/**
* given an AgentID, find the text span associated with this Agent and highlight the appropriate
* areas in the raw text panel
*
* @param agentRef the AgentID
*/
public void highlightText(Annotation an, Color highlightTextColor) {
if (an != null) {
// highlight the annotation
// also define color to the highlight
tvPanel.highlightSpan(
an.getStartOffset(), an.getEndOffset() - an.getStartOffset(), highlightTextColor);
}
}
@Override
public void run(Document doc, String annSetNames[]) {
String tagChunk = currentConfig.getTagChunk();
String listDir = currentConfig.getTagChunkLists();
AnnotationSet namedEntities = new AnnotationSet(annSetNames[0]);
// get the sentences from the input
AnnotationSet sentSet = doc.getAnnotationSet(Constants.SENT);
// get the tokens from each sentence
AnnotationSet tokenSet = doc.getAnnotationSet(Constants.TOKEN);
// Read in the text from the raw file
String text = doc.getText();
Iterator<Annotation> sents = sentSet.iterator();
ArrayList<String> lines = new ArrayList<String>();
ArrayList<Vector<Annotation>> tokenList = new ArrayList<Vector<Annotation>>();
while (sents.hasNext()) {
Vector<Annotation> annVector = new Vector<Annotation>();
Annotation sent = sents.next();
int sentStart = sent.getStartOffset();
int sentEnd = sent.getEndOffset();
String sentText = Annotation.getAnnotText(sent, text);
AnnotationSet sentTokens = tokenSet.getContained(sentStart, sentEnd);
// gather all sentences to tag
if (!sentText.matches("\\W+")) {
StringBuilder tmp = new StringBuilder();
for (Annotation a : sentTokens) {
tmp.append(Annotation.getAnnotTextClean(a, text)).append(" ");
annVector.add(a);
}
lines.add(tmp.toString());
tokenList.add(annVector);
}
}
// write out a tmp file that contains the words to be tagged
File tmpFile = new File(doc.getRootDir(), "tmp.ner");
try {
tmpFile.deleteOnExit();
FileWriter fw = new FileWriter(tmpFile);
BufferedWriter bw = new BufferedWriter(fw);
for (String l : lines) {
// System.out.println(l);
bw.write(l + "\n");
}
bw.close();
fw.close();
} catch (IOException ioe) {
ioe.printStackTrace();
}
// run the tagger
String command =
tagChunk
+ " -predict . "
+ modelDir
+ Utils.SEPARATOR
+ models[0]
+ " "
+ tmpFile.getAbsolutePath()
+ " "
+ listDir;
// collect the results
ArrayList<String> results;
int i = 0;
try {
results = Utils.runExternalCaptureOutput(command);
Annotation current = null;
for (String l : results) {
Vector<Annotation> annVector = tokenList.get(i);
// get rid of these extraneous tags
l = l.replace("_O-O", "");
String[] tokens = l.split(" ");
// System.out.println(l);
int j = 0;
int underscore;
int nes = 1;
String tag;
for (String t : tokens) {
underscore = t.lastIndexOf('_');
tag = t.substring(underscore + 1, t.length());
Annotation a = annVector.get(j);
// System.out.print(Utils.getAnnotTextClean(a, text) + "_" + tag + " ");
if (tag.equals("B-O")) {
j++;
if (current != null) {
namedEntities.add(current);
// System.out.println("NE Found: " + Utils.getAnnotTextClean(current, text) + ":" +
// current.getType());
nes++;
current = null;
}
continue;
}
String entityType = tag.substring(tag.indexOf("-") + 1, tag.length());
if (entityType.equals("ORG")) {
entityType = "ORGANIZATION";
} else if (entityType.equals("LOC")) {
entityType = "LOCATION";
} else if (entityType.equals("PER")) {
entityType = "PERSON";
} else if (entityType.equals("VEH")) {
entityType = "VEHICLE";
}
if (tag.startsWith("B-")) {
if (current != null) {
namedEntities.add(current);
nes++;
current = null;
// System.out.println("NE Found: " + Utils.getAnnotTextClean(current, text));
}
current = new Annotation(nes, a.getStartOffset(), a.getEndOffset(), entityType);
} else if (tag.startsWith("I-")) {
if (current != null) {
current.setEndOffset(a.getEndOffset());
} else {
current = new Annotation(nes, a.getStartOffset(), a.getEndOffset(), entityType);
}
}
j++;
}
// System.out.println();
i++;
}
FileUtils.delete(tmpFile);
} catch (IOException e) {
throw new RuntimeException(e);
} catch (InterruptedException e) {
throw new RuntimeException(e);
}
addResultSet(doc, namedEntities);
}