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Posted to commits@ctakes.apache.org by ja...@apache.org on 2013/05/06 18:40:37 UTC
svn commit: r1479635 - in /ctakes/trunk:
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/
ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/
ctakes-core/src/main/java/org/apache/ctakes/co...
Author: james-masanz
Date: Mon May 6 16:40:37 2013
New Revision: 1479635
URL: http://svn.apache.org/r1479635
Log:
CTAKES-190 dictionary lookup should create specific XxxxMention annotations instead of more generic EntityMention. Some will now be instances of (subclasses of) EventMention instead of EntityMention. This affected code that was looking at all EntityMentions. (Still need to update creation within drug-ner to be MedicationMention instead of MedicationEventMention yet for this JIRA issue.)
Modified:
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/AssertionCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/ (props changed)
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java
ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java
ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/PrintRelations.java
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=1479635&r1=1479634&r2=1479635&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 May 6 16:40:37 2013
@@ -247,25 +247,26 @@ public abstract class AssertionCleartkAn
// Map<IdentifiedAnnotation, Collection<Sentence>> coveringSentenceMap = JCasUtil.indexCovering(identifiedAnnotationView, IdentifiedAnnotation.class, Sentence.class);
// Map<Sentence, Collection<BaseToken>> tokensCoveredInSentenceMap = JCasUtil.indexCovered(identifiedAnnotationView, Sentence.class, BaseToken.class);
- Map<EntityMention, Collection<Zone>> coveringZoneMap =
- JCasUtil.indexCovering(jCas, EntityMention.class, Zone.class);
+ Map<IdentifiedAnnotation, Collection<Zone>> coveringZoneMap =
+ JCasUtil.indexCovering(jCas, IdentifiedAnnotation.class, Zone.class);
List<Instance<String>> instances = new ArrayList<Instance<String>>();
// generate a list of training instances for each sentence in the document
Collection<IdentifiedAnnotation> entities = JCasUtil.select(identifiedAnnotationView, IdentifiedAnnotation.class);
- for (IdentifiedAnnotation entityMention : entities)
+ for (IdentifiedAnnotation identifiedAnnotation : entities)
{
- if (!(entityMention instanceof EntityMention || entityMention instanceof EventMention))
+ if (!(identifiedAnnotation instanceof EntityMention || identifiedAnnotation instanceof EventMention))
{
continue;
}
- if (entityMention.getPolarity() == -1)
+ IdentifiedAnnotation entityOrEventMention = identifiedAnnotation;
+ if (entityOrEventMention.getPolarity() == -1)
{
logger.debug(String.format(" - identified annotation: [%d-%d] polarity %d (%s)",
- entityMention.getBegin(),
- entityMention.getEnd(),
- entityMention.getPolarity(),
- entityMention.getClass().getName()));
+ entityOrEventMention.getBegin(),
+ entityOrEventMention.getEnd(),
+ entityOrEventMention.getPolarity(),
+ entityOrEventMention.getClass().getName()));
}
Instance<String> instance = new Instance<String>();
@@ -316,11 +317,11 @@ public abstract class AssertionCleartkAn
*/
for (CleartkExtractor extractor : this.tokenCleartkExtractors) {
//instance.addAll(extractor.extractWithin(identifiedAnnotationView, entityMention, sentence));
- instance.addAll(extractor.extract(identifiedAnnotationView, entityMention));
+ instance.addAll(extractor.extract(identifiedAnnotationView, entityOrEventMention));
}
List<Feature> cuePhraseFeatures =
- cuePhraseInWindowExtractor.extract(jCas, entityMention);
+ cuePhraseInWindowExtractor.extract(jCas, entityOrEventMention);
//cuePhraseInWindowExtractor.extractWithin(jCas, entityMention, firstCoveringSentence);
if (cuePhraseFeatures != null && !cuePhraseFeatures.isEmpty())
@@ -332,26 +333,26 @@ public abstract class AssertionCleartkAn
