svn commit: r1471431 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java

[tm...@apache.org]

Author: tmill
Date: Wed Apr 24 14:25:10 2013
New Revision: 1471431

URL: http://svn.apache.org/r1471431
Log:
Added F1-targeting baseline to build.

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java   (with props)

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java?rev=1471431&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java Wed Apr 24 14:25:10 2013
@@ -0,0 +1,101 @@
+package org.apache.ctakes.temporal.ae.baselines;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+import org.apache.ctakes.relationextractor.ae.RelationExtractorAnnotator;
+import org.apache.ctakes.typesystem.type.syntax.BaseToken;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.cleartk.classifier.CleartkAnnotator;
+import org.cleartk.classifier.Feature;
+import org.cleartk.classifier.jar.GenericJarClassifierFactory;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.util.JCasUtil;
+
+import com.google.common.base.Function;
+import com.google.common.base.Functions;
+import com.google.common.collect.Lists;
+import com.google.common.collect.Ordering;
+
+public class F1BaselineEventTimeRelationAnnotator extends
+		RelationExtractorAnnotator {
+
+	  public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
+		      throws ResourceInitializationException {
+		    return AnalysisEngineFactory.createPrimitiveDescription(
+		        F1BaselineEventTimeRelationAnnotator.class,
+		        CleartkAnnotator.PARAM_IS_TRAINING,
+		        false,
+		        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
+		        new File(modelDirectory, "model.jar"));
+		  }
+
+	@Override
+	protected Class<? extends Annotation> getCoveringClass() {
+		return Sentence.class;
+	}
+
+	@Override
+	protected List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(
+			JCas jCas, Annotation sentence) {
+    	List<EventMention> events = JCasUtil.selectCovered(jCas, EventMention.class, sentence);
+	    	    
+	    if(events.size() == 0) {
+	      return Lists.newArrayList();
+	    }
+
+	    // compute token distance for each time-event pair
+	    HashMap<IdentifiedAnnotationPair, Integer> distanceLookup = new HashMap<IdentifiedAnnotationPair, Integer>();
+	    for (EventMention event : events) {
+	    	if (event.getClass().equals(EventMention.class)) {
+	    		// get only times preceding this event:
+	    		List<TimeMention> times = JCasUtil.selectCovered(jCas, TimeMention.class, sentence.getBegin(), event.getBegin());
+	    		if(times.size() == 0) continue;
+	    		for (TimeMention time : times) {
+	    			// ignore subclasses like Procedure and Disease/Disorder
+	    			IdentifiedAnnotationPair pair = new IdentifiedAnnotationPair(time, event);
+	    			List<BaseToken> baseTokens = JCasUtil.selectBetween(jCas, BaseToken.class, pair.getArg1(), pair.getArg2());
+	    			int distance = baseTokens.size();
+	    			distanceLookup.put(pair, distance);
+	    		}
+	    	}
+
+	    }
+	    
+	    if(distanceLookup.size() == 0) return Lists.newArrayList();
+	    
+	    // find the pair where the distance between entities is the smallest and return it
+	    List<IdentifiedAnnotationPair> rankedPairs = new ArrayList<IdentifiedAnnotationPair>(distanceLookup.keySet());
+	    Function<IdentifiedAnnotationPair, Integer> getValue = Functions.forMap(distanceLookup);
+	    Collections.sort(rankedPairs, Ordering.natural().onResultOf(getValue));
+	    
+	    List<IdentifiedAnnotationPair> results = new ArrayList<IdentifiedAnnotationPair>();
+	    Set<EventMention> relTimes = new HashSet<EventMention>();
+	    for(IdentifiedAnnotationPair result : rankedPairs){
+	    	if(!relTimes.contains(result.getArg2())){
+	    		relTimes.add((EventMention)result.getArg2());
+	    		results.add(result);
+	    		Sentence sent = JCasUtil.selectCovering(jCas, Sentence.class, result.getArg1().getBegin(), result.getArg1().getEnd()).get(0); 
+	    		System.out.println(sent.getCoveredText());
+	    		System.out.println("Relation found: CONTAINS(" + result.getArg1().getCoveredText() + "," + result.getArg2().getCoveredText() + ")\n");
+	    	}
+	    }
+	    return results;
+	}
+
+	  @Override
+	  public String classify(List<Feature> features) {
+	    return "CONTAINS";
+	  }
+}

Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/ae/baselines/F1BaselineEventTimeRelationAnnotator.java
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