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Posted to commits@ctakes.apache.org by dl...@apache.org on 2013/04/02 22:20:19 UTC
svn commit: r1463737 - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis:
EventContextAnalysisConsumer.java EventContextAnalysisPipeline.java
Author: dligach
Date: Tue Apr 2 20:20:18 2013
New Revision: 1463737
URL: http://svn.apache.org/r1463737
Log:
print events and their contexts to a file fur further analysis
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisConsumer.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisConsumer.java?rev=1463737&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisConsumer.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisConsumer.java Tue Apr 2 20:20:18 2013
@@ -0,0 +1,106 @@
+/**
+ * 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.FileWriter;
+import java.io.IOException;
+
+import org.apache.ctakes.typesystem.type.syntax.WordToken;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.util.JCasUtil;
+
+/**
+ * Print all tokens with contexts and all events with contexts for farther analysis.
+ *
+ * @author dmitriy dligach
+ *
+ */
+public class EventContextAnalysisConsumer extends JCasAnnotator_ImplBase {
+
+ String tokenFile = "/home/dima/thyme/event-context/tokens.txt";
+ String eventFile = "/home/dima/thyme/event-context/events.txt";
+
+ @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);
+ }
+
+ try {
+ BufferedWriter tokenWriter = getWriter(tokenFile, true);
+ for(WordToken wordToken : JCasUtil.select(systemView, WordToken.class)) {
+ String tokenText = wordToken.getCoveredText().toLowerCase();
+ String output = String.format("%s|%s\n", tokenText, getAnnotationContext(wordToken, 40));
+ tokenWriter.write(output);
+ }
+
+ BufferedWriter eventWriter = getWriter(eventFile, true);
+ for(EventMention eventMention : JCasUtil.select(goldView, EventMention.class)) {
+ String eventText = eventMention.getCoveredText().toLowerCase();
+ String output = String.format("%s|%s\n", eventText, getAnnotationContext(eventMention, 40));
+ eventWriter.write(output);
+ }
+
+ tokenWriter.close();
+ eventWriter.close();
+
+ } catch (IOException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+ }
+
+ private static String getAnnotationContext(Annotation annotation, int maxContextWindowSize) {
+
+ String text = annotation.getCAS().getDocumentText();
+ int begin = Math.max(0, annotation.getBegin() - maxContextWindowSize);
+ int end = Math.min(text.length(), annotation.getEnd() + maxContextWindowSize);
+
+ return text.substring(begin, end).replaceAll("[\r\n]", " ");
+ }
+
+ private 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;
+ }
+}
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java?rev=1463737&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/EventContextAnalysisPipeline.java Tue Apr 2 20:20:18 2013
@@ -0,0 +1,81 @@
+/**
+ * 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.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.eval.XMIReader;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.collection.CollectionReader;
+import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.Option;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+
+/**
+ *
+ * @author dmitriy dligach
+ */
+public class EventContextAnalysisPipeline {
+
+ 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;
+ }
+
+ 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 relationExtractorConsumer = AnalysisEngineFactory.createPrimitive(
+ EventContextAnalysisConsumer.class);
+
+ SimplePipeline.runPipeline(collectionReader, relationExtractorConsumer);
+ }
+
+ private 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);
+ }
+}