NeuronGroup (Simbrain API)

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

All Implemented Interfaces:

CopyableGroup<NeuronGroup>

Direct Known Subclasses:

CompetitiveGroup, KWTA, NeuronLayer, SOMGroup, WinnerTakeAll
```
public class NeuronGroup
extends Group
implements CopyableGroup<NeuronGroup>
```
A group of neurons. A primary abstraction for larger network structures. Layers in feed-forward networks are neuron groups. Self-organizing-maps subclass this class. Etc.

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`DEFAULT_GROUP_SIZE` The number of neurons in the group by default.
`static Layout`	`DEFAULT_LAYOUT` Default layout for neuron groups.
`static int`	`FLUSH_FREQUENCY` The default for how often `writeActsToFile()` should flush the output stream when writing to a file.

Constructor Summary

Constructors
Constructor and Description
`NeuronGroup(Network network)` Create a neuron group without any initial neurons.
`NeuronGroup(Network net, int numNeurons)` Construct a new neuron group with a specified number of neurons.
`NeuronGroup(Network net, java.util.List<Neuron> neurons)` Construct a new neuron group from a list of neurons.
`NeuronGroup(Network network, NeuronGroup toCopy)` Copy constructor.
`NeuronGroup(Network network, java.awt.geom.Point2D initialPosition)` Create a neuron group without any initial neurons and an initial position.
`NeuronGroup(Network net, java.awt.geom.Point2D initialPosition, int numNeurons)` Construct a new neuron group with a specified number of neurons.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addIncomingSg(SynapseGroup sg)`
`void`	`addNeuron(Neuron neuron)` Add neuron to group.
`void`	`addNeuron(Neuron neuron, boolean fireEvent)` Add a neuron to group.
`void`	`addOutgoingSg(SynapseGroup sg)`
`void`	`applyInputs()` Apply any input values to the activations of the neurons in this group.
`void`	`applyLayout()` Apply this group's layout to its neurons.
`void`	`applyLayout(java.awt.geom.Point2D initialPosition)` Apply this group's layout to its neurons based on a specified initial position.
`void`	`clearActivations()` Set all activations to 0.
`void`	`clearNeuronList()` Clear the neuron list.
`boolean`	`containsAsIncoming(SynapseGroup sg)`
`boolean`	`containsAsOutgoing(SynapseGroup sg)`
`boolean`	`containsNeuron(Neuron n)` True if the group contains the specified neuron.
`void`	`copyActivations(NeuronGroup toCopy)` Copy activations from one neuron group to this one.
`NeuronGroup`	`deepCopy(Network newParent)` Returns a deep copy of a copyable group using the same root network as the original.
`void`	`delete()` Perform necessary deletion cleanup.
`void`	`forceSetActivationLevels(double value)` Force set all activations to a specified value.
`void`	`forceSetActivations(double[] inputs)` Force set activations of neurons using an array of doubles.
`double[]`	`getActivations()` Return activations as a double array.
`int`	`getBetweenNeuronInterval()`
`double[]`	`getBiases()` Return biases as a double array.
`double`	`getCenterX()` Get the central x coordinate of this group, based on the positions of the neurons that comprise it.
`double`	`getCenterY()` Get the central y coordinate of this group, based on the positions of the neurons that comprise it.
`double[]`	`getExternalActivations()` Returns a vector of activations to be used by some object external to the neuron group.
`java.awt.geom.Point2D[]`	`getFourCorners()`
`int`	`getGridThreshold()`
`double`	`getHeight()` Return the height of this group, based on the positions of the neurons that comprise it.
`java.util.HashSet<SynapseGroup>`	`getIncomingSgs()`
`java.util.List<Synapse>`	`getIncomingWeights()` Return flat list of fanins for all neurons in group.
`java.lang.String`	`getLabelsOfActiveNeurons(double threshold)` Utility to method (used in couplings) to get a string showing the labels of all "active" neurons (neurons with activation above a threshold).
`Layout`	`getLayout()`
`double`	`getMaxDim()`
`double`	`getMaxX()` Returns the maximum X position of this group based on the neurons that comprise it.
`double`	`getMaxY()` Returns the maximum Y position of this group based on the neurons that comprise it.
`double`	`getMinX()` Returns the minimum X position of this group based on the neurons that comprise it.
`double`	`getMinY()` Returns the minimum Y position of this group based on the neurons that comprise it.
`java.lang.String`	`getMostActiveNeuron()` Returns the label of the most active neuron.
`java.util.List<Neuron>`	`getNeuronList()`
`java.util.List<Neuron>`	`getNeuronsInRadius(Neuron n, int radius)` Returns all the neurons in this group within a certain radius of the given neuron.
