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Posted to commits@ctakes.apache.org by dl...@apache.org on 2014/04/15 23:04:19 UTC
svn commit: r1587731 -
/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java
Author: dligach
Date: Tue Apr 15 21:04:19 2014
New Revision: 1587731
URL: http://svn.apache.org/r1587731
Log:
Print a sentence and all gold relations that are annotated in it.
Added:
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java (with props)
Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java?rev=1587731&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java Tue Apr 15 21:04:19 2014
@@ -0,0 +1,192 @@
+/**
+ * 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.io.FilenameFilter;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.core.cr.XMIReader;
+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.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.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+public class GoldRelationViewer {
+
+ static interface Options {
+
+ @Option(longName = "xmi-dir")
+ public File getInputDirectory();
+
+ @Option(longName = "patients")
+ public CommandLine.IntegerRanges getPatients();
+ }
+
+ public static void main(String[] args) throws Exception {
+
+ Options options = CliFactory.parseArguments(Options.class, args);
+
+ List<Integer> patientSets = options.getPatients().getList();
+ List<Integer> trainItems = THYMEData.getTrainPatientSets(patientSets);
+ List<File> trainFiles = getFilesFor(trainItems, options.getInputDirectory());
+ CollectionReader collectionReader = getCollectionReader(trainFiles);
+
+ AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+ RelationContextPrinter.class);
+
+ SimplePipeline.runPipeline(collectionReader, annotationConsumer);
+ }
+
+ private static CollectionReader getCollectionReader(List<File> inputFiles) throws Exception {
+
+ List<String> fileNames = new ArrayList<>();
+ 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);
+ }
+
+ private static List<File> getFilesFor(List<Integer> patientSets, File inputDirectory) {
+
+ List<File> files = new ArrayList<>();
+
+ for (Integer set : patientSets) {
+ final int setNum = set;
+ for (File file : inputDirectory.listFiles(new FilenameFilter(){
+ @Override
+ public boolean accept(File dir, String name) {
+ return name.contains(String.format("ID%03d", setNum));
+ }})) {
+ // skip hidden files like .svn
+ if (!file.isHidden()) {
+ files.add(file);
+ }
+ }
+ }
+
+ return files;
+ }
+
+ /**
+ * Print gold standard relations and their context.
+ *
+ * @author dmitriy dligach
+ */
+ public static class RelationContextPrinter extends JCasAnnotator_ImplBase {
+
+ @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 from pair of annotations to binary text relation
+ Map<List<Annotation>, BinaryTextRelation> relationLookup = new HashMap<>();
+ for(BinaryTextRelation relation : JCasUtil.select(goldView, BinaryTextRelation.class)) {
+ Annotation arg1 = relation.getArg1().getArgument();
+ Annotation arg2 = relation.getArg2().getArgument();
+ relationLookup.put(Arrays.asList(arg1, arg2), relation);
+ }
+
+ for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {
+ List<String> formattedRelationsInSentence = new ArrayList<>();
+ List<EventMention> eventMentions = JCasUtil.selectCovered(goldView, EventMention.class, sentence);
+ for(EventMention mention1 : eventMentions) {
+ for(EventMention mention2 : eventMentions) {
+ if(mention1 == mention2) {
+ continue;
+ }
+ BinaryTextRelation relation = relationLookup.get(Arrays.asList(mention1, mention2));
+ if(relation != null) {
+ String text = String.format("%s(%s, %s)", relation.getCategory(), mention1.getCoveredText(), mention2.getCoveredText());
+ formattedRelationsInSentence.add(text);
+ }
+ }
+ }
+ if(formattedRelationsInSentence.size() > 0) {
+ System.out.println(sentence.getCoveredText());
+ for(String text : formattedRelationsInSentence) {
+ System.out.println(text);
+ }
+ System.out.println();
+ }
+ }
+ }
+
+ @SuppressWarnings("unused")
+ private static String getTextBetweenAnnotations(JCas jCas, Annotation arg1, Annotation arg2) {
+
+ final int windowSize = 15;
+
+ String text = jCas.getDocumentText();
+ int leftArgBegin = Math.min(arg1.getBegin(), arg2.getBegin());
+ int rightArgEnd = Math.max(arg1.getEnd(), arg2.getEnd());
+ int begin = Math.max(0, leftArgBegin - windowSize);
+ int end = Math.min(text.length(), rightArgEnd + windowSize);
+
+ return text.substring(begin, end).replaceAll("[\r\n]", " ");
+ }
+ }
+}
Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/GoldRelationViewer.java
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