for (SimpleFeatureExtractor extractor : this.entityFeatureExtractors) {
- instance.addAll(extractor.extract(jCas, entityMention));
+ instance.addAll(extractor.extract(jCas, entityOrEventMention));
}
- List<Feature> zoneFeatures = extractZoneFeatures(coveringZoneMap, entityMention);
+ List<Feature> zoneFeatures = extractZoneFeatures(coveringZoneMap, entityOrEventMention);
if (zoneFeatures != null && !zoneFeatures.isEmpty())
{
instance.addAll(zoneFeatures);
}
- setClassLabel(entityMention, instance);
+ setClassLabel(entityOrEventMention, instance);
}
}
- public List<Feature> extractZoneFeatures(Map<EntityMention, Collection<Zone>> coveringZoneMap, IdentifiedAnnotation entityMention)
+ public List<Feature> extractZoneFeatures(Map<IdentifiedAnnotation, Collection<Zone>> coveringZoneMap, IdentifiedAnnotation entityOrEventMention)
{
- final Collection<Zone> zoneList = coveringZoneMap.get(entityMention);
+ final Collection<Zone> zoneList = coveringZoneMap.get(entityOrEventMention);
if (zoneList == null || zoneList.isEmpty())
{
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/ConditionalCleartkAnalysisEngine.java Mon May 6 16:40:37 2013
@@ -35,11 +35,11 @@ public class ConditionalCleartkAnalysisE
}
@Override
- public void setClassLabel(IdentifiedAnnotation entityMention,
+ public void setClassLabel(IdentifiedAnnotation entityOrEventMention,
Instance<String> instance) throws AnalysisEngineProcessException {
if (this.isTraining())
{
- String conditional = (entityMention.getConditional()) ? "conditional" : "nonconditional";
+ String conditional = (entityOrEventMention.getConditional()) ? "conditional" : "nonconditional";
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if ("nonconditional".equals(conditional)
@@ -60,7 +60,7 @@ public class ConditionalCleartkAnalysisE
{
conditional = false;
}
- entityMention.setConditional(conditional);
+ entityOrEventMention.setConditional(conditional);
}
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/GenericCleartkAnalysisEngine.java Mon May 6 16:40:37 2013
@@ -67,11 +67,11 @@ public class GenericCleartkAnalysisEngin
}
@Override
- public void setClassLabel(IdentifiedAnnotation entityMention,
+ public void setClassLabel(IdentifiedAnnotation entityOrEventMention,
Instance<String> instance) throws AnalysisEngineProcessException {
if (this.isTraining())
{
- String generic = entityMention.getGeneric()? "1":"0";
+ String generic = entityOrEventMention.getGeneric()? "1":"0";
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if ("0".equals(generic)
@@ -83,7 +83,7 @@ public class GenericCleartkAnalysisEngin
} else
{
String label = this.classifier.classify(instance.getFeatures());
- entityMention.setGeneric("1".equals(label));
+ entityOrEventMention.setGeneric("1".equals(label));
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/HistoryCleartkAnalysisEngine.java Mon May 6 16:40:37 2013
@@ -69,11 +69,11 @@ public class HistoryCleartkAnalysisEngin
}
@Override
- public void setClassLabel(IdentifiedAnnotation entityMention,
+ public void setClassLabel(IdentifiedAnnotation entityOrEventMention,
Instance<String> instance) throws AnalysisEngineProcessException {
if (this.isTraining())
{
- int history = entityMention.getHistoryOf();
+ int history = entityOrEventMention.getHistoryOf();
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if (history == CONST.NE_HISTORY_OF_ABSENT
@@ -86,7 +86,7 @@ public class HistoryCleartkAnalysisEngin
} else
{
String label = this.classifier.classify(instance.getFeatures());
- entityMention.setHistoryOf(Integer.parseInt(label));
+ entityOrEventMention.setHistoryOf(Integer.parseInt(label));
}
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/PolarityCleartkAnalysisEngine.java Mon May 6 16:40:37 2013
@@ -44,10 +44,10 @@ public class PolarityCleartkAnalysisEngi
this.entityFeatureExtractors.add(new ContextWordWindowExtractor("org/apache/ctakes/assertion/models/polarity.txt"));
}