`java.lang.String`	`getNeuronType()`
`static int`	`getNumSubSamples()`
`java.util.HashSet<SynapseGroup>`	`getOutgoingSg()`
`java.util.List<Synapse>`	`getOutgoingWeights()` Return flat list of fanouts for all neurons in group.
`java.awt.geom.Point2D.Double`	`getPosition()` Return current position (upper left corner of neuron in the farthest north-west position.
`double[]`	`getSpikeIndexes()` Returns an array of spike indices used in couplings, (e.g.
`double[][]`	`getTestData()`
`java.lang.String`	`getTypeDescription()` Return a human-readable name for this type of neuron group.
`java.lang.String`	`getUpdateMethodDesecription()` Returns a description of this group's update method, which is displayed in the update manager panel.
`double`	`getWidth()` Return the width of this group, based on the positions of the neurons that comprise it.
`boolean`	`inFanInOfSomeNode(Synapse synapse)` Returns true if the provided synapse is in the fan-in weight vector of some node in this neuron group.
`boolean`	`isAllClamped()` Returns true if all the neurons in this group are clamped.
`boolean`	`isAllUnclamped()` Returns true if all the neurons in this group are unclamped.
`boolean`	`isEmpty()` Whether this group is empty or not.
`boolean`	`isInputMode()`
`boolean`	`isRecordAsSpikes()`
`boolean`	`isRecording()`
`boolean`	`isSpikingNeuronGroup()`
`static boolean`	`isUseSubSampling()`
`void`	`offset(double offsetX, double offsetY)` Translate all neurons (the only objects with position information).
`void`	`printActivations()` Print activations as a vector.
`void`	`prune()` Removes all neurons with no incoming or outgoing synapses from the group.
`void`	`randomize()` Randomize all neurons in group.
`void`	`randomizeBiases(double lower, double upper)` Randomize bias for all neurons in group.
`void`	`randomizeIncomingWeights()` Randomize fan-in for all neurons in group.
`void`	`randomizeOutgoingWeights()` Randomize fan-out for all neurons in group.
`void`	`readNextInputs()` A forwarding method surrounding `readNextInputUnsafe()` in the appropriate checks to make it safe.
`boolean`	`removeIncomingSg(SynapseGroup sg)`
`void`	`removeNeuron(Neuron toDelete)` Delete the provided neuron.
`boolean`	`removeOutgoingSg(SynapseGroup sg)`
`void`	`resetSubsamplingIndices()` Reset the indices used for subsampling
`void`	`setActivationLevels(double value)` Set all activations to a specified value.
`void`	`setActivations(double[] inputs)` Set activations of neurons using an array of doubles.
`void`	`setBetweenNeuronInterval(int betweenNeuronInterval)`
`void`	`setClamped(boolean clamp)` Set clamping on all neurons in this group.
`void`	`setGridThreshold(int gridThreshold)`
`void`	`setIncrement(double increment)` Set the increment on all neurons in this group.
`void`	`setInputMode(boolean inputMode)` Sets whether or not this neuron group is in input mode.
`void`	`setInputValues(double[] inputs)` Set input values of neurons using an array of doubles.
`void`	`setLayout(Layout layout)` Set the layout.
`void`	`setLayoutBasedOnSize()` If more than gridThreshold neurons use a grid layout, else a horizontal line layout.
`void`	`setLayoutBasedOnSize(java.awt.geom.Point2D initialPosition)` If more than gridThreshold neurons use a grid layout, else a horizontal line layout.
`void`	`setLocation(double x, double y)`
`void`	`setLowerBound(double lb)` Set the lower bound on all neurons in this group.
`void`	`setNeuronType(NeuronUpdateRule base)` Set the update rule for the neurons in this group.
`void`	`setNeuronType(java.lang.String rule)` Set the string update rule for the neurons in this group.
`static void`	`setNumSubSamples(int numSubSamples)`
`void`	`setRecordAsSpikes(boolean recordAsSpikes)`
`void`	`setSpikingNeuronGroup(boolean isSpikingNeuronGroup)`
`void`	`setTestData(double[][] testData)`
`void`	`setUpperBound(double ub)` Set the upper bound on all neurons in this group.
`static void`	`setUseSubSampling(boolean useSubSampling)`
`void`	`setXYZCoordinatesFromFile(java.lang.String filename)`
`int`	`size()`
`void`	`startRecording(java.io.File outputFile)` Creates a file which activations will be written to and activates the necessary output streams.
`void`	`stopRecording()` Halts recording of activations.
`void`	`testAndSetIfSpiking()` Tests if this neuron group can be considered a spiking neuron group and sets that value to true/false acordingly.
`java.lang.String`	`toString()`
`void`	`update()` Updates all the neurons in the neuron group according to their NeuronUpdateRule(s).
`void`	`writeActsToFile()` Writes the activations of the network to a file.

