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 2015/02/24 18:10:47 UTC
svn commit: r1662028 - in
/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis:
./ GoldRelationViewer.java Utils.java
Author: dligach
Date: Tue Feb 24 17:10:47 2015
New Revision: 1662028
URL: http://svn.apache.org/r1662028
Log:
code to view relations in SHARP gold standard
Added:
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/GoldRelationViewer.java (with props)
ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/Utils.java (with props)
Added: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/GoldRelationViewer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/GoldRelationViewer.java?rev=1662028&view=auto
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/GoldRelationViewer.java (added)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/GoldRelationViewer.java Tue Feb 24 17:10:47 2015
@@ -0,0 +1,129 @@
+/**
+ * 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.relationextractor.data.analysis;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+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.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.cleartk.util.ViewUriUtil;
+
+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();
+ }
+
+ public static void main(String[] args) throws Exception {
+
+ Options options = CliFactory.parseArguments(Options.class, args);
+ CollectionReader collectionReader = Utils.getCollectionReader(options.getInputDirectory());
+ AnalysisEngine annotationConsumer = AnalysisEngineFactory.createEngine(RelationContextPrinter.class);
+ SimplePipeline.runPipeline(collectionReader, annotationConsumer);
+ }
+
+ /**
+ * 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);
+ }
+
+ File noteFile = new File(ViewUriUtil.getURI(jCas).toString());
+ String fileName = noteFile.getName();
+
+ for(Sentence sentence : JCasUtil.select(systemView, Sentence.class)) {
+ List<String> formattedRelationsInSentence = new ArrayList<>();
+ List<Annotation> annotationsInSentence = JCasUtil.selectCovered(goldView, Annotation.class, sentence);
+ for(Annotation annot1 : annotationsInSentence) {
+ for(Annotation annot2 : annotationsInSentence) {
+ if(annot1 == annot2) {
+ continue;
+ }
+ BinaryTextRelation relation = relationLookup.get(Arrays.asList(annot1, annot2));
+ if(relation != null) {
+ System.out.println(relation.getCategory());
+ String text = String.format("%s(%s, %s)", relation.getCategory(), annot1.getCoveredText(), annot2.getCoveredText());
+ formattedRelationsInSentence.add(text);
+ }
+ }
+ }
+
+ if(formattedRelationsInSentence.size() > 0) {
+ System.out.println(fileName + ": " + sentence.getCoveredText());
+ for(String text : formattedRelationsInSentence) {
+ System.out.println(text);
+ }
+ System.out.println();
+ }
+ }
+ }
+ }
+}
Propchange: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/GoldRelationViewer.java
------------------------------------------------------------------------------
svn:mime-type = text/plain
Added: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/Utils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/Utils.java?rev=1662028&view=auto
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/Utils.java (added)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/Utils.java Tue Feb 24 17:10:47 2015
@@ -0,0 +1,54 @@
+/**
+ * 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.relationextractor.data.analysis;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.ctakes.core.cr.XMIReader;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+
+/**
+ * Various useful classes and methods.
+ */
+public class Utils {
+
+ /**
+ * Instantiate an XMI collection reader.
+ */
+ public static CollectionReader getCollectionReader(File inputDirectory) throws Exception {
+
+ List<String> fileNames = new ArrayList<>();
+ for(File file : inputDirectory.listFiles()) {
+ if(! (file.isHidden())) {
+ fileNames.add(file.getPath());
+ }
+ }
+
+ String[] paths = new String[fileNames.size()];
+ fileNames.toArray(paths);
+
+ return CollectionReaderFactory.createReader(
+ XMIReader.class,
+ XMIReader.PARAM_FILES,
+ paths);
+ }
+}
Propchange: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/data/analysis/Utils.java
------------------------------------------------------------------------------
svn:mime-type = text/plain