You are viewing a plain text version of this content. The canonical link for it is here.
Posted to commits@ctakes.apache.org by dl...@apache.org on 2016/08/01 17:53:43 UTC
svn commit: r1754783 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/GoldEventPrinterWithLabels.java
Author: dligach
Date: Mon Aug 1 17:53:42 2016
New Revision: 1754783
URL: http://svn.apache.org/viewvc?rev=1754783&view=rev
Log:
printe event data / single label per word
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/GoldEventPrinterWithLabels.java
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/GoldEventPrinterWithLabels.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/GoldEventPrinterWithLabels.java?rev=1754783&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/GoldEventPrinterWithLabels.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/nn/GoldEventPrinterWithLabels.java Mon Aug 1 17:53:42 2016
@@ -0,0 +1,209 @@
+/**
+ * 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.Collections;
+import java.util.List;
+
+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.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 com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * Read cTAKES annotations from XMI files.
+ *
+ * @author dmitriy dligach
+ */
+public class GoldEventPrinterWithLabels {
+
+ 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);
+
+ // write training data to file
+ CollectionReader trainCollectionReader = Utils.getCollectionReader(trainFiles);
+ AnalysisEngine trainDataWriter = AnalysisEngineFactory.createEngine(
+ EventPrinter.class,
+ "OutputFile",
+ trainFile.getAbsoluteFile());
+ SimplePipeline.runPipeline(trainCollectionReader, trainDataWriter);
+
+ // write dev data to file
+ CollectionReader devCollectionReader = Utils.getCollectionReader(devFiles);
+ AnalysisEngine devDataWriter = AnalysisEngineFactory.createEngine(
+ EventPrinter.class,
+ "OutputFile",
+ devFile.getAbsolutePath());
+ SimplePipeline.runPipeline(devCollectionReader, devDataWriter);
+ }
+
+ /**
+ * Print events and entities.
+ *
+ * @author dmitriy dligach
+ */
+ public static class EventPrinter 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 {
+
+ // gold EventMention(s) are all in gold view
+ JCas goldView;
+ try {
+ goldView = jCas.getView("GoldView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ // system view has sentence segmentation, tokens, and dictionary lookup events
+ JCas systemView;
+ try {
+ systemView = jCas.getView("_InitialView");
+ } catch (CASException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+
+ List<String> labelsAndTokens = new ArrayList<>();
+ for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {
+ List<String> sentenceTokens = new ArrayList<>(); // tokens in this sentence
+ List<String> sentenceLabels = new ArrayList<>(); // label for each token in this sentence
+
+ for(BaseToken baseToken : JCasUtil.selectCovered(systemView, BaseToken.class, sentence)) {
+ sentenceTokens.add(tokenToString(baseToken));
+ List<EventMention> events = JCasUtil.selectCovering(goldView, EventMention.class, baseToken.getBegin(), baseToken.getEnd());
+ if(events.size() > 0) {
+ sentenceLabels.add("1"); // this is an event
+ } else {
+ sentenceLabels.add("0"); // this is not an event
+ }
+ }
+
+ String sentenceAsString = String.join(" ", sentenceTokens).replaceAll("[\r\n]", " ");
+ String labelsAsString = String.join(" ", sentenceLabels);
+ labelsAndTokens.add(labelsAsString + "|" + sentenceAsString);
+ }
+
+ try {
+ Files.write(Paths.get(outputFile), labelsAndTokens, StandardOpenOption.APPEND);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /*
+ * Make sure this matches how data was pre-processed for word2vec
+ */
+ public static String tokenToString(BaseToken token) {
+
+ String stringValue;
+ String tokenType = token.getClass().getSimpleName();
+ String tokenText = token.getCoveredText().toLowerCase();
+
+ switch(tokenType) {
+ case "ContractionToken":
+ stringValue = tokenText;
+ break;
+ case "NewlineToken":
+ // stringValue = null;
+ stringValue = "";
+ break;
+ case "NumToken":
+ stringValue = "number_token";
+ break;
+ case "PunctuationToken":
+ stringValue = tokenText;
+ break;
+ case "SymbolToken":
+ stringValue = tokenText;
+ break;
+ case "WordToken":
+ stringValue = tokenText;
+ break;
+ default:
+ throw new IllegalArgumentException("Invalid token type: " + tokenType);
+ }
+
+ return stringValue;
+ }
+}