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
  - FLUSH_FREQUENCY
```
public static final int FLUSH_FREQUENCY
```
    The default for how often writeActsToFile() should flush the output stream when writing to a file.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_GROUP_SIZE
```
public static final int DEFAULT_GROUP_SIZE
```
    The number of neurons in the group by default.
    
    See Also:
    
    Constant Field Values
  - DEFAULT_LAYOUT
```
public static final Layout DEFAULT_LAYOUT
```
    Default layout for neuron groups.
- Constructor Detail
  - NeuronGroup
```
public NeuronGroup(Network net,
                   java.util.List<Neuron> neurons)
```
    Construct a new neuron group from a list of neurons.
    
    Parameters:
    
    net - the network
    
    neurons - the neurons
  - NeuronGroup
```
public NeuronGroup(Network net,
                   int numNeurons)
```
    Construct a new neuron group with a specified number of neurons.
    
    Parameters:
    
    net - parent network
    
    numNeurons - how many neurons it will have
  - NeuronGroup
```
public NeuronGroup(Network net,
                   java.awt.geom.Point2D initialPosition,
                   int numNeurons)
```
    Construct a new neuron group with a specified number of neurons.
    
    Parameters:
    
    net - parent network
    
    initialPosition - initial location of the group
    
    numNeurons - how many neurons it will have
  - NeuronGroup
```
public NeuronGroup(Network network,
                   java.awt.geom.Point2D initialPosition)
```
    Create a neuron group without any initial neurons and an initial position.
    
    Parameters:
    
    network - parent network
    
    initialPosition - the starting position from which to lay-out the neurons in the group whenever they are added.
  - NeuronGroup
```
public NeuronGroup(Network network)
```
    Create a neuron group without any initial neurons.
    
    Parameters:
    
    network - parent network
  - NeuronGroup
```
public NeuronGroup(Network network,
                   NeuronGroup toCopy)
```
    Copy constructor. pass in network for cases where a group is pasted from one network to another
    
    Parameters:
    
    network - parent network
    
    toCopy - the neuron group this will become a (deep) copy of.
- Method Detail
  - resetSubsamplingIndices
```
public void resetSubsamplingIndices()
```
    Reset the indices used for subsampling
  - deepCopy
```
public NeuronGroup deepCopy(Network newParent)
```
    Description copied from interface: CopyableGroup
    
    Returns a deep copy of a copyable group using the same root network as the original.
    
    Specified by:
    
    deepCopy in interface CopyableGroup<NeuronGroup>
    
    Parameters:
    
    newParent - the parent network for this group, potentially different from the original (used when copying and pasting from one network to another)
    
    Returns:
    
    a deep copy of a group
  - delete
```
public void delete()
```
    Description copied from class: Group
    
    Perform necessary deletion cleanup.
    
    Specified by:
    
    delete in class Group
  - update
```
public void update()
```
    Updates all the neurons in the neuron group according to their NeuronUpdateRule(s). If the group is in input mode reads in the next set of values from the input table and sets the neuron values accordingly.
    
    Specified by:
    
    update in class Group
  - readNextInputs
```
public void readNextInputs()
```
    A forwarding method surrounding readNextInputUnsafe() in the appropriate checks to make it safe. This allows outside classes to force the neuron group to read in and set activations according to the value(s) in its input table.
  - startRecording
```
public void startRecording(java.io.File outputFile)
```
    Creates a file which activations will be written to and activates the necessary output streams. Uses the name of the the group for the name of the file, adding an incremented number to the name each time this method is called. Recording happens only if the appropriate neuron group recording action is a part of the network update. Also checks if this neuron group is populated entirely by spiking neurons and if so, sets recordAsSpikes to true, since writeActsToFile() writes activations differently if the neuron group contains only spiking neurons.
    
