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Posted to commits@ctakes.apache.org by st...@apache.org on 2014/02/01 00:54:34 UTC
svn commit: r1563350 - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal:
ae/THYMEAnaforaXMLReader.java eval/EvaluationOfEventEventRelations.java
eval/Evaluation_ImplBase.java
Author: stevenbethard
Date: Fri Jan 31 23:54:34 2014
New Revision: 1563350
URL: http://svn.apache.org/r1563350
Log:
Modifies temporal Evaluation_ImplBase so that the text directory does not need to be specified when Anafora format is used. (The text will be taken from the Anafora directories.)
Modified:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java?rev=1563350&r1=1563349&r2=1563350&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/THYMEAnaforaXMLReader.java Fri Jan 31 23:54:34 2014
@@ -55,6 +55,8 @@ public class THYMEAnaforaXMLReader exten
description = "list of suffixes that might be added to a file name to identify the Anafora "
+ "XML annotations file; only the first suffix corresponding to a file will be used")
private String[] anaforaXMLSuffixes = new String[] {
+ ".Gold_Temporal_Entities.xml",
+ ".Gold_Temporal_Relations.xml",
".temporal.Temporal-Adjudication.gold.completed.xml",
".temporal.Temporal-Entities.gold.completed.xml",
".Temporal-Entity.gold.completed.xml",
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java?rev=1563350&r1=1563349&r2=1563350&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/EvaluationOfEventEventRelations.java Fri Jan 31 23:54:34 2014
@@ -12,7 +12,6 @@ import org.apache.ctakes.relationextract
import org.apache.ctakes.temporal.ae.EventEventRelationAnnotator;
import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.ParameterSettings;
import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveCrossSentenceRelations;
-import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveNonContainsRelations;
import org.apache.ctakes.temporal.eval.EvaluationOfEventTimeRelations.RemoveRelations;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java?rev=1563350&r1=1563349&r2=1563350&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java Fri Jan 31 23:54:34 2014
@@ -24,8 +24,9 @@ import java.io.FileOutputStream;
import java.io.FilenameFilter;
import java.io.IOException;
import java.util.ArrayList;
-import java.util.Collections;
+import java.util.HashSet;
import java.util.List;
+import java.util.Set;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
@@ -60,6 +61,7 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.log4j.Logger;
import org.apache.uima.UIMAException;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngine;
@@ -100,13 +102,15 @@ import com.lexicalscope.jewel.cli.Option
public abstract class Evaluation_ImplBase<STATISTICS_TYPE> extends
org.cleartk.eval.Evaluation_ImplBase<Integer, STATISTICS_TYPE> {
+ private static Logger LOGGER = Logger.getLogger(Evaluation_ImplBase.class);
+
public static final String GOLD_VIEW_NAME = "GoldView";
enum XMLFormat { Knowtator, Anafora }
static interface Options {
- @Option(longName = "text")
+ @Option(longName = "text", defaultToNull = true)
public File getRawTextDirectory();
@Option(longName = "xml")
@@ -194,10 +198,28 @@ public abstract class Evaluation_ImplBas
}
private List<File> getFilesFor(List<Integer> patientSets) {
- if ( !rawTextDirectory.exists() ) {
- return Collections.emptyList();
- }
List<File> files = new ArrayList<File>();
+ if (this.rawTextDirectory == null
+ && this.xmlFormat == XMLFormat.Anafora) {
+ for (File dir : this.xmlDirectory.listFiles()) {
+ Set<String> ids = new HashSet<String>();
+ for (Integer set : patientSets) {
+ ids.add(String.format("ID%03d", set));
+ }
+ if (dir.isDirectory()) {
+ if (ids.contains(dir.getName().substring(0, 5))) {
+ File file = new File(dir, dir.getName());
+ if (file.exists()) {
+ files.add(file);
+ } else {
+ LOGGER.warn("Missing note: " + file);
+ }
+ } else {
+ LOGGER.info("Skipping note: " + dir);
+ }
+ }
+ }
+ } else {
for (Integer set : patientSets) {
final int setNum = set;
for (File file : rawTextDirectory.listFiles(new FilenameFilter(){
@@ -221,7 +243,8 @@ public abstract class Evaluation_ImplBas
}
}
}
- return files;
+ }
+ return files;
}
@Override