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Posted to commits@ctakes.apache.org by tm...@apache.org on 2014/04/09 22:40:38 UTC
svn commit: r1586138 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfMetaTimeExpressionExtractor.java
Author: tmill
Date: Wed Apr 9 20:40:37 2014
New Revision: 1586138
URL: http://svn.apache.org/r1586138
Log:
CTAKES-82: Modify meta time expression extractor to read i2b2 data.
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfMetaTimeExpressionExtractor.java
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfMetaTimeExpressionExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfMetaTimeExpressionExtractor.java?rev=1586138&r1=1586137&r2=1586138&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfMetaTimeExpressionExtractor.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfMetaTimeExpressionExtractor.java Wed Apr 9 20:40:37 2014
@@ -12,6 +12,7 @@ import org.apache.ctakes.temporal.ae.CRF
import org.apache.ctakes.temporal.ae.ConstituencyBasedTimeAnnotator;
import org.apache.ctakes.temporal.ae.MetaTimeAnnotator;
import org.apache.ctakes.temporal.ae.TimeAnnotator;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMLFormat;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -32,7 +33,7 @@ import com.google.common.collect.Maps;
import com.lexicalscope.jewel.cli.CliFactory;
public class EvaluationOfMetaTimeExpressionExtractor extends EvaluationOfAnnotationSpans_ImplBase {
- public static int nFolds = 2;
+ public static int nFolds = 5;
private List<Integer> allTrain = null;
public EvaluationOfMetaTimeExpressionExtractor(File baseDirectory,
@@ -48,9 +49,18 @@ public class EvaluationOfMetaTimeExpress
public static void main(String[] args) throws Exception {
Options options = CliFactory.parseArguments(Options.class, args);
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> trainItems = null;
+ List<Integer> devItems = null;
+ List<Integer> testItems = null;
+ if(options.getXMLFormat() == XMLFormat.I2B2){
+ trainItems = I2B2Data.getTrainPatientSets(options.getXMLDirectory());
+ devItems = I2B2Data.getDevPatientSets(options.getXMLDirectory());
+ testItems = I2B2Data.getTestPatientSets(options.getXMLDirectory());
+ }else{
+ trainItems = THYMEData.getTrainPatientSets(patientSets);
+ devItems = THYMEData.getDevPatientSets(patientSets);
+ testItems = THYMEData.getTestPatientSets(patientSets);
+ }
List<Integer> allTrain = new ArrayList<>(trainItems);
List<Integer> allTest = null;
@@ -71,6 +81,7 @@ public class EvaluationOfMetaTimeExpress
options.getTreebankDirectory(),
allTrain,
TimeMention.class);
+ if(options.getI2B2Output()!=null) eval.setI2B2Output(options.getI2B2Output());
AnnotationStatistics<String> stats = eval.trainAndTest(allTrain, allTest);
System.out.println(stats.toString());
}