    Parameters:
    
    outputFile - the file to write the activations to
  - stopRecording
```
public void stopRecording()
```
    Halts recording of activations. Closes all involved output streams.
  - writeActsToFile
```
public void writeActsToFile()
```
    Writes the activations of the network to a file. When #startRecording() is called, the group checks whether or not the group is entirely populated by spiking neurons. If it is then this methods writes the activations to a file as spike trains in [neuron id][spk time] couplets. Otherwise it writes the neurons' activation values as a state matrix to the file. Flushes the output stream every FLUSH_FREQUENCY invocations.
  - getNeuronType
```
public java.lang.String getNeuronType()
```
    Returns:
    
    the name of the neuron update rule used by all the neurons in this group (or mixed if more than one update rule governs the neurons).
  - getNeuronList
```
public java.util.List<Neuron> getNeuronList()
```
    Returns:
    
    the neurons in this group.
  - setNeuronType
```
public void setNeuronType(NeuronUpdateRule base)
```
    Set the update rule for the neurons in this group.
    
    Parameters:
    
    base - the neuron update rule to set.
  - setNeuronType
```
public void setNeuronType(java.lang.String rule)
```
    Set the string update rule for the neurons in this group.
    
    Parameters:
    
    rule - the neuron update rule to set.
  - getTypeDescription
```
public java.lang.String getTypeDescription()
```
    Return a human-readable name for this type of neuron group. Subclasses should override this. Used in the Gui for various purposes.
    
    Returns:
    
    the name of this type of neuron group.
  - inFanInOfSomeNode
```
public boolean inFanInOfSomeNode(Synapse synapse)
```
    Returns true if the provided synapse is in the fan-in weight vector of some node in this neuron group.
    
    Parameters:
    
    synapse - the synapse to check
    
    Returns:
    
    true if it's attached to a neuron in this group
  - randomizeIncomingWeights
```
public void randomizeIncomingWeights()
```
    Randomize fan-in for all neurons in group.
  - randomizeOutgoingWeights
```
public void randomizeOutgoingWeights()
```
    Randomize fan-out for all neurons in group.
  - getIncomingWeights
```
public java.util.List<Synapse> getIncomingWeights()
```
    Return flat list of fanins for all neurons in group.
    
    Returns:
    
    incoming weights
  - getOutgoingWeights
```
public java.util.List<Synapse> getOutgoingWeights()
```
    Return flat list of fanouts for all neurons in group.
    
    Returns:
    
    outgoing weights
  - randomize
```
public void randomize()
```
    Randomize all neurons in group.
  - randomizeBiases
```
public void randomizeBiases(double lower,
                            double upper)
```
    Randomize bias for all neurons in group.
    
    Parameters:
    
    lower - lower bound for randomization.
    
    upper - upper bound for randomization.
  - addNeuron
```
public void addNeuron(Neuron neuron,
                      boolean fireEvent)
```
    Add a neuron to group.
    
    Parameters:
    
    neuron - neuron to add
    
    fireEvent - whether to fire a neuron added event
  - addNeuron
```
public void addNeuron(Neuron neuron)
```
    Add neuron to group.
    
    Parameters:
    
    neuron - neuron to add
  - removeNeuron
```
public void removeNeuron(Neuron toDelete)
```
    Delete the provided neuron.
    
    Parameters:
    
    toDelete - the neuron to delete
  - prune
```
public void prune()
```
    Removes all neurons with no incoming or outgoing synapses from the group.
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString 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.
  - setInputValues
```
public void setInputValues(double[] inputs)
```
    Set input values of neurons using an array of doubles. Assumes the order of the items in the array matches the order of items in the neuronlist. Does not throw an exception if the provided input array and neuron list do not match in size.
    
    Parameters:
    
    inputs - the input vector as a double array.
  - setActivations
```
public void setActivations(double[] inputs)
```
    Set activations of neurons using an array of doubles. Assumes the order of the items in the array matches the order of items in the neuronlist. Does not throw an exception if the provided input array and neuron list do not match in size.
    
    Parameters:
    
    inputs - the input vector as a double array.
  - forceSetActivations
```
public void forceSetActivations(double[] inputs)
```
    Force set activations of neurons using an array of doubles. Assumes the order of the items in the array should match the order of items in the neuronlist. Does not throw an exception if the provided input array and neuron list do not match in size.
    
