A B C D E F G I J K L M N P Q R S T U V W _

A

activationThreshold - Variable in class neuroidnet.ntr.Area

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

add(Synapse) - Method in class neuroidnet.ntr.Dendrite

Adds a synapse to the vector.

addArbitrarySynapses(Synapse, Neuroid, int) - Method in class neuroidnet.ntr.Area

Hack to arbitrarily choose different neurons for each allocation of concepts.

addArbitrarySynapses(Synapse, Neuroid, int) - Method in interface neuroidnet.remote.AreaInt

addArea(Area) - Method in class neuroidnet.ntr.Network

Adds an area to the network.

addAxon(Neuroid, AxonArbor) - Method in class neuroidnet.ntr.Area

Adds the synapses to the outgoing synapse record of the Area.

addNeuroid(Neuroid) - Method in class neuroidnet.ntr.AxonArbor

Adds a postsynaptic neuroid to the AxonArbor.

addNeuroid(Neuroid) - Method in class neuroidnet.ntr.Area

Adds a neuroid to the Area.

addRandomSynapse() - Method in class neuroidnet.ntr.AxonArbor

Creates a new synapse connected to a random member of the Area.

addRandomSynapse() - Method in class neuroidnet.remote.Area

Deprecated. Overload method in Area to create Remote.Synapse instead.

addRandomSynapses(Synapse, Neuroid, int) - Method in class neuroidnet.ntr.Area

Creates new numberOfSynapses Synapses for a given srcNeuroid to a specified destination destArea.

addRandomSynapses(Synapse, Neuroid, int) - Method in interface neuroidnet.remote.AreaInt

addSynapse(Synapse) - Method in class neuroidnet.ntr.AxonArbor

Adds a synapse to list of synapses only if it doesn't already exist.

addSynapse(Synapse) - Method in class neuroidnet.ntr.Neuroid

Add synapse to synapses and return index to become the id of the Synapse.

addWatch(Neuroid) - Method in interface neuroidnet.ntr.DebuggerInterface

addWatch(Neuroid) - Method in class neuroidnet.ntr.Network

Sets the watch flag of the neuroid and includes in the list of watched entities.

addWatchAll(Set) - Method in interface neuroidnet.ntr.DebuggerInterface

addWatchAll(Set) - Method in class neuroidnet.ntr.Network

addWatchs all neuroids with names given in argument.

AdThNeuroid - class neuroidnet.ntr.AdThNeuroid.

SRM neuroid augmented with an adaptive threshold element that takes the maximum value reached by the membrane potential.

AdThNeuroid.AdaptiveThresholdDevice - class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice.

Describe class AdThNeuroid here.

AdThNeuroid.AdaptiveThresholdDevice() - Constructor for class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Dummy constructor, sets the baseline to infinity.

AdThNeuroid.AdaptiveThresholdDevice(double) - Constructor for class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Sets the baseline.

AdThNeuroid.Mode - class neuroidnet.ntr.AdThNeuroid.Mode.

Finite state part of the neuroid.

AdThNeuroid.Mode() - Constructor for class neuroidnet.ntr.AdThNeuroid.Mode

Initalizes state to quiescent.

AdThNeuroid(Area) - Constructor for class neuroidnet.ntr.AdThNeuroid

Creates a threshold with infinite baseline (can never be crossed!).

AdThNeuroid(Area, double, double) - Constructor for class neuroidnet.ntr.AdThNeuroid

Creates a proper neuroid.

advanceTime(double) - Method in class neuroidnet.ntr.Network

Simulate network for given duration starting from current state.

AM - Static variable in class neuroidnet.ntr.SRMNeuroid.Mode

AM1 - Static variable in class neuroidnet.ntr.SRMNeuroid.Mode

area - Variable in class neuroidnet.ntr.Neuroid

Parent Area.

Area - class neuroidnet.ntr.Area.

Entity Area that holds neurons and keeps track of time.

Area - class neuroidnet.remote.Area.

Deprecated. See neuroidnet.ntr.Area.

Area(Network, String, int, int, double, double, boolean, double, double, Class) - Constructor for class neuroidnet.ntr.Area

Constructor with option to add inhibitory inter-neuron.

Area(Network, String, int, int, double, double, double, double, Class) - Constructor for class neuroidnet.ntr.Area

Constructor for plain Area (no inhibitory interneuron).

Area(String, int, int, double, double, double) - Constructor for class neuroidnet.remote.Area

Deprecated.

AreaController - class neuroidnet.remote.AreaController.

Create an Area and register it to the RMI registry.

AreaController() - Constructor for class neuroidnet.remote.AreaController

AreaInt - interface neuroidnet.remote.AreaInt.

Distributed extensions to Area

areaName - Variable in class neuroidnet.ntr.NeuroidName

areas - Variable in class neuroidnet.ntr.Network

All Areas contained in Network.

ArtificialConcept - class neuroidnet.periphery.ArtificialConcept.

Implementation of a Concept that listens to a population of UM neuroids which represent a certain concept.

ArtificialConcept(Network, Set) - Constructor for class neuroidnet.periphery.ArtificialConcept

Create a concept from a conjunction of concepts.

ArtificialConcept(Network, String) - Constructor for class neuroidnet.periphery.ArtificialConcept

Create a simple concept.

attach(Neuroid) - Method in interface neuroidnet.ntr.Concept

Attaches the presynaptic neuroid to concept.

attach(Neuroid) - Method in class neuroidnet.periphery.ArtificialConcept

Attaches the neuroid to the concept population.

AxonArbor - class neuroidnet.ntr.AxonArbor.

Contains all outgoing synapses of a Neuroid that end up in a particular Area with a similar Synapse template.

AxonArbor(Synapse, Neuroid, Area) - Constructor for class neuroidnet.ntr.AxonArbor

Constructor.

AxonArbor(Synapse, Neuroid, Area, int) - Constructor for class neuroidnet.ntr.AxonArbor

Specifies initial capacity for the Vector holding the synapses.

axons - Variable in class neuroidnet.ntr.Area

Hash table holding the white matter, e.g.

B

baseline - Variable in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

The initial dictated by the area forming a threshold baseline thereafter.

body() - Method in class neuroidnet.ntr.MembranePotentialPlot

body() - Method in class neuroidnet.ntr.WeightedPotentialPlot

body() - Method in class neuroidnet.ntr.PotentialPlot

Iterates on the spikes receive times of the synapse and adds epsp() functions for each.

bodySuffix - Static variable in class neuroidnet.ntr.MembranePotentialPlot

Number for generating unique identifiers for the body functions created by this class in this execution.

bsh - Variable in class neuroidnet.ntr.Shell

build() - Method in class neuroidnet.ntr.Network

Describes the architecture of the network.

build() - Method in class neuroidnet.phasesegregator.StatisticalInputSequence

Builds properties of the peripheral object.

build() - Method in class neuroidnet.phasesegregator.Network

n input areas and n medial areas.

