org.ptolemy.machineLearning.hsmm

Class HSMMGenerator

java.lang.Object

ptolemy.kernel.util.NamedObj

ptolemy.kernel.InstantiableNamedObj

ptolemy.kernel.Entity<T>

ptolemy.kernel.ComponentEntity<T>

ptolemy.actor.AtomicActor<TypedIOPort>

ptolemy.actor.TypedAtomicActor

org.ptolemy.machineLearning.hsmm.HSMMGenerator

All Implemented Interfaces:

java.lang.Cloneable, Actor, Executable, FiringsRecordable, Initializable, TypedActor, Changeable, Debuggable, DebugListener, Derivable, Instantiable, ModelErrorHandler, MoMLExportable, Moveable, Nameable

Direct Known Subclasses:

HSMMGeneratorGaussianEmissions, HSMMGeneratorMultinomialEmissions

public abstract class HSMMGenerator
extends TypedAtomicActor

An abstract class that implements a Bayesian network used to simulate an Explicit-Duration Hidden Markov Model.

Since:

Ptolemy II 10.0

Version:

$Id$

Author:

Ilge Akkaya

Pt.AcceptedRating:

Pt.ProposedRating:

Red (ilgea)

Nested Class Summary

Nested classes/interfaces inherited from class ptolemy.kernel.Entity

Entity.ContainedObjectsIterator

Field Summary

Fields

Modifier and Type	Field and Description
protected double[][]	_A Cached transition matrix value.
protected double[][]	_D current duration distribution.
protected double[][]	_D0 initial duration distribution.
protected int	_dt Duration variable: d(t).
protected double[]	_durationPriors Duration priors: an nStates-by-nDurations matrix.
protected boolean	_firstIteration Boolean indicating the first iteration of the generator.
protected int	_maxDuration Cardinality of the support of duration distribution.
protected int	_nStates Cardinality of state space.
protected int	_windowSize Generation window size.
protected double[]	_x0 maximum duration ( in time steps).
protected int	_xt State variable: x(t).
protected double[][]	D_new new duration distribution.
PortParameter	durationPriors The user-provided initial guess on the prior probability distribution.
PortParameter	durationProbabilities The user-provided initial guess on the prior probability distribution.
TypedIOPort	hiddenState Output port for corresponding state sequence.
protected static int	MAX_TRIALS In the presence of window-based constraints, number of runs allowable until valid trace found.
TypedIOPort	observation Output port for observation array.
PortParameter	powerUpperBound Power limit on generation window.
PortParameter	statePriors Prior state distribution.
PortParameter	transitionMatrix Transition Probability matrix estimate.
TypedIOPort	trigger Trigger generation.
Parameter	windowSize Generation window size.

Fields inherited from class ptolemy.actor.TypedAtomicActor

_typesValid

Fields inherited from class ptolemy.actor.AtomicActor

_actorFiringListeners, _initializables, _notifyingActorFiring, _stopRequested

Fields inherited from class ptolemy.kernel.util.NamedObj

_changeListeners, _changeLock, _changeRequests, _debugging, _debugListeners, _deferChangeRequests, _elementName, _isPersistent, _verbose, _workspace, ATTRIBUTES, CLASSNAME, COMPLETE, CONTENTS, DEEP, FULLNAME, LINKS

Fields inherited from interface ptolemy.actor.Executable

COMPLETED, NOT_READY, STOP_ITERATING

Constructor Summary

Constructors

Constructor and Description
HSMMGenerator(CompositeEntity container, java.lang.String name) Construct an actor with the given container and name.

Method Summary

Modifier and Type	Method and Description
protected abstract int	_propagateState() Sample next state given current state.
protected abstract int	_sampleDurationForState() Sample a duration value given current state.
protected abstract int	_sampleDurationFromPrior() Sample duration value from prior duration distribution.
protected abstract int	_sampleHiddenStateFromPrior() Sample state at this iteration from the state prior.
protected abstract double[]	_sampleObservation() Sample an observation value given current state.
void	attributeChanged(Attribute attribute) React to a change in an attribute.
java.lang.Object	clone(Workspace workspace) Clone the actor into the specified workspace.
void	preinitialize() Create receivers and declare delay dependencies.

