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Posted to commits@ctakes.apache.org by tm...@apache.org on 2014/01/23 22:52:59 UTC
svn commit: r1560825 - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal:
ae/ClearTKLinkToTHYMELinkAnnotator.java
ae/TimexToClearTKTimexAnnotator.java eval/EvaluationOfClearTKRelations.java
Author: tmill
Date: Thu Jan 23 21:52:59 2014
New Revision: 1560825
URL: http://svn.apache.org/r1560825
Log:
Addresses CTAKES-82: Implements cleartk baselines for relations.
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKLinkToTHYMELinkAnnotator.java (with props)
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java (with props)
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java (with props)
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKLinkToTHYMELinkAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKLinkToTHYMELinkAnnotator.java?rev=1560825&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKLinkToTHYMELinkAnnotator.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKLinkToTHYMELinkAnnotator.java Thu Jan 23 21:52:59 2014
@@ -0,0 +1,70 @@
+package org.apache.ctakes.temporal.ae;
+
+import java.util.HashSet;
+
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.cleartk.timeml.type.Anchor;
+import org.cleartk.timeml.type.TemporalLink;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.util.JCasUtil;
+
+public class ClearTKLinkToTHYMELinkAnnotator extends JCasAnnotator_ImplBase {
+
+ static HashSet<String> ctkRels = new HashSet<String>();
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ for(TemporalLink link : JCasUtil.select(jCas, TemporalLink.class)){
+ BinaryTextRelation rel = new BinaryTextRelation(jCas);
+ RelationArgument arg1 = new RelationArgument(jCas);
+ Anchor source = link.getSource();
+ arg1.setArgument(new Annotation(jCas, source.getBegin(), source.getEnd()));
+ arg1.addToIndexes();
+
+ RelationArgument arg2 = new RelationArgument(jCas);
+ Anchor target = link.getTarget();
+ arg2.setArgument(new Annotation(jCas, target.getBegin(), target.getEnd()));
+ arg2.addToIndexes();
+
+ String cat = getMappedCategory(link.getRelationType());
+ if(cat.endsWith("-1")){
+ rel.setArg1(arg2);
+ rel.setArg2(arg1);
+ rel.setCategory(cat.substring(0, cat.length()-2));
+ }else{
+ rel.setCategory(getMappedCategory(link.getRelationType()));
+ rel.setArg1(arg1);
+ rel.setArg2(arg2);
+ }
+ rel.addToIndexes();
+ }
+ }
+
+ public static AnalysisEngineDescription getAnnotatorDescription() throws ResourceInitializationException {
+ return AnalysisEngineFactory.createPrimitiveDescription(ClearTKLinkToTHYMELinkAnnotator.class);
+ }
+
+ private static String getMappedCategory(String cleartkCat){
+ if(!ctkRels.contains(cleartkCat)){
+ System.err.println("New relation: " + cleartkCat);
+ ctkRels.add(cleartkCat);
+ }
+
+ if(cleartkCat.equals("AFTER")){
+ return "BEFORE-1";
+ }else if(cleartkCat.equals("INCLUDES")){
+ return "CONTAINS";
+ }else if(cleartkCat.equals("IS_INCLUDED")){
+ return "CONTAINS-1";
+ }else{
+ return cleartkCat;
+ }
+ }
+}
Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKLinkToTHYMELinkAnnotator.java
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Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java?rev=1560825&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java Thu Jan 23 21:52:59 2014
@@ -0,0 +1,29 @@
+package org.apache.ctakes.temporal.ae;
+
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.cleartk.timeml.type.Time;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.util.JCasUtil;
+
+public class TimexToClearTKTimexAnnotator extends JCasAnnotator_ImplBase {
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ for(TimeMention timex : JCasUtil.select(jCas, TimeMention.class)){
+ Time time = new Time(jCas);
+ time.setBegin(timex.getBegin());
+ time.setEnd(timex.getEnd());
+ time.addToIndexes();
+ }
+ }
+
+ public static AnalysisEngineDescription getAnnotatorDescription()
+ throws ResourceInitializationException {
+ return AnalysisEngineFactory.createPrimitiveDescription(TimexToClearTKTimexAnnotator.class);
+ }
+}
Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/TimexToClearTKTimexAnnotator.java
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svn:mime-type = text/plain
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java?rev=1560825&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java Thu Jan 23 21:52:59 2014
