayNeuronGroups to set
  - clearActivations
```
public void clearActivations()
```
    Set all activations to 0.
  - getUpdateMethodDesecription
```
public java.lang.String getUpdateMethodDesecription()
```
    Description copied from class: Group
    
    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.
  - addRowToTrainingSet
```
public void addRowToTrainingSet()
```
    If this subnetwork is trainable, then add the current activation of the "input" neuron group to the input data of the training set. Assumes the input neuron group is that last in the list of neuron groups (as is the case with Hopfield, Competitive, and SOM). Only makes sense with unsupervised learning, since only input data (and no target data) are added.
  - recursivelySetIds
```
public void recursivelySetIds()
```
    Description copied from class: Group
    
    Set the id for this group. A default label based on the id is also set. This is overridden by subnetowrk so that sub-groups also are given ids.
    
    Overrides:
    
    recursivelySetIds in class Group

Class Subnetwork

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Constructor Detail

Subnetwork

Method Detail

delete

isEmpty

addSynapseGroup

addNeuronGroup

connectNeuronGroups

connectNeuronGroups

connectNeuronGroups

addAndLabelSynapseGroup

removeNeuronGroup

removeSynapseGroup

getNeuronGroup

getNeuronGroupByLabel

getSynapseGroupByLabel

getNeuronGroup

getNeuronGroupCount

getNeuronGroupList

getNeuronGroupsAsList

getIndexOfNeuronGroup

getSynapseGroup

getSynapseGroup

getSynapseGroupCount

getSynapseGroupList

getFlatNeuronList

getModifiableNeuronList

getFlatSynapseList

toString

size

getLongDescription

getEnabled

setEnabled

update

displayNeuronGroups

setDisplayNeuronGroups

clearActivations

getUpdateMethodDesecription

addRowToTrainingSet

recursivelySetIds