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Serialized Form

Package neuroidnet.ntr

Class neuroidnet.ntr.AdThNeuroid implements Serializable

Serialized Fields

thresholdDevice

AdThNeuroid.AdaptiveThresholdDevice thresholdDevice
The adaptive threshold.

Class neuroidnet.ntr.AdThNeuroid.Mode implements Serializable

Serialized Fields

state

Neuroid.Mode.State state

quiescent

Neuroid.Mode.State quiescent

rising

Neuroid.Mode.State rising

Class neuroidnet.ntr.Area implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException
Method called when a serialized object is loaded. Only customization done is to create a new thread to reside in the transient thread variable.

Throws:
IOException - if an error occurs
ClassNotFoundException - if an error occurs
Serialized Fields

name

String name
Name of the Area for identification purposes.

time

double time
Time of the area.

deltaT

double deltaT
Increment of time for algorithms. Proxy for deltaT in network.

See Also:
Network.deltaT

id

int id
Id tag of the area.

numberOfNeuroids

int numberOfNeuroids
Number of Neuroids contained in Area. TODO: should be obsolete, redundant info with size of neuroids vector.

See Also:
Area.neuroids, Neuroid

replication

int replication
The replication factor, i.e. the number of Neuroids allocated for each concept.

period

double period
Oscillation period of Neuroids.

See Also:
Neuroid

neuroids

Vector neuroids
List of Neuroids contained in Area. TODO: Fix access modifier from public, becuase of peripherals..

See Also:
Neuroid

inhibitoryInterNeuroid

Neuroid inhibitoryInterNeuroid
The global inhibitory neuroid that gets input from all and projects to all in the area.

fromInhibitorySynapseTemplate

Synapse fromInhibitorySynapseTemplate
The template used for creating synapses from the inhibitoryInterNeuroid

See Also:
Area.inhibitoryInterNeuroid

toInhibitorySynapseTemplate

Synapse toInhibitorySynapseTemplate
The template used for creating synapses to the inhibitoryInterNeuroid

See Also:
Area.inhibitoryInterNeuroid

inhibitorySynapseVector

AxonArbor inhibitorySynapseVector
The axon emanating from the inhibitoryInterNeuroid

See Also:
Area.init()

axons

Hashtable axons
Hash table holding the white matter, e.g. the axons of neuroids residing in this Area connecting to Synapses of other Neuroids. Returns a Vector of Synapses for every Neuroid key.

See Also:
Synapse, Neuroid

stepRequested

boolean stepRequested
Flag showing incoming requets to step().

See Also:
Area.run(), Area.step()

conceptCount

int conceptCount
Count of concept allocations made (via call to addArbitrarySynapses) in this Area.

See Also:
Area.addArbitrarySynapses(neuroidnet.ntr.Synapse, neuroidnet.ntr.Neuroid, int), Peripheral.Concept

network

Network network
Pointer to parent network TODO: Fix access modifier from public, problem with SensoryNeuroid

inhibInter

boolean inhibInter
True if the area contains a inhibitory inter-neuroid.

timeConstantM

double timeConstantM
Membrane time constant of all neurons in this area.

activationThreshold

double activationThreshold
The threshold to change a Neuroid from AM to AM1 mode.

See Also:
Neuroid.step()

Class neuroidnet.ntr.AxonArbor implements Serializable

Serialized Fields

srcNeuroid

Neuroid srcNeuroid
Axon's owner neuroid.

See Also:
Neuroid

destArea

Area destArea
Describe variable destNeuroid here.

destSynapseTemplate

Synapse destSynapseTemplate
Template to create all synapses of this AxonArbor.

Class neuroidnet.ntr.Dendrite implements Serializable

Class neuroidnet.ntr.MembranePotentialPlot implements Serializable

Serialized Fields

plots

Vector plots
Vector of WeightedPotentialPlot

See Also:
WeightedPotentialPlot

neuroidProfile

NeuroidProfile neuroidProfile

Class neuroidnet.ntr.ModeProfile implements Serializable

Serialized Fields

neuroid

Neuroid neuroid
Neuroid enclosing the mode object profiled.

Class neuroidnet.ntr.NameNotFoundException implements Serializable

Class neuroidnet.ntr.Network implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException
Method called when a serialized object is loaded. Only customization done is to set the static numberFormat object via a call to setNumberFormatting().

