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Posted to commits@ctakes.apache.org by sh...@apache.org on 2013/07/30 01:59:24 UTC
svn commit: r1508251 - in
/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion:
eval/AssertionEvaluation.java
medfacts/cleartk/AssertionCleartkAnalysisEngine.java
Author: shalgrim
Date: Mon Jul 29 23:59:24 2013
New Revision: 1508251
URL: http://svn.apache.org/r1508251
Log:
improvements to historyOf. subsumedBy feature added. There may be some stuff to more easily create a file for EA, too.
Modified:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java?rev=1508251&r1=1508250&r2=1508251&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/eval/AssertionEvaluation.java Mon Jul 29 23:59:24 2013
@@ -1128,6 +1128,9 @@ private static void output(Object o) {
private static void printErrors(JCas jCas,
Collection<IdentifiedAnnotation> goldEntitiesAndEvents,
Collection<IdentifiedAnnotation> systemEntitiesAndEvents, String classifierType, Object trueCategory, Class<? extends Object> categoryClass) throws ResourceProcessException {
+
+ String documentId = DocumentIDAnnotationUtil.getDocumentID(jCas);
+
Map<HashableAnnotation, IdentifiedAnnotation> goldMap = Maps.newHashMap();
for (IdentifiedAnnotation mention : goldEntitiesAndEvents) {
goldMap.put(new HashableAnnotation(mention), mention);
@@ -1176,17 +1179,17 @@ private static void printErrors(JCas jCa
// used for multi-class case:
System.out.println(classifierType+" Incorrectly labeled as " + systemLabel + " when the example was " + goldLabel + ": " + formatError(jCas, goldAnnotation));
}else if(systemLabel.equals(trueCategory)){
- System.out.println(classifierType+" FP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+ System.out.println(classifierType+" FP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
}else{
- System.out.println(classifierType+" FN: " + typeId + " " + formatError(jCas, goldAnnotation)+ "| system:|" + formatError(jCas, systemAnnotation));
+ System.out.println(classifierType+" FN: " + typeId + " " + formatError(jCas, goldAnnotation)+ "| system:|" + formatError(jCas, systemAnnotation) + " " + documentId);
}
}else{
if(trueCategory == null){
// multi-class case -- probably don't want to print anything?
}else if(systemLabel.equals(trueCategory)){
- System.out.println(classifierType+" TP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+ System.out.println(classifierType+" TP: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
}else{
- System.out.println(classifierType+" TN: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation));
+ System.out.println(classifierType+" TN: " + typeId + " " + formatError(jCas, systemAnnotation) + "| gold:|" + formatError(jCas, goldAnnotation) + " " + documentId);
}
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java?rev=1508251&r1=1508250&r2=1508251&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java Mon Jul 29 23:59:24 2013
@@ -27,6 +27,7 @@ import java.util.Random;
import org.apache.ctakes.assertion.attributes.features.selection.FeatureSelection;
import org.apache.ctakes.assertion.zoner.types.Zone;
+import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.structured.DocumentID;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.temporary.assertion.AssertionCuePhraseAnnotation;
@@ -358,7 +359,18 @@ public abstract class AssertionCleartkAn
// }
- instance.add(new Feature("ENTITY_TYPE_" + entityOrEventMention.getTypeID()));
+ // 7/9/13 SRH trying to make it work just for anatomical site
+ int eemTypeId = entityOrEventMention.getTypeID();
+ if (eemTypeId == CONST.NE_TYPE_ID_ANATOMICAL_SITE) {
+ // 7/9/13 srh modified per tmiller so it's binary but not numeric feature
+ //instance.add(new Feature("ENTITY_TYPE_" + entityOrEventMention.getTypeID()));
+ instance.add(new Feature("ENTITY_TYPE_ANAT_SITE"));
+ } /* This hurts recall more than it helps precision
+ else if (eemTypeId == CONST.NE_TYPE_ID_DRUG) {
+ // 7/10 adding drug
+ instance.add(new Feature("ENTITY_TYPE_DRUG"));
+ }
+ */
for (SimpleFeatureExtractor extractor : this.entityFeatureExtractors) {
instance.addAll(extractor.extract(jCas, entityOrEventMention));