/**
* 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.utils;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.apache.ctakes.temporal.eval.CommandLine;
import org.apache.ctakes.temporal.eval.Evaluation_ImplBase;
import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.XMIReader;
import org.apache.ctakes.temporal.eval.THYMEData;
import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.ctakes.typesystem.type.textsem.TimeMention;
import org.apache.ctakes.utils.struct.CounterMap;
import org.apache.uima.UIMAException;
import org.apache.uima.collection.CollectionReader;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
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 RunCorpusDiagnostics {
static interface Options {
@Option(longName = "text")
public File getRawTextDirectory();
@Option(longName = "xmi")
public File getXMIDirectory();
@Option(longName = "patients")
public CommandLine.IntegerRanges getPatients();
@Option(longName = "treebank", defaultToNull=true)
public File getTreebankDirectory();
}
/**
* @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);
CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(getFilesFor(options.getRawTextDirectory(), trainItems));
AggregateBuilder aggregateBuilder = new AggregateBuilder();
aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
XMIReader.class,
XMIReader.PARAM_XMI_DIRECTORY,
options.getXMIDirectory()));
CounterMap<String> timeClassCounts = new CounterMap<String>();
JCasIterable casIter = new JCasIterable(reader, aggregateBuilder.createAggregate());
while(casIter.hasNext()){
JCas jcas = casIter.next();
JCas goldView = jcas.getView(Evaluation_ImplBase.GOLD_VIEW_NAME);
Collection<TemporalTextRelation> rels = JCasUtil.select(goldView, TemporalTextRelation.class);
for(BinaryTextRelation rel : rels){
Annotation arg1 = rel.getArg1().getArgument();
Annotation arg2 = rel.getArg2().getArgument();
String timeClass = null;
if(arg1 instanceof TimeMention && arg2 instanceof EventMention){
timeClass = ((TimeMention) arg1).getTimeClass();
}else if(arg1 instanceof EventMention && arg2 instanceof TimeMention){
timeClass = ((TimeMention) arg2).getTimeClass();
}
if(timeClass != null){
timeClassCounts.add(rel.getCategory()+"--"+timeClass);
}
// System.out.println("Found relation: " + rel.getCategory());
}
}
for(String key : timeClassCounts.keySet()){
System.out.println(key + " => " + timeClassCounts.get(key));
}
}
private static List<File> getFilesFor(File rawTextDirectory, List<Integer> patientSets) {
List<File> files = new ArrayList<File>();
for (Integer set : patientSets) {
File setTextDirectory = new File(rawTextDirectory, "doc" + set);
for (File file : setTextDirectory.listFiles()) {
// skip hidden files like .svn
if (!file.isHidden()) {
files.add(file);
}
}
}
return files;
}
}