Examples with JPEG2000Codec loci.formats.codec.JPEG2000Codec used on opensource projects

Example 6 with JPEG2000Codec

use of loci.formats.codec.JPEG2000Codec in project bioformats by openmicroscopy.

the class JPEG2000Writer method compressBuffer.

/**
 * Compresses the buffer.
 *
 * @param no the image index within the current file, starting from 0.
 * @param buf the byte array that represents the image tile.
 * @param x the X coordinate of the upper-left corner of the image tile.
 * @param y the Y coordinate of the upper-left corner of the image tile.
 * @param w the width (in pixels) of the image tile.
 * @param h the height (in pixels) of the image tile.
 * @throws FormatException if one of the parameters is invalid.
 * @throws IOException if there was a problem writing to the file.
 */
public byte[] compressBuffer(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    checkParams(no, buf, x, y, w, h);
    MetadataRetrieve retrieve = getMetadataRetrieve();
    boolean littleEndian = false;
    if (retrieve.getPixelsBigEndian(series) != null) {
        littleEndian = !retrieve.getPixelsBigEndian(series).booleanValue();
    } else if (retrieve.getPixelsBinDataCount(series) == 0) {
        littleEndian = !retrieve.getPixelsBinDataBigEndian(series, 0).booleanValue();
    }
    int bytesPerPixel = FormatTools.getBytesPerPixel(FormatTools.pixelTypeFromString(retrieve.getPixelsType(series).toString()));
    int nChannels = getSamplesPerPixel();
    // To be on the save-side
    if (options == null)
        options = JPEG2000CodecOptions.getDefaultOptions();
    options = new JPEG2000CodecOptions(options);
    options.width = w;
    options.height = h;
    options.channels = nChannels;
    options.bitsPerSample = bytesPerPixel * 8;
    options.littleEndian = littleEndian;
    options.interleaved = interleaved;
    options.lossless = compression == null || compression.equals(CompressionType.J2K.getCompression());
    options.colorModel = getColorModel();
    return new JPEG2000Codec().compress(buf, options);
}

Example 7 with JPEG2000Codec

use of loci.formats.codec.JPEG2000Codec in project bioformats by openmicroscopy.

the class JPXReader method openBytes.

/**
 * @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int)
 */
@Override
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    if (lastSeries == getSeries() && lastPlane == no && lastSeriesPlane != null) {
        RandomAccessInputStream s = new RandomAccessInputStream(lastSeriesPlane);
        readPlane(s, x, y, w, h, buf);
        s.close();
        return buf;
    }
    JPEG2000CodecOptions options = JPEG2000CodecOptions.getDefaultOptions();
    options.interleaved = isInterleaved();
    options.littleEndian = isLittleEndian();
    if (resolutionLevels != null) {
        options.resolution = Math.abs(getSeries() - resolutionLevels);
    } else if (getSeriesCount() > 1) {
        options.resolution = getSeries();
    }
    in.seek(pixelOffsets.get(no));
    lastSeriesPlane = new JPEG2000Codec().decompress(in, options);
    RandomAccessInputStream s = new RandomAccessInputStream(lastSeriesPlane);
    readPlane(s, x, y, w, h, buf);
    s.close();
    lastSeries = getSeries();
    lastPlane = no;
    return buf;
}