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Posted to commits@ctakes.apache.org by dl...@apache.org on 2016/12/13 14:34:38 UTC
svn commit: r1774027 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPositionPrinter.java
Author: dligach
Date: Tue Dec 13 14:34:38 2016
New Revision: 1774027
URL: http://svn.apache.org/viewvc?rev=1774027&view=rev
Log:
position feature data writer for event-event relations
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPositionPrinter.java
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPositionPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPositionPrinter.java?rev=1774027&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPositionPrinter.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventEventRelPositionPrinter.java Tue Dec 13 14:34:38 2016
@@ -0,0 +1,263 @@
+/**
+ * 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.data;
+
+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.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 EventEventRelPositionPrinter {
+
+ 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,
+ "IsTraining",
+ true,
+ "OutputFile",
+ trainFile.getAbsoluteFile());
+ SimplePipeline.runPipeline(trainCollectionReader, trainDataWriter);
+
+ // write dev data to file
+ CollectionReader devCollectionReader = Utils.getCollectionReader(devFiles);
+ AnalysisEngine devDataWriter = AnalysisEngineFactory.createEngine(
+ RelationSnippetPrinter.class,
+ "IsTraining",
+ false,
+ "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 = "IsTraining",
+ mandatory = true,
+ description = "are we training?")
+ private boolean isTraining;
+
+ @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<>();
+ ArrayList<EventMention> eventMentionsInSentence = new ArrayList<>(JCasUtil.selectCovered(goldView, EventMention.class, sentence));
+
+ // retrieve event-event relations in this sentence
+ for(int i = 0; i < eventMentionsInSentence.size(); i++) {
+ for(int j = i + 1; j < eventMentionsInSentence.size(); j++) {
+ EventMention mention1 = eventMentionsInSentence.get(i);
+ EventMention mention2 = eventMentionsInSentence.get(j);
+ BinaryTextRelation forwardRelation = relationLookup.get(Arrays.asList(mention1, mention2));
+ BinaryTextRelation reverseRelation = relationLookup.get(Arrays.asList(mention2, mention1));
+
+ String label = "none";
+ if(forwardRelation != null) {
+ if(forwardRelation.getCategory().equals("CONTAINS")) {
+ label = "contains"; // mention1 contains mention2
+ }
+ } else if(reverseRelation != null) {
+ if(reverseRelation.getCategory().equals("CONTAINS")) {
+ label = "contains-1"; // mention2 contains mention1
+ }
+ }
+
+ // sanity check
+ if(mention1.getBegin() > mention2.getBegin()) {
+ System.out.println("We assumed mention1 is always before mention2");
+ System.out.println(sentence.getCoveredText());
+ System.out.println(mention1.getCoveredText());
+ System.out.println(mention2.getCoveredText());
+ System.out.println();
+ }
+
+ String context = getPositionContext(systemView, sentence, mention1, mention2);
+ // String context = ArgContextProvider.getRegions(systemView, sentence, mention1, mention2, 2);
+
+ String text = String.format("%s|%s", label, context);
+ eventEventRelationsInSentence.add(text.toLowerCase());
+ }
+ }
+
+ try {
+ Files.write(Paths.get(outputFile), eventEventRelationsInSentence, StandardOpenOption.APPEND);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ /**
+ * Print indices
+ * @param contextSize number of tokens to include on the left of arg1 and on the right of arg2
+ */
+ public static String getPositionContext(
+ JCas jCas,
+ Sentence sent,
+ EventMention event1,
+ EventMention event2) {
+
+ // get sentence as a list of tokens
+ List<String> tokens = new ArrayList<>();
+ for(BaseToken baseToken : JCasUtil.selectCovered(jCas, BaseToken.class, sent)) {
+ tokens.add(baseToken.getCoveredText());
+ }
+
+ // find the positions of event mentions
+ // assume both events consists of just head words
+
+ int currentPosition = 0; // current token index
+ int event1Position = -1000; // event1's index
+ int event2Position = -1000; // event2's index
+
+ for(BaseToken token : JCasUtil.selectCovered(jCas, BaseToken.class, sent)) {
+ if(event1.getBegin() == token.getBegin()) {
+ event1Position = currentPosition; // event1 position found
+ }
+ if(event2.getBegin() == token.getBegin()) {
+ event2Position = currentPosition; // event2 postion found
+ }
+ currentPosition++;
+ }
+
+ List<String> positionsWrtToEvent1 = new ArrayList<>();
+ List<String> positionsWrtToEvent2 = new ArrayList<>();
+ int tokensInSentence = JCasUtil.selectCovered(jCas, BaseToken.class, sent).size();
+
+ for(int tokenIndex = 0; tokenIndex < tokensInSentence; tokenIndex++) {
+
+ positionsWrtToEvent1.add(Integer.toString(tokenIndex - event1Position));
+ positionsWrtToEvent2.add(Integer.toString(tokenIndex - event2Position));
+ }
+
+ String tokensAsString = String.join(" ", tokens).replaceAll("[\r\n]", " ");
+ String distanceToTime = String.join(" ", positionsWrtToEvent1);
+ String distanceToEvent = String.join(" ", positionsWrtToEvent2);
+
+ return tokensAsString + "|" + distanceToTime + "|" + distanceToEvent;
+ }
+}