Author: stevenbethard
Date: Thu Aug 8 16:01:44 2013
New Revision: 1511845
URL: http://svn.apache.org/r1511845
Log:
Fixes some bugs in the evaluation of ClearTK docTimeRels.
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java?rev=1511845&r1=1511844&r2=1511845&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/ClearTKDocTimeRelAnnotator.java Thu Aug 8 16:01:44 2013
@@ -1,23 +1,26 @@
package org.apache.ctakes.temporal.ae;
-import org.apache.ctakes.typesystem.type.refsem.Event;
-import org.apache.ctakes.typesystem.type.refsem.EventProperties;
+import java.util.Map;
+
import org.apache.ctakes.typesystem.type.textsem.EventMention;
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.cas.FSArray;
import org.apache.uima.resource.ResourceInitializationException;
import org.cleartk.timeml.type.Anchor;
+import org.cleartk.timeml.type.DocumentCreationTime;
import org.cleartk.timeml.type.TemporalLink;
import org.uimafit.component.JCasAnnotator_ImplBase;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.util.JCasUtil;
+import com.google.common.collect.Maps;
+
/**
* for every cTAKES EventMention annotation, create a ClearTK Event Annotation
+ *
* @author Chen Lin
- *
+ *
*/
public class ClearTKDocTimeRelAnnotator extends JCasAnnotator_ImplBase {
@@ -26,40 +29,35 @@ public class ClearTKDocTimeRelAnnotator
}
@Override
- public void process(JCas jCas)
- throws AnalysisEngineProcessException {
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ DocumentCreationTime dct = JCasUtil.selectSingle(jCas, DocumentCreationTime.class);
+ Map<EventMention, String> docTimeRels = Maps.newHashMap();
for (TemporalLink tlink : JCasUtil.select(jCas, TemporalLink.class)) {
- // create a cleartk event object
- String relation = tlink.getRelationType();
-// System.out.println("__find tlink relation: " + relation + " srouce: " + tlink.getSource().getCoveredText() + " target: " + tlink.getTarget().getType().getName());
-
- Anchor linksource = tlink.getSource();
-
- EventMention ement = new EventMention(jCas);
- ement.setBegin(linksource.getBegin());
- ement.setEnd(linksource.getEnd());
- Event event = new Event(jCas);
-
- EventProperties eventProperties = new EventProperties(jCas);
- if ("INCLUDES".equals(relation)){
- eventProperties.setDocTimeRel("OVERLAP");
- }else{
- eventProperties.setDocTimeRel(relation);
- }
- event.setProperties(eventProperties);
- event.setMentions(new FSArray(jCas, 1));
- event.setMentions(0, ement);
- ement.setEvent(event);
-
- eventProperties.addToIndexes();
- event.addToIndexes();
- ement.addToIndexes();
-
+ Anchor source = tlink.getSource();
+ Anchor target = tlink.getTarget();
+ if (source instanceof org.cleartk.timeml.type.Event && target.equals(dct)) {
+ for (EventMention event : JCasUtil.selectCovered(jCas, EventMention.class, source)) {
+ docTimeRels.put(event, tlink.getRelationType());
+ }
+ }
}
+ for (EventMention eventMention : JCasUtil.select(jCas, EventMention.class)) {
+ // needed because SignSymptomMention, etc. do not have EventProperties
+ if (eventMention.getClass().equals(EventMention.class)) {
+ String docTimeRel = docTimeRels.get(eventMention);
+
+ // convert missing or INCLUDES to OVERLAP
+ if (docTimeRel == null || "INCLUDES".equals(docTimeRel)) {
+ docTimeRel = "OVERLAP";
+ }
+ eventMention.getEvent().getProperties().setDocTimeRel(docTimeRel);
+ }
+ }
}
- public static AnalysisEngineDescription getAnnotatorDescription() throws ResourceInitializationException {
+ public static AnalysisEngineDescription getAnnotatorDescription()
+ throws ResourceInitializationException {
return AnalysisEngineFactory.createPrimitiveDescription(ClearTKDocTimeRelAnnotator.class);
}
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java?rev=1511845&r1=1511844&r2=1511845&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventToClearTKEventAnnotator.java Thu Aug 8 16:01:44 2013
@@ -12,8 +12,9 @@ import org.uimafit.util.JCasUtil;
/**
* for every cTAKES EventMention annotation, create a ClearTK Event Annotation
+ *
* @author Chen Lin
- *
+ *
*/
public class EventToClearTKEventAnnotator extends JCasAnnotator_ImplBase {
@@ -22,20 +23,23 @@ public class EventToClearTKEventAnnotato
}
@Override
- public void process(JCas jCas)
- throws AnalysisEngineProcessException {
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
for (EventMention eMention : JCasUtil.select(jCas, EventMention.class)) {
- // create a cleartk event object
- Event event = new Event(jCas);
- event.setBegin(eMention.getBegin());
- event.setEnd(eMention.getEnd());
-
- event.addToIndexes();
+ // needed because SignSymptomMention, etc. do not have EventProperties
+ if (eMention.getClass().equals(EventMention.class)) {
+ // create a cleartk event object
+ Event event = new Event(jCas);
+ event.setBegin(eMention.getBegin());
+ event.setEnd(eMention.getEnd());
+
+ event.addToIndexes();
+ }
}
}
- public static AnalysisEngineDescription getAnnotatorDescription() throws ResourceInitializationException {
+ public static AnalysisEngineDescription getAnnotatorDescription()
+ throws ResourceInitializationException {
return AnalysisEngineFactory.createPrimitiveDescription(EventToClearTKEventAnnotator.class);
}
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java?rev=1511845&r1=1511844&r2=1511845&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfClearTKEventProperties.java Thu Aug 8 16:01:44 2013
@@ -35,6 +35,7 @@ import org.apache.ctakes.temporal.ae.Cle
import org.apache.ctakes.temporal.ae.ClearTKDocTimeRelAnnotator;
import org.apache.ctakes.typesystem.type.refsem.EventProperties;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.cas.CAS;
@@ -119,14 +120,13 @@ public class EvaluationOfClearTKEventPro
CollectionReader collectionReader,
File directory) throws Exception {
AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
-// aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
+ aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class));
+ aggregateBuilder.add(CopyFromGold.getDescription(TimeMention.class));
aggregateBuilder.add(SentenceAnnotator.getDescription());
aggregateBuilder.add(TokenAnnotator.getDescription());
aggregateBuilder.add(PosTaggerAnnotator.getDescription());
aggregateBuilder.add(DefaultSnowballStemmer.getDescription("English"));
aggregateBuilder.add(ParserAnnotator.getDescription());
-// aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class));
-// aggregateBuilder.add(CopyFromGold.getDescription(TimeMention.class));
aggregateBuilder.add(EventToClearTKEventAnnotator.getAnnotatorDescription());//for every cTakes eventMention, create a cleartk event
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"));