- public void setClassLabel(IdentifiedAnnotation entityMention, Instance<String> instance) throws AnalysisEngineProcessException {
+ public void setClassLabel(IdentifiedAnnotation entityOrEventMention, Instance<String> instance) throws AnalysisEngineProcessException {
if (this.isTraining())
{
- String polarity = (entityMention.getPolarity() == -1) ? "negated" : "present";
+ String polarity = (entityOrEventMention.getPolarity() == -1) ? "negated" : "present";
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if ("negated".equals(polarity))
{
@@ -70,10 +70,10 @@ public class PolarityCleartkAnalysisEngi
{
polarity = -1;
}
- entityMention.setPolarity(polarity);
+ entityOrEventMention.setPolarity(polarity);
if ("negated".equals(label))
{
- logger.debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityMention.getBegin(), entityMention.getEnd(), entityMention.getClass().getName()));
+ logger.debug(String.format("DECODING/EVAL: %s//%s [%d-%d] (%s)", label, polarity, entityOrEventMention.getBegin(), entityOrEventMention.getEnd(), entityOrEventMention.getClass().getName()));
}
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/SubjectCleartkAnalysisEngine.java Mon May 6 16:40:37 2013
@@ -77,11 +77,11 @@ public class SubjectCleartkAnalysisEngin
}
@Override
- public void setClassLabel(IdentifiedAnnotation entityMention,
+ public void setClassLabel(IdentifiedAnnotation entityOrEventMention,
Instance<String> instance) throws AnalysisEngineProcessException {
if (this.isTraining())
{
- String subj = entityMention.getSubject();
+ String subj = entityOrEventMention.getSubject();
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if ("patient".equals(subj)
@@ -98,8 +98,8 @@ public class SubjectCleartkAnalysisEngin
} else
{
String label = this.classifier.classify(instance.getFeatures());
- entityMention.setSubject(label);
- logger.log(Level.DEBUG, "SUBJECT is being set on an IdentifiedAnnotation: "+label+" "+entityMention.getSubject());
+ entityOrEventMention.setSubject(label);
+ logger.log(Level.DEBUG, "SUBJECT is being set on an IdentifiedAnnotation: "+label+" "+entityOrEventMention.getSubject());
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/UncertaintyCleartkAnalysisEngine.java Mon May 6 16:40:37 2013
@@ -34,10 +34,10 @@ public class UncertaintyCleartkAnalysisE
}
@Override
- public void setClassLabel(IdentifiedAnnotation entityMention, Instance<String> instance) throws AnalysisEngineProcessException {
+ public void setClassLabel(IdentifiedAnnotation entityOrEventMention, Instance<String> instance) throws AnalysisEngineProcessException {
if (this.isTraining())
{
- String uncertainty = (entityMention.getUncertainty() == 1) ? "uncertain" : "certain";
+ String uncertainty = (entityOrEventMention.getUncertainty() == 1) ? "uncertain" : "certain";
// downsampling. initialize probabilityOfKeepingADefaultExample to 1.0 for no downsampling
if ("certain".equals(uncertainty)
@@ -57,7 +57,7 @@ public class UncertaintyCleartkAnalysisE
{
uncertainty = 0;
}
- entityMention.setUncertainty(uncertainty);
+ entityOrEventMention.setUncertainty(uncertainty);
}
}
Modified: ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java (original)
+++ ctakes/trunk/ctakes-assertion/src/main/java/org/apache/ctakes/assertion/medfacts/cleartk/extractors/SurroundingExtractor.java Mon May 6 16:40:37 2013
@@ -34,8 +34,8 @@ public class SurroundingExtractor implem
logger.info("SurroundingExtractor.extract() BEGIN");
//JCasUtil.indexCovering(jcas, IdentifiedAnnotation.class, this.ancestorAnnotationClass)
- Map<EntityMention, Collection<Zone>> coveringMap =
- JCasUtil.indexCovering(jcas, EntityMention.class, Zone.class);
+ Map<IdentifiedAnnotation, Collection<Zone>> coveringMap =
+ JCasUtil.indexCovering(jcas, IdentifiedAnnotation.class, Zone.class);
IdentifiedAnnotation targetEntityAnnotation = (IdentifiedAnnotation)targetAnnotation;
Propchange: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/
