org.apache.ctakes.temporal.eval

Class EvaluationOfTimeSpans

java.lang.Object

org.cleartk.eval.Evaluation_ImplBase<Integer,STATISTICS_TYPE>

org.apache.ctakes.temporal.eval.Evaluation_ImplBase<org.cleartk.eval.AnnotationStatistics<String>>

org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase

org.apache.ctakes.temporal.eval.EvaluationOfTimeSpans

public class EvaluationOfTimeSpans
extends EvaluationOfAnnotationSpans_ImplBase

Nested Class Summary

Nested classes/interfaces inherited from class org.apache.ctakes.temporal.eval.Evaluation_ImplBase

Evaluation_ImplBase.CopyFromGold, Evaluation_ImplBase.CopyFromSystem, Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations, Evaluation_ImplBase.EntityMentionRemover, Evaluation_ImplBase.EventMentionRemover, Evaluation_ImplBase.PittHeaderAnnotator, Evaluation_ImplBase.RemoveEnclosedLookupWindows, Evaluation_ImplBase.SegmentsFromBracketedSectionTagsAnnotator, Evaluation_ImplBase.Subcorpus, Evaluation_ImplBase.TimexAnnotationCorrector, Evaluation_ImplBase.UriToDocumentTextAnnotatorCtakes, Evaluation_ImplBase.WriteAnaforaXML, Evaluation_ImplBase.WriteI2B2XML, Evaluation_ImplBase.XMIReader, Evaluation_ImplBase.XMIWriter, Evaluation_ImplBase.XMLFormat

Field Summary

Fields inherited from class org.apache.ctakes.temporal.eval.Evaluation_ImplBase

anaforaOutput, badNotes, GOLD_VIEW_NAME, i2b2Output, kernelParams, printErrors, printOverlapping, PROB_VIEW_NAME, rawTextDirectory, subcorpus, treebankDirectory, xmiDirectory, xmlDirectory, xmlFormat

Fields inherited from class org.cleartk.eval.Evaluation_ImplBase

baseDirectory

Constructor Summary

Constructors

Constructor and Description

EvaluationOfTimeSpans(File baseDirectory, File rawTextDirectory, File xmlDirectory, Evaluation_ImplBase.XMLFormat xmlFormat, Evaluation_ImplBase.Subcorpus subcorpus, File xmiDirectory, File treebankDirectory, float featureSelectionThreshold, float numOfSmoteNeighbors, Class<? extends org.apache.uima.fit.component.JCasAnnotator_ImplBase> annotatorClass, boolean printOverlapping, String[] trainingArguments)

Method Summary

Modifier and Type	Method and Description
protected org.apache.uima.analysis_engine.AnalysisEngineDescription	getAnnotatorDescription(File directory)
protected org.apache.uima.analysis_engine.AnalysisEngineDescription	getDataWriterDescription(File directory)
protected Collection<? extends org.apache.uima.jcas.tcas.Annotation>	getGoldAnnotations(org.apache.uima.jcas.JCas jCas, Segment segment)
protected Collection<? extends org.apache.uima.jcas.tcas.Annotation>	getSystemAnnotations(org.apache.uima.jcas.JCas jCas, Segment segment)
static void	main(String[] args)
void	setSkipTrain(boolean val)
void	train(org.apache.uima.collection.CollectionReader reader, File directory)
protected void	trainAndPackage(File directory)

Methods inherited from class org.apache.ctakes.temporal.eval.EvaluationOfAnnotationSpans_ImplBase

setLogging, test

Methods inherited from class org.apache.ctakes.temporal.eval.Evaluation_ImplBase

getCollectionReader, getPreprocessorAggregateBuilder, getRelationId, getTestItems, getTrainItems, getXMIReadingPreprocessorAggregateBuilder, getXMIWritingPreprocessorAggregateBuilder, prepareXMIsFor, selectExact, setI2B2Output

Methods inherited from class org.cleartk.eval.Evaluation_ImplBase

crossValidation, selectFoldTestItems, selectFoldTrainItems, trainAndTest

Methods inherited from class java.lang.Object

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

Constructor Detail

EvaluationOfTimeSpans

public EvaluationOfTimeSpans(File baseDirectory,
                             File rawTextDirectory,
                             File xmlDirectory,
                             Evaluation_ImplBase.XMLFormat xmlFormat,
                             Evaluation_ImplBase.Subcorpus subcorpus,
                             File xmiDirectory,
                             File treebankDirectory,
                             float featureSelectionThreshold,
                             float numOfSmoteNeighbors,
                             Class<? extends org.apache.uima.fit.component.JCasAnnotator_ImplBase> annotatorClass,
                             boolean printOverlapping,
                             String[] trainingArguments)

Method Detail

main

public static void main(String[] args)
                 throws Exception

Throws:

Exception

setSkipTrain

public void setSkipTrain(boolean val)

train

public void train(org.apache.uima.collection.CollectionReader reader,
                  File directory)
           throws Exception

Overrides:

train in class EvaluationOfAnnotationSpans_ImplBase

Throws:

Exception

getDataWriterDescription

protected org.apache.uima.analysis_engine.AnalysisEngineDescription getDataWriterDescription(File directory)
                                                                                      throws org.apache.uima.resource.ResourceInitializationException

Specified by:

getDataWriterDescription in class EvaluationOfAnnotationSpans_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

trainAndPackage

protected void trainAndPackage(File directory)
                        throws Exception

Specified by:

trainAndPackage in class EvaluationOfAnnotationSpans_ImplBase

Throws:

Exception

getAnnotatorDescription

protected org.apache.uima.analysis_engine.AnalysisEngineDescription getAnnotatorDescription(File directory)
                                                                                     throws org.apache.uima.resource.ResourceInitializationException

Specified by:

getAnnotatorDescription in class EvaluationOfAnnotationSpans_ImplBase

Throws:

org.apache.uima.resource.ResourceInitializationException

getGoldAnnotations

protected Collection<? extends org.apache.uima.jcas.tcas.Annotation> getGoldAnnotations(org.apache.uima.jcas.JCas jCas,
                                                                                        Segment segment)

Specified by:

getGoldAnnotations in class EvaluationOfAnnotationSpans_ImplBase

getSystemAnnotations

protected Collection<? extends org.apache.uima.jcas.tcas.Annotation> getSystemAnnotations(org.apache.uima.jcas.JCas jCas,
                                                                                          Segment segment)

Specified by:

getSystemAnnotations in class EvaluationOfAnnotationSpans_ImplBase