MiNiNeuron (ERNST API)

java.lang.Object
- cnslab.cnsnetwork.MiNiNeuron

All Implemented Interfaces:

Neuron
```
public final class MiNiNeuron
extends Object
implements Neuron
```
MN model with STDP implemented. See Mihalas and Niebur 2009 paper.

Version:

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

Author:

Yi Dong, David Wallace Croft, M.Sc., Jeremy Cohen

Nested Class Summary

Nested Classes
Modifier and Type Class and Description

class MiNiNeuron.State

Nested Classes
Modifier and Type	Class and Description
`class`	`MiNiNeuron.State`

Field Summary

Fields
Modifier and Type	Field and Description
`double`	`clampThreshold` clamp the threshold during absolute refractory period
`double`	`clampVoltage` clamp the membrane voltage during absolute refractory period
`static double`	`cost` the expected cost of inserting a preliminary fire estimate into the event queue (as opposed to performing another NR iteration)
`static double`	`cost_Schedule` the cost associated with one queue schedule (see D'Haene, 2009)
`static double`	`cost_Update` the cost associated with one neuron update (see D’Haene, 2009)
`boolean`	`fire` whether the next fire event is a final calculation, as opposed to a preliminary estimate (see D'Haene, 2009)
`double`	`lastFireTime` last time the neuron fired; negative means no last spike
`double`	`lastInputTime` last time the neuron received a spike
`MiNiNeuronPara`	`para` neuron parameters
`static double`	`rEPS` the criterion for removing synapses: if a synaptic channel does not get an input for a long time such that its current decays below rEPS, it is removed from computations of the voltage and future updates up until it gets an input
`MiNiNeuron.State[][]`	`sta_p` two-dimensional array pointing to the state variables.
`TreeSet<MiNiNeuron.State>`	`state` linked list for state variables
`double`	`tAvg` running average of the time interval between input spikes
`static double`	`tEPS` the epsilon of a final firing time calculation
`long`	`tHost` long imposes a constraint on the maximum number of hosts to be 64

Constructor Summary

Constructors
Constructor and Description

MiNiNeuron(MiNiNeuronPara para)

Constructors
Constructor and Description
`MiNiNeuron(MiNiNeuronPara para)`

Method Summary

Methods
Modifier and Type	Method and Description
`double[]`	`getCurr(double currTime)` Used mainly for intracellular recording.
`double`	`getMemV(double currTime)` Used mainly for intracellular recording.
`boolean`	`getRecord()` record the neuron
`double`	`getSensoryWeight()`
`long`	`getTHost()`
`double`	`getTimeOfLastUpdate()`
`double`	`getTimeOfNextFire()` get the value of timeOfNextFire
`void`	`init(int expid, int trialid, Seed idum, Network net, int id)` initialize the neuron
`boolean`	`isSensory()` sensory report
`double`	`membraneVoltage(double t)` Compute the membrane voltage.
`boolean`	`realFire()`
`double`	`safeDerivative(double t)` Computes the "safe derivative" (see D'Haene, 2009) of the thresholdDiff function.
`void`	`setMemV(double memV)` set the membrane voltage
`void`	`setRecord(boolean record)` set the neuron record or not.
`void`	`setTHost(long id)` set the target host id, 0 means none, 1 means yes
`void`	`setTimeOfLastUpdate(double timeOfLastUpdate)`
`void`	`setTimeOfNextFire(double timeOfNextFire)` set a new value to timeOfNextFire
`double`	`thresholdDiff(double t)` Compute the difference between the membrane voltage and the membrane voltage threshold.
`String`	`toString()`
`double`	`updateFire()` update of the neuron after firing the current time is TimeOfNextFire
`double`	`updateInput(double time, Synapse input)` update of the neuron after receiving a spike the current time is time

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Field Detail
  - tEPS
```
public static double tEPS
```
    the epsilon of a final firing time calculation
  - rEPS
```
public static double rEPS
```
    the criterion for removing synapses: if a synaptic channel does not get an input for a long time such that its current decays below rEPS, it is removed from computations of the voltage and future updates up until it gets an input
  - cost_Update
```
public static double cost_Update
```
    the cost associated with one neuron update (see D’Haene, 2009)
  - cost_Schedule
```
public static double cost_Schedule
```
    the cost associated with one queue schedule (see D'Haene, 2009)
  - cost
```
public static double cost
```
    the expected cost of inserting a preliminary fire estimate into the event queue (as opposed to performing another NR iteration)
  - tAvg
```
public double tAvg
```
    running average of the time interval between input spikes
  - lastInputTime
```
public double lastInputTime
```
    last time the neuron received a spike
  - lastFireTime
```
public double lastFireTime
```
    last time the neuron fired; negative means no last spike
  - clampVoltage
```
public double clampVoltage
```
    clamp the membrane voltage during absolute refractory period
  - clampThreshold
```
public double clampThreshold
```
    clamp the threshold during absolute refractory period
  - fire
```
public boolean fire
```
    whether the next fire event is a final calculation, as opposed to a preliminary estimate (see D'Haene, 2009)
  - tHost
```
public long tHost
```
    long imposes a constraint on the maximum number of hosts to be 64
  - para
```
public MiNiNeuronPara para
```
    neuron parameters
  - state
```
public TreeSet<MiNiNeuron.State> state
```
    linked list for state variables
  - sta_p
```
public MiNiNeuron.State[][] sta_p
```
    two-dimensional array pointing to the state variables. The first dimension corresponds to type -- NG, NB, NJ_SPIKE, and NJ_SYNAPSE, in that order. The second dimension corresponds to index. The NG and NB arrays have only one element.
- Constructor Detail
  - MiNiNeuron
```
public MiNiNeuron(MiNiNeuronPara para)
```
- Method Detail
  - getCurr
```
public double[] getCurr(double currTime)
```
    Used mainly for intracellular recording.
    