------------------------------------------------------------------------------
--- svn:ignore (added)
+++ svn:ignore Mon May 6 16:40:37 2013
@@ -0,0 +1 @@
+SHARPKnowtatorXMLReader.java.TEXT
Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java (original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/ae/FilterAnnotator.java Mon May 6 16:40:37 2013
@@ -34,6 +34,7 @@ import org.apache.uima.jcas.tcas.Annotat
import org.apache.uima.resource.ResourceInitializationException;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
public class FilterAnnotator extends JCasAnnotator_ImplBase {
// TODO parameterize retainAttrTypeId = DISORDER_ANNOTATIONS = 2
@@ -77,7 +78,7 @@ public class FilterAnnotator extends JCa
}
private boolean isValid(Annotation ann) {
- if (((EntityMention) ann).getTypeID() != retainAttrTypeId)
+ if (((IdentifiedAnnotation) ann).getTypeID() != retainAttrTypeId)
return false;
return true;
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/AnnotationSelector.java Mon May 6 16:40:37 2013
@@ -35,6 +35,7 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
@@ -45,16 +46,19 @@ public class AnnotationSelector {
public static ArrayList<Annotation> selectNE (JCas jcas) {
ArrayList<Annotation> ret = new ArrayList<Annotation>();
- FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(EntityMention.type).iterator();
+ FSIterator<Annotation> iter = jcas.getJFSIndexRepository().getAnnotationIndex(IdentifiedAnnotation.type).iterator();
while (iter.hasNext()) {
- EntityMention a = (EntityMention) iter.next();
- if(a.getOntologyConceptArr() != null)
+ IdentifiedAnnotation a = (IdentifiedAnnotation) iter.next();
+ if (a instanceof EntityMention || a instanceof EventMention) {
+ if(a.getOntologyConceptArr() != null) {
// int tid = a.getTypeID();
// if (tid == TypeSystemConst.NE_TYPE_ID_ANATOMICAL_SITE ||
// tid == TypeSystemConst.NE_TYPE_ID_DISORDER ||
// tid == TypeSystemConst.NE_TYPE_ID_PROCEDURE ||
// tid == TypeSystemConst.NE_TYPE_ID_FINDING)
ret.add(a);
+ }
+ }
}
java.util.Collections.sort(ret, new AnnotOffsetComparator());
return ret;
@@ -62,7 +66,7 @@ public class AnnotationSelector {
public static ArrayList<BaseToken> selectBaseToken (JCas jcas) {
ArrayList<BaseToken> ret = new ArrayList<BaseToken>();
- FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(BaseToken.type).iterator();
+ FSIterator<?> iter = jcas.getJFSIndexRepository().getAnnotationIndex(BaseToken.type).iterator();
while (iter.hasNext())
ret.add((BaseToken)iter.next());
java.util.Collections.sort(ret, new AnnotOffsetComparator());
@@ -71,7 +75,7 @@ public class AnnotationSelector {
public static ArrayList<Sentence> selectSentence (JCas jcas) {
ArrayList<Sentence> ret = new ArrayList<Sentence>();
- FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(Sentence.type).iterator();
+ FSIterator<Annotation> iter = jcas.getJFSIndexRepository().getAnnotationIndex(Sentence.type).iterator();
while (iter.hasNext())
ret.add((Sentence)iter.next());
java.util.Collections.sort(ret, new AnnotOffsetComparator());
@@ -83,7 +87,7 @@ public class AnnotationSelector {
Logger logger) {
Hashtable<String, WordToken> offset2token = new Hashtable<String, WordToken>();
ArrayList<WordToken> ret = new ArrayList<WordToken>();
- FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(WordToken.type).iterator();
+ FSIterator<Annotation> iter = jcas.getJFSIndexRepository().getAnnotationIndex(WordToken.type).iterator();
while (iter.hasNext()) {
WordToken t = (WordToken)iter.next();
String s = t.getCoveredText();
@@ -138,8 +142,8 @@ public class AnnotationSelector {
findP(adjP, "SBAR", 1)!=null ||
findP(adjP, "S", 1)!=null))
return true;
- } else if (isBe((TreebankNode) par.getChildren(0))) {
- firstChild = (TreebankNode) vp.getChildren(0);
+ } else if (isBe(par.getChildren(0))) {
+ firstChild = vp.getChildren(0);
if (firstChild!=null && cogved.contains(firstChild.getCoveredText()) &&
(findP(vp, "SBAR", 1)!=null ||
findP(vp, "S", 1)!=null))
