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Posted to commits@ctakes.apache.org by st...@apache.org on 2014/04/06 00:54:19 UTC
svn commit: r1585211 - in /ctakes/trunk:
ctakes-temporal-res/src/main/resources/org/
ctakes-temporal-res/src/main/resources/org/apache/
ctakes-temporal-res/src/main/resources/org/apache/ctakes/
ctakes-temporal-res/src/main/resources/org/apache/ctakes/t...
Author: stevenbethard
Date: Sat Apr 5 22:54:19 2014
New Revision: 1585211
URL: http://svn.apache.org/r1585211
Log:
Adds trained EventAnnotator model and static createAnnotatorDescription() method for it. No tests yet as it's unclear whether we want to load all the prerequisites (e.g. UMLS) within a unit test. Also, all the other models are still missing.
Added:
ctakes/trunk/ctakes-temporal-res/src/main/resources/org/
ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/
ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/
ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/
ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/
ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventannotator/
ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventannotator/model.jar (with props)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
Added: ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventannotator/model.jar
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventannotator/model.jar?rev=1585211&view=auto
==============================================================================
Binary file - no diff available.
Propchange: ctakes/trunk/ctakes-temporal-res/src/main/resources/org/apache/ctakes/temporal/ae/eventannotator/model.jar
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svn:mime-type = application/octet-stream
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java?rev=1585211&r1=1585210&r2=1585211&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/EventAnnotator.java Sat Apr 5 22:54:19 2014
@@ -136,6 +136,18 @@ public class EventAnnotator extends Temp
EventAnnotator.createFeatureSelectionURI(modelDirectory));
}
+ public static AnalysisEngineDescription createAnnotatorDescription()
+ throws ResourceInitializationException {
+ return AnalysisEngineFactory.createPrimitiveDescription(
+ EventAnnotator.class,
+ CleartkAnnotator.PARAM_IS_TRAINING,
+ false,
+ GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+ String.format(
+ "/%s/model.jar",
+ EventAnnotator.class.getName().toLowerCase().replace('.', '/')));
+ }
+
private BIOChunking<BaseToken, IdentifiedAnnotation> entityChunking;
private BIOChunking<BaseToken, EventMention> eventChunking;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java?rev=1585211&r1=1585210&r2=1585211&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventSpans.java Sat Apr 5 22:54:19 2014
@@ -19,6 +19,7 @@
package org.apache.ctakes.temporal.eval;
import java.io.File;
+import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import java.util.logging.Level;
@@ -60,6 +61,16 @@ public class EvaluationOfEventSpans exte
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 = null;
+ if (options.getTest()) {
+ allTraining.addAll(devItems);
+ allTest = new ArrayList<Integer>(testItems);
+ } else {
+ allTest = new ArrayList<Integer>(devItems);
+ }
EvaluationOfEventSpans evaluation = new EvaluationOfEventSpans(
new File("target/eval/event-spans"),
options.getRawTextDirectory(),
@@ -71,7 +82,7 @@ public class EvaluationOfEventSpans exte
options.getSMOTENeighborNumber());
evaluation.prepareXMIsFor(patientSets);
evaluation.setLogging(Level.FINE, new File("target/eval/ctakes-event-errors.log"));
- AnnotationStatistics<String> stats = evaluation.trainAndTest(trainItems, devItems);
+ AnnotationStatistics<String> stats = evaluation.trainAndTest(allTraining, allTest);
System.err.println(stats);
}