    Specified by:
    
    getCurr in interface Neuron
    
    Parameters:
    currTime - the current time.
    
    Returns:
    the synaptic currents in this neuron at time currTime.
  - getMemV
```
public double getMemV(double currTime)
```
    Used mainly for intracellular recording.
    
    Specified by:
    
    getMemV in interface Neuron
    
    Parameters:
    currTime - the current time.
    
    Returns:
    the membrane voltage in this neuron at time currTime.
  - getRecord
```
public boolean getRecord()
```
    Description copied from interface: Neuron
    
    record the neuron
    
    Specified by:
    
    getRecord in interface Neuron
    
    Returns:
    boolean whether it should be recorded
  - getTHost
```
public long getTHost()
```
    Specified by:
    
    getTHost in interface Neuron
    
    Returns:
    the target host, maximum NetHost 64
  - getTimeOfNextFire
```
public double getTimeOfNextFire()
```
    Description copied from interface: Neuron
    
    get the value of timeOfNextFire
    
    Specified by:
    
    getTimeOfNextFire in interface Neuron
    
    Returns:
    the value of timeOfNextFire
  - isSensory
```
public boolean isSensory()
```
    Description copied from interface: Neuron
    
    sensory report
    
    Specified by:
    
    isSensory in interface Neuron
    
    Returns:
    true if the neuron is a sensory neuron
  - realFire
```
public boolean realFire()
```
    Specified by:
    
    realFire in interface Neuron
    
    Returns:
    whether the scheduled neuron fire means the neuron really fires
  - setRecord
```
public void setRecord(boolean record)
```
    Description copied from interface: Neuron
    
    set the neuron record or not.
    
    Specified by:
    
    setRecord in interface Neuron
  - setTHost
```
public void setTHost(long id)
```
    Description copied from interface: Neuron
    
    set the target host id, 0 means none, 1 means yes
    
    Specified by:
    
    setTHost in interface Neuron
  - setTimeOfNextFire
```
public void setTimeOfNextFire(double timeOfNextFire)
```
    Description copied from interface: Neuron
    
    set a new value to timeOfNextFire
    
    Specified by:
    
    setTimeOfNextFire in interface Neuron
    
    Parameters:
    timeOfNextFire - the new value to be used
  - init
```
public void init(int expid,
        int trialid,
        Seed idum,
        Network net,
        int id)
```
    Description copied from interface: Neuron
    
    initialize the neuron
    
    Specified by:
    
    init in interface Neuron
  - updateFire
```
public double updateFire()
```
    Description copied from interface: Neuron
    
    update of the neuron after firing the current time is TimeOfNextFire
    
    Specified by:
    
    updateFire in interface Neuron
    
    Returns:
    the time interval until the next fire event, or negative if no spike is generated
  - updateInput
```
public double updateInput(double time,
                 Synapse input)
```
    Description copied from interface: Neuron
    
    update of the neuron after receiving a spike the current time is time
    
    Specified by:
    
    updateInput in interface Neuron
    
    input - it is a InputEvent event in the input queue
    
    Returns:
    the time interval until next fire event, or negative if no spike is generated
  - getSensoryWeight
```
public double getSensoryWeight()
```
  - getTimeOfLastUpdate
```
public double getTimeOfLastUpdate()
```
  - setMemV
```
public void setMemV(double memV)
```
    set the membrane voltage
  - setTimeOfLastUpdate
```
public void setTimeOfLastUpdate(double timeOfLastUpdate)
```
  - toString
```
public String toString()
```
    Overrides:
    
    toString in class Object
  - membraneVoltage
```
public double membraneVoltage(double t)
```
    Compute the membrane voltage. This method transforms the thresholdDiff (Mihalas and Niebur, 2009, Equation 3.5) into the voltage ( V(t) in Equation 3.2)
    
    Parameters:
    t - absolute time t
    
    Returns:
    membrane voltage at time t.s
  - thresholdDiff
```
public double thresholdDiff(double t)
```
    Compute the difference between the membrane voltage and the membrane voltage threshold. The MNNeuron class is optimized to perform this function quickly, at the expense of membraneVoltage(). This method is based on Equation 3.5 in Mihalas and Niebur, 2009.
    
    Parameters:
    t - absolute time t
    
    Returns:
    voltage - threshold at time t
  - safeDerivative
```
public double safeDerivative(double t)
```
    Computes the "safe derivative" (see D'Haene, 2009) of the thresholdDiff function.
    
    Parameters:
    t - absolute time t

Class MiNiNeuron

Nested Class Summary

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

tEPS

rEPS

cost_Update

cost_Schedule

cost

tAvg

lastInputTime

lastFireTime

clampVoltage

clampThreshold

fire

tHost

para

state

sta_p

Constructor Detail

MiNiNeuron

Method Detail

getCurr

getMemV

getRecord

getTHost

getTimeOfNextFire

isSensory

realFire

setRecord

setTHost

setTimeOfNextFire

init

updateFire

updateInput

getSensoryWeight

getTimeOfLastUpdate

setMemV

setTimeOfLastUpdate

toString

membraneVoltage

thresholdDiff

safeDerivative