@@ -182,12 +186,13 @@ public class AnnotationSelector {
txt.equalsIgnoreCase("been") ||
txt.equalsIgnoreCase("be")))
return true;
- else return false;
+
+ return false;
}
public static ArrayList<Chunk> selectDemonAndRelative (JCas jcas) {
ArrayList<Chunk> ret = new ArrayList<Chunk>();
- FSIterator iter = jcas.getJFSIndexRepository().getAnnotationIndex(Chunk.type).iterator();
+ FSIterator<Annotation> iter = jcas.getJFSIndexRepository().getAnnotationIndex(Chunk.type).iterator();
while (iter.hasNext()) {
Chunk c = (Chunk)iter.next();
if (c.getChunkType().equals("NP")) {
Modified: ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java (original)
+++ ctakes/trunk/ctakes-coreference/src/main/java/org/apache/ctakes/coreference/util/PairAttributeCalculator.java Mon May 6 16:40:37 2013
@@ -18,37 +18,19 @@
*/
package org.apache.ctakes.coreference.util;
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.PrintWriter;
-import java.rmi.UnexpectedException;
import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Scanner;
-import org.apache.uima.cas.FSIterator;
-import org.apache.uima.cas.Type;
-import org.apache.uima.cas.text.AnnotationIndex;
-import org.apache.uima.jcas.JCas;
-import org.apache.uima.jcas.cas.FSArray;
-import org.apache.uima.jcas.cas.StringArray;
-import org.apache.uima.jcas.tcas.Annotation;
-
-import org.apache.ctakes.core.resource.FileLocator;
-import org.apache.ctakes.coreference.util.AnnotationSelector;
+import org.apache.ctakes.coreference.type.Markable;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
-import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation;
-import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.ctakes.coreference.type.DemMarkable;
-import org.apache.ctakes.coreference.type.Markable;
-import org.apache.ctakes.coreference.type.NEMarkable;
-import org.apache.ctakes.coreference.type.PronounMarkable;
+import org.apache.uima.cas.FSIterator;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.cas.FSArray;
+import org.apache.uima.jcas.tcas.Annotation;
public class PairAttributeCalculator extends AttributeCalculator {
@@ -551,9 +533,9 @@ public class PairAttributeCalculator ext
}
public boolean calcNegatedBoth(){
- if(a1 instanceof EntityMention && a2 instanceof EntityMention){
- if(((EntityMention)a1).getPolarity() == -1 &&
- ((EntityMention)a2).getPolarity() == -1){
+ if((a1 instanceof EntityMention && a2 instanceof EntityMention) || (a1 instanceof EventMention && a2 instanceof EventMention)){
+ if(((IdentifiedAnnotation)a1).getPolarity() == -1 &&
+ ((IdentifiedAnnotation)a2).getPolarity() == -1){
return true;
}
}
@@ -561,9 +543,9 @@ public class PairAttributeCalculator ext
}
public boolean calcNonNegatedBoth(){
- if(a1 instanceof EntityMention && a2 instanceof EntityMention){
- if(((EntityMention)a1).getPolarity() == 1.0 &&
- ((EntityMention)a2).getPolarity() == 1.0){
+ if(a1 instanceof EntityMention && a2 instanceof EntityMention || (a1 instanceof EventMention && a2 instanceof EventMention)){
+ if(((IdentifiedAnnotation)a1).getPolarity() == 1.0 &&
+ ((IdentifiedAnnotation)a2).getPolarity() == 1.0){
return true;
}
}
Modified: ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/NamedEntityLookupConsumerImpl.java Mon May 6 16:40:37 2013
@@ -22,9 +22,14 @@ import org.apache.ctakes.dictionary.look
import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
+import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
+import org.apache.ctakes.typesystem.type.textsem.LabMention;
+import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
+import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
+import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
@@ -107,11 +112,22 @@ public class NamedEntityLookupConsumerIm
codes.add( code );
}
}
- IdentifiedAnnotation neAnnot;
- if ( typeId == CONST.NE_TYPE_ID_DRUG || typeId == CONST.NE_TYPE_ID_UNKNOWN ) {
- neAnnot = new MedicationEventMention( jcas );
+
