cnslab.cnsnetwork

Class Network

java.lang.Object

cnslab.cnsnetwork.Network

Direct Known Subclasses:

ANetwork

public class Network
extends Object

Network structure to organize all the small pieces (neurons, layers, axons, recorders, etc.) together.

Version:

$Date: 2012-08-04 13:43:22 -0500 (Sat, 04 Aug 2012) $ $Rev: 104 $ $Author: croft $

Author:

Yi Dong, David Wallace Croft

Field Summary

Fields

Modifier and Type	Field and Description
Map<Integer,Axon>	axons A data structure mapping neuron id to the neuron's Axon.
int	base neuron index base, the real index is index+base
Map<String,Integer>	cellmap a data structure map "pre,x,y,suf" to neuron index
int	countTrial
protected DiscreteEventQueue	discreteEventQueue
double	endOfTrial the end of Trial time
Experiment	experiment
int	expIdBack
protected Queue<FireEvent>	fireQueue The neuron fire queue
JpvmInfo	info the parallel machine informations
protected Queue<InputEvent>	inputQueue The (internal) input spike queue
IntraRecBuffer	intraRecBuffers recorded intracellular info
double[]	localTime used by the root host to monitor other host's time
double	minSynapticDelay the minimum synaptic delay
protected ModelFactory	modelFactory
Neuron[]	neurons An array of neurons used in current Nethosts
PrintStream	p for the output of the slave hosts
protected Queue<PInputEvent>	poissonQueue The (external) input queue
int[]	received used for keep record of received spikes
RecordBuffer	recordBuff recorded info buffer
RecorderData	recorderData Store the recorded data.
double	rootTime the root broadcasting time
Seed	seed the seed value for this network
SimulatorParser	simulatorParser the system background firing rates
SpikeBuffer[]	spikeBuffers spike buffer to store the neuron spikes which needs to be sented
boolean	spikeState flag for trial end
boolean	startSig trial start flag
boolean	stop flag for the computation and communication threads to stop
int	subExpId Keep track of current simulated subExp id
boolean	trialDone Flag to indicate whether the trial is done or not
int	trialId Keep track of current Trials.
int	trialIdBack
int	xEdge Size of Xedge
int	yEdge Size of Yedge

Constructor Summary

Constructors

Constructor and Description
Network(ModelFactory modelFactory, DiscreteEventQueue discreteEventQueue, Seq<ModulatedSynapse> modulatedSynapseSeq, Experiment experiment, JpvmInfo info, int base, double minSynapticDelay, SimulatorParser simulatorParser, Seed seed)
Network(ModelFactory modelFactory, DiscreteEventQueue discreteEventQueue, Seq<ModulatedSynapse> modulatedSynapseSeq, Neuron[] neurons, Map<Integer,Axon> axons, double minSynapticDelay, SimulatorParser simulatorParser, Seed seed)
Network(ModelFactory modelFactory, DiscreteEventQueue discreteEventQueue, Seq<ModulatedSynapse> modulatedSynapseSeq, Neuron[] neurons, Map<Integer,Axon> axons, JpvmInfo info, int base, double minSynapticDelay, SimulatorParser simulatorParser, Seed seed, Experiment experiment)

Method Summary

Methods

Modifier and Type	Method and Description
void	clearQueues()
DiscreteEventQueue	getDiscreteEventQueue()
Slot<FireEvent>	getFireEventSlot()
FireEvent	getFirstFireEvent()
InputEvent	getFirstInputEvent()
PInputEvent	getFirstPInputEvent()
Slot<InputEvent>	getInputEventSlot()
double	getLocalTime(int i)
Slot<PInputEvent>	getPInputEventSlot()
void	init() Initialize the queues, put the first element into each of the queues.
void	initMain() One time initialization, initialize the structure to store the times.
void	initNet() Initializes the Network.
void	inputProcess(InputEvent firstInput) Deprecated.
void	pFireProcess(FireEvent firstFireEvent) Process the event from fireQueue in parallel.
void	pInputProcess(InputEvent firstInputEvent) Process the event from inputQueue in parallel.
void	pMainProcess(FireEvent firstFire, double freq, double weight, Seed seed) Deprecated.
void	poissonProcess(PInputEvent poiInput) Deprecated.
void	pPoissonProcess(PInputEvent poiInput) poisson input process (external input) in parallel
void	setLocalTime(double localTime, int i) set a new value to localTime
void	stopRun() stop the testRun();

Methods inherited from class java.lang.Object

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

Field Detail

countTrial

public int countTrial

expIdBack

public int expIdBack

trialIdBack

public int trialIdBack

experiment

public Experiment experiment

subExpId

public int subExpId

Keep track of current simulated subExp id

trialId

public int trialId

Keep track of current Trials.

