ca.nengo.model.nef.impl
Class DecodableEnsembleImpl

java.lang.Object
  ca.nengo.model.impl.AbstractEnsemble
      ca.nengo.model.impl.EnsembleImpl
          ca.nengo.model.plasticity.impl.PlasticEnsembleImpl
              ca.nengo.model.nef.impl.DecodableEnsembleImpl

All Implemented Interfaces:

Ensemble, ExpandableNode, DecodableEnsemble, Node, PlasticEnsemble, Probeable, Resettable, SimulationMode.ModeConfigurable, TaskSpawner, VisiblyMutable, java.io.Serializable, java.lang.Cloneable

Direct Known Subclasses:

NEFEnsembleImpl

public class DecodableEnsembleImpl
extends PlasticEnsembleImpl
implements DecodableEnsemble

Default implementation of DecodableEnsemble.

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface ca.nengo.util.VisiblyMutable

VisiblyMutable.Event, VisiblyMutable.Listener, VisiblyMutable.NameChangeEvent, VisiblyMutable.NodeRemovedEvent

Field Summary

protected java.util.Map<java.lang.String,DecodedOrigin>	myDecodedOrigins
protected java.util.Map<java.lang.String,DecodedTermination>	myDecodedTerminations

Fields inherited from class ca.nengo.model.plasticity.impl.PlasticEnsembleImpl

myPlasticEnsembleTerminations

Fields inherited from class ca.nengo.model.impl.EnsembleImpl

myExpandableNodes, myExpandedTerminations

Constructor Summary

DecodableEnsembleImpl(java.lang.String name, Node[] nodes, ApproximatorFactory factory)

Method Summary

Origin	addDecodedOrigin(java.lang.String name, Function[] functions, java.lang.String nodeOrigin, Network environment, Probe probe, float startTime, float endTime) Adds an Origin that corresponds to a decoding of the activities of Nodes in this Ensemble.
Origin	addDecodedOrigin(java.lang.String name, Function[] functions, java.lang.String nodeOrigin, Network environment, Probe probe, Probe state, float startTime, float endTime, float tau) Lloyd Elliot's decodable origin for decoding band-limited noise using a psc optimized decoder
Origin	addDecodedOrigin(java.lang.String name, Function[] functions, java.lang.String nodeOrigin, Network environment, Probe probe, Termination termination, float[][] evalPoints, float transientTime) Adds an Origin that corresponds to a decoding of the activities of Nodes in this Ensemble.
Termination	addDecodedTermination(java.lang.String name, float[][] matrix, float[] tfNumerator, float[] tfDenominator, float passthrough, boolean isModulatory)
Termination	addDecodedTermination(java.lang.String name, float[][] matrix, float tauPSC, boolean isModulatory)
DecodableEnsemble	clone()
void	doneOrigins() This method can optionally be called after all decoded Origins have been added, in order to free resources that are needed for adding new decodings.
ApproximatorFactory	getApproximatorFactory()
DecodedOrigin[]	getDecodedOrigins() Used to get decoded origins to give to GPU.
DecodedTermination[]	getDecodedTerminations() Used to get decoded terminations to give to GPU.
TimeSeries	getHistory(java.lang.String stateName) Note that the units of TimeSeries' for a given state do not change over time (ie at different time steps).
Origin	getOrigin(java.lang.String name)
Origin[]	getOrigins()
Termination	getTermination(java.lang.String name)
Termination[]	getTerminations()
java.util.Properties	listStates()
DecodedOrigin	removeDecodedOrigin(java.lang.String name)
DecodedTermination	removeDecodedTermination(java.lang.String name)
void	run(float startTime, float endTime) Runs each neuron in the Ensemble.
void	setTime(float time) Allows subclasses to set the simulation time, which is used to support Probeable.
void	stopProbing(java.lang.String stateName)

Methods inherited from class ca.nengo.model.plasticity.impl.PlasticEnsembleImpl

addTasks, getLearning, getPlasticityInterval, getTasks, isPopulationPlastic, reset, setLearning, setPlasticityInterval, setStates, setTasks

Methods inherited from class ca.nengo.model.impl.EnsembleImpl

addTermination, getDimension, removeTermination, setMode

Methods inherited from class ca.nengo.model.impl.AbstractEnsemble

addChangeListener, collectSpikes, findCommon1DOrigins, fireVisibleChangeEvent, getCollectSpikesRatio, getDocumentation, getMode, getName, getNodes, getSpikePattern, isCollectingSpikes, redefineNodes, removeChangeListener, removeOrigin, setCollectSpikesRatio, setDocumentation, setName, setSpikePattern