Methods inherited from class ptolemy.actor.TypedAtomicActor

_containedTypeConstraints, _customTypeConstraints, _defaultTypeConstraints, _fireAt, _fireAt, attributeTypeChanged, clone, isBackwardTypeInferenceEnabled, newPort, typeConstraintList, typeConstraints

Methods inherited from class ptolemy.actor.AtomicActor

_actorFiring, _actorFiring, _declareDelayDependency, addActorFiringListener, addInitializable, connectionsChanged, createReceivers, declareDelayDependency, fire, getCausalityInterface, getDirector, getExecutiveDirector, getManager, initialize, inputPortList, isFireFunctional, isStrict, iterate, newReceiver, outputPortList, postfire, prefire, pruneDependencies, recordFiring, removeActorFiringListener, removeDependency, removeInitializable, setContainer, stop, stopFire, terminate, wrapup

Methods inherited from class ptolemy.kernel.ComponentEntity

_adjustDeferrals, _checkContainer, _getContainedObject, _propagateExistence, getContainer, instantiate, isAtomic, isOpaque, moveDown, moveToFirst, moveToIndex, moveToLast, moveUp, propagateExistence, setName

Methods inherited from class ptolemy.kernel.Entity

_addPort, _description, _exportMoMLContents, _removePort, _validateSettables, connectedPortList, connectedPorts, containedObjectsIterator, getAttribute, getPort, getPorts, linkedRelationList, linkedRelations, portList, removeAllPorts, setClassDefinition, uniqueName

Methods inherited from class ptolemy.kernel.InstantiableNamedObj

_setParent, exportMoML, getChildren, getElementName, getParent, getPrototypeList, isClassDefinition, isWithinClassDefinition

Methods inherited from class ptolemy.kernel.util.NamedObj

_addAttribute, _adjustOverride, _attachText, _cloneFixAttributeFields, _containedDecorators, _copyChangeRequestList, _debug, _debug, _debug, _debug, _debug, _executeChangeRequests, _getIndentPrefix, _isMoMLSuppressed, _markContentsDerived, _notifyHierarchyListenersAfterChange, _notifyHierarchyListenersBeforeChange, _propagateValue, _removeAttribute, _splitName, _stripNumericSuffix, addChangeListener, addDebugListener, addHierarchyListener, attributeDeleted, attributeList, attributeList, decorators, deepContains, depthInHierarchy, description, description, event, executeChangeRequests, exportMoML, exportMoML, exportMoML, exportMoML, exportMoMLPlain, getAttribute, getAttributes, getChangeListeners, getClassName, getDecoratorAttribute, getDecoratorAttributes, getDerivedLevel, getDerivedList, getDisplayName, getFullName, getModelErrorHandler, getName, getName, getSource, handleModelError, isDeferringChangeRequests, isOverridden, isPersistent, lazyContainedObjectsIterator, message, notifyOfNameChange, propagateValue, propagateValues, removeAttribute, removeChangeListener, removeDebugListener, removeHierarchyListener, requestChange, setClassName, setDeferringChangeRequests, setDerivedLevel, setDisplayName, setModelErrorHandler, setPersistent, setSource, sortContainedObjects, toplevel, toString, validateSettables, workspace

Methods inherited from class java.lang.Object

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

Methods inherited from interface ptolemy.actor.Actor

createReceivers, getCausalityInterface, getDirector, getExecutiveDirector, getManager, inputPortList, newReceiver, outputPortList

Methods inherited from interface ptolemy.actor.Executable

fire, isFireFunctional, isStrict, iterate, postfire, prefire, stop, stopFire, terminate

Methods inherited from interface ptolemy.actor.Initializable

addInitializable, initialize, removeInitializable, wrapup

Methods inherited from interface ptolemy.kernel.util.Nameable

description, getContainer, getDisplayName, getFullName, getName, getName, setName

Methods inherited from interface ptolemy.kernel.util.Derivable

getDerivedLevel, getDerivedList, propagateValue

Field Detail

durationPriors

public PortParameter durationPriors

The user-provided initial guess on the prior probability distribution.

durationProbabilities

public PortParameter durationProbabilities

The user-provided initial guess on the prior probability distribution.

transitionMatrix

public PortParameter transitionMatrix

Transition Probability matrix estimate.

statePriors

public PortParameter statePriors

Prior state distribution.

trigger

public TypedIOPort trigger

Trigger generation.

observation

public TypedIOPort observation

Output port for observation array.

hiddenState

public TypedIOPort hiddenState

Output port for corresponding state sequence.

windowSize

public Parameter windowSize

Generation window size.

powerUpperBound

public PortParameter powerUpperBound

Power limit on generation window.