C

c1 - Variable in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Circuit parameters: r1 & c1 are fast acting component (1/10th of mTC), and r2 & c2 are slow acting component (10 times of mTC) of the threshold.

c2 - Variable in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Circuit parameters: r1 & c1 are fast acting component (1/10th of mTC), and r2 & c2 are slow acting component (10 times of mTC) of the threshold.

calculatePotential() - Method in class neuroidnet.ntr.AdThNeuroid

Steps the threshold.

calculatePotential() - Method in class neuroidnet.ntr.Neuroid

Calculate the potential here.

calculatePotential() - Method in class neuroidnet.ntr.SRMNeuroid

Iterate through Synapses and add kernel values and decrease refractoriness at this time value.

clear() - Method in class neuroidnet.periphery.ConceptArea

commandLineMode() - Method in class neuroidnet.ntr.Shell

compareTo(Object) - Method in class neuroidnet.ntr.NeuroidName

compareTo(Object) - Method in class neuroidnet.periphery.ArtificialConcept

Required for implementing the Comparable interface for use in TreeMap implementation in ConceptArea.

concept - Variable in class neuroidnet.ntr.Neuroid

Associated concept if neuroid has memorized anything.

concept - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence.SimObject

Concept - interface neuroidnet.ntr.Concept.

Interface for read-out devices for the network.

conceptArea - Variable in class neuroidnet.ntr.Network

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

ConceptArea - class neuroidnet.periphery.ConceptArea.

Artificial area for holding Concepts.

ConceptArea(Network) - Constructor for class neuroidnet.periphery.ConceptArea

Creates an Area named ConceptArea with initially no neuroids.

conceptCount - Variable in class neuroidnet.ntr.Area

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

conceptLookup - Variable in class neuroidnet.periphery.ConceptArea

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

conceptName(Set) - Static method in class neuroidnet.periphery.ArtificialConcept

ConceptSaturatedException - exception neuroidnet.periphery.ConceptSaturatedException.

ConceptSaturatedException.java Exception thrown from ArtificialConcept.attach() whenever a Neuroid is recruited tries to attach to a Concept which has already Area.replication members.

ConceptSaturatedException(String) - Constructor for class neuroidnet.periphery.ConceptSaturatedException

conceptSet - Variable in class neuroidnet.periphery.ArtificialConcept

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

conceptSet - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence.SimObject

connectToArea(AreaInt, double, double, double) - Method in class neuroidnet.ntr.Area

Makes connections between this Area and the given destArea.

connectToArea(AreaInt, double, double, double) - Method in interface neuroidnet.remote.AreaInt

containsKey(Object) - Method in class neuroidnet.periphery.ConceptArea

containsValue(Object) - Method in class neuroidnet.periphery.ConceptArea

convertKey(Object) - Method in class neuroidnet.periphery.ConceptArea

Convert Vector to (Tree)Set for avoiding mistake of vector with same content but different order pointing to different buckets!

correctConcepts() - Method in class neuroidnet.phasesegregator.StatisticalInputSequence

Builds a sorted set from simObjects.

correctTimesRequired - Static variable in class neuroidnet.ntr.SRMNeuroid

Learning parameter for the Winnow learning algorithm.

createSensoryInputs() - Method in class neuroidnet.phasesegregator.Peripheral

Creates sensoryAreas that hold sensoryNeuroids.

crossTime - Variable in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

The last time the threshold is crossed by the membrane potential.

D

dddPotential - Variable in class neuroidnet.ntr.PeakerNeuroid

ddPotential - Variable in class neuroidnet.ntr.PeakerNeuroid

debug - Variable in class neuroidnet.ntr.Neuroid

If set, outputs debugging info about this neuroid.

DebuggerInterface - interface neuroidnet.ntr.DebuggerInterface.

DebuggerInterface.java

defaultPeriod() - Static method in class neuroidnet.ntr.SRMNeuroid

Helper method to get a period for initiating calculations in Network.

delay - Variable in class neuroidnet.ntr.Synapse

Axonal delay associated with this synapse (simplified).

delay - Variable in class neuroidnet.phasesegregator.Network

deltaT - Variable in class neuroidnet.ntr.Area

Increment of time for algorithms.

deltaT - Variable in class neuroidnet.ntr.Network

Increment of time for algorithms.

Dendrite - class neuroidnet.ntr.Dendrite.

Dendrite is a Vector that holds incoming Synapses belonging to a neuroid.

Dendrite() - Constructor for class neuroidnet.ntr.Dendrite

destArea - Variable in class neuroidnet.ntr.AxonArbor

Describe variable destNeuroid here.

destNeuroid - Variable in class neuroidnet.ntr.Synapse

Postsynaptic neuroid

destSynapseTemplate - Variable in class neuroidnet.ntr.AxonArbor

Template to create all synapses of this AxonArbor.

detach(Neuroid) - Method in interface neuroidnet.ntr.Concept

Detaches the presynaptic neuroid from concept.

detach(Neuroid) - Method in class neuroidnet.periphery.ArtificialConcept

Detaches the neuroid from the concept population.

doubleValue() - Method in class neuroidnet.ntr.Synapse.Weight

doubleValue() - Method in class neuroidnet.ntr.Neuroid.Mode

dPotential - Variable in class neuroidnet.ntr.PeakerNeuroid

dPotentialOld - Variable in class neuroidnet.ntr.PeakerNeuroid

dumpData() - Method in class neuroidnet.ntr.Synapse

Deprecated. Use plots instead.

dumpData() - Method in interface neuroidnet.ntr.DumpsData

Creates a Matlab script depicting the activity of the element on a graph or simply exports the information in matlab style variables.

dumpData() - Method in class neuroidnet.ntr.Neuroid

Deprecated. Use plots and the profile gathering system.

dumpData() - Method in class neuroidnet.periphery.ConceptArea

Deprecated. Use plots instead.

DumpsData - interface neuroidnet.ntr.DumpsData.

DumpsData.java

E

entrySet() - Method in class neuroidnet.periphery.ConceptArea

equals(Object) - Method in class neuroidnet.phasesegregator.StatisticalInputSequence.SimObject

Checks equality according to conceptSets.

evaluateResults() - Method in class neuroidnet.phasesegregator.StatisticalInputSequence

After simulation, checks if desired concepts were allocated in the NTR during simulation.

eventIterator - Variable in class neuroidnet.phasesegregator.Peripheral

events - Variable in class neuroidnet.phasesegregator.Peripheral

Peripheral input events map.

eventsAtThisTime() - Method in class neuroidnet.ntr.Peripheral

Called by step(), determines periperal actions.

eventsAtThisTime() - Method in class neuroidnet.phasesegregator.Peripheral

If nextTime is reached, call job().

excitatorySynapse - Variable in class neuroidnet.periphery.ArtificialConcept

Excitatory synapse template to instantiate new synapses.

Expressive - interface neuroidnet.ntr.Expressive.

