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

Example 6 with ZlibCodec

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

the class OMEXMLReader 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 {
    if (binDataOffsets.size() == 0)
        return buf;
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    int index = no;
    int series = getSeries();
    for (int i = 0; i < series; i++) {
        index += core.get(i).imageCount;
    }
    if (index >= binDataOffsets.size()) {
        index = binDataOffsets.size() - 1;
    }
    long offset = binDataOffsets.get(index).longValue();
    String compress = compression.get(index);
    in.seek(offset);
    int depth = FormatTools.getBytesPerPixel(getPixelType());
    int planeSize = getSizeX() * getSizeY() * depth;
    CodecOptions options = new CodecOptions();
    options.width = getSizeX();
    options.height = getSizeY();
    options.bitsPerSample = depth * 8;
    options.channels = getRGBChannelCount();
    options.maxBytes = planeSize;
    options.littleEndian = isLittleEndian();
    options.interleaved = isInterleaved();
    String encoded = in.readString("<");
    encoded = encoded.trim();
    if (encoded.length() == 0 || encoded.equals("<")) {
        LOGGER.debug("No pixel data for plane #{}", no);
        return buf;
    }
    encoded = encoded.substring(0, encoded.length() - 1);
    byte[] pixels = BaseEncoding.base64().decode(encoded);
    // return a blank plane if no pixel data was stored
    if (pixels.length == 0) {
        LOGGER.debug("No pixel data for plane #{}", no);
        return buf;
    }
    // TODO: Create a method uncompress to handle all compression methods
    if (compress.equals("bzip2")) {
        byte[] tempPixels = pixels;
        pixels = new byte[tempPixels.length - 2];
        System.arraycopy(tempPixels, 2, pixels, 0, pixels.length);
        ByteArrayInputStream bais = new ByteArrayInputStream(pixels);
        CBZip2InputStream bzip = new CBZip2InputStream(bais);
        pixels = new byte[planeSize];
        bzip.read(pixels, 0, pixels.length);
        tempPixels = null;
        bais.close();
        bzip.close();
        bais = null;
        bzip = null;
    } else if (compress.equals("zlib")) {
        pixels = new ZlibCodec().decompress(pixels, options);
    } else if (compress.equals("J2K")) {
        pixels = new JPEG2000Codec().decompress(pixels, options);
    } else if (compress.equals("JPEG")) {
        pixels = new JPEGCodec().decompress(pixels, options);
    }
    for (int row = 0; row < h; row++) {
        int off = (row + y) * getSizeX() * depth + x * depth;
        System.arraycopy(pixels, off, buf, row * w * depth, w * depth);
    }
    pixels = null;
    return buf;
}