Throws:
IOException - if an error occurs
ClassNotFoundException - if an error occurs
Serialized Fields

areas

Vector areas
All Areas contained in Network.

See Also:
Area

peripheral

Peripheral peripheral
Peripheral control device

conceptArea

ConceptArea conceptArea
Redundant pointer to instance of the ConceptArea (it is also in areas)

See Also:
Network.areas, ConceptArea

deltaT

double deltaT
Increment of time for algorithms. TODO: Put it elsewhere; too far to reach!

stepArea

Task stepArea
Defines what do to every step given Area object. That is, Task object that will run Area.step() for all areas contained.

See Also:
AreaInt

simulateAreas

Simulation simulateAreas
Lock variable and thread controller for event dispatching to remote (or local) areas.

isConcurrent

boolean isConcurrent
Flag to mean multi thread usage.

watchList

Set watchList

Class neuroidnet.ntr.Neuroid implements Serializable

Serialized Fields

potential

double potential
Membrane potential.

synapses

Dendrite synapses
List of incoming synapses.

timeLastFired

double timeLastFired
Last firing time of this Neuroid.

area

Area area
Parent Area.

concept

Concept concept
Associated concept if neuroid has memorized anything.

See Also:
Concept

id

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

Neuroid.Mode mode
Represents the state and dynamic parameters of the neuroid.

debug

boolean debug
If set, outputs debugging info about this neuroid.

watch

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

Class neuroidnet.ntr.Neuroid.Mode implements Serializable

Serialized Fields

state

int state
State of neuroid, can only take values defined here. TODO: Use byte?

threshold

double threshold
Threshold of the neuroid.

Class neuroidnet.ntr.NeuroidName implements Serializable

Serialized Fields

areaName

String areaName

neuroidId

int neuroidId

Class neuroidnet.ntr.NeuroidProfile implements Serializable

Serialized Fields

modeProfile

ModeProfile modeProfile

synapseProfiles

Vector synapseProfiles

neuroid

Neuroid neuroid

Class neuroidnet.ntr.PeakerNeuroid implements Serializable

Serialized Fields

dPotential

double dPotential

dPotentialOld

double dPotentialOld

ddPotential

double ddPotential

dddPotential

double dddPotential

Class neuroidnet.ntr.PeakerNeuroid.Mode implements Serializable

Serialized Fields

_state

Neuroid.Mode.State _state
The state for the continuous-time state machine. The name is chosen to be distinct from dicrete-time state machine.

quiescent

Neuroid.Mode.State quiescent

rising

Neuroid.Mode.State rising

plateau

Neuroid.Mode.State plateau

Class neuroidnet.ntr.Peripheral implements Serializable

Serialized Fields

network

Network network
Pointer to associated Network object

See Also:
ntr.Network

time

double time
Peripheral system's own account of time.

Class neuroidnet.ntr.PotentialPlot implements Serializable

Serialized Fields

synapseProfile

SynapseProfile synapseProfile

Class neuroidnet.ntr.ResynapseException implements Serializable

Class neuroidnet.ntr.SRMNeuroid implements Serializable

Serialized Fields

refractoryTimeConstant

double refractoryTimeConstant

externalCurrent

double externalCurrent
Constant external current for all neuroids in network (not used!)

sumOfCurrentWeights

double sumOfCurrentWeights
Internal.

Class neuroidnet.ntr.SRMNeuroid.Mode implements Serializable

Serialized Fields

fitnessCounter

int fitnessCounter

suggestedThreshold

double suggestedThreshold

sumOfWeights

double sumOfWeights
The total sum of incoming weights to a Neuroid should be fixed. (Why?)

See Also:
Neuroid.Neuroid(neuroidnet.ntr.Area)

Class neuroidnet.ntr.SRMNeuroid.SRMMode implements Serializable

Serialized Fields

fitnessCounter

int fitnessCounter

suggestedThreshold

double suggestedThreshold

sumOfWeights

double sumOfWeights

Class neuroidnet.ntr.Synapse implements Serializable

Serialized Fields

spikeTrain

Vector spikeTrain
List of times when spikes are received

id

int id
Identifier number of this synapse as index in the list of synapses at the postsynaptic neuroid, therefore in reference to that neuroid.