    Parameters:
    
    inputs - the input vector as a double array.
  - getActivations
```
public double[] getActivations()
```
    Return activations as a double array.
    
    Returns:
    
    the activation array
  - getSpikeIndexes
```
public double[] getSpikeIndexes()
```
    Returns an array of spike indices used in couplings, (e.g. to a raster plot). For example, if a neuron group has 9 neurons, and neurons 1 and 4 just spiked, the producer will send the list (1,0,0,4,0,0,0,0,0).
    
    Returns:
    
    the spike index array
  - getBiases
```
public double[] getBiases()
```
    Return biases as a double array.
    
    Returns:
    
    the bias array
  - containsNeuron
```
public boolean containsNeuron(Neuron n)
```
    True if the group contains the specified neuron.
    
    Parameters:
    
    n - neuron to check for.
    
    Returns:
    
    true if the group contains this neuron, false otherwise
  - size
```
public int size()
```
    Specified by:
    
    size in class Group
    
    Returns:
    
    the number of neurons in the group
  - getNeuronsInRadius
```
public java.util.List<Neuron> getNeuronsInRadius(Neuron n,
                                                 int radius)
```
    Returns all the neurons in this group within a certain radius of the given neuron. This method will never return the given neuron as part of the list of neurons within the given radius, nor will it return neurons with the exact same position as the given neuron as a part of the returned list.
    
    Parameters:
    
    n - the neurons
    
    radius - the radius to search within.
    
    Returns:
    
    neurons in the group within a certain radius
  - getCenterX
```
public double getCenterX()
```
    Get the central x coordinate of this group, based on the positions of the neurons that comprise it.
    
    Returns:
    
    the center x coordinate.
  - getCenterY
```
public double getCenterY()
```
    Get the central y coordinate of this group, based on the positions of the neurons that comprise it.
    
    Returns:
    
    the center y coordinate.
  - getMaxX
```
public double getMaxX()
```
    Returns the maximum X position of this group based on the neurons that comprise it.
    
    Returns:
    
    the x position of the farthest right neuron in the group.
  - getMinX
```
public double getMinX()
```
    Returns the minimum X position of this group based on the neurons that comprise it.
    
    Returns:
    
    the x position of the farthest left neuron in the group.
  - getMaxY
```
public double getMaxY()
```
    Returns the maximum Y position of this group based on the neurons that comprise it.
    
    Returns:
    
    the y position of the farthest north neuron in the group.
  - getMinY
```
public double getMinY()
```
    Returns the minimum Y position of this group based on the neurons that comprise it.
    
    Returns:
    
    the y position of the farthest south neuron in the group.
  - getWidth
```
public double getWidth()
```
    Return the width of this group, based on the positions of the neurons that comprise it.
    
    Returns:
    
    the width of the group
  - getHeight
```
public double getHeight()
```
    Return the height of this group, based on the positions of the neurons that comprise it.
    
    Returns:
    
    the height of the group
  - getMaxDim
```
public double getMaxDim()
```
    Returns:
    
    the longest dimensions upon which neurons are laid out.
  - getFourCorners
```
public java.awt.geom.Point2D[] getFourCorners()
```
    Returns:
    
    the spatial positions of the corners of the neuron group (X and Y only)
  - setLocation
```
public void setLocation(double x,
                        double y)
```
    Parameters:
    
    x - x coordinate for neuron group
    
    y - y coordinate for neuron group
  - offset
```
public void offset(double offsetX,
                   double offsetY)
```
    Translate all neurons (the only objects with position information).
    
    Parameters:
    
    offsetX - x offset for translation.
    
    offsetY - y offset for translation.
  - clearActivations
```
public void clearActivations()
```
    Set all activations to 0.
  - setClamped
```
public void setClamped(boolean clamp)
```
    Set clamping on all neurons in this group.
    
    Parameters:
    
    clamp - true to clamp them, false otherwise
  - setActivationLevels
```
public void setActivationLevels(double value)
```
    Set all activations to a specified value.
    
    Parameters:
    
    value - the value to set the neurons to
  - forceSetActivationLevels
```
public void forceSetActivationLevels(double value)
```
    Force set all activations to a specified value.
    
