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Posted to commits@ctakes.apache.org by dl...@apache.org on 2016/06/24 15:44:44 UTC
svn commit: r1750125 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java
Author: dligach
Date: Fri Jun 24 15:44:44 2016
New Revision: 1750125
URL: http://svn.apache.org/viewvc?rev=1750125&view=rev
Log:
printing event-time relations for nn experiments
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java?rev=1750125&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/eventTimeRelationPrinter.java Fri Jun 24 15:44:44 2016
@@ -0,0 +1,254 @@
+/**
+ * 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.nn;
+
+import java.io.File;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Paths;
+import java.nio.file.StandardOpenOption;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.temporal.duration.Utils;
+import org.apache.ctakes.temporal.eval.CommandLine;
+import org.apache.ctakes.temporal.eval.THYMEData;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+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.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
+import org.apache.uima.fit.descriptor.ConfigurationParameter;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+public class eventTimeRelationPrinter {
+
+ static interface Options {
+
+ @Option(longName = "xmi-dir")
+ public File getInputDirectory();
+
+ @Option(longName = "patients")
+ public CommandLine.IntegerRanges getPatients();
+
+ @Option(longName = "output-train")
+ public File getTrainOutputDirectory();
+
+ @Option(longName = "output-test")
+ public File getTestOutputDirectory();
+ }
+
+ public static void main(String[] args) throws Exception {
+
+ Options options = CliFactory.parseArguments(Options.class, args);
+
+ File trainFile = options.getTrainOutputDirectory();
+ if(trainFile.exists()) {
+ trainFile.delete();
+ }
+ trainFile.createNewFile();
+ File devFile = options.getTestOutputDirectory();
+ if(devFile.exists()) {
+ devFile.delete();
+ }
+ devFile.createNewFile();
+
+ List<Integer> patientSets = options.getPatients().getList();
+ List<Integer> trainItems = THYMEData.getPatientSets(patientSets, THYMEData.TRAIN_REMAINDERS);
+ List<Integer> devItems = THYMEData.getPatientSets(patientSets, THYMEData.DEV_REMAINDERS);
+
+ List<File> trainFiles = Utils.getFilesFor(trainItems, options.getInputDirectory());
+ List<File> devFiles = Utils.getFilesFor(devItems, options.getInputDirectory());
+
+ // write training data to file
+ CollectionReader trainCollectionReader = Utils.getCollectionReader(trainFiles);
+ AnalysisEngine trainDataWriter = AnalysisEngineFactory.createEngine(
+ RelationSnippetPrinter.class,
+ "OutputFile",
+ trainFile.getAbsoluteFile());
+ SimplePipeline.runPipeline(trainCollectionReader, trainDataWriter);
+
+ // write dev data to file
+ CollectionReader devCollectionReader = Utils.getCollectionReader(devFiles);
+ AnalysisEngine devDataWriter = AnalysisEngineFactory.createEngine(
+ RelationSnippetPrinter.class,
+ "OutputFile",
+ devFile.getAbsolutePath());
+ SimplePipeline.runPipeline(devCollectionReader, devDataWriter);
+ }
+
+ /**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+ public static class RelationSnippetPrinter extends JCasAnnotator_ImplBase {
+
+ @ConfigurationParameter(
+ name = "OutputFile",
+ mandatory = true,
+ description = "path to the output file")
+ private String outputFile;
+
+ @Override
+ public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+ JCas goldView;
+ try {
+ goldView = jCas.getView("GoldView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ JCas systemView;
+ try {
+ systemView = jCas.getView("_InitialView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ // can't iterate over binary text relations in a sentence, so need
+ // a lookup from pair of annotations to binary text relation
+ Map<List<Annotation>, BinaryTextRelation> relationLookup = new HashMap<>();
+ for(BinaryTextRelation relation : JCasUtil.select(goldView, BinaryTextRelation.class)) {
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+ relationLookup.put(Arrays.asList(arg1, arg2), relation);
+ }
+
+ // go over sentences, extracting event-event relation instances
+ for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {
+ List<String> eventEventRelationsInSentence = new ArrayList<>();
+
+ // retrieve event-time relations in this sentence
+ for(EventMention event : JCasUtil.selectCovered(goldView, EventMention.class, sentence)) {
+ for(TimeMention time : JCasUtil.selectCovered(goldView, TimeMention.class, sentence)) {
+ BinaryTextRelation timeEventRelation = relationLookup.get(Arrays.asList(time, event));
+
+ String label;
+ if(timeEventRelation != null) {
+ if(timeEventRelation.getCategory().equals("CONTAINS")) {
+ label = "contains";
+ } else {
+ label = "none"; // e.g. before or overlap
+ }
+ } else {
+ label = "none"; // no relation between this time and event
+ }
+
+ String context;
+ if(time.getBegin() < event.getBegin()) {
+ // ... time ... event ... scenario
+ context = getTokensBetween(systemView, sentence, time, "t", event, "e", 2);
+ } else {
+ // ... event ... time ... scenario
+ context = getTokensBetween(systemView, sentence, event, "e", time, "t", 2);
+ }
+
+ String text = String.format("%s|%s", label, context);
+ eventEventRelationsInSentence.add(text.toLowerCase());
+ }
+ }
+
+ // BinaryTextRelation eventTimeRelation = relationLookup.get(Arrays.asList(event, time));
+
+ //
+ // String label;
+ // if(forwardRelation != null) {
+ // if(forwardRelation.getCategory().equals("CONTAINS")) {
+ // label = "contains"; // this is contains relation
+ // } else {
+ // label = "none"; // this is some other relation
+ // }
+ // } else if(reverseRelation != null) {
+ // if(reverseRelation.getCategory().equals("CONTAINS")) {
+ // label = "contains-1"; // this is contains relation
+ // } else {
+ // label = "none"; // this is some other relation
+ // }
+ // } else {
+ // label = "none"; // no relation between mentions
+ // }
+
+ try {
+ Files.write(Paths.get(outputFile), eventEventRelationsInSentence, StandardOpenOption.APPEND);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ /**
+ * Return tokens between arg1 and arg2 as string
+ * @param contextSize number of tokens to include on the left of arg1 and on the right of arg2
+ */
+ public static String getTokensBetween(
+ JCas jCas,
+ Sentence sent,
+ Annotation left,
+ String leftType,
+ Annotation right,
+ String rightType,
+ int contextSize) {
+
+ List<String> tokens = new ArrayList<>();
+ for(BaseToken baseToken : JCasUtil.selectPreceding(jCas, BaseToken.class, left, contextSize)) {
+ if(sent.getBegin() <= baseToken.getBegin()) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ }
+ tokens.add("<" + leftType + ">");
+ tokens.add(left.getCoveredText());
+ tokens.add("</" + leftType + ">");
+ for(BaseToken baseToken : JCasUtil.selectBetween(jCas, BaseToken.class, left, right)) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ tokens.add("<" + rightType + ">");
+ tokens.add(right.getCoveredText());
+ tokens.add("</" + rightType + ">");
+ for(BaseToken baseToken : JCasUtil.selectFollowing(jCas, BaseToken.class, right, contextSize)) {
+ if(baseToken.getEnd() <= sent.getEnd()) {
+ tokens.add(baseToken.getCoveredText());
+ }
+ }
+
+ return String.join(" ", tokens).replaceAll("[\r\n]", " ");
+ }
+}