Methods inherited from class java.lang.Object

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

Methods inherited from interface ca.nengo.model.plasticity.PlasticEnsemble

getPlasticityInterval, setPlasticityInterval

Methods inherited from interface ca.nengo.model.Ensemble

collectSpikes, getNodes, getSpikePattern, isCollectingSpikes, redefineNodes

Methods inherited from interface ca.nengo.model.Node

getDocumentation, getName, setDocumentation, setName

Methods inherited from interface ca.nengo.model.Resettable

reset

Methods inherited from interface ca.nengo.model.SimulationMode.ModeConfigurable

getMode, setMode

Methods inherited from interface ca.nengo.util.VisiblyMutable

addChangeListener, removeChangeListener

Field Detail

myDecodedOrigins

protected final java.util.Map<java.lang.String,DecodedOrigin> myDecodedOrigins

myDecodedTerminations

protected final java.util.Map<java.lang.String,DecodedTermination> myDecodedTerminations

Constructor Detail

DecodableEnsembleImpl

public DecodableEnsembleImpl(java.lang.String name,
                             Node[] nodes,
                             ApproximatorFactory factory)
                      throws StructuralException

Parameters:

name - Name of the Ensemble

nodes - Nodes that make up the Ensemble

factory - Source of LinearApproximators to use in decoding output

Throws:

StructuralException - if super constructor fails

Method Detail

addDecodedOrigin

public Origin addDecodedOrigin(java.lang.String name,
                               Function[] functions,
                               java.lang.String nodeOrigin,
                               Network environment,
                               Probe probe,
                               float startTime,
                               float endTime)
                        throws StructuralException,
                               SimulationException

Description copied from interface: DecodableEnsemble

Adds an Origin that corresponds to a decoding of the activities of Nodes in this Ensemble. The decoding is found by running the Ensemble within a Network, and using its output to approximate a vector function of time.

Specified by:

addDecodedOrigin in interface DecodableEnsemble

Parameters:

name - Name of decoding

functions - 1D Functions of time which represent the meaning of the Ensemble output when it runs in the Network provided (see environment arg)

nodeOrigin - The name of the Node-level Origin to decode

environment - A Network in which the Ensemble runs (may include inputs, feedback, etc)

probe - A Probe that is connected to the named Node-level Origin

startTime - Simulation time at which to start

endTime - Simulation time at which to finish

Returns:

An Origin that approximates the given Functions as a linear combination of output from the given nodeOrigin

Throws:

StructuralException - May arise in instantiating the Origin

SimulationException - If there is a problem running the simulation

See Also:

DecodableEnsemble.addDecodedOrigin(java.lang.String, ca.nengo.math.Function[], java.lang.String, ca.nengo.model.Network, ca.nengo.util.Probe, float, float)

addDecodedOrigin

public Origin addDecodedOrigin(java.lang.String name,
                               Function[] functions,
                               java.lang.String nodeOrigin,
                               Network environment,
                               Probe probe,
                               Termination termination,
                               float[][] evalPoints,
                               float transientTime)
                        throws StructuralException,
                               SimulationException

Description copied from interface: DecodableEnsemble

Adds an Origin that corresponds to a decoding of the activities of Nodes in this Ensemble. The decoding is found by running the Ensemble repeatedly with different inputs, and using the steady-state output for each input to approximate a vector function of the input. Input is applied to a caller-defined Termination which may or may not be directly onto the Ensemble.

Specified by:

addDecodedOrigin in interface DecodableEnsemble

Parameters:

name - Name of decoding

functions - Functions of input that represent the meaning of Ensemble output when it runs in the Network provided (see environment arg)

nodeOrigin - The name of the Node-level Origin to decode

environment - A Network in which the Ensemble runs (may include inputs, feedback, etc)

probe - A Probe that is connected to the named Node-level Origin

termination - The Termination through which input is to be applied to the Ensemble

evalPoints - The set of vector inputs that are to be applied at the above Termination

transientTime - The amount of time the Network is to run with each input, so that transients die away (output is averaged over the last 10% of each simulation)

Returns:

An Origin that approximates the given Functions as a linear combination of output from the given nodeOrigin

