org.apache.ctakes.temporal.eval

Class Evaluation_ImplBase<STATISTICS_TYPE>

java.lang.Object

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

Direct Known Subclasses:

EvaluationOfAnnotationSpans_ImplBase, EvaluationOfClearTKEventProperties, EvaluationOfEventProperties, EvaluationOfTemporalRelations_ImplBase

public abstract class Evaluation_ImplBase<STATISTICS_TYPE>
extends 

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Evaluation_ImplBase.CopyFromGold
static class	Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations
static class	Evaluation_ImplBase.EntityMentionRemover
static class	Evaluation_ImplBase.EventMentionRemover
static interface	Evaluation_ImplBase.Options
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
static java.lang.String	GOLD_VIEW_NAME
protected java.lang.String	i2b2Output
protected java.lang.String[]	kernelParams
private static Logger	LOGGER
protected boolean	printErrors
protected boolean	printOverlapping
protected java.io.File	rawTextDirectory
protected Evaluation_ImplBase.Subcorpus	subcorpus
protected java.io.File	treebankDirectory
protected java.io.File	xmiDirectory
private boolean	xmiExists
protected java.io.File	xmlDirectory
protected Evaluation_ImplBase.XMLFormat	xmlFormat

Constructor Summary

Constructors

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

Method Summary

Methods

Modifier and Type	Method and Description
protected CollectionReader	getCollectionReader(java.util.List<java.lang.Integer> patientSets)
private java.util.List<java.io.File>	getFilesFor(java.util.List<java.lang.Integer> patientSets)
protected AggregateBuilder	getPreprocessorAggregateBuilder()
static java.util.List<java.lang.Integer>	getTestItems(Evaluation_ImplBase.Options options)
static java.util.List<java.lang.Integer>	getTrainItems(Evaluation_ImplBase.Options options)
(package private) static java.io.File	getXMIFile(java.io.File xmiDirectory, java.io.File textFile)
(package private) static java.io.File	getXMIFile(java.io.File xmiDirectory, JCas jCas)
protected AggregateBuilder	getXMIReadingPreprocessorAggregateBuilder()
protected AggregateBuilder	getXMIWritingPreprocessorAggregateBuilder()
void	prepareXMIsFor(java.util.List<java.lang.Integer> patientSets)
static <T extends Annotation> java.util.List<T>	selectExact(JCas jCas, java.lang.Class<T> annotationClass, Segment segment)
void	setI2B2Output(java.lang.String outDir)

Methods inherited from class java.lang.Object

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

Field Detail

LOGGER

private static Logger LOGGER

GOLD_VIEW_NAME

public static final java.lang.String GOLD_VIEW_NAME

See Also:

Constant Field Values

rawTextDirectory

protected java.io.File rawTextDirectory

xmlDirectory

protected java.io.File xmlDirectory

xmlFormat

protected Evaluation_ImplBase.XMLFormat xmlFormat

subcorpus

protected Evaluation_ImplBase.Subcorpus subcorpus

xmiDirectory

protected java.io.File xmiDirectory

xmiExists

private boolean xmiExists

treebankDirectory

protected java.io.File treebankDirectory

printErrors

protected boolean printErrors

printOverlapping

protected boolean printOverlapping

i2b2Output

protected java.lang.String i2b2Output

kernelParams

protected java.lang.String[] kernelParams

Constructor Detail

Evaluation_ImplBase

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

Method Detail

getTrainItems

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

getTestItems

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

setI2B2Output

public void setI2B2Output(java.lang.String outDir)

prepareXMIsFor

public void prepareXMIsFor(java.util.List<java.lang.Integer> patientSets)
                    throws java.lang.Exception

Throws:

java.lang.Exception

getFilesFor

private java.util.List<java.io.File> getFilesFor(java.util.List<java.lang.Integer> patientSets)
                                          throws java.io.FileNotFoundException

Throws:

java.io.FileNotFoundException

getCollectionReader

protected CollectionReader getCollectionReader(java.util.List<java.lang.Integer> patientSets)
                                        throws java.lang.Exception

Throws:

java.lang.Exception

getPreprocessorAggregateBuilder

protected AggregateBuilder getPreprocessorAggregateBuilder()
                                                    throws java.lang.Exception

Throws:

java.lang.Exception

getXMIReadingPreprocessorAggregateBuilder

protected AggregateBuilder getXMIReadingPreprocessorAggregateBuilder()
                                                              throws UIMAException

Throws:

UIMAException

getXMIWritingPreprocessorAggregateBuilder

protected AggregateBuilder getXMIWritingPreprocessorAggregateBuilder()
                                                              throws java.lang.Exception

Throws:

java.lang.Exception

selectExact

public static <T extends Annotation> java.util.List<T> selectExact(JCas jCas,
                                                   java.lang.Class<T> annotationClass,
                                                   Segment segment)

getXMIFile

static java.io.File getXMIFile(java.io.File xmiDirectory,
                      java.io.File textFile)

getXMIFile

static java.io.File getXMIFile(java.io.File xmiDirectory,
                      JCas jCas)
                        throws AnalysisEngineProcessException

Throws:

AnalysisEngineProcessException