    Parameters:
    
    value - the value to set the neurons to
  - copyActivations
```
public void copyActivations(NeuronGroup toCopy)
```
    Copy activations from one neuron group to this one.
    
    Parameters:
    
    toCopy - the group to copy activations from.
  - printActivations
```
public void printActivations()
```
    Print activations as a vector.
  - 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.
  - applyInputs
```
public void applyInputs()
```
    Apply any input values to the activations of the neurons in this group.
  - getLayout
```
public Layout getLayout()
```
    Returns:
    
    the layout
  - setLayout
```
public void setLayout(Layout layout)
```
    Set the layout. Does not apply it. Call apply layout for that.
    
    Parameters:
    
    layout - the layout to set
  - getPosition
```
public java.awt.geom.Point2D.Double getPosition()
```
    Return current position (upper left corner of neuron in the farthest north-west position.
    
    Returns:
    
    position upper left position of group
  - setXYZCoordinatesFromFile
```
public void setXYZCoordinatesFromFile(java.lang.String filename)
```
  - applyLayout
```
public void applyLayout()
```
    Apply this group's layout to its neurons.
  - applyLayout
```
public void applyLayout(java.awt.geom.Point2D initialPosition)
```
    Apply this group's layout to its neurons based on a specified initial position.
    
    Parameters:
    
    initialPosition - the position from which to begin the layout.
  - getIncomingSgs
```
public java.util.HashSet<SynapseGroup> getIncomingSgs()
```
  - getOutgoingSg
```
public java.util.HashSet<SynapseGroup> getOutgoingSg()
```
  - containsAsIncoming
```
public boolean containsAsIncoming(SynapseGroup sg)
```
  - containsAsOutgoing
```
public boolean containsAsOutgoing(SynapseGroup sg)
```
  - addIncomingSg
```
public void addIncomingSg(SynapseGroup sg)
```
  - addOutgoingSg
```
public void addOutgoingSg(SynapseGroup sg)
```
  - removeIncomingSg
```
public boolean removeIncomingSg(SynapseGroup sg)
```
  - removeOutgoingSg
```
public boolean removeOutgoingSg(SynapseGroup sg)
```
  - isAllClamped
```
public boolean isAllClamped()
```
    Returns true if all the neurons in this group are clamped.
    
    Returns:
    
    true if all neurons are clamped, false otherwise
  - isAllUnclamped
```
public boolean isAllUnclamped()
```
    Returns true if all the neurons in this group are unclamped.
    
    Returns:
    
    true if all neurons are unclamped, false otherwise
  - setLowerBound
```
public void setLowerBound(double lb)
```
    Set the lower bound on all neurons in this group.
    
    Parameters:
    
    lb - the lower bound to set.
  - setUpperBound
```
public void setUpperBound(double ub)
```
    Set the upper bound on all neurons in this group.
    
    Parameters:
    
    ub - the upper bound to set.
  - setIncrement
```
public void setIncrement(double increment)
```
    Set the increment on all neurons in this group.
    
    Parameters:
    
    increment - the increment to set.
  - getTestData
```
public double[][] getTestData()
```
    Returns:
    
    the testData
  - setTestData
```
public void setTestData(double[][] testData)
                 throws java.lang.IllegalArgumentException
```
    Parameters:
    
    testData - the testData to set
    
    Throws:
    
    java.lang.IllegalArgumentException
  - testAndSetIfSpiking
```
public void testAndSetIfSpiking()
```
    Tests if this neuron group can be considered a spiking neuron group and sets that value to true/false acordingly.
  - setLayoutBasedOnSize
```
public void setLayoutBasedOnSize()
```
    If more than gridThreshold neurons use a grid layout, else a horizontal line layout.
  - setLayoutBasedOnSize
```
public void setLayoutBasedOnSize(java.awt.geom.Point2D initialPosition)
```
    If more than gridThreshold neurons use a grid layout, else a horizontal line layout.
    
    Parameters:
    
    initialPosition - the initial Position for the layout
  - getBetweenNeuronInterval
```
public int getBetweenNeuronInterval()
```
    Returns:
    
    the betweenNeuronInterval
  - setBetweenNeuronInterval
```
public void setBetweenNeuronInterval(int betweenNeuronInterval)
```
    Parameters:
    
    betweenNeuronInterval - the betweenNeuronInterval to set
  - getGridThreshold
```
public int getGridThreshold()
```
    Returns:
    
    the gridThreshold
  - setGridThreshold
```
public void setGridThreshold(int gridThreshold)
```
    Parameters:
    
    gridThreshold - the gridThreshold to set
  - clearNeuronList
```
public void clearNeuronList()
```
    Clear the neuron list.
  - getLabelsOfActiveNeurons
```
public java.lang.String getLabelsOfActiveNeurons(double threshold)
```
    Utility to method (used in couplings) to get a string showing the labels of all "active" neurons (neurons with activation above a threshold).
    