Defines an interface on how an entity should express its identity and state.

externalCurrent - Variable in class neuroidnet.ntr.SRMNeuroid

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

F

finale() - Method in class neuroidnet.ntr.Network

To be called after everthing else is done.

fire() - Method in class neuroidnet.ntr.AxonArbor

Spikes are received at contained synapses.

fire() - Method in interface neuroidnet.ntr.Concept

Fire the neuroids associated with the Concept.

fire() - Method in interface neuroidnet.ntr.Input

Fires the device, the recipients are notified.

fire() - Method in class neuroidnet.ntr.Neuroid

Fires the neuroid.

fire() - Method in class neuroidnet.ntr.SRMNeuroid

Saves firing time to spikeTrain.

fire() - Method in class neuroidnet.phasesegregator.StatisticalInputSequence.SimObject

Loops over all percepts and fires them.

fireNeuroid(Neuroid) - Method in class neuroidnet.ntr.Area

Fires neuroid.

fireObject(int, int, int, int) - Method in class neuroidnet.phasesegregator.ThreeLevelInputSequence

fireObjectA() - Method in class neuroidnet.phasesegregator.TwoLevelInputSequence

fireObjectA() - Method in class neuroidnet.phasesegregator.ThreeLevelInputSequence

fireObjectB() - Method in class neuroidnet.phasesegregator.TwoLevelInputSequence

fireObjectB() - Method in class neuroidnet.phasesegregator.ThreeLevelInputSequence

fireObjectC() - Method in class neuroidnet.phasesegregator.TwoLevelInputSequence

fireObjectC() - Method in class neuroidnet.phasesegregator.ThreeLevelInputSequence

fireObjectInArea(int, int) - Method in class neuroidnet.phasesegregator.Peripheral

Deprecated. See methods in StatisticalInputSequence.java

fit() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

fitless() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

fitnessCounter - Variable in class neuroidnet.ntr.SRMNeuroid.Mode

fitter() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

fromInhibitorySynapseTemplate - Variable in class neuroidnet.ntr.Area

The template used for creating synapses from the inhibitoryInterNeuroid

G

get(Object) - Method in class neuroidnet.periphery.ConceptArea

getActivationThreshold() - Method in class neuroidnet.ntr.Area

Get the value of activationThreshold.

getArea() - Method in class neuroidnet.ntr.Neuroid

Get the value of area.

getArea(String) - Method in interface neuroidnet.ntr.DebuggerInterface

getArea(String) - Method in class neuroidnet.ntr.Network

Returns the Area object given the name.

getAreaName() - Method in class neuroidnet.ntr.NeuroidName

Get the value of areaName.

getAxons() - Method in class neuroidnet.ntr.Area

Get the value of axons.

getConcept() - Method in class neuroidnet.ntr.Neuroid

Get the value of concept.

getConceptArea() - Method in class neuroidnet.ntr.Network

Get the value of conceptArea.

getConceptSet() - Method in interface neuroidnet.ntr.Concept

Returns the conceptSet that constitutes this concept

getConceptSet() - Method in class neuroidnet.periphery.ArtificialConcept

Get the value of conceptSet.

getDelay() - Method in class neuroidnet.ntr.Synapse

Get the value of delay.

getDestNeuroid() - Method in class neuroidnet.ntr.Synapse

Get the value of destNeuroid.

getDestSynapseTemplate() - Method in class neuroidnet.ntr.AxonArbor

Get the value of destSynapseTemplate.

getFitnessCounter() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Get the value of fitnessCounter.

getFitnessPlot() - Method in class neuroidnet.ntr.ModeProfile

getFitnessProfile() - Method in class neuroidnet.ntr.ModeProfile

getId() - Method in class neuroidnet.ntr.Synapse

Get the value of id.

getId() - Method in class neuroidnet.ntr.Neuroid

Get the value of id.

getLocalSynapse() - Method in class neuroidnet.remote.Synapse

Deprecated. Get the value of localSynapse.

getMembranePotentialPlot() - Method in class neuroidnet.ntr.NeuroidProfile

getMode() - Method in class neuroidnet.ntr.Neuroid

Get the value of mode.

getModeProfile() - Method in class neuroidnet.ntr.NeuroidProfile

Get the value of modeProfile.

getName() - Method in class neuroidnet.ntr.Area

Get the value of name.

getName() - Method in class neuroidnet.periphery.ArtificialConcept

getNeuroid() - Method in class neuroidnet.ntr.NeuroidProfile

Get the value of neuroid.

getNeuroid() - Method in class neuroidnet.ntr.Neuroid.Mode

Returns a reference to the enclosing Neuroid.

getNeuroid(Area, int) - Method in interface neuroidnet.ntr.DebuggerInterface

getNeuroid(Area, int) - Method in class neuroidnet.ntr.Network

Returns the Neuroid object, given the area and id.

getNeuroid(NeuroidName) - Method in class neuroidnet.ntr.Network

getNeuroid(String, int) - Method in interface neuroidnet.ntr.DebuggerInterface

getNeuroid(String, int) - Method in class neuroidnet.ntr.Network

Returns the Neuroid object, given the area and id.

getNeuroidId() - Method in class neuroidnet.ntr.NeuroidName

Get the value of neuroidId.

getNext() - Method in class neuroidnet.phasesegregator.Peripheral

Iterates to next event.

getNumberOfNeuroids() - Method in class neuroidnet.ntr.Area

Get the value of numberOfNeuroids.

getNumberOfNeuroids() - Method in interface neuroidnet.remote.AreaInt

getPeripheral() - Method in class neuroidnet.ntr.Network

Get the value of peripheral.

getPlots() - Method in class neuroidnet.ntr.MembranePotentialPlot

Get the value of plots.

getPotential() - Method in class neuroidnet.ntr.Synapse

Total effect of potentiation from Synapse.

getPotentialPlot() - Method in class neuroidnet.ntr.SynapseProfile

getProfile() - Method in class neuroidnet.ntr.ModeProfile.ProfileTask

getProfile() - Method in class neuroidnet.ntr.Synapse

Get the value of profile.

getProfile() - Method in class neuroidnet.ntr.Neuroid

Get the value of profile.

getProperties() - Method in class neuroidnet.ntr.Peripheral

getProperties() - Method in class neuroidnet.ntr.Area

Describe Area in more detail, including static properties.

getProperties() - Method in class neuroidnet.ntr.Synapse

Describe in higher detail.

getProperties() - Method in class neuroidnet.ntr.Network

Return detailed info about network components.

getProperties() - Method in interface neuroidnet.ntr.Expressive

In addition to getStatus() contents, give all static properties also.

getProperties() - Method in class neuroidnet.ntr.Neuroid

Describe in higher detail.

getProperties() - Method in class neuroidnet.ntr.Neuroid.Mode

Nothing special.

getProperties() - Method in class neuroidnet.periphery.ConceptArea

Report on concepts in this area one by one.

getProperties() - Method in class neuroidnet.periphery.ArtificialConcept

Describe concept in more detail, including static properties.

getProperties() - Method in class neuroidnet.phasesegregator.StatisticalInputSequence

getRandomNeuroid() - Method in class neuroidnet.ntr.Area

Returns a Neuroid which is a random member of the destArea.

getRefractoryTimeConstant() - Method in class neuroidnet.ntr.SRMNeuroid

Get the value of refractoryTimeConstant.

getReplication() - Method in class neuroidnet.ntr.Area

Get the value of replication.

getReplication() - Method in interface neuroidnet.remote.AreaInt

getSpikesEmitted() - Method in class neuroidnet.ntr.NeuroidProfile

Get the value of spikesEmitted.

