/**
   * We assume that the initial indexing has been done and a set of reference objects has been found
   * and indexed in the separate directory. However further documents were added and they now need
   * to get a ranked list of reference objects. So we (i) get all these new documents missing the
   * field "ro-order" and (ii) add this field.
   *
   * @param indexPath the index to update
   * @throws IOException
   */
  public void updateIndex(String indexPath) throws IOException {
    IndexReader reader = DirectoryReader.open(FSDirectory.open(new File(indexPath)));
    int numDocs = reader.numDocs();
    boolean hasDeletions = reader.hasDeletions();
    int countUpdated = 0;

    IndexReader readerRo = DirectoryReader.open(FSDirectory.open(new File(indexPath + "-ro")));
    ImageSearcher searcher =
        new GenericImageSearcher(numReferenceObjectsUsed, featureClass, featureFieldName);
    Map<String, Analyzer> perField = new HashMap<String, Analyzer>(1);
    perField.put("ro-order", new WhitespaceAnalyzer(LuceneUtils.LUCENE_VERSION));
    PerFieldAnalyzerWrapper aWrapper =
        new PerFieldAnalyzerWrapper(new SimpleAnalyzer(LuceneUtils.LUCENE_VERSION), perField);

    IndexWriter iw =
        new IndexWriter(
            FSDirectory.open(new File(indexPath)),
            new IndexWriterConfig(LuceneUtils.LUCENE_VERSION, aWrapper)
                .setOpenMode(IndexWriterConfig.OpenMode.CREATE));
    StringBuilder sb = new StringBuilder(256);
    // Needed for check whether the document is deleted.
    Bits liveDocs = MultiFields.getLiveDocs(reader);

    for (int i = 0; i < numDocs; i++) {
      if (reader.hasDeletions() && !liveDocs.get(i)) continue; // if it is deleted, just ignore it.
      Document document = reader.document(i);
      if (document.getField("ro-order") == null) { // if the field is not here we create it.
        ImageSearchHits hits = searcher.search(document, readerRo);
        sb.delete(0, sb.length());
        for (int j = 0; j < numReferenceObjectsUsed; j++) {
          sb.append(hits.doc(j).getValues("ro-id")[0]);
          sb.append(' ');
        }
        // System.out.println(sb.toString());
        document.add(new TextField("ro-order", sb.toString(), Field.Store.YES));
        iw.updateDocument(
            new Term(
                DocumentBuilder.FIELD_NAME_IDENTIFIER,
                document.getValues(DocumentBuilder.FIELD_NAME_IDENTIFIER)[0]),
            document);
        countUpdated++;
      }

      // progress report
      progress.setNumDocsProcessed(progress.getNumDocsProcessed() + 1);

      // debug:
      System.out.println("countUpdated = " + countUpdated);
    }
    iw.commit();
    iw.close();
  }
  /**
   * Creates a set of reference objects and stores it in a new index (name "<indexPath>-ro"). Then
   * creates ordered lists of reference object positions for each data item in the index with given
   * feature. Finally a new index (name "<indexPath>-ms") is created where all the original
   * documents as well as the new data are stored.
   *
   * @param indexPath the path to the original index
   * @throws IOException
   */
  public void createIndex(String indexPath) throws IOException {
    IndexReader reader = DirectoryReader.open(FSDirectory.open(new File(indexPath)));
    int numDocs = reader.numDocs();

    if (numDocs < numReferenceObjects) {
      throw new UnsupportedOperationException("Too few documents in index.");
    }

    // progress report
    progress.setNumDocsAll(numDocs);
    progress.setCurrentState(State.RoSelection);

    boolean hasDeletions = reader.hasDeletions();

    // init reference objects:
    IndexWriter iw = LuceneUtils.createIndexWriter(indexPath + "-ro", true);
    HashSet<Integer> referenceObjsIds = new HashSet<Integer>(numReferenceObjects);

    double numDocsDouble = (double) numDocs;
    while (referenceObjsIds.size() < numReferenceObjects) {
      referenceObjsIds.add((int) (numDocsDouble * Math.random()));
    }
    int count = 0;

    if (hasDeletions) {
      System.err.println(
          "WARNING: There are deleted docs in your index. You should "
              + "optimize your index before using this method.");
    }

    // progress report
    progress.setCurrentState(State.RoIndexing);

    // find them in the index and put them into a separate index:
    for (int i : referenceObjsIds) {
      count++;
      Document document = reader.document(i);
      document.add(new Field("ro-id", count + "", StringField.TYPE_STORED));
      iw.addDocument(document);
    }
    iw.commit();
    iw.close();

    // progress report
    progress.setCurrentState(State.Indexing);

    // now find the reference objects for each entry ;)
    IndexReader readerRo = DirectoryReader.open(FSDirectory.open(new File(indexPath + "-ro")));
    ImageSearcher searcher =
        new GenericImageSearcher(numReferenceObjectsUsed, featureClass, featureFieldName);
    Map<String, Analyzer> analyzerPerField = new HashMap<String, Analyzer>();
    analyzerPerField.put("ro-order", new WhitespaceAnalyzer(LuceneUtils.LUCENE_VERSION));
    PerFieldAnalyzerWrapper aWrapper =
        new PerFieldAnalyzerWrapper(
            new SimpleAnalyzer(LuceneUtils.LUCENE_VERSION), analyzerPerField);

    iw =
        new IndexWriter(
            FSDirectory.open(new File(indexPath)),
            new IndexWriterConfig(LuceneUtils.LUCENE_VERSION, aWrapper)
                .setOpenMode(IndexWriterConfig.OpenMode.CREATE));
    StringBuilder sb = new StringBuilder(256);
    // Needed for check whether the document is deleted.
    Bits liveDocs = MultiFields.getLiveDocs(reader);

    for (int i = 0; i < numDocs; i++) {
      if (reader.hasDeletions() && !liveDocs.get(i)) continue; // if it is deleted, just ignore it.
      Document document = reader.document(i);
      ImageSearchHits hits = searcher.search(document, readerRo);
      sb.delete(0, sb.length());
      for (int j = 0; j < numReferenceObjectsUsed; j++) {
        sb.append(hits.doc(j).getValues("ro-id")[0]);
        sb.append(' ');
      }
      // System.out.println(sb.toString());
      document.add(new TextField("ro-order", sb.toString(), Field.Store.YES));
      iw.updateDocument(
          new Term(
              DocumentBuilder.FIELD_NAME_IDENTIFIER,
              document.getValues(DocumentBuilder.FIELD_NAME_IDENTIFIER)[0]),
          document);

      // progress report
      progress.setNumDocsProcessed(progress.getNumDocsProcessed() + 1);
    }
    iw.commit();
    iw.close();

    // progress report
    progress.setCurrentState(State.Idle);
  }