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

Example 1 with CodecOptions

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

the class NativeND2Reader 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);
    lastChannel = split ? no % getSizeC() : 0;
    int planeIndex = split ? no / getSizeC() : no;
    in.seek(offsets[getSeries()][planeIndex]);
    int bpp = FormatTools.getBytesPerPixel(getPixelType());
    int pixel = bpp * getRGBChannelCount();
    if (split)
        pixel *= getSizeC();
    int totalPlanes = split ? getImageCount() / getSizeC() : getImageCount();
    long maxFP = planeIndex == totalPlanes - 1 ? in.length() : offsets[getSeries()][planeIndex + 1];
    CodecOptions options = new CodecOptions();
    options.littleEndian = isLittleEndian();
    options.interleaved = isInterleaved();
    options.maxBytes = (int) maxFP;
    int scanlinePad = getScanlinePad();
    if (isJPEG || isLossless) {
        if (codec == null)
            codec = createCodec(isJPEG);
        byte[] t = null;
        try {
            t = codec.decompress(in, options);
        } catch (IOException e) {
            LOGGER.debug("Failed to decompress; plane may be corrupt", e);
            return buf;
        }
        if ((getSizeX() + scanlinePad) * getSizeY() * pixel > t.length) {
            // one padding pixel per row total, instead of one padding pixel
            // per channel per row
            int rowLength = getSizeX() * pixel + scanlinePad * bpp;
            int destLength = w * pixel;
            int p = rowLength * y + x * pixel;
            byte[] pix = new byte[destLength * h];
            for (int row = 0; row < h; row++) {
                if (p + destLength <= t.length) {
                    System.arraycopy(t, p, pix, row * destLength, destLength);
                    int skip = pixel * (getSizeX() - w - x) + scanlinePad * bpp;
                    p += destLength + skip;
                } else {
                    break;
                }
            }
            if (split) {
                pix = ImageTools.splitChannels(pix, lastChannel, getEffectiveSizeC(), bpp, false, true);
            }
            System.arraycopy(pix, 0, buf, 0, pix.length);
        } else {
            copyPixels(x, y, w, h, bpp, scanlinePad, t, buf, split);
        }
        t = null;
    } else if (split && (getSizeC() <= 4 || scanlinePad == 0) && nXFields == 1) {
        byte[] pix = new byte[(getSizeX() + scanlinePad) * getSizeY() * pixel];
        in.read(pix);
        copyPixels(x, y, w, h, bpp, scanlinePad, pix, buf, split);
        pix = null;
    } else if (split) {
        // one padding pixel per row total, instead of one padding pixel
        // per channel per row
        int rowLength = getSizeX() * pixel + scanlinePad * bpp;
        int destLength = w * pixel;
        in.skipBytes(rowLength * y);
        byte[] pix = new byte[destLength * h];
        for (int row = 0; row < h; row++) {
            in.skipBytes(x * pixel);
            in.read(pix, row * destLength, destLength);
            in.skipBytes(pixel * (getSizeX() - w - x) + scanlinePad * bpp);
        }
        pix = ImageTools.splitChannels(pix, lastChannel, getEffectiveSizeC(), bpp, false, true);
        System.arraycopy(pix, 0, buf, 0, pix.length);
    } else {
        // plane is not compressed
        readPlane(in, x, y, w, h, scanlinePad, buf);
    }
    return buf;
}

Example 2 with CodecOptions

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

the class PhotoshopTiffReader 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 (getSeries() == 0)
        return super.openBytes(no, buf, x, y, w, h);
    FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
    int offsetIndex = 0;
    for (int i = 1; i < getSeries(); i++) {
        offsetIndex += core.get(i).sizeC;
    }
    tag.seek(layerOffset[offsetIndex]);
    int bpp = FormatTools.getBytesPerPixel(getPixelType());
    if (compression[getSeries() - 1] == PACKBITS || compression[getSeries() - 1] == ZIP) {
        Codec codec = compression[getSeries() - 1] == ZIP ? new ZlibCodec() : new PackbitsCodec();
        CodecOptions options = new CodecOptions();
        options.maxBytes = FormatTools.getPlaneSize(this) / getSizeC();
        ByteArrayHandle pix = new ByteArrayHandle();
        for (int c = 0; c < getSizeC(); c++) {
            int index = channelOrder[getSeries() - 1][c];
            tag.seek(layerOffset[offsetIndex + index]);
            pix.write(codec.decompress(tag, options));
        }
        RandomAccessInputStream plane = new RandomAccessInputStream(pix);
        plane.seek(0);
        readPlane(plane, x, y, w, h, buf);
        plane.close();
        pix = null;
    } else
        readPlane(tag, x, y, w, h, buf);
    return buf;
}

