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

Example 1 with JPEGCodec

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

the class NativeQTReader method uncompress.

/**
 * Uncompresses an image plane according to the the codec identifier.
 */
private byte[] uncompress(byte[] pixs, String code) throws FormatException, IOException {
    CodecOptions options = new MJPBCodecOptions();
    options.width = getSizeX();
    options.height = getSizeY();
    options.bitsPerSample = bitsPerPixel;
    options.channels = bitsPerPixel < 40 ? bitsPerPixel / 8 : (bitsPerPixel - 32) / 8;
    options.previousImage = canUsePrevious ? prevPixels : null;
    options.littleEndian = isLittleEndian();
    options.interleaved = isRGB();
    if (code.equals("raw "))
        return pixs;
    else if (code.equals("rle ")) {
        return new QTRLECodec().decompress(pixs, options);
    } else if (code.equals("rpza")) {
        return new RPZACodec().decompress(pixs, options);
    } else if (code.equals("mjpb")) {
        ((MJPBCodecOptions) options).interlaced = interlaced;
        return new MJPBCodec().decompress(pixs, options);
    } else if (code.equals("jpeg")) {
        return new JPEGCodec().decompress(pixs, options);
    } else {
        throw new UnsupportedCompressionException("Unsupported codec : " + code);
    }
}

Example 2 with JPEGCodec

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

the class OMEXMLWriter method compress.

// -- Helper methods --
/**
 * Compress the given byte array using the current codec.
 * The compressed data is then base64-encoded.
 */
private byte[] compress(byte[] b) throws FormatException, IOException {
    MetadataRetrieve r = getMetadataRetrieve();
    String type = r.getPixelsType(series).toString();
    int pixelType = FormatTools.pixelTypeFromString(type);
    int bytes = FormatTools.getBytesPerPixel(pixelType);
    CodecOptions options = new CodecOptions();
    options.width = r.getPixelsSizeX(series).getValue().intValue();
    options.height = r.getPixelsSizeY(series).getValue().intValue();
    options.channels = 1;
    options.interleaved = false;
    options.signed = FormatTools.isSigned(pixelType);
    boolean littleEndian = false;
    if (r.getPixelsBigEndian(series) != null) {
        littleEndian = !r.getPixelsBigEndian(series).booleanValue();
    } else if (r.getPixelsBinDataCount(series) == 0) {
        littleEndian = !r.getPixelsBinDataBigEndian(series, 0).booleanValue();
    }
    options.littleEndian = littleEndian;
    options.bitsPerSample = bytes * 8;
    if (compression.equals("J2K")) {
        b = new JPEG2000Codec().compress(b, options);
    } else if (compression.equals("JPEG")) {
        b = new JPEGCodec().compress(b, options);
    } else if (compression.equals("zlib")) {
        b = new ZlibCodec().compress(b, options);
    }
    return new Base64Codec().compress(b, options);
}

