Author: dligach
Date: Fri Sep 30 19:53:00 2016
New Revision: 1762961
URL: http://svn.apache.org/viewvc?rev=1762961&view=rev
Log:
printing positions for the arguments
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java?rev=1762961&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java
(added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/data/EventTimeRelPositionPrinter.java
Fri Sep 30 19:53:00 2016
@@ -0,0 +1,358 @@
+/**
+ * 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.Collections;
+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.relation.TemporalTextRelation;
+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 EventTimeRelPositionPrinter {
+
+ 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());
+
+ // sort training files to eliminate platform specific dir listings
+ Collections.sort(trainFiles);
+ // Collections.shuffle(trainFiles, new Random(100));
+
+ // 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.
+ */
+ 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
+ Map<List<Annotation>, BinaryTextRelation> relationLookup = new HashMap<>();
+ if(isTraining) {
+ for(BinaryTextRelation relation : JCasUtil.select(goldView, TemporalTextRelation.class))
{
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+
+ if(relationLookup.get(Arrays.asList(arg1, arg2)) != null) {
+ // there is already a relation between arg1 and arg2
+ // only store if it is 'contains' relation
+ if(relation.getCategory().equals("CONTAINS")) {
+ relationLookup.put(Arrays.asList(arg1, arg2), relation);
+ } else {
+ System.out.println("skipping relation: " + arg1.getCoveredText() + " ... "
+ arg2.getCoveredText());
+ }
+ } else {
+ relationLookup.put(Arrays.asList(arg1, arg2), relation);
+ }
+ }
+ } else {
+ for(BinaryTextRelation relation : JCasUtil.select(goldView, TemporalTextRelation.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> eventTimeRelationsInSentence = 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));
+ BinaryTextRelation eventTimeRelation = relationLookup.get(Arrays.asList(event,
time));
+
+ String label = "none";
+ if(timeEventRelation != null) {
+ if(timeEventRelation.getCategory().equals("CONTAINS")) {
+ label = "contains"; // this is contains
+ }
+ }
+ // there is at least one instance where both event-time and time-event rels exist?
+ if(eventTimeRelation != null) {
+ if(eventTimeRelation.getCategory().equals("CONTAINS")) {
+ label = "contains-1"; // this is contains
+ }
+ }
+
+ String context = getPositionContext(systemView, sentence, time, event);
+ String text = String.format("%s|%s", label, context);
+ eventTimeRelationsInSentence.add(text.toLowerCase());
+ }
+ }
+
+ try {
+ Files.write(Paths.get(outputFile), eventTimeRelationsInSentence, StandardOpenOption.APPEND);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+ }
+
+ /**
+ * Print words from left to right.
+ * @param contextSize number of tokens to include on the left of arg1 and on the right
of arg2
+ */
+ public static String getTokenContext(
+ 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]", " ");
+ }
+
+ /**
+ * Print POS tags from left to right.
+ * @param contextSize number of tokens to include on the left of arg1 and on the right
of arg2
+ */
+ public static String getPosContext(
+ 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.getPartOfSpeech());
+ }
+ }
+ tokens.add("<" + leftType + ">");
+ for(BaseToken baseToken : JCasUtil.selectCovered(jCas, BaseToken.class, left)) {
+ tokens.add(baseToken.getPartOfSpeech());
+ }
+ tokens.add("</" + leftType + ">");
+ for(BaseToken baseToken : JCasUtil.selectBetween(jCas, BaseToken.class, left, right))
{
+ tokens.add(baseToken.getPartOfSpeech());
+ }
+ tokens.add("<" + rightType + ">");
+ for(BaseToken baseToken : JCasUtil.selectCovered(jCas, BaseToken.class, right)) {
+ tokens.add(baseToken.getPartOfSpeech());
+ }
+ tokens.add("</" + rightType + ">");
+ for(BaseToken baseToken : JCasUtil.selectFollowing(jCas, BaseToken.class, right, contextSize))
{
+ if(baseToken.getEnd() <= sent.getEnd()) {
+ tokens.add(baseToken.getPartOfSpeech());
+ }
+ }
+
+ return String.join(" ", tokens).replaceAll("[\r\n]", " ");
+ }
+
+ /**
+ * 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,
+ TimeMention time,
+ EventMention event) {
+
+ // 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());
+ }
+
+ // assume time consists of multipe words; event of one
+ int currentPosition = 0; // current token index
+ int timeFirstPosition = -1000; // timex's start index
+ int timeLastPosition = -1000; // timex's end index
+ int eventPosition = -1000; // event's index
+ for(BaseToken token : JCasUtil.selectCovered(jCas, BaseToken.class, sent)) {
+ if(time.getBegin() == token.getBegin()) {
+ timeFirstPosition = currentPosition; // start of time expression found
+ }
+ if(time.getEnd() == token.getEnd()) {
+ timeLastPosition = currentPosition; // end of time expression found
+ }
+ if(event.getBegin() == token.getBegin()) {
+ eventPosition = currentPosition; // event postion found
+ }
+ currentPosition++;
+ }
+
+ List<String> positionsWrtToTime = new ArrayList<>();
+ List<String> positionsWrtToEvent = new ArrayList<>();
+ int tokensInSentence = JCasUtil.selectCovered(jCas, BaseToken.class, sent).size();
+ for(int tokenIndex = 0; tokenIndex < tokensInSentence; tokenIndex++) {
+ if(tokenIndex < timeFirstPosition) {
+ positionsWrtToTime.add(Integer.toString(tokenIndex - timeFirstPosition));
+ } else if(tokenIndex >= timeFirstPosition && tokenIndex <= timeLastPosition)
{
+ positionsWrtToTime.add("0");
+ } else {
+ positionsWrtToTime.add(Integer.toString(tokenIndex - timeLastPosition));
+ }
+ positionsWrtToEvent.add(Integer.toString(tokenIndex - eventPosition));
+ }
+
+ String tokensAsString = String.join(" ", tokens).replaceAll("[\r\n]", " ");
+ String wrtToTimeAsString = String.join(" ", positionsWrtToTime);
+ String wrtToEventAsString = String.join(" ", positionsWrtToEvent);
+
+ return tokensAsString + "|" + wrtToTimeAsString + "|" + wrtToEventAsString;
+ }
+}
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