+ IdentifiedAnnotation neAnnot = new IdentifiedAnnotation(jcas);
+ if ( typeId == CONST.NE_TYPE_ID_DRUG ) {
+ neAnnot = new MedicationMention( jcas );
+ } else if ( typeId == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) {
+ neAnnot = new AnatomicalSiteMention( jcas );
+ } else if ( typeId == CONST.NE_TYPE_ID_DISORDER ) {
+ neAnnot = new DiseaseDisorderMention( jcas );
+ } else if ( typeId == CONST.NE_TYPE_ID_FINDING ) {
+ neAnnot = new SignSymptomMention( jcas );
+ } else if ( typeId == CONST.NE_TYPE_ID_LAB ) {
+ neAnnot = new LabMention( jcas );
+ } else if ( typeId == CONST.NE_TYPE_ID_PROCEDURE ) {
+ neAnnot = new ProcedureMention( jcas );
} else {
- neAnnot = new EntityMention( jcas );
+ neAnnot = new EntityMention( jcas );
}
final int neBegin = entry.getKey().__start;
final int neEnd = entry.getKey().__end;
Modified: ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java Mon May 6 16:40:37 2013
@@ -23,9 +23,14 @@ import org.apache.ctakes.dictionary.look
import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
+import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
+import org.apache.ctakes.typesystem.type.textsem.LabMention;
+import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
+import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
+import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
@@ -250,9 +255,19 @@ public abstract class UmlsToSnomedConsum
IdentifiedAnnotation neAnnot;
final int conceptKey = conceptEntry.getKey();
if ( conceptKey == CONST.NE_TYPE_ID_DRUG ) {
- neAnnot = new MedicationEventMention( jcas );
+ neAnnot = new MedicationMention( jcas );
+ } else if ( conceptKey == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) {
+ neAnnot = new AnatomicalSiteMention( jcas );
+ } else if ( conceptKey == CONST.NE_TYPE_ID_DISORDER ) {
+ neAnnot = new DiseaseDisorderMention( jcas );
+ } else if ( conceptKey == CONST.NE_TYPE_ID_FINDING ) {
+ neAnnot = new SignSymptomMention( jcas );
+ } else if ( conceptKey == CONST.NE_TYPE_ID_LAB ) {
+ neAnnot = new LabMention( jcas );
+ } else if ( conceptKey == CONST.NE_TYPE_ID_PROCEDURE ) {
+ neAnnot = new ProcedureMention( jcas );
} else {
- neAnnot = new EntityMention( jcas );
+ neAnnot = new EntityMention( jcas );
}
neAnnot.setTypeID( conceptKey );
neAnnot.setBegin( neBegin );
Modified: ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java (original)
+++ ctakes/trunk/ctakes-drug-ner/src/main/java/org/apache/ctakes/drugner/ae/DrugMentionAnnotator.java Mon May 6 16:40:37 2013
@@ -106,7 +106,7 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.syntax.SymbolToken;
import org.apache.ctakes.typesystem.type.syntax.WordToken;
import org.apache.ctakes.typesystem.type.textsem.DateAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
@@ -989,7 +989,7 @@ public class DrugMentionAnnotator extend
}
} catch (ArrayIndexOutOfBoundsException aioobe) {
allNEs =
- FSUtil.getAnnotationsInSpan(jcas, EntityMention.type, begin, end, validNeTypes);
+ FSUtil.getAnnotationsInSpan(jcas, EventMention.type, begin, end, validNeTypes);
uniqueNEs = findUniqueMentions(allNEs.toArray());
Modified: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java (original)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/baselines/Utils.java Mon May 6 16:40:37 2013
@@ -6,6 +6,7 @@ import java.util.HashSet;
import java.util.List;
import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator.IdentifiedAnnotationPair;
+import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
@@ -28,14 +29,16 @@ public class Utils {
public static boolean validateLocationOfArgumentTypes(IdentifiedAnnotationPair pair) {
// allowable arg2 types for location_of
- HashSet<Integer> okArg2Types = new HashSet<Integer>(Arrays.asList(2, 3, 5));
+ // Per CTAKES-190, only link anatomical sites in LocationOf to EventMentions, but these three are EventMentions now,
+ // so this check of type ID now already handles if it is an EventMention.