Example 7 with ZlibCodec

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

the class PhotoshopTiffReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    Object sourceData = ifds.get(0).getIFDValue(IMAGE_SOURCE_DATA);
    byte[] b = null;
    if (sourceData instanceof byte[]) {
        b = (byte[]) sourceData;
    } else if (sourceData instanceof TiffIFDEntry) {
        b = (byte[]) tiffParser.getIFDValue((TiffIFDEntry) sourceData);
    }
    if (b == null)
        return;
    tag = new RandomAccessInputStream(b);
    tag.order(isLittleEndian());
    String checkString = tag.readCString();
    String signature, type;
    int length;
    while (tag.getFilePointer() < tag.length() - 12 && tag.getFilePointer() > 0) {
        signature = tag.readString(4);
        type = tag.readString(4);
        length = tag.readInt();
        int skip = length % 4;
        if (skip != 0)
            skip = 4 - skip;
        if (type.equals("ryaL")) {
            int nLayers = (int) Math.abs(tag.readShort());
            compression = new int[nLayers];
            layerNames = new String[nLayers];
            channelOrder = new int[nLayers][];
            int[][] dataSize = new int[nLayers][];
            int offsetCount = 0;
            for (int layer = 0; layer < nLayers; layer++) {
                int top = tag.readInt();
                int left = tag.readInt();
                int bottom = tag.readInt();
                int right = tag.readInt();
                CoreMetadata layerCore = new CoreMetadata();
                layerCore = new CoreMetadata();
                layerCore.sizeX = right - left;
                layerCore.sizeY = bottom - top;
                layerCore.pixelType = getPixelType();
                layerCore.sizeC = tag.readShort();
                layerCore.sizeZ = 1;
                layerCore.sizeT = 1;
                layerCore.imageCount = 1;
                layerCore.rgb = isRGB();
                layerCore.interleaved = isInterleaved();
                layerCore.littleEndian = isLittleEndian();
                layerCore.dimensionOrder = getDimensionOrder();
                if (layerCore.sizeX == 0 || layerCore.sizeY == 0 || (layerCore.sizeC > 1 && !isRGB())) {
                    // Set size to 1
                    CoreMetadata ms0 = core.get(0);
                    core.clear();
                    core.add(ms0);
                    break;
                }
                offsetCount += layerCore.sizeC;
                channelOrder[layer] = new int[layerCore.sizeC];
                dataSize[layer] = new int[layerCore.sizeC];
                for (int c = 0; c < layerCore.sizeC; c++) {
                    int channelID = tag.readShort();
                    if (channelID < 0)
                        channelID = layerCore.sizeC - 1;
                    channelOrder[layer][channelID] = c;
                    dataSize[layer][c] = tag.readInt();
                }
                tag.skipBytes(12);
                int len = tag.readInt();
                long fp = tag.getFilePointer();
                int mask = tag.readInt();
                if (mask != 0)
                    tag.skipBytes(mask);
                int blending = tag.readInt();
                tag.skipBytes(blending);
                int nameLength = tag.read();
                int pad = nameLength % 4;
                if (pad != 0)
                    pad = 4 - pad;
                layerNames[layer] = tag.readString(nameLength + pad);
                layerNames[layer] = layerNames[layer].replaceAll("[^\\p{ASCII}]", "").trim();
                if (layerNames[layer].length() == nameLength + pad && !layerNames[layer].equalsIgnoreCase("Layer " + layer + "M")) {
                    addGlobalMetaList("Layer name", layerNames[layer]);
                    core.add(layerCore);
                }
                tag.skipBytes((int) (fp + len - tag.getFilePointer()));
            }
            nLayers = core.size() - 1;
            layerOffset = new long[offsetCount];
            int nextOffset = 0;
            for (int layer = 0; layer < nLayers; layer++) {
                for (int c = 0; c < core.get(layer + 1).sizeC; c++) {
                    long startFP = tag.getFilePointer();
                    compression[layer] = tag.readShort();
                    layerOffset[nextOffset] = tag.getFilePointer();
                    if (compression[layer] == ZIP) {
                        layerOffset[nextOffset] = tag.getFilePointer();
                        ZlibCodec codec = new ZlibCodec();
                        codec.decompress(tag, null);
                    } else if (compression[layer] == PACKBITS) {
                        if (layer == 0) {
                            tag.skipBytes(256 * 6 + 36);
                        } else
                            tag.skipBytes(192);
                        layerOffset[nextOffset] = tag.getFilePointer();
                        PackbitsCodec codec = new PackbitsCodec();
                        CodecOptions options = new CodecOptions();
                        options.maxBytes = core.get(layer + 1).sizeX * core.get(layer + 1).sizeY;
                        codec.decompress(tag, options);
                    }
                    tag.seek(startFP + dataSize[layer][c]);
                    nextOffset++;
                }
            }
        } else
            tag.skipBytes(length + skip);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setImageName("Merged", 0);
    if (layerNames != null) {
        int end = (int) Math.min(getSeriesCount() - 1, layerNames.length);
        for (int layer = 0; layer < end; layer++) {
            store.setImageName(layerNames[layer], layer + 1);
        }
    }
}