Example 3 with JPEGCodec

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

the class PictReader 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 (jpegOffsets.size() > 0) {
        ByteArrayHandle v = new ByteArrayHandle();
        in.seek(jpegOffsets.get(0));
        byte[] b = new byte[(int) (in.length() - in.getFilePointer())];
        in.read(b);
        RandomAccessInputStream s = new RandomAccessInputStream(b);
        for (long jpegOffset : jpegOffsets) {
            s.seek(jpegOffset - jpegOffsets.get(0));
            CodecOptions options = new CodecOptions();
            options.interleaved = isInterleaved();
            options.littleEndian = isLittleEndian();
            v.write(new JPEGCodec().decompress(s, options));
        }
        s.close();
        s = new RandomAccessInputStream(v);
        s.seek(0);
        readPlane(s, x, y, w, h, buf);
        s.close();
        return buf;
    }
    if (legacy || strips.size() == 0) {
        in.seek(512);
        byte[] pix = new byte[(int) (in.length() - in.getFilePointer())];
        in.read(pix);
        byte[][] b = AWTImageTools.getBytes(AWTImageTools.makeBuffered(qtTools.pictToImage(pix)));
        pix = null;
        for (int i = 0; i < b.length; i++) {
            System.arraycopy(b[i], 0, buf, i * b[i].length, b[i].length);
        }
        b = null;
        return buf;
    }
    if ((getSizeY() * 4 < strips.size()) && (((strips.size() / 3) % getSizeY()) != 0)) {
        core.get(0).sizeY = strips.size();
    }
    int plane = w * h;
    if (lookup != null) {
        // 8 bit data
        byte[] row;
        for (int i = y; i < y + h; i++) {
            row = (byte[]) strips.get(i);
            int len = (int) Math.min(row.length, w);
            System.arraycopy(row, x, buf, (i - y) * w, len);
        }
    } else if (getSizeY() * 3 == strips.size() || getSizeY() * 4 == strips.size()) {
        // 24 or 32 bit data
        int nc = strips.size() / getSizeY();
        byte[] c0 = null;
        byte[] c1 = null;
        byte[] c2 = null;
        for (int i = y; i < h + y; i++) {
            c0 = (byte[]) strips.get(i * nc + nc - 3);
            c1 = (byte[]) strips.get(i * nc + nc - 2);
            c2 = (byte[]) strips.get(i * nc + nc - 1);
            int baseOffset = (i - y) * w;
            System.arraycopy(c0, x, buf, baseOffset, w);
            System.arraycopy(c1, x, buf, plane + baseOffset, w);
            System.arraycopy(c2, x, buf, 2 * plane + baseOffset, w);
        }
    } else {
        // RGB value is packed into a single short: xRRR RRGG GGGB BBBB
        int[] row = null;
        for (int i = y; i < h + y; i++) {
            row = (int[]) strips.get(i);
            for (int j = x; j < w + x; j++) {
                int base = (i - y) * w + (j - x);
                buf[base] = (byte) ((row[j] & 0x7c00) >> 10);
                buf[plane + base] = (byte) ((row[j] & 0x3e0) >> 5);
                buf[2 * plane + base] = (byte) (row[j] & 0x1f);
            }
        }
    }
    return buf;
}

Example 4 with JPEGCodec

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

the class CellSensReader method decodeTile.

private byte[] decodeTile(int no, int row, int col) throws FormatException, IOException {
    if (tileMap.get(getCoreIndex()) == null) {
        return new byte[getTileSize()];
    }
    int[] zct = getZCTCoords(no);
    TileCoordinate t = new TileCoordinate(nDimensions.get(getCoreIndex()));
    t.coordinate[0] = col;
    t.coordinate[1] = row;
    int resIndex = getResolution();
    int pyramidIndex = getSeries();
    if (hasFlattenedResolutions()) {
        int index = 0;
        pyramidIndex = 0;
        for (int i = 0; i < core.size(); ) {
            if (index + core.get(i).resolutionCount <= getSeries()) {
                index += core.get(i).resolutionCount;
                i += core.get(i).resolutionCount;
                pyramidIndex++;
            } else {
                resIndex = getSeries() - index;
                break;
            }
        }
    }
    Pyramid pyramid = pyramids.get(pyramidIndex);
    for (String dim : pyramid.dimensionOrdering.keySet()) {
        int index = pyramid.dimensionOrdering.get(dim) + 2;
        if (dim.equals("Z")) {
            t.coordinate[index] = zct[0];
        } else if (dim.equals("C")) {
            t.coordinate[index] = zct[1];
        } else if (dim.equals("T")) {
            t.coordinate[index] = zct[2];
        }
    }
    if (resIndex > 0) {
        t.coordinate[t.coordinate.length - 1] = resIndex;
    }
    ArrayList<TileCoordinate> map = tileMap.get(getCoreIndex());
    Integer index = map.indexOf(t);
    if (index == null || index < 0) {
        // fill in the tile with the stored background color
        // usually this is either black or white
        byte[] tile = new byte[getTileSize()];
        byte[] color = backgroundColor.get(getCoreIndex());
        if (color != null) {
            for (int q = 0; q < getTileSize(); q += color.length) {
                for (int i = 0; i < color.length; i++) {
                    tile[q + i] = color[i];
                }
            }
        }
        return tile;
    }
    Long offset = tileOffsets.get(getCoreIndex())[index];
    RandomAccessInputStream ets = new RandomAccessInputStream(fileMap.get(getCoreIndex()));
    ets.seek(offset);
    CodecOptions options = new CodecOptions();
    options.interleaved = isInterleaved();
    options.littleEndian = isLittleEndian();
    int tileSize = getTileSize();
    if (tileSize == 0) {
        tileSize = tileX.get(getCoreIndex()) * tileY.get(getCoreIndex()) * 10;
    }
    options.maxBytes = (int) (offset + tileSize);
    byte[] buf = null;
    long end = index < tileOffsets.get(getCoreIndex()).length - 1 ? tileOffsets.get(getCoreIndex())[index + 1] : ets.length();
    IFormatReader reader = null;
    String file = null;
    switch(compressionType.get(getCoreIndex())) {
        case RAW:
            buf = new byte[tileSize];
            ets.read(buf);
            break;
        case JPEG:
            Codec codec = new JPEGCodec();
            buf = codec.decompress(ets, options);
            break;
        case JPEG_2000:
            codec = new JPEG2000Codec();
            buf = codec.decompress(ets, options);
            break;
        case JPEG_LOSSLESS:
            codec = new LosslessJPEGCodec();
            buf = codec.decompress(ets, options);
            break;
        case PNG:
            file = "tile.png";
            reader = new APNGReader();
        case BMP:
            if (reader == null) {
                file = "tile.bmp";
                reader = new BMPReader();
            }
            byte[] b = new byte[(int) (end - offset)];
            ets.read(b);
            Location.mapFile(file, new ByteArrayHandle(b));
            reader.setId(file);
            buf = reader.openBytes(0);
            Location.mapFile(file, null);
            break;
    }
    if (reader != null) {
        reader.close();
    }
    ets.close();
    return buf;
}