+ HashSet<Integer> okArg2Types = new HashSet<Integer>(Arrays.asList(CONST.NE_TYPE_ID_DISORDER, CONST.NE_TYPE_ID_FINDING, CONST.NE_TYPE_ID_PROCEDURE));
IdentifiedAnnotation arg1 = pair.getArg1(); // Argument (should be anatomical site)
IdentifiedAnnotation arg2 = pair.getArg2(); // Related_to (should be either disorder, sign/symptom, or procedure)
int type1 = arg1.getTypeID();
int type2 = arg2.getTypeID();
- if(type1 == 6 && okArg2Types.contains(type2)) {
+ if(type1 == CONST.NE_TYPE_ID_ANATOMICAL_SITE && okArg2Types.contains(type2)) {
return true;
}
@@ -52,7 +55,9 @@ public class Utils {
public static boolean validateDegreeOfArgumentTypes(IdentifiedAnnotationPair pair) {
// allowable arg1 types
- HashSet<Integer> okArg1Types = new HashSet<Integer>(Arrays.asList(2, 3));
+ // Per CTAKES-190, only link SeverityModifiers to EventMention, but the 2 type IDs below are EventMentions now,
+ // so this check of type ID now already handles if it is an EventMention.
+ HashSet<Integer> okArg1Types = new HashSet<Integer>(Arrays.asList(CONST.NE_TYPE_ID_DISORDER, CONST.NE_TYPE_ID_FINDING));
IdentifiedAnnotation arg1 = pair.getArg1(); // Argument (should be either disease/disorder or sign/symptom
int type1 = arg1.getTypeID();
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=1479635&r1=1479634&r2=1479635&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 Mon May 6 16:40:37 2013
@@ -54,6 +54,7 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.syntax.Chunk;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.LookupWindowAnnotation;
import org.apache.ctakes.typesystem.type.textspan.Segment;
@@ -454,6 +455,16 @@ public abstract class Evaluation_ImplBas
}
}
+ public static class EventMentionRemover extends JCasAnnotator_ImplBase {
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+ for (EventMention mention : Lists.newArrayList(JCasUtil.select(jCas, EventMention.class))) {
+ mention.removeFromIndexes();
+ }
+ }
+ }
+
// replace this with SimpleSegmentWithTagsAnnotator if that code ever gets fixed
public static class SegmentsFromBracketedSectionTagsAnnotator extends JCasAnnotator_ImplBase {
private static Pattern SECTION_PATTERN = Pattern.compile(
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/PrintRelations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/PrintRelations.java?rev=1479635&r1=1479634&r2=1479635&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/PrintRelations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/PrintRelations.java Mon May 6 16:40:37 2013
@@ -30,6 +30,8 @@ import java.util.TreeSet;
import org.apache.ctakes.temporal.ae.THYMEKnowtatorXMLReader;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
@@ -89,8 +91,10 @@ public class PrintRelations {
List<BinaryTextRelation> relationList = new ArrayList<BinaryTextRelation>(relations);
Collections.sort(relationList, BY_RELATION_OFFSETS);
- for (EntityMention entityMention : JCasUtil.select(jCas, EntityMention.class)) {
- System.err.printf("%s (%s)\n", entityMention.getCoveredText(), entityMention.getTypeID());
+ for (IdentifiedAnnotation identifiedAnnotation : JCasUtil.select(jCas, IdentifiedAnnotation.class)) {
+ if (identifiedAnnotation instanceof EventMention || identifiedAnnotation instanceof EntityMention) {
+ System.err.printf("%s (%s)\n", identifiedAnnotation.getCoveredText(), identifiedAnnotation.getTypeID());
+ }
}
// print out the relations for visual inspection