xEdge

public int xEdge

Size of Xedge

yEdge

public int yEdge

Size of Yedge

cellmap

public Map<String,Integer> cellmap

a data structure map "pre,x,y,suf" to neuron index

seed

public Seed seed

the seed value for this network

simulatorParser

public SimulatorParser simulatorParser

the system background firing rates

minSynapticDelay

public double minSynapticDelay

the minimum synaptic delay

p

public PrintStream p

for the output of the slave hosts

info

public JpvmInfo info

the parallel machine informations

localTime

public double[] localTime

used by the root host to monitor other host's time

spikeBuffers

public SpikeBuffer[] spikeBuffers

spike buffer to store the neuron spikes which needs to be sented

received

public int[] received

used for keep record of received spikes

intraRecBuffers

public IntraRecBuffer intraRecBuffers

recorded intracellular info

recordBuff

public RecordBuffer recordBuff

recorded info buffer

base

public int base

neuron index base, the real index is index+base

rootTime

public double rootTime

the root broadcasting time

endOfTrial

public double endOfTrial

the end of Trial time

neurons

public Neuron[] neurons

An array of neurons used in current Nethosts

axons

public Map<Integer,Axon> axons

A data structure mapping neuron id to the neuron's Axon.

recorderData

public RecorderData recorderData

Store the recorded data.

stop

public boolean stop

flag for the computation and communication threads to stop

trialDone

public boolean trialDone

Flag to indicate whether the trial is done or not

startSig

public boolean startSig

trial start flag

spikeState

public boolean spikeState

flag for trial end

modelFactory

protected final ModelFactory modelFactory

discreteEventQueue

protected final DiscreteEventQueue discreteEventQueue

fireQueue

protected Queue<FireEvent> fireQueue

The neuron fire queue

inputQueue

protected Queue<InputEvent> inputQueue

The (internal) input spike queue

poissonQueue

protected Queue<PInputEvent> poissonQueue

The (external) input queue

Constructor Detail

Network

public Network(ModelFactory modelFactory,
       DiscreteEventQueue discreteEventQueue,
       Seq<ModulatedSynapse> modulatedSynapseSeq,
       Neuron[] neurons,
       Map<Integer,Axon> axons,
       double minSynapticDelay,
       SimulatorParser simulatorParser,
       Seed seed)

Network

public Network(ModelFactory modelFactory,
       DiscreteEventQueue discreteEventQueue,
       Seq<ModulatedSynapse> modulatedSynapseSeq,
       Neuron[] neurons,
       Map<Integer,Axon> axons,
       JpvmInfo info,
       int base,
       double minSynapticDelay,
       SimulatorParser simulatorParser,
       Seed seed,
       Experiment experiment)

Network

public Network(ModelFactory modelFactory,
       DiscreteEventQueue discreteEventQueue,
       Seq<ModulatedSynapse> modulatedSynapseSeq,
       Experiment experiment,
       JpvmInfo info,
       int base,
       double minSynapticDelay,
       SimulatorParser simulatorParser,
       Seed seed)

Method Detail

getDiscreteEventQueue

public DiscreteEventQueue getDiscreteEventQueue()

getLocalTime

public double getLocalTime(int i)

getFireEventSlot

public Slot<FireEvent> getFireEventSlot()

getFirstFireEvent

public FireEvent getFirstFireEvent()

getFirstInputEvent

public InputEvent getFirstInputEvent()

getFirstPInputEvent

public PInputEvent getFirstPInputEvent()

getInputEventSlot

public Slot<InputEvent> getInputEventSlot()

getPInputEventSlot

public Slot<PInputEvent> getPInputEventSlot()

clearQueues

public void clearQueues()

setLocalTime

public void setLocalTime(double localTime,
                int i)

set a new value to localTime

Parameters:

localTime - the new value to be used

stopRun

public void stopRun()

stop the testRun();

initNet

public void initNet()

Initializes the Network. fill up the first item for inputQueue, fireQueue, poissonQueue (the implementation of the queue is changed here), Initialized SyncNeuron (Index is the number of neurons).

init

public void init()

Initialize the queues, put the first element into each of the queues. Called from PRun.run().

initMain

public void initMain()

One time initialization, initialize the structure to store the times.

pFireProcess

public void pFireProcess(FireEvent firstFireEvent)
                  throws jpvmException,
                         Exception

Process the event from fireQueue in parallel.

Throws:

jpvmException

Exception

pMainProcess

@Deprecated
public void pMainProcess(FireEvent firstFire,
                           double freq,
                           double weight,
                           Seed seed)

Deprecated.

inputProcess

@Deprecated
public void inputProcess(InputEvent firstInput)

Deprecated.

process the event from (internal) inputQueue

Parameters:

firstInput -

poissonProcess

@Deprecated
public void poissonProcess(PInputEvent poiInput)

Deprecated.

poisson input process

pPoissonProcess

public void pPoissonProcess(PInputEvent poiInput)

poisson input process (external input) in parallel

pInputProcess

public void pInputProcess(InputEvent firstInputEvent)

Process the event from inputQueue in parallel.