org.apache.ctakes.temporal.ae.baselines.PrecisionBaselineEventTimeRelationAnnotator.java Source code

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Here is the source code for org.apache.ctakes.temporal.ae.baselines.PrecisionBaselineEventTimeRelationAnnotator.java

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/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */
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.ml.CleartkAnnotator;
import org.cleartk.ml.Feature;
import org.cleartk.ml.jar.GenericJarClassifierFactory;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.fit.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 PrecisionBaselineEventTimeRelationAnnotator extends RelationExtractorAnnotator {

    public static AnalysisEngineDescription createAnnotatorDescription(File modelDirectory)
            throws ResourceInitializationException {
        return AnalysisEngineFactory.createEngineDescription(PrecisionBaselineEventTimeRelationAnnotator.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
    public List<IdentifiedAnnotationPair> getCandidateRelationArgumentPairs(JCas jCas, Annotation sentence) {

        List<EventMention> events = JCasUtil.selectCovered(jCas, EventMention.class, sentence);
        List<TimeMention> times = JCasUtil.selectCovered(jCas, TimeMention.class, sentence);

        if (times.size() < 1 || events.size() < 1) {
            return Lists.newArrayList();
        }

        // compute token distance for each time-event pair
        HashMap<IdentifiedAnnotationPair, Integer> distanceLookup = new HashMap<IdentifiedAnnotationPair, Integer>();
        for (EventMention event : events) {
            // ignore subclasses like Procedure and Disease/Disorder
            if (event.getClass().equals(EventMention.class)) {
                for (TimeMention time : times) {
                    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);
                }
            }
        }

        // 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<TimeMention> relTimes = new HashSet<TimeMention>();
        for (IdentifiedAnnotationPair result : rankedPairs) {
            if (!relTimes.contains(result.getArg1())) {
                relTimes.add((TimeMention) result.getArg1());
                results.add(result);
            }
        }

        return results;
    }

    @Override
    public String classify(List<Feature> features) {
        return "CONTAINS";
    }
}