getSpikesEmittedPlot() - Method in class neuroidnet.ntr.NeuroidProfile

getSpikesReceivedPlot() - Method in class neuroidnet.ntr.SynapseProfile

getSpikeTrain() - Method in class neuroidnet.ntr.Synapse

Get the value of spikeTrain.

getSpikeTrain() - Method in class neuroidnet.ntr.Neuroid

Get the value of spikeTrain.

getSrcNeuroid() - Method in class neuroidnet.ntr.Synapse

Get the value of srcNeuroid.

getState() - Method in class neuroidnet.ntr.Neuroid.Mode

Get the value of state.

getStatePlot() - Method in class neuroidnet.ntr.ModeProfile

getStateProfile() - Method in class neuroidnet.ntr.ModeProfile

getStatus() - Method in class neuroidnet.ntr.PeakerNeuroid.Mode

getStatus() - Method in class neuroidnet.ntr.Peripheral

getStatus() - Method in class neuroidnet.ntr.Area

Mentions the time in addition to toString() contents.

getStatus() - Method in class neuroidnet.ntr.Synapse

Include output of toString() plus potential and weight.

getStatus() - Method in class neuroidnet.ntr.Network

Adds time from conceptArea.

getStatus() - Method in interface neuroidnet.ntr.Expressive

In addition to toString() contents, give transient properties of the entity without the static properties.

getStatus() - Method in class neuroidnet.ntr.Neuroid

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

getStatus() - Method in class neuroidnet.ntr.Neuroid.Mode

toString() plus state, threshold.

getStatus() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Add suggested threshold and fitnessCounter to super.getStatus().

getStatus() - Method in class neuroidnet.periphery.ArtificialConcept

Add concept set size to result of toString().

getSuggestedThreshold() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Get the value of suggestedThreshold.

getSuggestedThresholdPlot() - Method in class neuroidnet.ntr.ModeProfile

getSuggestedThresholdProfile() - Method in class neuroidnet.ntr.ModeProfile

getSumOfWeights() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Get the value of sumOfWeights.

getSynapse() - Method in class neuroidnet.ntr.SynapseProfile

Get the value of synapse.

getSynapseProfiles() - Method in class neuroidnet.ntr.NeuroidProfile

Get the value of synapseProfiles.

getSynapses() - Method in class neuroidnet.ntr.Neuroid

Get the value of synapses.

getThread() - Method in class neuroidnet.ntr.Area

Get the value of thread.

getThreshold() - Method in class neuroidnet.ntr.Neuroid.Mode

Get the value of threshold.

getThresholdPlot() - Method in class neuroidnet.ntr.ModeProfile

getThresholdProfile() - Method in class neuroidnet.ntr.ModeProfile

getTimeConstantM() - Method in class neuroidnet.ntr.Synapse

Get the value of timeConstantM.

getTimeConstantS() - Method in class neuroidnet.ntr.Synapse

Get the value of timeConstantS.

getTimeLastFired() - Method in class neuroidnet.ntr.Neuroid

Get the value of timeLastFired.

getValue() - Method in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Get the value of value.

getValue() - Method in class neuroidnet.ntr.ModeProfile.ProfileTask

getValue() - Method in class neuroidnet.ntr.Synapse.Weight

Get the value.

getValue() - Method in class neuroidnet.ntr.Neuroid.SynapseActivityTask

getVar(Neuroid.Mode) - Method in class neuroidnet.ntr.ModeProfile.ProfileTask

getWatchList() - Method in class neuroidnet.ntr.Network

Get the value of watchList.

getWeight() - Method in class neuroidnet.ntr.Synapse

Get the value from weight.

getWeightedPotentialPlot() - Method in class neuroidnet.ntr.SynapseProfile

getWeightObject() - Method in class neuroidnet.ntr.Synapse

Returns a reference to the weight object.

getWeightPlot() - Method in class neuroidnet.ntr.SynapseProfile

getWeightProfile() - Method in class neuroidnet.ntr.SynapseProfile

Get the value of weightProfile.

I

id - Variable in class neuroidnet.ntr.Area

Id tag of the area.

id - Variable in class neuroidnet.ntr.Synapse

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

id - Variable in class neuroidnet.ntr.Neuroid

Sequence of Neuroid in the array held in Area.

inhibInter - Variable in class neuroidnet.ntr.Area

True if the area contains a inhibitory inter-neuroid.

inhibitoryInterNeuroid - Variable in class neuroidnet.ntr.Area

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

inhibitorySynapseVector - Variable in class neuroidnet.ntr.Area

The axon emanating from the inhibitoryInterNeuroid

init() - Method in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Dummy.

init() - Method in class neuroidnet.ntr.Area

Does nothing.

init() - Method in class neuroidnet.ntr.Synapse

Initialization code called from various constructors.

init() - Method in class neuroidnet.ntr.Network

Does nothing.

init() - Method in class neuroidnet.ntr.Neuroid

N/A

init() - Method in class neuroidnet.ntr.Neuroid.Mode

init() - Method in class neuroidnet.ntr.Neuroid.Mode.State

Dummy.

init(Synapse, Neuroid, Area) - Method in class neuroidnet.ntr.AxonArbor

Called from all constructors.

init2() - Method in class neuroidnet.periphery.ArtificialConcept

Called by all contructors.

initEvents() - Method in class neuroidnet.phasesegregator.TwoLevelInputSequence

Overloaded to define event for inputs going three levels deep.

initEvents() - Method in class neuroidnet.phasesegregator.ThreeLevelInputSequence

Overloaded to define event for inputs going three levels deep.

initEvents() - Method in class neuroidnet.phasesegregator.StatisticalInputSequence

initEvents() - Method in class neuroidnet.phasesegregator.Peripheral

Sets the eventIterator to first position.

Input - interface neuroidnet.ntr.Input.

Interface for devices to provide input to the network.

inputAreas - Variable in class neuroidnet.phasesegregator.Peripheral

inputAreas - Variable in class neuroidnet.phasesegregator.Network

isCalculating - Variable in class neuroidnet.ntr.Area

Lock variable showing the thread is busy doing the calculations.

isConcurrent - Variable in class neuroidnet.ntr.Network

Flag to mean multi thread usage.

isDebug() - Method in class neuroidnet.ntr.Neuroid

Get the value of debug.

isEmpty() - Method in class neuroidnet.periphery.ConceptArea

isInhibitory - Variable in class neuroidnet.ntr.Synapse

isitnotfit() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

isPotentiated() - Method in class neuroidnet.ntr.Synapse

Returns true if Synapse received a spike a short time back.

isWaiting - Variable in class neuroidnet.ntr.Area

Lock variable showing the thread is waiting for a step request.

isWatch() - Method in class neuroidnet.ntr.Synapse

Get the value of watch.

isWatch() - Method in class neuroidnet.ntr.Neuroid

Get the value of watch.

iterate() - Method in class neuroidnet.ntr.Neuroid.SynapseActivityTask

Initiates the iteration over synapses of the enclosing Neuroid.

J

job(Object) - Method in class neuroidnet.ntr.ModeProfile.ProfileTask

job(Object) - Method in class neuroidnet.ntr.Neuroid.SynapseActivityTask

Calls potentiatedSynapse and silentSynapse deciding by scanning Synapses.

