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From tm...@apache.org
Subject svn commit: r1611026 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CoreferenceChainAnnotator.java
Date Wed, 16 Jul 2014 14:37:39 GMT
Author: tmill
Date: Wed Jul 16 14:37:38 2014
New Revision: 1611026

URL: http://svn.apache.org/r1611026
Log:
CTAKES-199: Moved chain annotator coref classes into temporal for event coreference.

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CoreferenceChainAnnotator.java

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CoreferenceChainAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CoreferenceChainAnnotator.java?rev=1611026&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CoreferenceChainAnnotator.java
(added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/CoreferenceChainAnnotator.java
Wed Jul 16 14:37:38 2014
@@ -0,0 +1,123 @@
+package org.apache.ctakes.temporal.ae;
+
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.Comparator;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.ctakes.typesystem.type.relation.CollectionTextRelation;
+import org.apache.ctakes.typesystem.type.relation.CoreferenceRelation;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.cas.EmptyFSList;
+import org.apache.uima.jcas.cas.NonEmptyFSList;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.util.JCasUtil;
+
+/*
+ * Does not find coreference -- simply turns annotated pairs into chains of clustered mentions
+ */
+public class CoreferenceChainAnnotator extends JCasAnnotator_ImplBase {
+
+  @Override
+  public void process(JCas jCas) throws AnalysisEngineProcessException {
+    Collection<CoreferenceRelation> pairs = JCasUtil.select(jCas, CoreferenceRelation.class);
+    Map<Annotation,Set<Annotation>> chains = new HashMap<>();
+    
+    for(CoreferenceRelation pair : pairs){
+      Annotation ante = pair.getArg1().getArgument();
+      Annotation ana = pair.getArg2().getArgument();
+      
+      /* 3 cases:
+       * 1) Only antecedent is in a chain -- add anaphor to that chain
+       * 2) Only anaphor is in a chain -- add antecedent to that chain
+       * 3) Both in different chains -- join the chains
+       * 4) Both in same chain -- do nothing
+       * 5) Neither in a chain -- create new chain
+       */
+      if(chains.containsKey(ante) && !chains.containsKey(ana)){
+        // 1
+        chains.get(ante).add(ana);
+        chains.put(ana, chains.get(ante));
+      }else if(chains.containsKey(ana) && !chains.containsKey(ante)){
+        // 2
+        chains.get(ana).add(ante);
+        chains.put(ante, chains.get(ana));
+      }else if(chains.containsKey(ante) && chains.containsKey(ana)){
+        if(!chains.get(ante).equals(chains.get(ana))){
+          // 3
+          Set<Annotation> anteChain = chains.get(ante);
+          Set<Annotation> anaChain = chains.get(ana);
+          anteChain.addAll(anaChain);
+          chains.put(ana, anteChain);
+          // make all annotations in ana chain point to ante chain:
+          for(Annotation markable : anaChain){
+            chains.put(markable, anteChain);
+          }
+        }
+        // else 4, which do nothing
+      }else{
+        // 5
+        Set<Annotation> newChain = new HashSet<Annotation>();
+        newChain.add(ante);
+        newChain.add(ana);
+        chains.put(ante, newChain);
+        chains.put(ana, newChain);
+      }
+    }
+    
+    // convert java Sets into ordered UIMA lists.
+    for(Set<Annotation> mentionSet : new HashSet<Set<Annotation>>(chains.values())){
+      List<Annotation> sortedMentions = new ArrayList<>(mentionSet);
+      Collections.sort(sortedMentions, new AnnotationComparator());
+      CollectionTextRelation chain = new CollectionTextRelation(jCas);
+      NonEmptyFSList list = new NonEmptyFSList(jCas);
+      chain.setMembers(list);
+      list.addToIndexes();
+      for(int i = 0; i < sortedMentions.size(); i++){
+        Annotation mention = sortedMentions.get(i);
+        list.setHead(mention);
+        if(i == (sortedMentions.size() - 1)){
+          list.setTail(new EmptyFSList(jCas));
+          list.getTail().addToIndexes();
+        }else{
+          list.setTail(new NonEmptyFSList(jCas));
+          list = (NonEmptyFSList) list.getTail();
+          list.addToIndexes();
+        }
+      }
+      chain.addToIndexes();
+    }
+  }
+
+  private class AnnotationComparator implements Comparator<Annotation> {
+
+    @Override
+    public int compare(Annotation o1, Annotation o2) {
+      if(o1.getBegin() < o2.getBegin()){
+        return -1;
+      }else if(o1.getBegin() == o2.getBegin() && o1.getEnd() < o2.getEnd()){
+        return -1;
+      }else if(o1.getBegin() == o2.getBegin() && o1.getEnd() > o2.getEnd()){
+        return 1;
+      }else if(o2.getBegin() < o1.getBegin()){
+        return 1;
+      }else{
+        return 0;
+      }
+    }
+  }
+  
+  public static AnalysisEngineDescription createAnnotatorDescription() throws ResourceInitializationException{
+    return AnalysisEngineFactory.createPrimitiveDescription(CoreferenceChainAnnotator.class);
+  }
+}



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