org.apache.ctakes.temporal.eval

Class EvaluationOfAnnotationSpans_ImplBase

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

Direct Known Subclasses:

EvaluationOfClearTKEventSpans, EvaluationOfClearTKTimeSpans, EvaluationOfEventSpans, EvaluationOfMetaTimeExpressionExtractor, EvaluationOfNEPredicateEventSpans, EvaluationOfTimeSpans

public abstract class EvaluationOfAnnotationSpans_ImplBase
extends Evaluation_ImplBase<org.cleartk.eval.AnnotationStatistics<String>>

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.Options, 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
EvaluationOfAnnotationSpans_ImplBase(File baseDirectory, File rawTextDirectory, File xmlDirectory, Evaluation_ImplBase.XMLFormat xmlFormat, Evaluation_ImplBase.Subcorpus subcorpus, File xmiDirectory, Class<? extends org.apache.uima.jcas.tcas.Annotation> annotationClass)
EvaluationOfAnnotationSpans_ImplBase(File baseDirectory, File rawTextDirectory, File xmlDirectory, Evaluation_ImplBase.XMLFormat xmlFormat, Evaluation_ImplBase.Subcorpus subcorpus, File xmiDirectory, File treebankDirectory, Class<? extends org.apache.uima.jcas.tcas.Annotation> annotationClass)

Method Summary

Modifier and Type	Method and Description
protected abstract org.apache.uima.analysis_engine.AnalysisEngineDescription	getAnnotatorDescription(File directory)
protected abstract org.apache.uima.analysis_engine.AnalysisEngineDescription	getDataWriterDescription(File directory)
protected abstract Collection<? extends org.apache.uima.jcas.tcas.Annotation>	getGoldAnnotations(org.apache.uima.jcas.JCas jCas, Segment segment)
protected abstract Collection<? extends org.apache.uima.jcas.tcas.Annotation>	getSystemAnnotations(org.apache.uima.jcas.JCas jCas, Segment segment)
void	setLogging(Level level, File outputFile)
protected org.cleartk.eval.AnnotationStatistics<String>	test(org.apache.uima.collection.CollectionReader collectionReader, File directory)
protected void	train(org.apache.uima.collection.CollectionReader collectionReader, File directory)
protected abstract void	trainAndPackage(File directory)

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

EvaluationOfAnnotationSpans_ImplBase

public EvaluationOfAnnotationSpans_ImplBase(File baseDirectory,
                                            File rawTextDirectory,
                                            File xmlDirectory,
                                            Evaluation_ImplBase.XMLFormat xmlFormat,
                                            Evaluation_ImplBase.Subcorpus subcorpus,
                                            File xmiDirectory,
                                            File treebankDirectory,
                                            Class<? extends org.apache.uima.jcas.tcas.Annotation> annotationClass)

EvaluationOfAnnotationSpans_ImplBase

public EvaluationOfAnnotationSpans_ImplBase(File baseDirectory,
                                            File rawTextDirectory,
                                            File xmlDirectory,
                                            Evaluation_ImplBase.XMLFormat xmlFormat,
                                            Evaluation_ImplBase.Subcorpus subcorpus,
                                            File xmiDirectory,
                                            Class<? extends org.apache.uima.jcas.tcas.Annotation> annotationClass)

Method Detail

setLogging

public void setLogging(Level level,
                       File outputFile)
                throws IOException

Throws:

IOException

getDataWriterDescription

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

Throws:

org.apache.uima.resource.ResourceInitializationException

trainAndPackage

protected abstract void trainAndPackage(File directory)
                                 throws Exception

Throws:

Exception

train

protected void train(org.apache.uima.collection.CollectionReader collectionReader,
                     File directory)
              throws Exception

Specified by:

train in class org.cleartk.eval.Evaluation_ImplBase<Integer,org.cleartk.eval.AnnotationStatistics<String>>

Throws:

Exception

getAnnotatorDescription

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

Throws:

org.apache.uima.resource.ResourceInitializationException

getGoldAnnotations

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

getSystemAnnotations

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

test

protected org.cleartk.eval.AnnotationStatistics<String> test(org.apache.uima.collection.CollectionReader collectionReader,
                                                             File directory)
                                                      throws Exception

Specified by:

test in class org.cleartk.eval.Evaluation_ImplBase<Integer,org.cleartk.eval.AnnotationStatistics<String>>

Throws:

Exception