org.apache.ctakes.assertion.medfacts.cleartk

Class UncertaintyCleartkAnalysisEngine

java.lang.Object

org.apache.uima.analysis_component.AnalysisComponent_ImplBase

org.apache.uima.analysis_component.Annotator_ImplBase

org.apache.uima.analysis_component.JCasAnnotator_ImplBase

org.apache.uima.fit.component.JCasAnnotator_ImplBase

org.cleartk.ml.CleartkAnnotator<String>

org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine

org.apache.ctakes.assertion.medfacts.cleartk.UncertaintyCleartkAnalysisEngine

All Implemented Interfaces:

org.apache.uima.analysis_component.AnalysisComponent, org.apache.uima.fit.factory.initializable.Initializable

public class UncertaintyCleartkAnalysisEngine
extends AssertionCleartkAnalysisEngine

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine

AssertionCleartkAnalysisEngine.FEATURE_CONFIG

Field Summary

Fields inherited from class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine

coin, contextFeatureExtractors, cuePhraseInWindowExtractor, entityFeatureExtractors, entityTreeExtractors, featConfig, FEATURE_SELECTION_NAME, featureFunctionExtractors, featureSelection, featureSelectionThreshold, featureSelectionURI, ffDomainAdaptor, FILE_TO_DOMAIN_MAP, fileDomainMap, fileToDomain, goldViewName, lastLabel, PARAM_FEATURE_CONFIG, PARAM_FEATURE_SELECTION_THRESHOLD, PARAM_FEATURE_SELECTION_URI, PARAM_GOLD_VIEW_NAME, PARAM_PORTION_OF_DATA_TO_USE, PARAM_PRINT_ERRORS, PARAM_PROBABILITY_OF_KEEPING_DEFAULT_EXAMPLE, portionOfDataToUse, probabilityOfKeepingADefaultExample, relationId, tokenCleartkExtractors, tokenContextFeatureExtractors

Fields inherited from class org.cleartk.ml.CleartkAnnotator

classifier, dataWriter, PARAM_CLASSIFIER_FACTORY_CLASS_NAME, PARAM_DATA_WRITER_FACTORY_CLASS_NAME, PARAM_IS_TRAINING

Constructor Summary

Constructors

Constructor and Description
UncertaintyCleartkAnalysisEngine()

Method Summary

Modifier and Type	Method and Description
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createAnnotatorDescription()
static org.apache.uima.analysis_engine.AnalysisEngineDescription	createAnnotatorDescription(String modelPath)
static FeatureSelection<String>	createFeatureSelection(double threshold)
static URI	createFeatureSelectionURI(File outputDirectoryName)
void	initialize(org.apache.uima.UimaContext context)
protected void	initializeFeatureSelection()
void	setClassLabel(IdentifiedAnnotation entityOrEventMention, org.cleartk.ml.Instance<String> instance)

Methods inherited from class org.apache.ctakes.assertion.medfacts.cleartk.AssertionCleartkAnalysisEngine

getDescription, getTrainFileToDomain, normalizeToDomain, process, setTrainFileToDomain

Methods inherited from class org.cleartk.ml.CleartkAnnotator

collectionProcessComplete, isTraining

Methods inherited from class org.apache.uima.fit.component.JCasAnnotator_ImplBase

getLogger

Methods inherited from class org.apache.uima.analysis_component.JCasAnnotator_ImplBase

getRequiredCasInterface, process

Methods inherited from class org.apache.uima.analysis_component.Annotator_ImplBase

getCasInstancesRequired, hasNext, next

Methods inherited from class org.apache.uima.analysis_component.AnalysisComponent_ImplBase

batchProcessComplete, destroy, getContext, getResultSpecification, reconfigure, setResultSpecification

Methods inherited from class java.lang.Object

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

Constructor Detail

UncertaintyCleartkAnalysisEngine

public UncertaintyCleartkAnalysisEngine()

Method Detail

initialize

public void initialize(org.apache.uima.UimaContext context)
                throws org.apache.uima.resource.ResourceInitializationException

Specified by:

initialize in interface org.apache.uima.analysis_component.AnalysisComponent

Specified by:

initialize in interface org.apache.uima.fit.factory.initializable.Initializable

Overrides:

initialize in class AssertionCleartkAnalysisEngine

Throws:

org.apache.uima.resource.ResourceInitializationException

setClassLabel

public void setClassLabel(IdentifiedAnnotation entityOrEventMention,
                          org.cleartk.ml.Instance<String> instance)
                   throws org.apache.uima.analysis_engine.AnalysisEngineProcessException

Specified by:

setClassLabel in class AssertionCleartkAnalysisEngine

Throws:

org.apache.uima.analysis_engine.AnalysisEngineProcessException

createFeatureSelection

public static FeatureSelection<String> createFeatureSelection(double threshold)

createFeatureSelectionURI

public static URI createFeatureSelectionURI(File outputDirectoryName)

initializeFeatureSelection

protected void initializeFeatureSelection()
                                   throws org.apache.uima.resource.ResourceInitializationException

Specified by:

initializeFeatureSelection in class AssertionCleartkAnalysisEngine

Throws:

org.apache.uima.resource.ResourceInitializationException

createAnnotatorDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createAnnotatorDescription(String modelPath)
                                                                                            throws org.apache.uima.resource.ResourceInitializationException

Throws:

org.apache.uima.resource.ResourceInitializationException

createAnnotatorDescription

public static org.apache.uima.analysis_engine.AnalysisEngineDescription createAnnotatorDescription()
                                                                                            throws org.apache.uima.resource.ResourceInitializationException

Throws:

org.apache.uima.resource.ResourceInitializationException