K

kernel() - Method in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Returns current value of threshold according to crossTime and maxPotential.

kernel(double) - Method in class neuroidnet.ntr.Synapse

Synapse effect kernel function taken from "Pulsed neural networks" of Maass and Bishop 1999, Eq 1.49, p.31 for equivalence to the integrate and fire model and its period calculation.

keySet() - Method in class neuroidnet.periphery.ConceptArea

L

localSynapse - Variable in class neuroidnet.remote.Synapse

Deprecated.

M

main(String[]) - Static method in class neuroidnet.ntr.Shell

main(String[]) - Static method in class neuroidnet.phasesegregator.Network

Deprecated. OBSOLETE! Use the Shell

main(String[]) - Static method in class neuroidnet.remote.AreaController

Describe main method here.

makeConcept() - Method in class neuroidnet.ntr.Neuroid

Create new concept.

maxPotential - Variable in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

The value of membrane potential at crossTime (i.e.

maxWeight - Static variable in class neuroidnet.ntr.Synapse

Constant maxWeight is the upper limit any synapse weight can have.

meanPotential - Variable in class neuroidnet.ntr.Neuroid.SynapseActivityTask

medialAreas - Variable in class neuroidnet.phasesegregator.Network

MembranePotentialPlot - class neuroidnet.ntr.MembranePotentialPlot.

MembranePotentialPlot.java

MembranePotentialPlot(String, Range, NeuroidProfile) - Constructor for class neuroidnet.ntr.MembranePotentialPlot

mode - Variable in class neuroidnet.ntr.Neuroid

Represents the state and dynamic parameters of the neuroid.

modeProfile - Variable in class neuroidnet.ntr.NeuroidProfile

ModeProfile - class neuroidnet.ntr.ModeProfile.

Profile of Mode objects.

ModeProfile.ProfileTask - class neuroidnet.ntr.ModeProfile.ProfileTask.

ModeProfile.ProfileTask() - Constructor for class neuroidnet.ntr.ModeProfile.ProfileTask

ModeProfile(Profilable, Object) - Constructor for class neuroidnet.ntr.ModeProfile

N

name - Variable in class neuroidnet.ntr.Area

Name of the Area for identification purposes.

name - Variable in class neuroidnet.ntr.Neuroid.Mode.State

The name of the state.

name - Variable in class neuroidnet.periphery.ArtificialConcept

Name of the concept

NameNotFoundException - exception neuroidnet.ntr.NameNotFoundException.

NameNotFoundException.java

NameNotFoundException(String) - Constructor for class neuroidnet.ntr.NameNotFoundException

nameString() - Method in class neuroidnet.ntr.Synapse

network - Variable in class neuroidnet.ntr.Peripheral

Pointer to associated Network object

network - Variable in class neuroidnet.ntr.Area

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

Network - class neuroidnet.ntr.Network.

Container for all Areas that hold Neuroids.

Network - class neuroidnet.phasesegregator.Network.

Builds a network to test theoretical phase segregation properties.

Network(boolean) - Constructor for class neuroidnet.phasesegregator.Network

Network(boolean, double) - Constructor for class neuroidnet.phasesegregator.Network

Network(boolean, double, double) - Constructor for class neuroidnet.phasesegregator.Network

Network(double, boolean) - Constructor for class neuroidnet.ntr.Network

Creates a new Network instance.

neuroid - Variable in class neuroidnet.ntr.ModeProfile

Neuroid enclosing the mode object profiled.

neuroid - Variable in class neuroidnet.ntr.NeuroidProfile

Neuroid - class neuroidnet.ntr.Neuroid.

Abstract neuroid entity.

Neuroid.Mode - class neuroidnet.ntr.Neuroid.Mode.

Modes that a neuron can have.

Neuroid.Mode.State - class neuroidnet.ntr.Neuroid.Mode.State.

Neuroid.Mode.State() - Constructor for class neuroidnet.ntr.Neuroid.Mode.State

Dummy constructor, calls init().

Neuroid.Mode.State(String) - Constructor for class neuroidnet.ntr.Neuroid.Mode.State

Assigns state name.

Neuroid.Mode() - Constructor for class neuroidnet.ntr.Neuroid.Mode

Dummy constructor.

Neuroid.Mode(int, double) - Constructor for class neuroidnet.ntr.Neuroid.Mode

Neuroid.SynapseActivityTask - class neuroidnet.ntr.Neuroid.SynapseActivityTask.

Iterator task class which scans synapses of the neuroid.

Neuroid.SynapseActivityTask() - Constructor for class neuroidnet.ntr.Neuroid.SynapseActivityTask

Neuroid(Area) - Constructor for class neuroidnet.ntr.Neuroid

and connects to area.

neuroidId - Variable in class neuroidnet.ntr.NeuroidName

NeuroidName - class neuroidnet.ntr.NeuroidName.

Identifier for accessing a neuroid in a network.

NeuroidName(String, int) - Constructor for class neuroidnet.ntr.NeuroidName

neuroidnet.ntr - package neuroidnet.ntr

Holds the main classes for the simulator.

neuroidnet.periphery - package neuroidnet.periphery

Holds classes related to the peripheral controller of the neuroidal network.

neuroidnet.phasesegregator - package neuroidnet.phasesegregator

Example for the phase segregation hypothesis.

neuroidnet.remote - package neuroidnet.remote

Holds extensions for distributed processing of the Neuroidal Network Simulator.

neuroidProfile - Variable in class neuroidnet.ntr.MembranePotentialPlot

NeuroidProfile - class neuroidnet.ntr.NeuroidProfile.

Keeping track of changes of Neuroids.

NeuroidProfile(Neuroid) - Constructor for class neuroidnet.ntr.NeuroidProfile

Set the value of spikesEmitted.

neuroids - Variable in class neuroidnet.ntr.Area

List of Neuroids contained in Area.

neuroidType - Variable in class neuroidnet.phasesegregator.Network

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

nextTime - Variable in class neuroidnet.phasesegregator.Peripheral

nuBoost - Variable in class neuroidnet.phasesegregator.Network

numberFormat - Static variable in class neuroidnet.ntr.Network

For formatting real values

numberOfActiveSynapses - Variable in class neuroidnet.ntr.Neuroid.SynapseActivityTask

numberOfItemsPerArea - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence

numberOfItemsPerArea - Variable in class neuroidnet.phasesegregator.Peripheral

numberOfItemsPerArea - Variable in class neuroidnet.phasesegregator.Network

numberOfMedialAreas - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence

numberOfMedialAreas - Variable in class neuroidnet.phasesegregator.Network

numberOfNeuroids - Variable in class neuroidnet.ntr.Area

Number of Neuroids contained in Area.

numberOfNeuroids - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence

numberOfNeuroids - Variable in class neuroidnet.phasesegregator.Network

numberOfObjects - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence

Can be manipulated by beanshell scripts under scripts/.

P

PeakerNeuroid - class neuroidnet.ntr.PeakerNeuroid.

Intermediate neuroid augmenting SRMNeuroid before proceeding into a more completely liquid-state machine neuroid.

PeakerNeuroid.Mode - class neuroidnet.ntr.PeakerNeuroid.Mode.

