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Posted to commits@ctakes.apache.org by dl...@apache.org on 2013/08/06 20:37:43 UTC
svn commit: r1511067 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
Author: dligach
Date: Tue Aug 6 18:37:43 2013
New Revision: 1511067
URL: http://svn.apache.org/r1511067
Log:
Script for printing gold standard events of a given UMLS semantic type
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java?rev=1511067&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventPrinterPipeline.java Tue Aug 6 18:37:43 2013
@@ -0,0 +1,235 @@
+/**
+ * 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.data.analysis;
+
+import java.io.BufferedWriter;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
+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.relationextractor.eval.XMIReader;
+import org.apache.ctakes.typesystem.type.syntax.TerminalTreebankNode;
+import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
+import org.apache.ctakes.typesystem.type.textsem.EntityMention;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+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.jcas.JCas;
+import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.Option;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.descriptor.ConfigurationParameter;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+import com.google.common.base.Function;
+import com.google.common.base.Functions;
+import com.google.common.collect.Ordering;
+
+/**
+ * Print events of given UMLS semantic type.
+ *
+ * @author dmitriy dligach
+ */
+public class EventPrinterPipeline {
+
+ public static class Options extends Options_ImplBase {
+
+ @Option(
+ name = "--input-dir",
+ usage = "specify the path to the directory containing the clinical notes to be processed",
+ required = true)
+ public File inputDirectory;
+
+ @Option(
+ name = "--umls-type",
+ usage = "specify the UMLS semantic type (e.g. 5, i.e. procedure)",
+ required = true)
+ public int umlsSemanticType;
+
+ @Option(
+ name = "--event-output-file",
+ usage = "specify the path to the directory containing the clinical notes to be processed",
+ required = true)
+ public File eventOutputFile;
+ }
+
+ public static void main(String[] args) throws Exception {
+
+ Options options = new Options();
+ options.parseOptions(args);
+
+ List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
+ CollectionReader collectionReader = getCollectionReader(trainFiles);
+
+ AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+ EventAndTokenContextWriter.class,
+ "UmlsSemanticType",
+ options.umlsSemanticType,
+ "EventOutputFile",
+ options.eventOutputFile);
+
+ SimplePipeline.runPipeline(collectionReader, annotationConsumer);
+ }
+
+ /**
+ * Print events with a given UMLS semantic type.
+ */
+ public static class EventAndTokenContextWriter extends JCasAnnotator_ImplBase {
+
+ @ConfigurationParameter(
+ name = "EventOutputFile",
+ mandatory = true,
+ description = "path to the file that stores the events")
+ private String eventOutputFile;
+
+ @ConfigurationParameter(
+ name = "UmlsSemanticType",
+ mandatory = true,
+ description = "umls semantic type")
+ private int umlsSemanticType;
+
+ @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);
+ }
+
+ BufferedWriter eventWriter = getWriter(eventOutputFile, true);
+ try {
+ for(EventMention eventMention : JCasUtil.select(goldView, EventMention.class)) {
+
+ List<EntityMention> coveringEntityMentions = JCasUtil.selectCovered(
+ systemView,
+ EntityMention.class,
+ eventMention.getBegin(),
+ eventMention.getEnd());
+
+ for(EntityMention entityMention : coveringEntityMentions) {
+ if(entityMention.getTypeID() == umlsSemanticType) {
+ String output = String.format(
+ "%s|%s\n",
+ entityMention.getCoveredText().toLowerCase(),
+ expandToNP(systemView, eventMention).toLowerCase());
+ try {
+ eventWriter.write(output);
+ } catch (IOException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+ }
+ }
+ }
+ } finally {
+ try {
+ eventWriter.close();
+ } catch (IOException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+ }
+ }
+ }
+
+ public static BufferedWriter getWriter(String filePath, boolean append) {
+
+ BufferedWriter bufferedWriter = null;
+ try {
+ FileWriter fileWriter = new FileWriter(filePath, append);
+ bufferedWriter = new BufferedWriter(fileWriter);
+ } catch (IOException e) {
+ e.printStackTrace();
+ }
+
+ return bufferedWriter;
+ }
+
+ public static CollectionReader getCollectionReader(List<File> inputFiles) throws Exception {
+
+ List<String> fileNames = new ArrayList<String>();
+ for(File file : inputFiles) {
+ if(! (file.isHidden())) {
+ fileNames.add(file.getPath());
+ }
+ }
+
+ String[] paths = new String[fileNames.size()];
+ fileNames.toArray(paths);
+
+ return CollectionReaderFactory.createCollectionReader(
+ XMIReader.class,
+ XMIReader.PARAM_FILES,
+ paths);
+ }
+
+ public static String expandToNP(JCas jCas, IdentifiedAnnotation identifiedAnnotation) {
+
+ // map each covering treebank node to its character length
+ Map<TreebankNode, Integer> treebankNodeSizes = new HashMap<TreebankNode, Integer>();
+ for(TreebankNode treebankNode : JCasUtil.selectCovering(
+ jCas,
+ TreebankNode.class,
+ identifiedAnnotation.getBegin(),
+ identifiedAnnotation.getEnd())) {
+
+ // only expand nouns (and not verbs or adjectives)
+ if(treebankNode instanceof TerminalTreebankNode) {
+ if(! treebankNode.getNodeType().startsWith("N")) {
+ return identifiedAnnotation.getCoveredText();
+ }
+ }
+
+ // because only nouns are expanded, look for covering NPs
+ if(treebankNode.getNodeType().equals("NP")) {
+ treebankNodeSizes.put(treebankNode, treebankNode.getCoveredText().length());
+ }
+ }
+
+ // find the shortest covering treebank node
+ List<TreebankNode> sortedTreebankNodes = new ArrayList<TreebankNode>(treebankNodeSizes.keySet());
+ Function<TreebankNode, Integer> getValue = Functions.forMap(treebankNodeSizes);
+ Collections.sort(sortedTreebankNodes, Ordering.natural().onResultOf(getValue));
+
+ if(sortedTreebankNodes.size() > 0) {
+ return sortedTreebankNodes.get(0).getCoveredText();
+ }
+
+ return identifiedAnnotation.getCoveredText();
+ }
+}