org.ecoinformatics.seek.garp

Class GarpPresampleLayers

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.garp.GarpPresampleLayers

All Implemented Interfaces:

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

public class GarpPresampleLayers
extends TypedAtomicActor

GARP is a computer program for predicting species locations based on various spatial data sets of environment variables and known species locations. GARP is an acronym for Genetic Algorithm for Rule Set Production. GARP was originally ceated by David Stockwell. The version in Kepler is based on 'Desktop GARP', http://www.lifemapper.org/desktopgarp/. The GarpPresampleLayers actor carries out the first step in a GARP calculation to be executes as a Kepler workflow. It samples the environment data and known locations to create a 'CellSet' of information to be used in later steps. As input, it takes several file names. One is a summary of spatial grids containing things like environmental data (e.g. temperature, precipitation, etc.) A number of these spatial grids are summarized in an xml file (named *.dxl). The second major input is locations file that contains a list of known spatial locations where the species of interest has been found. This information is 'presampled' to create a CellSet to be used in subsequent pieces of the GARP calculation. There is also an input that should give the file name to be used to store this CellSet data. The output port provides the file name when the file has been actually written. (The output is thus a 'trigger'.) This is a JNI-based actor. It requires the following: linux: libgarp.so windows: garp.dll, libexpat.dll MacOSX - currently not available for the Mac (3/16/2006)

Author:

Chad Berkeley, Dan Higgins, NCEAS, UC Santa Barbara

Nested Class Summary

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

Entity.ContainedObjectsIterator

Field Summary

Fields

Modifier and Type	Field and Description
TypedIOPort	cellSetFileName input port can be used to supply the file name to be used in saving the cell set information.
TypedIOPort	cellSetFileNameOutput This output port supplies the file name of the cellSetFile.
FileParameter	cellSetFileNameParameter This parameter is the file name to be used in saving the cell set information.
TypedIOPort	dataPointFileName This input port can be used to supply the file name of the file that contains the known locations to be used to determine a ruleset for predicting other locations from the spatial environment layers.
FileParameter	dataPointFileNameParameter This parameter is the file name of the file that contains the known locations to be used to determine a ruleset for predicting other locations from the spatial environment layers.
TypedIOPort	layersetFilename This input port can be used to supply the file name of the xml file that summarizes all the spatial layers to be used in the GARP calculation.
FileParameter	layersetFilenameParameter This parameter is the file name of the xml file that summarizes all the spatial layers to be used in the GARP calculation.

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
GarpPresampleLayers(CompositeEntity container, java.lang.String name) Garp presample layer actor

Method Summary

Modifier and Type	Method and Description
void	fire() Do nothing.
void	initialize() Initialize this actor.
boolean	prefire() Return true.

Methods inherited from class ptolemy.actor.TypedAtomicActor

_containedTypeConstraints, _customTypeConstraints, _defaultTypeConstraints, _fireAt, _fireAt, attributeTypeChanged, clone, 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, postfire, preinitialize, 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, postfire, stop, stopFire, terminate

Methods inherited from interface ptolemy.actor.Initializable

addInitializable, preinitialize, 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

layersetFilenameParameter

public FileParameter layersetFilenameParameter

This parameter is the file name of the xml file that summarizes all the spatial layers to be used in the GARP calculation. The file name is of the *.dxl format. Examine samples to see the content.

dataPointFileNameParameter

public FileParameter dataPointFileNameParameter

This parameter is the file name of the file that contains the known locations to be used to determine a ruleset for predicting other locations from the spatial environment layers. The file is a text file with one location per line. Each line contains a point location (x,y) with the numeric values of x and y separated by a 'tab' character. Typically the (x,y) is (longitude, latitude).

cellSetFileNameParameter

public FileParameter cellSetFileNameParameter

This parameter is the file name to be used in saving the cell set information. This information is a sample to be used by GARP in creating the rule set for predicting occurrences.

layersetFilename

public TypedIOPort layersetFilename

This input port can be used to supply the file name of the xml file that summarizes all the spatial layers to be used in the GARP calculation. The file name is of the *.dxl format. Examine samples to see the content.

dataPointFileName

public TypedIOPort dataPointFileName

This input port can be used to supply the file name of the file that contains the known locations to be used to determine a ruleset for predicting other locations from the spatial environment layers. The file is a text file with one location per line. Each line contains a point location (x,y) with the numeric values of x and separated by a 'tab' character. Typically the (x,y) is (longitude, latitude).

cellSetFileName

public TypedIOPort cellSetFileName

input port can be used to supply the file name to be used in saving the cell set information. This information is a sample to be used by GARP in creating the rule set for predicting occurrences.

cellSetFileNameOutput

public TypedIOPort cellSetFileNameOutput

This output port supplies the file name of the cellSetFile. It has the same name as supplied in the input port, but it is only fired after the data has been calculated. It is thus used as a 'trigger' for the next step in the GARP calculation.

Constructor Detail

GarpPresampleLayers

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

Garp presample layer actor

Throws:

NameDuplicationException

IllegalActionException

Method Detail

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.

prefire

public boolean prefire()
                throws IllegalActionException

Description copied from class: AtomicActor

Return true. Derived classes override this method to define operations to be performed at the beginning of every iteration of its execution, prior the invocation of the fire() method. Derived classes may also use it to check preconditions for an iteration, if there are any.

Specified by:

prefire in interface Executable

Overrides:

prefire in class AtomicActor<TypedIOPort>

Returns:

True if this actor is ready for firing, false otherwise.

Throws:

IllegalActionException - Not thrown in this base class.

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.