PeakerNeuroid.Mode() - Constructor for class neuroidnet.ntr.PeakerNeuroid.Mode

PeakerNeuroid.Mode(double) - Constructor for class neuroidnet.ntr.PeakerNeuroid.Mode

PeakerNeuroid(Area) - Constructor for class neuroidnet.ntr.PeakerNeuroid

TODO: Initialize mode? Does the polymorphism work from super class to use Mode defined here? [No]

PeakerNeuroid(Area, double, double) - Constructor for class neuroidnet.ntr.PeakerNeuroid

percepts - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence.SimObject

percepts - Variable in class neuroidnet.phasesegregator.Peripheral

period - Variable in class neuroidnet.ntr.Area

Oscillation period of Neuroids.

period - Variable in class neuroidnet.phasesegregator.Network

peripheral - Variable in class neuroidnet.ntr.Network

Peripheral control device

peripheral - Variable in class neuroidnet.phasesegregator.Network

Peripheral - class neuroidnet.ntr.Peripheral.

Controls inputs to the Network.

Peripheral - class neuroidnet.phasesegregator.Peripheral.

Creates inputs in one SensoryArea that projects to neuroids in 3 input Areas.

Peripheral(Network) - Constructor for class neuroidnet.ntr.Peripheral

Creates a new Peripheral instance.

Peripheral(Network, Area[], int, double) - Constructor for class neuroidnet.phasesegregator.Peripheral

plateau - Variable in class neuroidnet.ntr.PeakerNeuroid.Mode

plots - Variable in class neuroidnet.ntr.MembranePotentialPlot

Vector of WeightedPotentialPlot

potential - Variable in class neuroidnet.ntr.Neuroid

Membrane potential.

PotentialPlot - class neuroidnet.ntr.PotentialPlot.

Plot for synapse potential.

PotentialPlot(String, Range, SynapseProfile) - Constructor for class neuroidnet.ntr.PotentialPlot

potentiatedSynapse(Synapse) - Method in class neuroidnet.ntr.Neuroid.SynapseActivityTask

Called for each potentiated synapse.

preamble() - Method in class neuroidnet.ntr.MembranePotentialPlot

Copies the epsp() function definition from PotentialPlots, defines refrac(), the refractory potential function, and then puts them together as bodyXX() function to appear as the body of this plot.

preamble() - Method in class neuroidnet.ntr.PotentialPlot

Define the epsp() function here.

profile - Variable in class neuroidnet.ntr.ModeProfile.ProfileTask

profile - Variable in class neuroidnet.ntr.Synapse

profile - Variable in class neuroidnet.ntr.Neuroid

put(Object, Object) - Method in class neuroidnet.periphery.ConceptArea

putAll(Map) - Method in class neuroidnet.periphery.ConceptArea

Q

qualityOfConcepts(Set) - Method in class neuroidnet.phasesegregator.StatisticalInputSequence

Calculates a quality value in the range [0, 1], 1 indicating full replication has been reached in recruitment for each intended simulation object.

quiescent - Variable in class neuroidnet.ntr.PeakerNeuroid.Mode

quiescent - Variable in class neuroidnet.ntr.AdThNeuroid.Mode

R

r1 - Variable in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Circuit parameters: r1 & c1 are fast acting component (1/10th of mTC), and r2 & c2 are slow acting component (10 times of mTC) of the threshold.

r2 - Variable in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Circuit parameters: r1 & c1 are fast acting component (1/10th of mTC), and r2 & c2 are slow acting component (10 times of mTC) of the threshold.

rcFile - Variable in class neuroidnet.ntr.Shell

readObject(ObjectInputStream) - Method in class neuroidnet.ntr.Area

Method called when a serialized object is loaded.

readObject(ObjectInputStream) - Method in class neuroidnet.ntr.Network

Method called when a serialized object is loaded.

readObject(ObjectInputStream) - Method in class neuroidnet.phasesegregator.Peripheral

For serialization support.

receiveSpike() - Method in class neuroidnet.ntr.Synapse

Receive a spike at this time instant.

receiveSpike() - Method in interface neuroidnet.remote.SynapseInt

receiveSpike(Synapse) - Method in class neuroidnet.ntr.Area

Public method to receive spikes from other areas.

refractoriness(double) - Method in class neuroidnet.ntr.SRMNeuroid

Refractory kernel taken from Maass and Bishop 1999, Eq.

refractoryTimeConstant - Variable in class neuroidnet.ntr.SRMNeuroid

refractoryTimeConstant - Variable in class neuroidnet.phasesegregator.Network

remove(Object) - Method in class neuroidnet.periphery.ConceptArea

replication - Variable in class neuroidnet.ntr.Area

The replication factor, i.e.

replication - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence

replication - Variable in class neuroidnet.phasesegregator.Network

reset() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Resets the neuroid to its initial pristine state.

ResynapseException - exception neuroidnet.ntr.ResynapseException.

ResynapseException.java Exception thrown in case two synaptic boutons of an axon end up on the same postsynaptic neuroid.

ResynapseException(String) - Constructor for class neuroidnet.ntr.ResynapseException

rising - Variable in class neuroidnet.ntr.PeakerNeuroid.Mode

rising - Variable in class neuroidnet.ntr.AdThNeuroid.Mode

run() - Method in class neuroidnet.ntr.Area

Check if step()ing requested, and serve the request.

run() - Method in class neuroidnet.ntr.Network

Build the network (USED TO: and run the simulation.) Calls build().

S

segregation - Variable in class neuroidnet.phasesegregator.Peripheral

segregation - Variable in class neuroidnet.phasesegregator.Network

sensoryArea - Variable in class neuroidnet.phasesegregator.Peripheral

SensoryArea - class neuroidnet.periphery.SensoryArea.

Area that holds inputs, ie.

SensoryArea(Network, String) - Constructor for class neuroidnet.periphery.SensoryArea

SensoryConcept - class neuroidnet.periphery.SensoryConcept.

Concept created by peripheral controller.

SensoryConcept(Network, String) - Constructor for class neuroidnet.periphery.SensoryConcept

SensoryNeuroid - class neuroidnet.periphery.SensoryNeuroid.

Neuroid that is not contained in a SensoryArea and which does not listen to its inputs.