_durationPriors

protected double[] _durationPriors

Duration priors: an nStates-by-nDurations matrix.

D_new

protected double[][] D_new

new duration distribution.

_D0

protected double[][] _D0

initial duration distribution.

_D

protected double[][] _D

current duration distribution.

_x0

protected double[] _x0

maximum duration ( in time steps).

_A

protected double[][] _A

Cached transition matrix value.

_firstIteration

protected boolean _firstIteration

Boolean indicating the first iteration of the generator.

_nStates

protected int _nStates

Cardinality of state space.

_maxDuration

protected int _maxDuration

Cardinality of the support of duration distribution.

_dt

protected int _dt

Duration variable: d(t).

_xt

protected int _xt

State variable: x(t).

_windowSize

protected int _windowSize

Generation window size.

MAX_TRIALS

protected static int MAX_TRIALS

In the presence of window-based constraints, number of runs allowable until valid trace found.

Constructor Detail

HSMMGenerator

public HSMMGenerator(CompositeEntity container,
                     java.lang.String name)
              throws NameDuplicationException,
                     IllegalActionException

Construct an actor with the given container and name.

Parameters:

container - The container.

name - The name of this actor

Throws:

IllegalActionException - If the actor cannot be contained by the proposed container.

NameDuplicationException - If the container already has an actor with this name.

Method Detail

clone

public java.lang.Object clone(Workspace workspace)
                       throws java.lang.CloneNotSupportedException

Description copied from class: TypedAtomicActor

Clone the actor into the specified workspace.

Overrides:

clone in class TypedAtomicActor

Parameters:

workspace - The workspace for the new object.

Returns:

A new actor.

Throws:

java.lang.CloneNotSupportedException - If a derived class contains an attribute that cannot be cloned.

See Also:

NamedObj.exportMoML(Writer, int, String), NamedObj.setDeferringChangeRequests(boolean)

preinitialize

public void preinitialize()
                   throws IllegalActionException

Description copied from class: AtomicActor

Create receivers and declare delay dependencies. Derived classes can override this method to perform additional initialization functions, but they should call this base class methods or create the receivers themselves. This method gets executed exactly once prior to any other action methods. It cannot produce output data since type resolution is typically not yet done. It also gets invoked prior to any static scheduling that might occur in the domain, so it can change scheduling information.

Specified by:

preinitialize in interface Initializable

Overrides:

preinitialize in class AtomicActor<TypedIOPort>

Throws:

IllegalActionException - Not thrown in this base class.

attributeChanged

public void attributeChanged(Attribute attribute)
                      throws IllegalActionException

Description copied from class: NamedObj

React to a change in an attribute. This method is called by a contained attribute when its value changes. In this base class, the method does nothing. In derived classes, this method may throw an exception, indicating that the new attribute value is invalid. It is up to the caller to restore the attribute to a valid value if an exception is thrown.

Overrides:

attributeChanged in class NamedObj

Parameters:

attribute - The attribute that changed.

Throws:

IllegalActionException - If the change is not acceptable to this container (not thrown in this base class).

_sampleObservation

protected abstract double[] _sampleObservation()

Sample an observation value given current state.

Returns:

Observation

_sampleDurationForState

protected abstract int _sampleDurationForState()

Sample a duration value given current state.

Returns:

Duration

_propagateState

protected abstract int _propagateState()
                                throws IllegalActionException

Sample next state given current state.

Returns:

Next state index.

Throws:

IllegalActionException

_sampleHiddenStateFromPrior

protected abstract int _sampleHiddenStateFromPrior()

Sample state at this iteration from the state prior.

Returns:

The hidden state at this iteration

_sampleDurationFromPrior

protected abstract int _sampleDurationFromPrior()

Sample duration value from prior duration distribution.

Returns:

sampled duration value