@@ -0,0 +1,195 @@
+package org.apache.ctakes.temporal.eval;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.eval.RelationExtractorEvaluation.HashableArguments;
+import org.apache.ctakes.temporal.ae.ClearTKDocTimeRelAnnotator;
+import org.apache.ctakes.temporal.ae.ClearTKDocumentCreationTimeAnnotator;
+import org.apache.ctakes.temporal.ae.ClearTKLinkToTHYMELinkAnnotator;
+import org.apache.ctakes.temporal.ae.EventToClearTKEventAnnotator;
+import org.apache.ctakes.temporal.ae.TimexToClearTKTimexAnnotator;
+import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations;
+import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveEventEventRelations;
+import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveNonContainsRelations;
+import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveRelations;
+import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.PreserveEventEventRelations;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.cleartk.eval.AnnotationStatistics;
+import org.cleartk.syntax.opennlp.ParserAnnotator;
+import org.cleartk.syntax.opennlp.PosTaggerAnnotator;
+import org.cleartk.syntax.opennlp.SentenceAnnotator;
+import org.cleartk.timeml.event.EventAspectAnnotator;
+import org.cleartk.timeml.event.EventClassAnnotator;
+import org.cleartk.timeml.event.EventModalityAnnotator;
+import org.cleartk.timeml.event.EventPolarityAnnotator;
+import org.cleartk.timeml.event.EventTenseAnnotator;
+import org.cleartk.timeml.time.TimeTypeAnnotator;
+import org.cleartk.timeml.tlink.TemporalLinkEventToDocumentCreationTimeAnnotator;
+import org.cleartk.timeml.tlink.TemporalLinkEventToSameSentenceTimeAnnotator;
+import org.cleartk.timeml.tlink.TemporalLinkEventToSubordinatedEventAnnotator;
+import org.cleartk.timeml.type.TemporalLink;
+import org.cleartk.token.stem.snowball.DefaultSnowballStemmer;
+import org.cleartk.token.tokenizer.TokenAnnotator;
+import org.uimafit.factory.AggregateBuilder;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.pipeline.JCasIterable;
+import org.uimafit.util.JCasUtil;
+
+import com.google.common.base.Function;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+public class EvaluationOfClearTKRelations extends
+ EvaluationOfTemporalRelations_ImplBase {
+
+ /**
+ * @param args
+ * @throws Exception
+ */
+ static interface EvalOptions extends Options{
+ @Option(shortName="iee") boolean getIgnoreEventEvent();
+ @Option(shortName="iet") boolean getIgnoreEventTime();
+ }
+
+ private boolean doEventEvent = true;
+ private boolean doEventTime = true;
+
+
+ public static void main(String[] args) throws Exception {
+ EvalOptions options = CliFactory.parseArguments(EvalOptions.class, args);
+ if(options.getIgnoreEventEvent() && options.getIgnoreEventTime()){
+ System.err.println("Ignoring all relation types is not a valid configuration.");
+ System.exit(-1);
+ }
+ List<Integer> patientSets = options.getPatients().getList();
+ List<Integer> trainItems = THYMEData.getTrainPatientSets(patientSets);
+ List<Integer> devItems = THYMEData.getDevPatientSets(patientSets);
+ List<Integer> testItems = THYMEData.getTestPatientSets(patientSets);
+
+ List<Integer> allTraining = new ArrayList<Integer>(trainItems);
+ List<Integer> allTest;
+ if (options.getTest()) {
+ allTraining.addAll(devItems);
+ allTest = new ArrayList<Integer>(testItems);
+ } else {
+ allTest = new ArrayList<Integer>(devItems);
+ }
+
+ EvaluationOfClearTKRelations evaluation = new EvaluationOfClearTKRelations(
+ new File("target/eval/cleartk-event-time-links"),
+ options.getRawTextDirectory(),
+ options.getXMLDirectory(),
+ options.getXMLFormat(),
+ options.getXMIDirectory());
+ evaluation.setExtractEventEvent(!options.getIgnoreEventEvent());
+ evaluation.setExtractEventTime(!options.getIgnoreEventTime());
+
+ evaluation.prepareXMIsFor(patientSets);
+ AnnotationStatistics<String> stats = evaluation.trainAndTest(allTraining, allTest);
+ System.err.println(stats);
+ }
+
+
+
+ public EvaluationOfClearTKRelations(File baseDirectory, File rawTextDirectory,
+ File xmlDirectory,
+ org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat xmlFormat,
+ File xmiDirectory) {
+ super(baseDirectory, rawTextDirectory, xmlDirectory, xmlFormat, xmiDirectory, null, false, false, defaultParams);
+ }
+
+ private void setExtractEventTime(boolean eventTime) {
+ this.doEventTime = eventTime;
+ }
+
+ private void setExtractEventEvent(boolean eventEvent) {