SensoryNeuroid(Area, Area, String) - Constructor for class neuroidnet.periphery.SensoryNeuroid

Create neuroid and associate a new SensoryConcept with it.

setActivationThreshold(double) - Method in class neuroidnet.ntr.Area

Set the value of activationThreshold.

setArea(Area) - Method in class neuroidnet.ntr.Neuroid

Set the value of area.

setAxons(Hashtable) - Method in class neuroidnet.ntr.Area

Set the value of axons.

setConceptArea(ConceptArea) - Method in class neuroidnet.ntr.Network

Set the value of conceptArea.

setConceptSet(Set) - Method in class neuroidnet.periphery.ArtificialConcept

Set the value of conceptSet.

setDebug(boolean) - Method in class neuroidnet.ntr.Neuroid

Set the value of debug.

setDelay(double) - Method in class neuroidnet.ntr.Synapse

Set the value of delay.

setDestNeuroid(Neuroid) - Method in class neuroidnet.ntr.Synapse

Set the value of destNeuroid.

setDestSynapseTemplate(Synapse) - Method in class neuroidnet.ntr.AxonArbor

Set the value of destSynapseTemplate.

setFitnessCounter(int) - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Set the value of fitnessCounter.

setId(int) - Method in class neuroidnet.ntr.Synapse

Set the value of id.

setLocalSynapse(Synapse) - Method in class neuroidnet.remote.Synapse

Deprecated. Set the value of localSynapse.

setMode(Neuroid.Mode) - Method in class neuroidnet.ntr.Neuroid

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

setModeProfile(ModeProfile) - Method in class neuroidnet.ntr.NeuroidProfile

Set the value of modeProfile.

setName(String) - Method in class neuroidnet.ntr.Area

Set the value of name.

setNeuroid(Neuroid) - Method in class neuroidnet.ntr.NeuroidProfile

Set the value of neuroid.

setNeuroidNetEnvironment() - Method in class neuroidnet.ntr.Shell

setNumberFormatting() - Method in class neuroidnet.ntr.Network

Number formatting for text numberFormat

setNumberOfNeuroids(int) - Method in class neuroidnet.ntr.Area

Set the value of numberOfNeuroids.

setPeripheral(Peripheral) - Method in class neuroidnet.ntr.Network

Set the value of peripheral.

setProfile(NeuroidProfile) - Method in class neuroidnet.ntr.Neuroid

Set the value of profile.

setProfile(SynapseProfile) - Method in class neuroidnet.ntr.Synapse

Set the value of profile.

setRefractoryTimeConstant(double) - Method in class neuroidnet.ntr.SRMNeuroid

Set the value of refractoryTimeConstant.

setReplication(int) - Method in class neuroidnet.ntr.Area

Set the value of replication.

setSpikeTrain(Vector) - Method in class neuroidnet.ntr.Neuroid

Set the value of spikeTrain.

setSrcNeuroid(Neuroid) - Method in class neuroidnet.ntr.Synapse

Set the value of srcNeuroid.

setState(int) - Method in class neuroidnet.ntr.Neuroid.Mode

Set the value of state.

setSuggestedThreshold(double) - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Set the value of suggestedThreshold.

setSumOfWeights(double) - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Set the value of sumOfWeights.

setSynapse(Synapse) - Method in class neuroidnet.ntr.SynapseProfile

Set the value of synapse.

setThread(Thread) - Method in class neuroidnet.ntr.Area

Set the value of thread.

setThreshold(double) - Method in class neuroidnet.ntr.Neuroid.Mode

Set the value of threshold.

setTimeConstantM(double) - Method in class neuroidnet.ntr.Synapse

Set the value of timeConstantM.

setTimeConstantS(double) - Method in class neuroidnet.ntr.Synapse

Set the value of timeConstantS.

setValue(double) - Method in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Set the value of value.

setValue(double) - Method in class neuroidnet.ntr.Synapse.Weight

Set the value of weight.

setWatch(boolean) - Method in class neuroidnet.ntr.Synapse

Set the value of watch.

setWatch(boolean) - Method in class neuroidnet.ntr.Neuroid

Set the value of watch.

setWatchList(Set) - Method in class neuroidnet.ntr.Network

Set the value of watchList.

setWeight(double) - Method in class neuroidnet.ntr.Synapse

Set the value of weight.

setWeightProfile(Profile) - Method in class neuroidnet.ntr.SynapseProfile

Set the value of weightProfile.

Shell - class neuroidnet.ntr.Shell.

Shell(boolean) - Constructor for class neuroidnet.ntr.Shell

silentSynapse(Synapse) - Method in class neuroidnet.ntr.Neuroid.SynapseActivityTask

Called for each non-potentiated synapse.

simObjects - Variable in class neuroidnet.phasesegregator.StatisticalInputSequence

Objects to be fired in the input sequence.

simulateAreas - Variable in class neuroidnet.ntr.Network

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

simulation() - Method in class neuroidnet.ntr.Network

Deprecated. See advanceTime

size() - Method in class neuroidnet.periphery.ConceptArea

spikeTrain - Variable in class neuroidnet.ntr.Synapse

List of times when spikes are received

spikeTrain - Variable in class neuroidnet.ntr.Neuroid

List of times that the neuroid fired.

spuriousConcepts() - Method in class neuroidnet.phasesegregator.StatisticalInputSequence

Computes the set of spurious concepts by pruning from the contents of the ConceptArea the subsets of all simObjects.

srcNeuroid - Variable in class neuroidnet.ntr.AxonArbor

Axon's owner neuroid.

srcNeuroid - Variable in class neuroidnet.ntr.Synapse

Presynaptic neuroid.

SRMNeuroid - class neuroidnet.ntr.SRMNeuroid.

First attempt to implement the central neuroidal entity with programmability capability as defined by Valiant.

SRMNeuroid.Mode - class neuroidnet.ntr.SRMNeuroid.Mode.

SRMNeuroid.Mode() - Constructor for class neuroidnet.ntr.SRMNeuroid.Mode

Initializes to AM state and sets the threshold to be infinity.

SRMNeuroid.Mode(double) - Constructor for class neuroidnet.ntr.SRMNeuroid.Mode

Initializes to AM state and sets the threshold.

SRMNeuroid(Area) - Constructor for class neuroidnet.ntr.SRMNeuroid

Sets mode and calls super().

SRMNeuroid(Area, double, double) - Constructor for class neuroidnet.ntr.SRMNeuroid

Sets initial parameters.

state - Variable in class neuroidnet.ntr.AdThNeuroid.Mode

state - Variable in class neuroidnet.ntr.Neuroid.Mode

State of neuroid, can only take values defined here.

StatisticalInputSequence - class neuroidnet.phasesegregator.StatisticalInputSequence.

Creates a random input sequence out of possible input patterns (objects).

StatisticalInputSequence.SimObject - class neuroidnet.phasesegregator.StatisticalInputSequence.SimObject.

StatisticalInputSequence.SimObject() - Constructor for class neuroidnet.phasesegregator.StatisticalInputSequence.SimObject

StatisticalInputSequence(Network) - Constructor for class neuroidnet.phasesegregator.StatisticalInputSequence

In order to be used from bsh: As constructor only take necessary parameters, like connect to a network.

statusString() - Method in class neuroidnet.ntr.Synapse

step() - Method in class neuroidnet.ntr.PeakerNeuroid

Calculates up to the third derivative of the membrane potential to detect max plateaus.

step() - Method in class neuroidnet.ntr.PeakerNeuroid.Mode

step() - Method in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

If membrane potential crosses the threshold value, then assign it to maxPotential and set crossTime to now.

step() - Method in class neuroidnet.ntr.AdThNeuroid.Mode

Calls state.step().

step() - Method in class neuroidnet.ntr.Peripheral

Peripheral control of timepass, initiates peripheral events associated with time.

step() - Method in class neuroidnet.ntr.Area

Updates the state of the Area.

step() - Method in class neuroidnet.ntr.Network

Updates the state of the Network.

step() - Method in class neuroidnet.ntr.Neuroid

Update state of the Neuroid.

step() - Method in class neuroidnet.ntr.Neuroid.Mode

step() - Method in class neuroidnet.ntr.Neuroid.Mode.State

step() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Takes care of mode related changes to the neuroid.

