org.apache.ctakes.temporal.eval

Class Evaluation_ImplBase<STATISTICS_TYPE>

java.lang.Object

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

org.apache.ctakes.temporal.eval.Evaluation_ImplBase<STATISTICS_TYPE>

Direct Known Subclasses:

EvaluationOfAnnotationSpans_ImplBase, EvaluationOfClearTKEventProperties, EvaluationOfEventDocTimeRelDeepPhe, EvaluationOfEventProperties, EvaluationOfMarkableSalience, EvaluationOfTemporalRelations_ImplBase

public abstract class Evaluation_ImplBase<STATISTICS_TYPE>
extends org.cleartk.eval.Evaluation_ImplBase<Integer,STATISTICS_TYPE>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Evaluation_ImplBase.CopyFromGold
static class	Evaluation_ImplBase.CopyFromSystem
static class	Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations
static class	Evaluation_ImplBase.EntityMentionRemover
static class	Evaluation_ImplBase.EventMentionRemover
static interface	Evaluation_ImplBase.Options
static class	Evaluation_ImplBase.PittHeaderAnnotator Grabs the document time from the header
static class	Evaluation_ImplBase.RemoveEnclosedLookupWindows
static class	Evaluation_ImplBase.SegmentsFromBracketedSectionTagsAnnotator
static class	Evaluation_ImplBase.Subcorpus
static class	Evaluation_ImplBase.TimexAnnotationCorrector
static class	Evaluation_ImplBase.UriToDocumentTextAnnotatorCtakes
static class	Evaluation_ImplBase.WriteAnaforaXML
static class	Evaluation_ImplBase.WriteI2B2XML
static class	Evaluation_ImplBase.XMIReader
static class	Evaluation_ImplBase.XMIWriter
static class	Evaluation_ImplBase.XMLFormat

Field Summary

Fields

Modifier and Type	Field and Description
protected String	anaforaOutput
static HashSet<String>	badNotes
static String	GOLD_VIEW_NAME
protected String	i2b2Output
protected String[]	kernelParams
protected boolean	printErrors
protected boolean	printOverlapping
static String	PROB_VIEW_NAME
protected File	rawTextDirectory
protected Evaluation_ImplBase.Subcorpus	subcorpus
protected File	treebankDirectory
protected File	xmiDirectory
protected File	xmlDirectory
protected Evaluation_ImplBase.XMLFormat	xmlFormat

Fields inherited from class org.cleartk.eval.Evaluation_ImplBase

baseDirectory

Constructor Summary

Constructors

Constructor and Description
Evaluation_ImplBase(File baseDirectory, File rawTextDirectory, File xmlDirectory, Evaluation_ImplBase.XMLFormat xmlFormat, Evaluation_ImplBase.Subcorpus subcorpus, File xmiDirectory, File treebankDirectory)

Method Summary

Modifier and Type	Method and Description
protected org.apache.uima.collection.CollectionReader	getCollectionReader(List<Integer> patientSets)
protected org.apache.uima.fit.factory.AggregateBuilder	getPreprocessorAggregateBuilder()
static String	getRelationId(TemporalTextRelation rel)
static List<Integer>	getTestItems(Evaluation_ImplBase.Options options)
static List<Integer>	getTrainItems(Evaluation_ImplBase.Options options)
protected org.apache.uima.fit.factory.AggregateBuilder	getXMIReadingPreprocessorAggregateBuilder()
protected org.apache.uima.fit.factory.AggregateBuilder	getXMIWritingPreprocessorAggregateBuilder()
void	prepareXMIsFor(List<Integer> patientSets)
static <T extends org.apache.uima.jcas.tcas.Annotation> List<T>	selectExact(org.apache.uima.jcas.JCas jCas, Class<T> annotationClass, Segment segment)
void	setI2B2Output(String outDir)

Methods inherited from class org.cleartk.eval.Evaluation_ImplBase

crossValidation, selectFoldTestItems, selectFoldTrainItems, test, train, trainAndTest

Methods inherited from class java.lang.Object

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

Field Detail

badNotes

public static HashSet<String> badNotes

GOLD_VIEW_NAME

public static final String GOLD_VIEW_NAME

See Also:

Constant Field Values

PROB_VIEW_NAME

public static final String PROB_VIEW_NAME

See Also:

Constant Field Values

rawTextDirectory

protected File rawTextDirectory

xmlDirectory

protected File xmlDirectory

xmlFormat

protected Evaluation_ImplBase.XMLFormat xmlFormat

subcorpus

protected Evaluation_ImplBase.Subcorpus subcorpus

xmiDirectory

protected File xmiDirectory

treebankDirectory

protected File treebankDirectory

printErrors

protected boolean printErrors

printOverlapping

protected boolean printOverlapping

i2b2Output

protected String i2b2Output

anaforaOutput

protected String anaforaOutput

kernelParams

protected String[] kernelParams

Constructor Detail

Evaluation_ImplBase

public Evaluation_ImplBase(File baseDirectory,
                           File rawTextDirectory,
                           File xmlDirectory,
                           Evaluation_ImplBase.XMLFormat xmlFormat,
                           Evaluation_ImplBase.Subcorpus subcorpus,
                           File xmiDirectory,
                           File treebankDirectory)

Method Detail

getTrainItems

public static List<Integer> getTrainItems(Evaluation_ImplBase.Options options)

getTestItems

public static List<Integer> getTestItems(Evaluation_ImplBase.Options options)

setI2B2Output

public void setI2B2Output(String outDir)

prepareXMIsFor

public void prepareXMIsFor(List<Integer> patientSets)
                    throws Exception

Throws:

Exception

getCollectionReader

protected org.apache.uima.collection.CollectionReader getCollectionReader(List<Integer> patientSets)
                                                                   throws Exception

Specified by:

getCollectionReader in class org.cleartk.eval.Evaluation_ImplBase<Integer,STATISTICS_TYPE>

Throws:

Exception

getPreprocessorAggregateBuilder

protected org.apache.uima.fit.factory.AggregateBuilder getPreprocessorAggregateBuilder()
                                                                                throws Exception

Throws:

Exception

getXMIReadingPreprocessorAggregateBuilder

protected org.apache.uima.fit.factory.AggregateBuilder getXMIReadingPreprocessorAggregateBuilder()
                                                                                          throws org.apache.uima.UIMAException

Throws:

org.apache.uima.UIMAException

getXMIWritingPreprocessorAggregateBuilder

protected org.apache.uima.fit.factory.AggregateBuilder getXMIWritingPreprocessorAggregateBuilder()
                                                                                          throws Exception

Throws:

Exception

selectExact

public static <T extends org.apache.uima.jcas.tcas.Annotation> List<T> selectExact(org.apache.uima.jcas.JCas jCas,
                                                                                   Class<T> annotationClass,
                                                                                   Segment segment)

getRelationId

public static String getRelationId(TemporalTextRelation rel)