+ this.doEventEvent = eventEvent;
+ }
+
+ @Override
+ protected void train(CollectionReader collectionReader, File directory)
+ throws Exception {
+ // not training a model - just using the ClearTK one
+ }
+
+ @Override
+ protected AnnotationStatistics<String> test(
+ CollectionReader collectionReader, File directory) throws Exception {
+ AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
+ aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class));
+ aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+ RemoveCrossSentenceRelations.class,
+ RemoveCrossSentenceRelations.PARAM_SENTENCE_VIEW,
+ CAS.NAME_DEFAULT_SOFA,
+ RemoveCrossSentenceRelations.PARAM_RELATION_VIEW,
+ GOLD_VIEW_NAME));
+ if(!this.doEventEvent){
+ aggregateBuilder.add(
+ AnalysisEngineFactory.createPrimitiveDescription(RemoveEventEventRelations.class),
+ CAS.NAME_DEFAULT_SOFA,
+ GOLD_VIEW_NAME);
+ }
+ if(!this.doEventTime){
+ aggregateBuilder.add(
+ AnalysisEngineFactory.createPrimitiveDescription(PreserveEventEventRelations.class),
+ CAS.NAME_DEFAULT_SOFA,
+ GOLD_VIEW_NAME);
+ }
+ aggregateBuilder.add(SentenceAnnotator.getDescription());
+ aggregateBuilder.add(TokenAnnotator.getDescription());
+ aggregateBuilder.add(PosTaggerAnnotator.getDescription());
+ aggregateBuilder.add(DefaultSnowballStemmer.getDescription("English"));
+ aggregateBuilder.add(ParserAnnotator.getDescription());
+ aggregateBuilder.add(EventToClearTKEventAnnotator.getAnnotatorDescription());//for every cTakes eventMention, create a cleartk event
+ aggregateBuilder.add(TimexToClearTKTimexAnnotator.getAnnotatorDescription());
+// aggregateBuilder.add(ClearTKDocumentCreationTimeAnnotator.getAnnotatorDescription());//for every jCAS create an empty DCT, and add it to index
+ aggregateBuilder.add(EventTenseAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventtenseannotator/model.jar"));
+ aggregateBuilder.add(EventAspectAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventaspectannotator/model.jar"));
+ aggregateBuilder.add(EventClassAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventclassannotator/model.jar"));
+ aggregateBuilder.add(EventPolarityAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventpolarityannotator/model.jar"));
+ aggregateBuilder.add(EventModalityAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventmodalityannotator/model.jar"));
+ aggregateBuilder.add(TimeTypeAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/time/timetypeannotator/model.jar"));
+// aggregateBuilder.add(TemporalLinkEventToDocumentCreationTimeAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/tlink/temporallinkeventtodocumentcreationtimeannotator/model.jar"));
+// aggregateBuilder.add(ClearTKDocTimeRelAnnotator.getAnnotatorDescription());// for every tlink, check if it cover and event, add the tlink type to the event's docTimeRel attribute
+
+ if(this.doEventTime){
+ aggregateBuilder.add(TemporalLinkEventToSameSentenceTimeAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/tlink/temporallinkeventtosamesentencetimeannotator/model.jar"));
+ }
+ if(this.doEventEvent){
+ aggregateBuilder.add(TemporalLinkEventToSubordinatedEventAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/tlink/temporallinkeventtosubordinatedeventannotator/model.jar"));
+ }
+
+ aggregateBuilder.add(ClearTKLinkToTHYMELinkAnnotator.getAnnotatorDescription());
+
+ Function<BinaryTextRelation, ?> getSpan = new Function<BinaryTextRelation, HashableArguments>() {
+ public HashableArguments apply(BinaryTextRelation relation) {
+ return new HashableArguments(relation);
+ }
+ };
+ Function<BinaryTextRelation, String> getOutcome = AnnotationStatistics.annotationToFeatureValue("category");
+ AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
+ for (JCas jCas : new JCasIterable(collectionReader, aggregateBuilder.createAggregate())) {
+ JCas goldView = jCas.getView(GOLD_VIEW_NAME);
+ JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+ Collection<BinaryTextRelation> goldRelations = JCasUtil.select(
+ goldView,
+ BinaryTextRelation.class);
+ Collection<BinaryTextRelation> systemRelations = JCasUtil.select(
+ systemView,
+ BinaryTextRelation.class);
+ stats.add(goldRelations, systemRelations, getSpan, getOutcome);
+ }
+
+ return stats;
+ }
+
+
+}
Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKRelations.java
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