org.ecoinformatics.seek.R

Class RExpression2

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.ecoinformatics.seek.R.RExpression2

All Implemented Interfaces:

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

public class RExpression2
extends TypedAtomicActor

The RExpression actor is an actor designed to run an R script or function with inputs and outputs determined by the ports created by the user. Port names will correspond to R object names. The RExpression actor is modeled after the Ptolemy expression actor, except that that instead of using a single mathematical expression in Ptolemy's expression language, it uses a set of the more powerful, higher order expressions available under R. Both input and output port will usually be added to the actor; The names of these ports correspond to R variables used in the R script.

Author:

Dan Higgins and Matt Jones, NCEAS, UC Santa Barbara

UserLevelDocumentation:

This actor let the user insert R scripts in a Kepler workflow. It requires the R system to be installed on the computer executing the workflow

Nested Class Summary

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

Entity.ContainedObjectsIterator

Field Summary

Fields

Modifier and Type	Field and Description
Parameter	displayGraphicsOutput If true, then display plot.
StringAttribute	expression The expression that is evaluated to produce the output.
TypedIOPort	graphicsFileName The name of the default graphics output file created by the actor
StringParameter	graphicsFormat The graphics output format.
Parameter	graphicsOutput If true, then create a graphics output port.
static org.apache.commons.logging.Log	log
StringParameter	numXPixels The width of the output graphics bitmap in pixels
StringParameter	numYPixels The height of the output graphics bitmap in pixels
TypedIOPort	output The output port.
StringParameter	Rcwd The 'R' working directory (home dir by default)
Parameter	serializeData If true, then daata frames (and other complexe data objects will be transferred by serialization to disk.
Parameter	showDebug If true, then shoe debugging information about script.

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
RExpression2(CompositeEntity container, java.lang.String name) Construct an actor with the given container and name.

Method Summary

Modifier and Type	Method and Description
static boolean[][]	asBooleanMatrix(org.rosuda.JRI.REXP x)
static int[][]	asIntMatrix(double[][] doubles)
java.lang.Object	clone(Workspace workspace) Override the base class to set type constraints.
void	fire() Do nothing.
void	initialize() Initialize this actor.
boolean	postfire() Return true, unless stop() has been called, in which case, return false.
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, getCausalityInterface, getDirector, getExecutiveDirector, getManager, inputPortList, isFireFunctional, isStrict, iterate, newReceiver, outputPortList, 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, attributeChanged, 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

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

Methods inherited from interface ptolemy.actor.Initializable

addInitializable, 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

log

public static org.apache.commons.logging.Log log

output

public TypedIOPort output

The output port.

expression

public StringAttribute expression

The expression that is evaluated to produce the output.

Rcwd

public StringParameter Rcwd

The 'R' working directory (home dir by default)

showDebug

public Parameter showDebug

If true, then shoe debugging information about script. If false, then don't. (the default)

serializeData

public Parameter serializeData

If true, then daata frames (and other complexe data objects will be transferred by serialization to disk. If false, then they will be converted as losslessly as possible to a Ptolemy data structure

displayGraphicsOutput

public Parameter displayGraphicsOutput

If true, then display plot. If false, then don't. (the default)

graphicsFormat

public StringParameter graphicsFormat

The graphics output format. Currently the format is either a *.pdf or a *.png

graphicsOutput

public Parameter graphicsOutput

If true, then create a graphics output port. (the default); If false, then don't.

numXPixels

public StringParameter numXPixels

The width of the output graphics bitmap in pixels

numYPixels

public StringParameter numYPixels

The height of the output graphics bitmap in pixels

graphicsFileName

public TypedIOPort graphicsFileName

The name of the default graphics output file created by the actor

Constructor Detail

RExpression2

public RExpression2(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

Override the base class to set type constraints.

Overrides:

clone in class TypedAtomicActor

Parameters:

workspace - The workspace for the new object.

Returns:

A new instance of RExpression.

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)

fire

public void fire()
          throws IllegalActionException

Description copied from class: AtomicActor

Do nothing. Derived classes override this method to define their primary run-time action.

Specified by:

fire in interface Executable

Overrides:

fire in class AtomicActor<TypedIOPort>

Throws:

IllegalActionException - Not thrown in this base class.

initialize

public void initialize()
                throws IllegalActionException

Description copied from class: AtomicActor

Initialize this actor. Derived classes override this method to perform actions that should occur once at the beginning of an execution, but after type resolution. Derived classes can produce output data and schedule events.

Specified by:

initialize in interface Initializable

Overrides:

initialize in class AtomicActor<TypedIOPort>

Throws:

IllegalActionException - If a derived class throws it.

postfire

public boolean postfire()
                 throws IllegalActionException

Description copied from class: AtomicActor

Return true, unless stop() has been called, in which case, return false. Derived classes override this method to define operations to be performed at the end of every iteration of its execution, after one invocation of the prefire() method and any number of invocations of the fire() method. This method typically wraps up an iteration, which may involve updating local state. In derived classes, this method returns false to indicate that this actor should not be fired again.

Specified by:

postfire in interface Executable

Overrides:

postfire in class AtomicActor<TypedIOPort>

Returns:

True if execution can continue into the next iteration.

Throws:

IllegalActionException - Not thrown in this base class.

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.

asIntMatrix

public static int[][] asIntMatrix(double[][] doubles)

asBooleanMatrix

public static boolean[][] asBooleanMatrix(org.rosuda.JRI.REXP x)