Throws:

StructuralException - May arise in instantiating the Origin

SimulationException - If there is a problem running the simulations

See Also:

DecodableEnsemble.addDecodedOrigin(java.lang.String, ca.nengo.math.Function[], java.lang.String, ca.nengo.model.Network, ca.nengo.util.Probe, ca.nengo.model.Termination, float[][], float)

addDecodedOrigin

public Origin addDecodedOrigin(java.lang.String name,
                               Function[] functions,
                               java.lang.String nodeOrigin,
                               Network environment,
                               Probe probe,
                               Probe state,
                               float startTime,
                               float endTime,
                               float tau)
                        throws StructuralException,
                               SimulationException

Lloyd Elliot's decodable origin for decoding band-limited noise using a psc optimized decoder

Parameters:

name - Name of decoding

functions - 1D Functions of time which represent the meaning of the Ensemble output when it runs in the Network provided (see environment arg)

nodeOrigin - The name of the Node-level Origin to decode

environment - A Network in which the Ensemble runs (may include inputs, feedback, etc)

probe - A Probe that is connected to the named Node-level Origin

state - Another probe?

startTime - Simulation time at which to start

endTime - Simulation time at which to finish

tau - Time constant

Returns:

The added Origin

Throws:

StructuralException - if origin name is taken

SimulationException - if environment can't run

addDecodedTermination

public Termination addDecodedTermination(java.lang.String name,
                                         float[][] matrix,
                                         float tauPSC,
                                         boolean isModulatory)
                                  throws StructuralException

Parameters:

name - Unique name for this Termination (in the scope of this Ensemble)

matrix - Transformation matrix which defines a linear map on incoming information, onto the space of vectors that can be represented by this NEFEnsemble. The first dimension is taken as matrix rows, and must have the same length as the Origin that will be connected to this Termination. The second dimension is taken as matrix columns, and must have the same length as the encoders of this NEFEnsemble. TODO: this is transposed?

tauPSC - Time constant of post-synaptic current decay (all Terminations have this property but it may have slightly different interpretations depending other properties of the Termination).

isModulatory - If true, inputs to this Termination do not drive Nodes in the Ensemble directly but may have modulatory influences (eg related to plasticity). If false, the transformation matrix output dimension must match the dimension of this Ensemble.

Returns:

Added Termination

Throws:

StructuralException - if termination name is taken

See Also:

NEFEnsemble.addDecodedTermination(java.lang.String, float[][], float, boolean)

addDecodedTermination

public Termination addDecodedTermination(java.lang.String name,
                                         float[][] matrix,
                                         float[] tfNumerator,
                                         float[] tfDenominator,
                                         float passthrough,
                                         boolean isModulatory)
                                  throws StructuralException

Parameters:

name - Unique name for this Termination (in the scope of this Ensemble)

matrix - Transformation matrix which defines a linear map on incoming information, onto the space of vectors that can be represented by this NEFEnsemble. The first dimension is taken as matrix rows, and must have the same length as the Origin that will be connected to this Termination. The second dimension is taken as matrix columns, and must have the same length as the encoders of this NEFEnsemble. TODO: this is transposed?

tfNumerator - Coefficients of transfer function numerator (see CanonicalModel.getRealization(...) for details)

tfDenominator - Coefficients of transfer function denominator

passthrough - How much should pass through?

isModulatory - Is the termination modulatory?

Returns:

The added Termination

Throws:

StructuralException - if termination name is taken

See Also:

NEFEnsemble.addDecodedTermination(java.lang.String, float[][], float[], float[], float, boolean)

removeDecodedTermination

public DecodedTermination removeDecodedTermination(java.lang.String name)
                                            throws StructuralException

Specified by:

removeDecodedTermination in interface DecodableEnsemble

Parameters:

name - Name of an existing termination to remove

Returns:

The removed DecodedTermination

Throws:

StructuralException - if DecodedTermination doesn't exist

See Also:

DecodableEnsemble.removeDecodedTermination(java.lang.String)

removeDecodedOrigin

public DecodedOrigin removeDecodedOrigin(java.lang.String name)
                                  throws StructuralException

Specified by:

removeDecodedOrigin in interface DecodableEnsemble

Parameters:

name - Name of an existing decoding to remove

Returns:

The removed DecodedOrigin

Throws:

StructuralException - if DecodedOrigin doesn't exist

See Also:

DecodableEnsemble.removeDecodedTermination(java.lang.String)

getDecodedTerminations

public DecodedTermination[] getDecodedTerminations()

Used to get decoded terminations to give to GPU.

