Ejemplo n.º 1
0
  /* @see loci.formats.FormatReader#initFile(String) */
  protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    reader = new ImageReader();

    reader.setMetadataOptions(getMetadataOptions());
    reader.setMetadataFiltered(isMetadataFiltered());
    reader.setOriginalMetadataPopulated(isOriginalMetadataPopulated());
    reader.setNormalized(isNormalized());
    reader.setMetadataStore(getMetadataStore());

    // NB: We need a raw handle on the ZIP data itself, not a ZipHandle.
    IRandomAccess rawHandle = Location.getHandle(id, false, false);
    in = new RandomAccessInputStream(rawHandle, id);

    ZipInputStream zip = new ZipInputStream(in);
    while (true) {
      ZipEntry ze = zip.getNextEntry();
      if (ze == null) break;
      ZipHandle handle = new ZipHandle(id, ze);
      Location.mapFile(ze.getName(), handle);
      mappedFiles.add(ze.getName());
    }

    ZipHandle base = new ZipHandle(id);
    reader.setId(base.getEntryName());

    metadataStore = reader.getMetadataStore();
    core = reader.getCoreMetadata();
    metadata = reader.getGlobalMetadata();

    base.close();
  }
Ejemplo n.º 2
0
  /**
   * Wrapper for bio-formats
   *
   * @param config - ImportConfit
   */
  public OMEROWrapper(ImportConfig config) {
    if (config == null) {
      throw new IllegalArgumentException(
          "An ImportConfig must be instantitated \n "
              + "in order to properly configure all readers.");
    }

    this.config = config;
    try {
      String readersPath = config.readersPath.get();
      // Since we now use all readers apart from the ZipReader, just
      // initialize in this manner which helps us by not requiring
      // us to keep up with all changes in readers.txt and removes
      // the requirement for importer_readers.txt (See #2859).
      // Chris Allan <*****@*****.**> -- Fri 10 Sep 2010 17:24:49 BST
      ClassList<IFormatReader> readers = ImageReader.getDefaultReaderClasses();
      readers.removeClass(ZipReader.class);
      if (readersPath != null) {
        Class<?> k = getClass();
        if (new File(readersPath).exists()) {
          k = null;
        }
        readers = new ClassList<IFormatReader>(readersPath, IFormatReader.class, k);
      }
      iReader = new ImageReader(readers);
      filler = new ChannelFiller(iReader);
    } catch (IOException e) {
      throw new RuntimeException("Unable to load readers.txt.");
    }
    reader = separator = new ChannelSeparator(filler);

    // Force unreadable characters to be removed from metadata key/value pairs
    iReader.setMetadataFiltered(true);
    filler.setMetadataFiltered(true);
    separator.setMetadataFiltered(true);
  };