Examples with IRandomAccess loci.common.IRandomAccess used on opensource projects

Example 6 with IRandomAccess

use of loci.common.IRandomAccess in project bioformats by openmicroscopy.

the class ZipReader method close.

/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
    super.close(fileOnly);
    if (reader != null)
        reader.close(fileOnly);
    if (!fileOnly)
        reader = null;
    for (String name : mappedFiles) {
        IRandomAccess handle = Location.getMappedFile(name);
        Location.mapFile(name, null);
        if (handle != null) {
            handle.close();
        }
    }
    mappedFiles.clear();
    entryName = null;
}

Example 7 with IRandomAccess

use of loci.common.IRandomAccess in project bioformats by openmicroscopy.

the class IM3Reader method openRaw.

/**
 * Open the current series in raw-mode, returning the
 * interleaved image bytes. The data format for a pixel is
 * a run of 63 unsigned short little endian values.
 *
 * @return a byte array containing the data organized by
 *         spectral channel, then x, then y. Returns null
 *         if, for some incomprehensible reason, the DATA
 *         block was missing.
 * @throws IOException
 */
public byte[] openRaw() throws IOException {
    IRandomAccess is = Location.getHandle(getCurrentFile(), false);
    try {
        is.setOrder(ByteOrder.LITTLE_ENDIAN);
        final ContainerRecord dataSet = dataSets.get(getSeries());
        for (IM3Record subRec : dataSet.parseChunks(is)) {
            if (subRec.name.equals(FIELD_DATA)) {
                is.seek(subRec.offset + 4);
                int width = is.readInt();
                int height = is.readInt();
                int channels = is.readInt();
                final byte[] result = new byte[width * height * channels * 2];
                is.read(result);
                return result;
            }
        }
    } finally {
        is.close();
    }
    return null;
}