/*
* 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 opennlp.tools.formats.brat;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import opennlp.tools.namefind.NameSample;
import opennlp.tools.sentdetect.SentenceDetector;
import opennlp.tools.sentdetect.SentenceDetectorME;
import opennlp.tools.sentdetect.SentenceModel;
import opennlp.tools.tokenize.Tokenizer;
import opennlp.tools.tokenize.TokenizerME;
import opennlp.tools.tokenize.TokenizerModel;
import opennlp.tools.util.ObjectStream;
import opennlp.tools.util.Span;
/**
* Generates Name Sample objects for a Brat Document object.
*/
public class BratNameSampleStream extends SegmenterObjectStream<BratDocument, NameSample> {
private SentenceDetector sentDetector;
private Tokenizer tokenizer;
protected BratNameSampleStream(SentenceDetector sentDetector,
Tokenizer tokenizer, ObjectStream<BratDocument> samples) {
super(samples);
this.sentDetector = sentDetector;
this.tokenizer = tokenizer;
}
protected BratNameSampleStream(SentenceModel sentModel, TokenizerModel tokenModel,
ObjectStream<BratDocument> samples) {
super(samples);
// TODO: We can pass in custom validators here ...
this.sentDetector = new SentenceDetectorME(sentModel);
this.tokenizer = new TokenizerME(tokenModel);
}
@Override
protected List<NameSample> read(BratDocument sample) throws IOException {
// Note: Some entities might not match sentence boundaries,
// to be able to print warning a set of entities id must be maintained
// to check if all entities have been used up after the matching is done
Set<String> entityIdSet = new HashSet<String>();
for (BratAnnotation ann : sample.getAnnotations()) {
if (ann instanceof SpanAnnotation) {
entityIdSet.add(ann.getId());
}
}
Span sentences[] = sentDetector.sentPosDetect(sample.getText());
// TODO: Sentence breaks should be avoided inside name annotations
// a) Merge two sentences, if an end/begin pair is part of a name annotation
// b) Implement a custom sentence validator which can be injected into the SD
// How could a custom validator be injected into an already instantiated sentence detector ?1
// Via a set method ...
// Via constructor ... probably best option, but a bit tricky to work with the SD interface then
//
// TODO: Token breaks should be enforced on name span boundaries
// a) Just split tokens
// b) Implement a custom token split validator which can be injected into the Tokenizer
// Currently we are missing all
List<NameSample> samples = new ArrayList<NameSample>(sentences.length);
for (Span sentence : sentences) {
String sentenceText = sentence.getCoveredText(
sample.getText()).toString();
Span tokens[] = tokenizer.tokenizePos(sentenceText);
// Note:
// A begin and end token index can be identical, but map to different
// tokens, to distinguish between between the two begin indexes are
// stored with a negative sign, and end indexes are stored with a positive sign
// in the tokenIndexMap.
// The tokenIndexMap maps to the sentence local token index.
Map<Integer, Integer> tokenIndexMap = new HashMap<Integer, Integer>();
for (int i = 0; i < tokens.length; i++) {
tokenIndexMap.put(-(sentence.getStart() + tokens[i].getStart()), i);
tokenIndexMap.put(sentence.getStart() + tokens[i].getEnd(), i + 1);
}
List<Span> names = new ArrayList<Span>();
for (BratAnnotation ann : sample.getAnnotations()) {
if (ann instanceof SpanAnnotation) {
SpanAnnotation entity = (SpanAnnotation) ann;
Span entitySpan = entity.getSpan();
if (sentence.contains(entitySpan)) {
entityIdSet.remove(ann.getId());
entitySpan = entitySpan.trim(sample.getText());
Integer nameBeginIndex = tokenIndexMap.get(-entitySpan.getStart());
Integer nameEndIndex = tokenIndexMap.get(entitySpan.getEnd());
if (nameBeginIndex != null && nameEndIndex != null) {
names.add(new Span(nameBeginIndex, nameEndIndex, entity.getType()));
}
else {
System.err.println("Dropped entity " + entity.getId() + " (" + entitySpan.getCoveredText(sample.getText()) + ") " + " in document " +
sample.getId() + ", it is not matching tokenization!");
}
}
}
}
samples.add(new NameSample(sample.getId(), Span.spansToStrings(tokens, sentenceText),
names.toArray(new Span[names.size()]), null, samples.size() == 0));
}
for (String id : entityIdSet) {
System.err.println("Dropped entity " + id + " in document " +
sample.getId() + ", is not matching sentence segmentation!");
}
return samples;
}
}