    Parameters:
    
    threshold - threshold above which to consider a neuron "active"
    
    Returns:
    
    the "active labels"
  - getMostActiveNeuron
```
public java.lang.String getMostActiveNeuron()
```
    Returns the label of the most active neuron.
    
    Returns:
    
    the label of the most active neuron
  - isRecording
```
public boolean isRecording()
```
  - setRecordAsSpikes
```
public void setRecordAsSpikes(boolean recordAsSpikes)
```
  - isRecordAsSpikes
```
public boolean isRecordAsSpikes()
```
  - isInputMode
```
public boolean isInputMode()
```
  - setInputMode
```
public void setInputMode(boolean inputMode)
                  throws java.lang.IllegalArgumentException
```
    Sets whether or not this neuron group is in input mode. When in input mode the neuron group will draw activations from its testData field instead of from any impinging synapses or its own neuron update functions. This function removes the neurons from the neuron set in ConcurrentBufferedUpdate, preventing it from updating the neurons in this group, and re-adds those neurons when input mode is turned off. Thus the update action associated with this neuron group MUST be added to the network update sequence even if ParallelBufferedUpdate is selected in order for input values to update the group properly.
    
    Parameters:
    
    inputMode - whether or not this group will run in input mode during network and workspace updates.
    
    Throws:
    
    java.lang.IllegalArgumentException - if input mode is set to true, but the testData field is set to null.
  - isSpikingNeuronGroup
```
public boolean isSpikingNeuronGroup()
```
  - setSpikingNeuronGroup
```
public void setSpikingNeuronGroup(boolean isSpikingNeuronGroup)
```
  - getExternalActivations
```
public double[] getExternalActivations()
```
    Returns a vector of activations to be used by some object external to the neuron group. If subsampling is turned on only some sample of these activations will be returned. Thus if plotting activations of a thousand node network, a sample of 100 activations might be returned.
    
    Returns:
    
    the vector of external activations.
  - isUseSubSampling
```
public static boolean isUseSubSampling()
```
    Returns:
    
    the useSubSampling
  - setUseSubSampling
```
public static void setUseSubSampling(boolean useSubSampling)
```
    Parameters:
    
    useSubSampling - the useSubSampling to set
  - getNumSubSamples
```
public static int getNumSubSamples()
```
    Returns:
    
    the numSubSamples
  - setNumSubSamples
```
public static void setNumSubSamples(int numSubSamples)
```
    Parameters:
    
    numSubSamples - the numSubSamples to set

Class NeuronGroup

Field Summary

Constructor Summary

Method Summary

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

Methods inherited from class java.lang.Object

Field Detail

FLUSH_FREQUENCY

DEFAULT_GROUP_SIZE

DEFAULT_LAYOUT

Constructor Detail

NeuronGroup

NeuronGroup

NeuronGroup

NeuronGroup

NeuronGroup

NeuronGroup

Method Detail

resetSubsamplingIndices

deepCopy

delete

update

readNextInputs

startRecording

stopRecording

writeActsToFile

getNeuronType

getNeuronList

setNeuronType

setNeuronType

getTypeDescription

inFanInOfSomeNode

randomizeIncomingWeights

randomizeOutgoingWeights

getIncomingWeights

getOutgoingWeights

randomize

randomizeBiases

addNeuron

addNeuron

removeNeuron

prune

toString

isEmpty

setInputValues

setActivations

forceSetActivations

getActivations

getSpikeIndexes

getBiases

containsNeuron

size

getNeuronsInRadius

getCenterX

getCenterY

getMaxX

getMinX

getMaxY

getMinY

getWidth

getHeight

getMaxDim

getFourCorners

setLocation

offset

clearActivations

setClamped

setActivationLevels

forceSetActivationLevels

copyActivations

printActivations

getUpdateMethodDesecription

applyInputs

getLayout

setLayout

getPosition

setXYZCoordinatesFromFile

applyLayout

applyLayout

getIncomingSgs