Example 5 with JPEGCodec

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

the class ZeissZVIReader 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);
    lastPlane = no;
    if (poi == null) {
        initPOIService();
    }
    int bytes = FormatTools.getBytesPerPixel(getPixelType());
    int pixel = bytes * getRGBChannelCount();
    CodecOptions options = new CodecOptions();
    options.littleEndian = isLittleEndian();
    options.interleaved = isInterleaved();
    int index = -1;
    int[] coords = getZCTCoords(no);
    for (int q = 0; q < coordinates.length; q++) {
        if (coordinates[q][0] == coords[0] && coordinates[q][1] == coords[1] && coordinates[q][2] == coords[2] && coordinates[q][3] == getSeries()) {
            index = q;
            break;
        }
    }
    LOGGER.trace("no = " + no + ", index = " + index);
    if (index < 0 || index >= imageFiles.length) {
        return buf;
    }
    RandomAccessInputStream s = poi.getDocumentStream(imageFiles[index]);
    s.seek(offsets[index]);
    int len = w * pixel;
    int row = getSizeX() * pixel;
    if (isJPEG) {
        byte[] t = new JPEGCodec().decompress(s, options);
        for (int yy = 0; yy < h; yy++) {
            System.arraycopy(t, (yy + y) * row + x * pixel, buf, yy * len, len);
        }
    } else if (isZlib) {
        byte[] t = new ZlibCodec().decompress(s, options);
        for (int yy = 0; yy < h; yy++) {
            int src = (yy + y) * row + x * pixel;
            int dest = yy * len;
            if (src + len <= t.length && dest + len <= buf.length) {
                System.arraycopy(t, src, buf, dest, len);
            } else
                break;
        }
    } else {
        readPlane(s, x, y, w, h, buf);
    }
    s.close();
    if (isRGB() && !isJPEG) {
        // reverse bytes in groups of 3 to account for BGR storage
        byte[] bb = new byte[bytes];
        for (int i = 0; i < buf.length; i += bpp) {
            System.arraycopy(buf, i + 2 * bytes, bb, 0, bytes);
            System.arraycopy(buf, i, buf, i + 2 * bytes, bytes);
            System.arraycopy(bb, 0, buf, i, bytes);
        }
    }
    return buf;
}