See Also:
toString

isInhibitory

boolean isInhibitory

timeConstantM

double timeConstantM
Synapse constant dynamic properties. The membrane time constant of the postsynaptic neuron. (Why in Snapse? See constructor documentation.)

See Also:
Synapse.Synapse(neuroidnet.ntr.Neuroid, neuroidnet.ntr.Neuroid, neuroidnet.ntr.Synapse)

timeConstantS

double timeConstantS
Synapse constant dynamic properties. The synaptic rise time constant.

delay

double delay
Axonal delay associated with this synapse (simplified). delay is required for the phasesegregator.Network

See Also:
phasesegregator.Network

weight

Synapse.Weight weight
Incoming weight.

srcNeuroid

Neuroid srcNeuroid
Presynaptic neuroid. TODO: The remote interfaces for this connection is not done yet. Presynaptic link can be made to either the neuroid itself or its axon, through which the neuron can be reached.

destNeuroid

Neuroid destNeuroid
Postsynaptic neuroid

profile

SynapseProfile profile

watch

boolean watch
If set, it saves information about its (weight) changes.

Class neuroidnet.ntr.SynapseProfile implements Serializable

Serialized Fields

weightProfile

Profile weightProfile

synapse

Synapse synapse

Class neuroidnet.ntr.WeightedPotentialPlot implements Serializable

Package neuroidnet.periphery

Class neuroidnet.periphery.ArtificialConcept implements Serializable

Serialized Fields

name

String name
Name of the concept

See Also:
#ArtificialConcept(Network,HashSet)

conceptSet

Set conceptSet
Set of other concepts that this concept represents, if available.

excitatorySynapse

Synapse excitatorySynapse
Excitatory synapse template to instantiate new synapses.

Class neuroidnet.periphery.ConceptArea implements Serializable

Serialized Fields

conceptLookup

Hashtable conceptLookup
Hashtable pointing from vector (set?) of concepts to concepts contained in here.

Class neuroidnet.periphery.ConceptSaturatedException implements Serializable

Class neuroidnet.periphery.SensoryArea implements Serializable

Class neuroidnet.periphery.SensoryConcept implements Serializable

Class neuroidnet.periphery.SensoryNeuroid implements Serializable

Package neuroidnet.phasesegregator

Class neuroidnet.phasesegregator.Network implements Serializable

Serialized Fields

peripheral

Peripheral peripheral

numberOfNeuroids

int numberOfNeuroids

replication

int replication

numberOfMedialAreas

int numberOfMedialAreas

numberOfItemsPerArea

int numberOfItemsPerArea

period

double period

delay

double delay

timeConstantS

double timeConstantS

timeConstantM

double timeConstantM

refractoryTimeConstant

double refractoryTimeConstant

segregation

double segregation

threshold

double threshold

nuBoost

double nuBoost

neuroidType

Class neuroidType
Type of neuroid to be employed in all areas of the network.

inputAreas

Area[] inputAreas

medialAreas

Area[] medialAreas

Class neuroidnet.phasesegregator.Peripheral implements Serializable

Serialization Methods

readObject

private void readObject(ObjectInputStream in)
                 throws IOException,
                        ClassNotFoundException
For serialization support.

Throws:
IOException - if an error occurs
ClassNotFoundException - if an error occurs
Serialized Fields

inputAreas

Area[] inputAreas

numberOfItemsPerArea

int numberOfItemsPerArea

sensoryArea

SensoryArea sensoryArea

segregation

double segregation

events

Map events
Peripheral input events map.

nextTime

Double nextTime

percepts

Hashtable percepts

Class neuroidnet.phasesegregator.StatisticalInputSequence implements Serializable

Serialized Fields

numberOfObjects

int numberOfObjects
Can be manipulated by beanshell scripts under scripts/.

numberOfNeuroids

int numberOfNeuroids

replication

int replication

numberOfMedialAreas

int numberOfMedialAreas

numberOfItemsPerArea

int numberOfItemsPerArea

simObjects

Vector simObjects
Objects to be fired in the input sequence.

Class neuroidnet.phasesegregator.ThreeLevelInputSequence implements Serializable

Class neuroidnet.phasesegregator.TwoLevelInputSequence implements Serializable

Package neuroidnet.remote

Class neuroidnet.remote.Area implements Serializable

Class neuroidnet.remote.Synapse implements Serializable

Serialized Fields

localSynapse

Synapse localSynapse
Deprecated. 

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