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Posted to commits@ctakes.apache.org by dl...@apache.org on 2013/04/30 16:31:54 UTC
svn commit: r1477662 - in
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis:
RelationContextAnalysisConsumer.java RelationContextAnalysisPipeline.java
Author: dligach
Date: Tue Apr 30 14:31:54 2013
New Revision: 1477662
URL: http://svn.apache.org/r1477662
Log:
code to print gold standard relations and their contexts
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisConsumer.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisPipeline.java
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisConsumer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisConsumer.java?rev=1477662&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisConsumer.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisConsumer.java Tue Apr 30 14:31:54 2013
@@ -0,0 +1,110 @@
+/**
+ * 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.relation.BinaryTextRelation;
+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.descriptor.ConfigurationParameter;
+import org.uimafit.util.JCasUtil;
+
+/**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ *
+ */
+public class RelationContextAnalysisConsumer extends JCasAnnotator_ImplBase {
+
+ @ConfigurationParameter(
+ name = "OutputFile",
+ mandatory = true,
+ description = "path to the file that stores relation data")
+ 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);
+ }
+
+ BufferedWriter writer = getWriter(outputFile, true);
+
+ for(BinaryTextRelation binaryTextRelation : JCasUtil.select(goldView, BinaryTextRelation.class)) {
+
+ Annotation arg1 = binaryTextRelation.getArg1().getArgument();
+ Annotation arg2 = binaryTextRelation.getArg2().getArgument();
+
+ String category = binaryTextRelation.getCategory();
+ String text = getTextBetweenAnnotations(systemView, arg1, arg2);
+ String output = String.format("%s|%s|%s|%s\n", category, arg1.getCoveredText(), arg2.getCoveredText(), text);
+
+ try {
+ writer.write(output);
+ } catch (IOException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+ }
+
+ try {
+ writer.close();
+ } catch (IOException e) {
+ throw new AnalysisEngineProcessException(e);
+ }
+ }
+
+ private static String getTextBetweenAnnotations(JCas jCas, Annotation arg1, Annotation arg2) {
+
+ int begin = Math.min(arg1.getBegin(), arg2.getBegin());
+ int end = Math.max(arg1.getEnd(), arg2.getEnd());
+
+ return jCas.getDocumentText().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/RelationContextAnalysisPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisPipeline.java?rev=1477662&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisPipeline.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/RelationContextAnalysisPipeline.java Tue Apr 30 14:31:54 2013
@@ -0,0 +1,90 @@
+/**
+ * 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;
+
+/**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+public class RelationContextAnalysisPipeline {
+
+ 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 = "--output-file",
+ usage = "specify the path to the directory containing the clinical notes to be processed",
+ required = true)
+ public File outputFile;
+ }
+
+ 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(
+ RelationContextAnalysisConsumer.class,
+ "OutputFile",
+ options.outputFile);
+
+ SimplePipeline.runPipeline(collectionReader, annotationConsumer);
+ }
+
+ 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);
+ }
+}