neuroidnet.ntr
Class Neuroid

java.lang.Object
  |
  +--neuroidnet.ntr.Neuroid

All Implemented Interfaces:

Expressive, Input, Serializable, Simulation

Direct Known Subclasses:

SRMNeuroid

public abstract class Neuroid

extends Object

implements Simulation, Input, Expressive

Abstract neuroid entity. Instances are contained in Areas.

Since:

1.0

Version:

$Revision: 1.25 $ for this file

Author:

Cengiz Gunay

See Also:

Area, Serialized Form

Nested Class Summary

protected class	Neuroid.Mode Modes that a neuron can have.
(package private) class	Neuroid.SynapseActivityTask Iterator task class which scans synapses of the neuroid.

Field Summary

protected Area	area Parent Area.
protected Concept	concept Associated concept if neuroid has memorized anything.
(package private) boolean	debug If set, outputs debugging info about this neuroid.
(package private) int	id Sequence of Neuroid in the array held in Area.
protected Neuroid.Mode	mode Represents the state and dynamic parameters of the neuroid.
(package private) double	potential Membrane potential.
(package private) NeuroidProfile	profile
(package private) Vector	spikeTrain List of times that the neuroid fired.
protected Dendrite	synapses List of incoming synapses.
(package private) double	timeLastFired Last firing time of this Neuroid.
protected boolean	watch If set, the neuroid saves informatoin about its state changes.

Constructor Summary

Neuroid(Area area)
and connects to area.

Method Summary

int	addSynapse(Synapse synapse) Add synapse to synapses and return index to become the id of the Synapse.
protected abstract void	calculatePotential() Calculate the potential here.
String	dumpData() Deprecated. Use plots and the profile gathering system.
void	fire() Fires the neuroid.
Area	getArea() Get the value of area.
Concept	getConcept() Get the value of concept.
int	getId() Get the value of id.
Neuroid.Mode	getMode() Get the value of mode.
NeuroidProfile	getProfile() Get the value of profile.
String	getProperties() Describe in higher detail.
Vector	getSpikeTrain() Get the value of spikeTrain.
String	getStatus() Output of toString() plus potential, mode status, last fire time, and concept name.
Dendrite	getSynapses() Get the value of synapses.
double	getTimeLastFired() Get the value of timeLastFired.
void	init() N/A
boolean	isDebug() Get the value of debug.
boolean	isWatch() Get the value of watch.
(package private) void	makeConcept() Create new concept.
void	setArea(Area v) Set the value of area.
void	setDebug(boolean v) Set the value of debug.
void	setMode(Neuroid.Mode v) Set the value of mode and connects any profilers if watched.
void	setProfile(NeuroidProfile v) Set the value of profile.
void	setSpikeTrain(Vector v) Set the value of spikeTrain.
void	setWatch(boolean v) Set the value of watch.
void	step() Update state of the Neuroid.
void	stop() N/A
String	toString() Identify the neuroid with its id and area.

Methods inherited from class java.lang.Object

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

Field Detail

potential

double potential

Membrane potential.

synapses

protected Dendrite synapses

List of incoming synapses.

timeLastFired

double timeLastFired

Last firing time of this Neuroid.

area

protected Area area

Parent Area.

concept

protected Concept concept

Associated concept if neuroid has memorized anything.

See Also:

Concept

id

final int id

Sequence of Neuroid in the array held in Area. Good for representation. Used to override Object.hashCode() and don't pass around this id, but hascode is dynamic and changes at every runtime, leaving us with a volatile identifier. Oh, well. Set in Area.addNeuroid()

See Also:

Area.neuroids, Area.addNeuroid(neuroidnet.ntr.Neuroid)

mode

protected Neuroid.Mode mode

Represents the state and dynamic parameters of the neuroid.

debug

boolean debug

If set, outputs debugging info about this neuroid.

watch

protected boolean watch

If set, the neuroid saves informatoin about its state changes.

spikeTrain

Vector spikeTrain

List of times that the neuroid fired. Redundant with the spikeTrain defined in Synapse.