step() - Method in class neuroidnet.periphery.SensoryNeuroid

N/A

step() - Method in interface neuroidnet.remote.AreaInt

stepArea - Variable in class neuroidnet.ntr.Network

Defines what do to every step given Area object.

stepRequested - Variable in class neuroidnet.ntr.Area

Flag showing incoming requets to step().

stop() - Method in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

Dummy.

stop() - Method in class neuroidnet.ntr.Area

Terminates the thread dedicated to this area.

stop() - Method in class neuroidnet.ntr.Network

Delegates the termination request to areas.

stop() - Method in class neuroidnet.ntr.Neuroid

N/A

stop() - Method in class neuroidnet.ntr.Neuroid.Mode

N/A

stop() - Method in class neuroidnet.ntr.Neuroid.Mode.State

Dummy.

suggestedThreshold - Variable in class neuroidnet.ntr.SRMNeuroid.Mode

suggestThreshold() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

sumOfCurrentWeights - Variable in class neuroidnet.ntr.SRMNeuroid

Internal.

sumOfWeights - Variable in class neuroidnet.ntr.SRMNeuroid.Mode

The total sum of incoming weights to a Neuroid should be fixed.

synapse - Variable in class neuroidnet.ntr.SynapseProfile

Synapse - class neuroidnet.ntr.Synapse.

Presynaptic connection to a Neuroid.

Synapse - class neuroidnet.remote.Synapse.

Deprecated. See neuroidnet.ntr.Synapse

Synapse.Weight - class neuroidnet.ntr.Synapse.Weight.

Synapse.Weight() - Constructor for class neuroidnet.ntr.Synapse.Weight

Synapse(Neuroid, Neuroid, double, double, boolean, double) - Constructor for class neuroidnet.ntr.Synapse

Creates a new Synapse instance.

Synapse(Neuroid, Neuroid, double, double, boolean, double) - Constructor for class neuroidnet.remote.Synapse

Deprecated.

Synapse(Neuroid, Neuroid, Synapse) - Constructor for class neuroidnet.ntr.Synapse

Creates a new Synapse instance with help of a templateSynapse.

SynapseInt - interface neuroidnet.remote.SynapseInt.

Distributed extensions of neuroidnet.ntr.Synapse.

synapsePotentials - Variable in class neuroidnet.ntr.Neuroid.SynapseActivityTask

synapseProfile - Variable in class neuroidnet.ntr.PotentialPlot

SynapseProfile - class neuroidnet.ntr.SynapseProfile.

SynapseProfile.java

SynapseProfile(Synapse) - Constructor for class neuroidnet.ntr.SynapseProfile

synapseProfiles - Variable in class neuroidnet.ntr.NeuroidProfile

synapses - Variable in class neuroidnet.ntr.Neuroid

List of incoming synapses.

T

testOneInput() - Method in class neuroidnet.phasesegregator.Peripheral

Fire one input in sensory area.

thread - Variable in class neuroidnet.ntr.Area

Thread to do the actual calculations.

ThreeLevelInputSequence - class neuroidnet.phasesegregator.ThreeLevelInputSequence.

Provides sequence of inputs for a three level deep network for demonstrating phase segregation.

ThreeLevelInputSequence(Network, Area[], int, double) - Constructor for class neuroidnet.phasesegregator.ThreeLevelInputSequence

threshold - Variable in class neuroidnet.ntr.Neuroid.Mode

Threshold of the neuroid.

threshold - Variable in class neuroidnet.phasesegregator.Network

thresholdDevice - Variable in class neuroidnet.ntr.AdThNeuroid

The adaptive threshold.

time - Variable in class neuroidnet.ntr.Peripheral

Peripheral system's own account of time.

time - Variable in class neuroidnet.ntr.Area

Time of the area.

timeConstantM - Variable in class neuroidnet.ntr.Area

Membrane time constant of all neurons in this area.

timeConstantM - Variable in class neuroidnet.ntr.Synapse

Synapse constant dynamic properties.

timeConstantM - Variable in class neuroidnet.phasesegregator.Network

timeConstantS - Variable in class neuroidnet.ntr.Synapse

Synapse constant dynamic properties.

timeConstantS - Variable in class neuroidnet.phasesegregator.Network

timeLastFired - Variable in class neuroidnet.ntr.Neuroid

Last firing time of this Neuroid.

toInhibitorySynapseTemplate - Variable in class neuroidnet.ntr.Area

The template used for creating synapses to the inhibitoryInterNeuroid

toString() - Method in class neuroidnet.ntr.NeuroidName

toString() - Method in class neuroidnet.ntr.Peripheral

toString() - Method in class neuroidnet.ntr.Area

Identifies are with its name.

toString() - Method in class neuroidnet.ntr.Synapse

Identifies the synapse using id and destNeuroid.

toString() - Method in class neuroidnet.ntr.Network

Return brief info about the network.

toString() - Method in interface neuroidnet.ntr.Expressive

Give enough information on the entity for identification.

toString() - Method in class neuroidnet.ntr.Neuroid

Identify the neuroid with its id and area.

toString() - Method in class neuroidnet.ntr.Neuroid.Mode

Strip fully qualified class name to leave only the class name.

toString() - Method in class neuroidnet.ntr.Neuroid.Mode.State

Returns state name.

toString() - Method in class neuroidnet.periphery.ArtificialConcept

Describe concept.

toString() - Method in class neuroidnet.phasesegregator.StatisticalInputSequence.SimObject

TwoLevelInputSequence - class neuroidnet.phasesegregator.TwoLevelInputSequence.

Provides sequence of inputs for a three level deep network for demonstrating phase segregation.

TwoLevelInputSequence(Network, Area[], int, double) - Constructor for class neuroidnet.phasesegregator.TwoLevelInputSequence

U

UM - Static variable in class neuroidnet.ntr.SRMNeuroid.Mode

updateTime() - Method in class neuroidnet.ntr.Area

Just increments the time by deltaT.

updateWeights() - Method in class neuroidnet.ntr.SRMNeuroid.Mode

Updates presynaptic weights according to a variant of Winnow learning rule.

usage() - Static method in class neuroidnet.ntr.Shell

V

value - Variable in class neuroidnet.ntr.AdThNeuroid.AdaptiveThresholdDevice

The threshold value;

value - Variable in class neuroidnet.ntr.Synapse.Weight

values() - Method in class neuroidnet.periphery.ConceptArea

W

watch - Variable in class neuroidnet.ntr.Synapse

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

watch - Variable in class neuroidnet.ntr.Neuroid

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

watchList - Variable in class neuroidnet.ntr.Network

weight - Variable in class neuroidnet.ntr.Synapse

Incoming weight.

WeightedPotentialPlot - class neuroidnet.ntr.WeightedPotentialPlot.

Weighted potential plot of a synapse.

WeightedPotentialPlot(String, Range, SynapseProfile) - Constructor for class neuroidnet.ntr.WeightedPotentialPlot

weightProfile - Variable in class neuroidnet.ntr.SynapseProfile

_

_state - Variable in class neuroidnet.ntr.PeakerNeuroid.Mode

The state for the continuous-time state machine.

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