Returns:

all DecodedTerminations

doneOrigins

public void doneOrigins()

Description copied from interface: DecodableEnsemble

This method can optionally be called after all decoded Origins have been added, in order to free resources that are needed for adding new decodings.

Specified by:

doneOrigins in interface DecodableEnsemble

See Also:

DecodableEnsemble.doneOrigins()

getOrigin

public Origin getOrigin(java.lang.String name)
                 throws StructuralException

Specified by:

getOrigin in interface Node

Overrides:

getOrigin in class AbstractEnsemble

Parameters:

name - Name of an Origin on this Node

Returns:

The named Origin if it exists

Throws:

StructuralException - if the named Origin does not exist

See Also:

Node.getOrigin(java.lang.String)

getTermination

public Termination getTermination(java.lang.String name)
                           throws StructuralException

Specified by:

getTermination in interface Node

Overrides:

getTermination in class PlasticEnsembleImpl

Parameters:

name - Name of a Termination onto this Node

Returns:

The named Termination if it exists

Throws:

StructuralException - if the named Termination does not exist

See Also:

Node.getTermination(java.lang.String)

getOrigins

public Origin[] getOrigins()

Specified by:

getOrigins in interface Node

Overrides:

getOrigins in class AbstractEnsemble

Returns:

Sets of ouput channels (eg spiking outputs, gap junctional outputs, etc.)

See Also:

Node.getOrigins()

getDecodedOrigins

public DecodedOrigin[] getDecodedOrigins()

Used to get decoded origins to give to GPU.

Returns:

All DecodedOrigins

getTerminations

public Termination[] getTerminations()

Specified by:

getTerminations in interface Node

Overrides:

getTerminations in class PlasticEnsembleImpl

Returns:

Sets of input channels (these have the same dimension as corresponding Origins to which they are connected).

See Also:

Node.getTerminations()

run

public void run(float startTime,
                float endTime)
         throws SimulationException

Description copied from class: AbstractEnsemble

Runs each neuron in the Ensemble.

Specified by:

run in interface Node

Overrides:

run in class PlasticEnsembleImpl

Parameters:

startTime - simulation time at which running starts (s)

endTime - simulation time at which running ends (s)

Throws:

SimulationException - if a problem is encountered while trying to run

See Also:

Node.run(float, float)

setTime

public void setTime(float time)

Allows subclasses to set the simulation time, which is used to support Probeable. This is normally set in the run() method. Subclasses that override run() without calling it should set the time.

Parameters:

time - Simulation time

getApproximatorFactory

public ApproximatorFactory getApproximatorFactory()

Returns:

The source of LinearApproximators for this ensemble (used to find linear decoding vectors).

getHistory

public TimeSeries getHistory(java.lang.String stateName)
                      throws SimulationException

Description copied from interface: Probeable

Note that the units of TimeSeries' for a given state do not change over time (ie at different time steps). CAUTION: The TimeSeries should not contain a reference to any arrays that you are going to change later. The caller owns what you return.

Specified by:

getHistory in interface Probeable

Overrides:

getHistory in class AbstractEnsemble

Parameters:

stateName - A state variable name

Returns:

Composite of Node states by given name. States of different nodes may be defined at different times, so only the states at the end of the most recent step are given. Only the first dimension of each Node state is included in the composite.

Throws:

SimulationException - if the Probeable does not have the requested state

See Also:

Probeable.getHistory(java.lang.String)

listStates

public java.util.Properties listStates()

Specified by:

listStates in interface Probeable

Overrides:

listStates in class AbstractEnsemble

Returns:

List of state variable names, eg "V", and associated descriptions eg "membrane potential (mV)"

See Also:

Probeable.listStates()

stopProbing

public void stopProbing(java.lang.String stateName)

Specified by:

stopProbing in interface Ensemble

Overrides:

stopProbing in class AbstractEnsemble

clone

public DecodableEnsemble clone()
                        throws java.lang.CloneNotSupportedException

Specified by:

clone in interface Node

Overrides:

clone in class PlasticEnsembleImpl

Returns:

An independent copy of the Node

Throws:

java.lang.CloneNotSupportedException - if clone can't be made