Example 3 with CodecOptions

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

the class TargaReader 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);
    in.seek(offset);
    int planeSize = FormatTools.getPlaneSize(this);
    TargaRLECodec codec = new TargaRLECodec();
    CodecOptions options = new CodecOptions();
    options.maxBytes = planeSize;
    options.bitsPerSample = bits;
    RandomAccessInputStream s = in;
    if (compressed) {
        byte[] b = codec.decompress(in, options);
        s = new RandomAccessInputStream(b);
        s.order(isLittleEndian());
    }
    int bpp = bits;
    while (bpp % 8 != 0) bpp++;
    bpp /= 8;
    int rowSkip = orientation < 2 ? (getSizeY() - h - y) : y;
    int colSkip = (orientation % 2) == 1 ? (getSizeX() - w - x) : x;
    s.skipBytes(rowSkip * getSizeX() * bpp);
    for (int row = 0; row < h; row++) {
        if (s.getFilePointer() >= s.length())
            break;
        s.skipBytes(colSkip * bpp);
        for (int col = 0; col < w; col++) {
            if (s.getFilePointer() >= s.length())
                break;
            int rowIndex = orientation < 2 ? h - row - 1 : row;
            int colIndex = (orientation % 2) == 1 ? w - col - 1 : col;
            int index = getSizeC() * (rowIndex * w + colIndex);
            if (bpp == 2) {
                int v = s.readShort();
                buf[index] = (byte) ((v & 0x7c00) >> 10);
                buf[index + 1] = (byte) ((v & 0x3e0) >> 5);
                buf[index + 2] = (byte) (v & 0x1f);
            } else if (bpp == 4) {
                buf[index + 2] = s.readByte();
                buf[index + 1] = s.readByte();
                buf[index] = s.readByte();
                s.skipBytes(1);
            } else {
                for (int c = getSizeC() - 1; c >= 0; c--) {
                    buf[index + c] = s.readByte();
                }
            }
        }
        s.skipBytes(bpp * (getSizeX() - w - colSkip));
    }
    return buf;
}

Example 4 with CodecOptions

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

the class TiffCompressionCompressTest method testGROUP_4_FAX.

@Test(expectedExceptions = { FormatException.class })
public void testGROUP_4_FAX() throws FormatException, IOException {
    TiffCompression compression = TiffCompression.GROUP_3_FAX;
    CodecOptions options = compression.getCompressionCodecOptions(ifd);
    compression.compress(data, options);
}

Example 5 with CodecOptions

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

the class TiffCompressionCompressTest method testJPEG_2000_ResetNumberDecompositionLevel.

@Test(enabled = true)
public void testJPEG_2000_ResetNumberDecompositionLevel() throws FormatException, IOException {
    TiffCompression compression = TiffCompression.JPEG_2000;
    JPEG2000CodecOptions opt = JPEG2000CodecOptions.getDefaultOptions();
    int v = 16;
    opt.numDecompositionLevels = v;
    CodecOptions options = compression.getCompressionCodecOptions(ifd, opt);
    assertTrue(options instanceof JPEG2000CodecOptions);
    JPEG2000CodecOptions j2k = (JPEG2000CodecOptions) options;
    assertEquals(j2k.numDecompositionLevels, opt.numDecompositionLevels);
    compression = TiffCompression.JPEG_2000_LOSSY;
    options = compression.getCompressionCodecOptions(ifd, opt);
    assertTrue(options instanceof JPEG2000CodecOptions);
    j2k = (JPEG2000CodecOptions) options;
    assertEquals(j2k.numDecompositionLevels, opt.numDecompositionLevels);
    compression = TiffCompression.ALT_JPEG2000;
    options = compression.getCompressionCodecOptions(ifd, opt);
    j2k = (JPEG2000CodecOptions) options;
    assertEquals(j2k.numDecompositionLevels, opt.numDecompositionLevels);
}