See Also:

Synapse.spikeTrain

profile

NeuroidProfile profile

Constructor Detail

Neuroid

public Neuroid(Area area)

and connects to area.

Method Detail

getSynapses

public Dendrite getSynapses()

Get the value of synapses.

Returns:

value of synapses.

getTimeLastFired

public double getTimeLastFired()

Get the value of timeLastFired.

Returns:

value of timeLastFired.

getArea

public Area getArea()

Get the value of area.

Returns:

value of area.

setArea

public void setArea(Area v)

Set the value of area.

Parameters:

v - Value to assign to area.

getConcept

public Concept getConcept()

Get the value of concept.

Returns:

value of concept.

getId

public int getId()

Get the value of id.

Returns:

value of id.

getMode

public Neuroid.Mode getMode()

Get the value of mode.

Returns:

value of mode.

setMode

public void setMode(Neuroid.Mode v)

Set the value of mode and connects any profilers if watched.

Parameters:

v - Value to assign to mode.

isDebug

public boolean isDebug()

Get the value of debug.

Returns:

value of debug.

setDebug

public void setDebug(boolean v)

Set the value of debug.

Parameters:

v - Value to assign to debug.

isWatch

public boolean isWatch()

Get the value of watch.

Returns:

value of watch.

setWatch

public void setWatch(boolean v)

Set the value of watch. if watched, create a NeuroidProfile object.

Parameters:

v - Value to assign to watch.

getSpikeTrain

public Vector getSpikeTrain()

Get the value of spikeTrain.

Returns:

value of spikeTrain.

setSpikeTrain

public void setSpikeTrain(Vector v)

Set the value of spikeTrain.

Parameters:

v - Value to assign to spikeTrain.

getProfile

public NeuroidProfile getProfile()

Get the value of profile.

Returns:

value of profile.

setProfile

public void setProfile(NeuroidProfile v)

Set the value of profile.

Parameters:

v - Value to assign to profile.

init

public final void init()

N/A

Specified by:

init in interface Simulation

fire

public void fire()

Fires the neuroid. Neuroid contact container Area to propagate the spike along its axon. Adds an entry to spikeTrain if being watched.

Specified by:

fire in interface Input

See Also:

Area.fireNeuroid(neuroidnet.ntr.Neuroid), watch

step

public void step()

Update state of the Neuroid. Use the UMT algorithm by default, though behavior will depend on Synapse parameters.

Specified by:

step in interface Simulation

See Also:

Synapse

stop

public void stop()

N/A

Specified by:

stop in interface Simulation

calculatePotential

protected abstract void calculatePotential()

Calculate the potential here.

See Also:

potential

makeConcept

void makeConcept()
           throws ConceptSaturatedException

Create new concept. Trace back synapses that made this neuroid go to UM mode to find concept set. Then look for associated concept in conceptArea, otherwise create new Concept using this concept set.

TODO: destroy old concept if it exists.

Throws:

ConceptSaturatedException

See Also:

ConceptArea, Concept, ConceptSaturatedException

addSynapse

public int addSynapse(Synapse synapse)

Add synapse to synapses and return index to become the id of the Synapse. Analogous to Area.addNeuroid()

Parameters:

synapse - a Synapse to add to synapses

Returns:

an int value, the index of new synapse in synapses

See Also:

Area.addNeuroid(neuroidnet.ntr.Neuroid)

toString

public String toString()

Identify the neuroid with its id and area.

Specified by:

toString in interface Expressive

Overrides:

toString in class Object

Returns:

a String value

getStatus

public String getStatus()

Output of toString() plus potential, mode status, last fire time, and concept name.

Specified by:

getStatus in interface Expressive

Returns:

a String value

See Also:

Expressive.toString()

getProperties

public String getProperties()

Describe in higher detail. List all contained synapses.

Specified by:

getProperties in interface Expressive

Returns:

a String value

See Also:

Expressive.getStatus()

dumpData

public String dumpData()

Deprecated. Use plots and the profile gathering system.

Dump synaptic activity to output (matlab format). Called by: TODO: optionally in gnuplot format?

See Also:

ConceptArea#dumpData