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Posted to commits@ctakes.apache.org by cl...@apache.org on 2016/04/22 17:59:55 UTC
svn commit: r1740550 - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval:
EvaluationOfEventEventThymeRelations.java EvaluationOfEventTimeRelations.java
Author: clin
Date: Fri Apr 22 15:59:55 2016
New Revision: 1740550
URL: http://svn.apache.org/viewvc?rev=1740550&view=rev
Log:
For EE and ET evaluation scripts, change the XML writing parameter names from i2b2writer to anafora writer.
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java?rev=1740550&r1=1740549&r2=1740550&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventThymeRelations.java Fri Apr 22 15:59:55 2016
@@ -45,6 +45,7 @@ import org.apache.ctakes.temporal.ae.bas
import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.Overlap2Contains;
import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveGoldAttributes;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteAnaforaXML;
//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML;
//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
import org.apache.ctakes.temporal.utils.AnnotationIdCollection;
@@ -76,6 +77,7 @@ import org.apache.uima.fit.component.JCa
import org.apache.uima.fit.descriptor.ConfigurationParameter;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.ConfigurationParameterFactory;
import org.apache.uima.fit.pipeline.JCasIterator;
import org.apache.uima.fit.pipeline.SimplePipeline;
import org.apache.uima.fit.util.JCasUtil;
@@ -190,6 +192,7 @@ EvaluationOfTemporalRelations_ImplBase{
params);
// evaluation.prepareXMIsFor(patientSets);
if(options.getI2B2Output()!=null) evaluation.setI2B2Output(options.getI2B2Output() + "/temporal-relations/event-event");
+ if(options.getAnaforaOutput()!=null) evaluation.anaforaOutput = options.getAnaforaOutput();
List<Integer> training = trainItems;
List<Integer> testing = null;
if(options.getTest()){
@@ -437,8 +440,8 @@ EvaluationOfTemporalRelations_ImplBase{
//count how many system predicted relations, their arguments are close to each other, without any other event in between
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CountCloseRelation.class));
- if(this.i2b2Output != null){
- aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
+ if(this.anaforaOutput != null){
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteAnaforaXML.class, WriteAnaforaXML.PARAM_OUTPUT_DIR, this.anaforaOutput), "TimexView", CAS.NAME_DEFAULT_SOFA);
}
File outf = null;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java?rev=1740550&r1=1740549&r2=1740550&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java Fri Apr 22 15:59:55 2016
@@ -43,6 +43,7 @@ import org.apache.ctakes.temporal.ae.Tem
//import org.apache.ctakes.temporal.ae.EventEventRelationAnnotator;
import org.apache.ctakes.temporal.ae.baselines.RecallBaselineEventTimeRelationAnnotator;
import org.apache.ctakes.temporal.eval.EvaluationOfTemporalRelations_ImplBase.RemoveGoldAttributes;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteAnaforaXML;
//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.WriteI2B2XML;
//import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
import org.apache.ctakes.temporal.utils.AnnotationIdCollection;
@@ -190,6 +191,7 @@ EvaluationOfTemporalRelations_ImplBase{
params);
if(options.getI2B2Output()!=null) evaluation.setI2B2Output(options.getI2B2Output() + "/temporal-relations/event-time");
+ if(options.getAnaforaOutput()!=null) evaluation.anaforaOutput = options.getAnaforaOutput();
List<Integer> training = trainItems;
List<Integer> testing = null;
if(options.getTest()){
@@ -428,8 +430,8 @@ EvaluationOfTemporalRelations_ImplBase{
//count how many system predicted relations, their arguments are close to each other, without any other event in between
aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(CountCloseRelation.class));
- if(this.i2b2Output != null){
- aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
+ if(this.anaforaOutput != null){
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(WriteAnaforaXML.class, WriteAnaforaXML.PARAM_OUTPUT_DIR, this.anaforaOutput), "TimexView", CAS.NAME_DEFAULT_SOFA);
}
File outf = null;