/**
* 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.IOException;
import java.util.Collection;
import java.util.List;
import org.apache.ctakes.constituency.parser.util.TreeUtils;
import org.apache.ctakes.temporal.eval.CommandLine;
import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader;
import org.apache.ctakes.temporal.eval.THYMEData;
import org.apache.ctakes.typesystem.type.syntax.TreebankNode;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.jcas.JCas;
import org.cleartk.util.ae.UriToDocumentTextAnnotator;
import org.cleartk.util.cr.UriCollectionReader;
import org.uimafit.factory.AggregateBuilder;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.pipeline.JCasIterable;
import org.uimafit.util.JCasUtil;
import com.lexicalscope.jewel.cli.CliFactory;
import com.lexicalscope.jewel.cli.Option;
public class TimexTreeAlignmentStatistics {
static interface Options{
@Option(longName = "xmi")
public File getXMIDirectory();
@Option(longName = "patients")
public CommandLine.IntegerRanges getPatients();
@Option(longName = "text")
public File getRawTextDirectory();
}
/**
* @param args
* @throws IOException
* @throws UIMAException
*/
public static void main(String[] args) throws UIMAException, IOException {
Options options = CliFactory.parseArguments(Options.class, args);
List<Integer> patientSets = options.getPatients().getList();
List<Integer> trainItems = THYMEData.getTrainPatientSets(patientSets);
//List<Integer> devItems = THYMEData.getDevPatientSets(patientSets);
//List<Integer> testItems = THYMEData.getTestPatientSets(patientSets);
CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(THYMEData.getFilesFor(trainItems, options.getRawTextDirectory()));
AggregateBuilder aggregateBuilder = new AggregateBuilder();
aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
XMIReader.class,
XMIReader.PARAM_XMI_DIRECTORY,
options.getXMIDirectory()));
AnalysisEngine ae = aggregateBuilder.createAggregate();
int numMentions=0;
int numMatches=0;
for(JCas jCas : new JCasIterable(reader, ae)){
// String docId = DocumentIDAnnotationUtil.getDocumentID(jCas);
// String docId = jCas.
// System.out.println("Document: " + docId);
for(Segment segment : JCasUtil.select(jCas, Segment.class)){
if(THYMEData.SEGMENTS_TO_SKIP.contains(segment.getId())) continue;
Collection<TimeMention> mentions = JCasUtil.selectCovered(jCas.getView("GoldView"), TimeMention.class, segment);
for(TimeMention mention : mentions){
numMentions++;
boolean match = false;
List<TreebankNode> nodes = JCasUtil.selectCovered(jCas, TreebankNode.class, mention);
for(TreebankNode node : nodes){
if(node.getBegin() == mention.getBegin() && node.getEnd() == mention.getEnd()){
numMatches++;
match = true;
break;
}
}
if(!match){
List<TreebankNode> coveringNodes = JCasUtil.selectCovering(jCas, TreebankNode.class, mention.getBegin(), mention.getEnd());
TreebankNode smallestCoveringNode = null;
int smallestLen = Integer.MAX_VALUE;
for(TreebankNode node : coveringNodes){
int len = node.getEnd() - node.getBegin();
if(len < smallestLen){
smallestLen = len;
smallestCoveringNode = node;
}
}
System.out.println("No alignment for: " + mention.getCoveredText());
System.out.println(" Smallest covering treebank node is: " + (smallestCoveringNode == null ? "null" : smallestCoveringNode.getCoveredText()));
System.out.println(" " + (smallestCoveringNode == null ? "no tree" : TreeUtils.tree2str(smallestCoveringNode)));
}
}
}
}
System.out.printf("Found %d mentions, %d match with node spans\n", numMentions, numMatches);
}
}