org.apache.ctakes.assertion.eval

Class AssertionEvaluation

java.lang.Object

org.cleartk.eval.Evaluation_ImplBase<File,Map<String,AnnotationStatisticsCompact<String>>>

org.apache.ctakes.assertion.eval.AssertionEvaluation

public class AssertionEvaluation
extends org.cleartk.eval.Evaluation_ImplBase<File,Map<String,AnnotationStatisticsCompact<String>>>

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	AssertionEvaluation.HashableAnnotation
static class	AssertionEvaluation.OnlyGoldAssertions Class that copies the manual Modifier annotations to the default CAS.
static class	AssertionEvaluation.Options
static class	AssertionEvaluation.ReferenceAnnotationsSystemAssertionClearer Class that copies the manual Modifier annotations to the default CAS.
static class	AssertionEvaluation.ReferenceIdentifiedAnnotationsSystemToGoldCopier Class that copies the manual Modifier annotations to the default CAS.
static class	AssertionEvaluation.ReferenceSupportingAnnotationsSystemToGoldCopier Class that copies the manual Modifier annotations to the default CAS.
static class	AssertionEvaluation.ReplaceCTakesEntityMentionsAndModifiersWithGold Annotator that removes cTAKES EntityMentions and Modifiers from the system view, and copies over the manually annotated EntityMentions and Modifiers from the gold view.

Field Summary

Fields

Modifier and Type	Field and Description
protected ArrayList<String>	annotationTypes
static String	evaluationLogFilePath
static String	GOLD_VIEW_NAME
protected static AssertionEvaluation.Options	options
static boolean	useEvaluationLogFile

Fields inherited from class org.cleartk.eval.Evaluation_ImplBase

baseDirectory

Constructor Summary

Constructors

Constructor and Description
AssertionEvaluation(File modelDirectory, File evaluationOutputDirectory, ArrayList<String> annotationTypes, Class<? extends org.cleartk.ml.DataWriter<String>> dataWriterClass, String... trainingArguments)

Method Summary

Modifier and Type	Method and Description
org.apache.uima.collection.CollectionReader	getCollectionReader(List<File> items)
protected Class<? extends org.cleartk.ml.DataWriter<String>>	getDataWriterClass()
static void	main(String[] args)
static void	preprocess(File rawDir)
static void	printScore(Map<String,AnnotationStatisticsCompact<String>> map, String directory)
protected Map<String,AnnotationStatisticsCompact<String>>	test(org.apache.uima.collection.CollectionReader collectionReader, File directory)
void	train(org.apache.uima.collection.CollectionReader collectionReader, File directory)
protected void	trainAndPackage(String currentAssertionAttribute, File directory, String[] arguments)

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

annotationTypes

protected ArrayList<String> annotationTypes

evaluationLogFilePath

public static String evaluationLogFilePath

useEvaluationLogFile

public static boolean useEvaluationLogFile

options

protected static AssertionEvaluation.Options options

GOLD_VIEW_NAME

public static final String GOLD_VIEW_NAME

See Also:

Constant Field Values

Constructor Detail

AssertionEvaluation

public AssertionEvaluation(File modelDirectory,
                           File evaluationOutputDirectory,
                           ArrayList<String> annotationTypes,
                           Class<? extends org.cleartk.ml.DataWriter<String>> dataWriterClass,
                           String... trainingArguments)

Method Detail

main

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

Throws:

Exception

printScore

public static void printScore(Map<String,AnnotationStatisticsCompact<String>> map,
                              String directory)

getCollectionReader

public org.apache.uima.collection.CollectionReader getCollectionReader(List<File> items)
                                                                throws org.apache.uima.resource.ResourceInitializationException

Specified by:

getCollectionReader in class org.cleartk.eval.Evaluation_ImplBase<File,Map<String,AnnotationStatisticsCompact<String>>>

Throws:

org.apache.uima.resource.ResourceInitializationException

preprocess

public static void preprocess(File rawDir)
                       throws org.apache.uima.resource.ResourceInitializationException,
                              org.apache.uima.UIMAException,
                              IOException

Throws:

org.apache.uima.resource.ResourceInitializationException

org.apache.uima.UIMAException

IOException

train

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

Specified by:

train in class org.cleartk.eval.Evaluation_ImplBase<File,Map<String,AnnotationStatisticsCompact<String>>>

Throws:

Exception

test

protected Map<String,AnnotationStatisticsCompact<String>> test(org.apache.uima.collection.CollectionReader collectionReader,
                                                               File directory)
                                                        throws Exception

Specified by:

test in class org.cleartk.eval.Evaluation_ImplBase<File,Map<String,AnnotationStatisticsCompact<String>>>

Throws:

Exception

trainAndPackage

protected void trainAndPackage(String currentAssertionAttribute,
                               File directory,
                               String[] arguments)
                        throws Exception

Throws:

Exception

getDataWriterClass

protected Class<? extends org.cleartk.ml.DataWriter<String>> getDataWriterClass()