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Posted to commits@ctakes.apache.org by cl...@apache.org on 2014/11/04 18:22:18 UTC
svn commit: r1636652 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java
Author: clin
Date: Tue Nov 4 17:22:18 2014
New Revision: 1636652
URL: http://svn.apache.org/r1636652
Log:
allow evaluation script for event-time only serialize test patients' xmis.
Modified:
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/EvaluationOfEventTimeRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventTimeRelations.java?rev=1636652&r1=1636651&r2=1636652&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 Tue Nov 4 17:22:18 2014
@@ -173,7 +173,7 @@ EvaluationOfTemporalRelations_ImplBase{
options.getUseGoldAttributes(),
options.getKernelParams(),
params);
- evaluation.prepareXMIsFor(patientSets);
+
if(options.getI2B2Output()!=null) evaluation.setI2B2Output(options.getI2B2Output() + "/temporal-relations/event-time");
List<Integer> training = trainItems;
List<Integer> testing = null;
@@ -185,6 +185,12 @@ EvaluationOfTemporalRelations_ImplBase{
}
//do closure on system, but not on gold, to calculate recall
evaluation.skipTrain = options.getSkipTrain();
+ if(evaluation.skipTrain && options.getTest()){
+ evaluation.prepareXMIsFor(testing);
+ }else{
+ evaluation.prepareXMIsFor(patientSets);
+ }
+
params.stats = evaluation.trainAndTest(training, testing);//training);//
// System.err.println(options.getKernelParams() == null ? params : options.getKernelParams());
System.err.println("No closure on gold::Closure on System::Recall Mode");
@@ -580,7 +586,7 @@ EvaluationOfTemporalRelations_ImplBase{
// }
- public static class RemoveEventEventRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+ public static class RemoveEventEventRelations extends JCasAnnotator_ImplBase {
public static final String PARAM_RELATION_VIEW = "RelationView";
@ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
private String relationViewName = CAS.NAME_DEFAULT_SOFA;
@@ -613,7 +619,7 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
- public static class AddPotentialRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+ public static class AddPotentialRelations extends JCasAnnotator_ImplBase {
public static final String PARAM_RELATION_VIEW = "RelationView";
@ConfigurationParameter(name = PARAM_RELATION_VIEW,mandatory=false)
private String relationViewName = CAS.NAME_DEFAULT_SOFA;
@@ -688,7 +694,7 @@ EvaluationOfTemporalRelations_ImplBase{
}
}*/
- public static class RemoveCrossSentenceRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+ public static class RemoveCrossSentenceRelations extends JCasAnnotator_ImplBase {
public static final String PARAM_SENTENCE_VIEW = "SentenceView";
@@ -739,7 +745,7 @@ EvaluationOfTemporalRelations_ImplBase{
}
- public static class RemoveRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+ public static class RemoveRelations extends JCasAnnotator_ImplBase {
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
for (BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(
@@ -836,7 +842,7 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
- public static class AddTransitiveContainsRelations extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+ public static class AddTransitiveContainsRelations extends JCasAnnotator_ImplBase {
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
@@ -901,7 +907,7 @@ EvaluationOfTemporalRelations_ImplBase{
}
- public static class AddContain2Overlap extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+ public static class AddContain2Overlap extends JCasAnnotator_ImplBase {
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
@@ -927,7 +933,7 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
- public static class AddFlippedOverlap extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+ public static class AddFlippedOverlap extends JCasAnnotator_ImplBase {
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
@@ -967,7 +973,7 @@ EvaluationOfTemporalRelations_ImplBase{
}
}
- public static class AddClosure extends org.apache.uima.fit.component.JCasAnnotator_ImplBase {
+ public static class AddClosure extends JCasAnnotator_ImplBase {
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {