org.apache.ctakes.temporal.eval

Class EvaluationOfEventDocTimeRelDeepPhe

java.lang.Object

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

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

org.apache.ctakes.temporal.eval.EvaluationOfEventDocTimeRelDeepPhe

public class EvaluationOfEventDocTimeRelDeepPhe
extends Evaluation_ImplBase<Map<String,org.cleartk.eval.AnnotationStatistics<String>>>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	EvaluationOfEventDocTimeRelDeepPhe.ClearEventProperties
static class	EvaluationOfEventDocTimeRelDeepPhe.CopyHeadEventDocTimeRel2GoldEvent copy covered event's DocTimeRel to the gold event remove non-gold eventMentions
static class	EvaluationOfEventDocTimeRelDeepPhe.KeepEventMentionsCoveredByGoldMentions
static class	EvaluationOfEventDocTimeRelDeepPhe.ReplaceCTakesMentionsWithGoldMentions Annotator that removes cTAKES Mentions and Modifiers from the system view, and copies over the manually annotated Mentions and Modifiers from the gold view.

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

Modifier and Type	Field and Description
protected static EvaluationOfEventTimeRelations.ParameterSettings	allParams
protected static boolean	DEFAULT_BOTH_DIRECTIONS
protected static float	DEFAULT_DOWNSAMPLE
protected boolean	skipTrain
boolean	skipWrite
protected boolean	testOnTrain
protected boolean	useClosure
protected boolean	useGoldAttributes

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
EvaluationOfEventDocTimeRelDeepPhe(File baseDirectory, File rawTextDirectory, File xmlDirectory, Evaluation_ImplBase.XMLFormat xmlFormat, Evaluation_ImplBase.Subcorpus subcorpus, File xmiDirectory, File treebankDirectory, boolean useClosure, boolean printErrors, boolean useGoldAttributes, EvaluationOfEventTimeRelations.ParameterSettings params)

Method Summary

Modifier and Type	Method and Description
void	logClassificationErrors(File outputDir, String outputFilePrefix)
static void	main(String[] args)
protected Map<String,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)

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

Field Detail

DEFAULT_BOTH_DIRECTIONS

protected static boolean DEFAULT_BOTH_DIRECTIONS

DEFAULT_DOWNSAMPLE

protected static float DEFAULT_DOWNSAMPLE

allParams

protected static EvaluationOfEventTimeRelations.ParameterSettings allParams

useClosure

protected boolean useClosure

useGoldAttributes

protected boolean useGoldAttributes

skipTrain

protected boolean skipTrain

skipWrite

public boolean skipWrite

testOnTrain

protected boolean testOnTrain

Constructor Detail

EvaluationOfEventDocTimeRelDeepPhe

public EvaluationOfEventDocTimeRelDeepPhe(File baseDirectory,
                                          File rawTextDirectory,
                                          File xmlDirectory,
                                          Evaluation_ImplBase.XMLFormat xmlFormat,
                                          Evaluation_ImplBase.Subcorpus subcorpus,
                                          File xmiDirectory,
                                          File treebankDirectory,
                                          boolean useClosure,
                                          boolean printErrors,
                                          boolean useGoldAttributes,
                                          EvaluationOfEventTimeRelations.ParameterSettings params)

Method Detail

main

public static void main(String[] args)
                 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,Map<String,org.cleartk.eval.AnnotationStatistics<String>>>

Throws:

Exception

test

protected Map<String,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,Map<String,org.cleartk.eval.AnnotationStatistics<String>>>

Throws:

Exception

logClassificationErrors

public void logClassificationErrors(File outputDir,
                                    String outputFilePrefix)
                             throws IOException

Throws:

IOException