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

Example 1 with ZlibCodec

use of loci.formats.codec.ZlibCodec 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 2 with ZlibCodec

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

the class CellomicsReader method getDecompressedStream.

private RandomAccessInputStream getDecompressedStream(String filename) throws FormatException, IOException {
    RandomAccessInputStream s = new RandomAccessInputStream(filename);
    if (checkSuffix(filename, "c01")) {
        LOGGER.info("Decompressing file");
        s.seek(4);
        ZlibCodec codec = new ZlibCodec();
        byte[] file = codec.decompress(s, null);
        s.close();
        return new RandomAccessInputStream(file);
    }
    return s;
}

Example 3 with ZlibCodec

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

the class NativeQTReader method parse.

// -- Helper methods --
/**
 * Parse all of the atoms in the file.
 */
private void parse(int depth, long offset, long length) throws FormatException, IOException {
    while (offset < length) {
        in.seek(offset);
        // first 4 bytes are the atom size
        long atomSize = in.readInt() & 0xffffffffL;
        // read the atom type
        String atomType = in.readString(4);
        // if atomSize is 1, then there is an 8 byte extended size
        if (atomSize == 1) {
            atomSize = in.readLong();
        }
        if (atomSize < 0) {
            LOGGER.warn("QTReader: invalid atom size: {}", atomSize);
        } else if (atomSize > in.length()) {
            offset += 4;
            continue;
        }
        LOGGER.debug("Seeking to {}; atomType={}; atomSize={}", new Object[] { offset, atomType, atomSize });
        // if this is a container atom, parse the children
        if (isContainer(atomType)) {
            parse(depth++, in.getFilePointer(), offset + atomSize);
        } else {
            if (atomSize == 0)
                atomSize = in.length();
            long oldpos = in.getFilePointer();
            if (atomType.equals("mdat")) {
                // we've found the pixel data
                pixelOffset = in.getFilePointer();
                pixelBytes = atomSize;
                if (pixelBytes > (in.length() - pixelOffset)) {
                    pixelBytes = in.length() - pixelOffset;
                }
            } else if (atomType.equals("tkhd")) {
                // we've found the dimensions
                in.skipBytes(38);
                int[][] matrix = new int[3][3];
                for (int i = 0; i < matrix.length; i++) {
                    for (int j = 0; j < matrix[0].length; j++) {
                        matrix[i][j] = in.readInt();
                    }
                }
                // The contents of the matrix we just read determine whether or not
                // we should flip the width and height.  We can check the first two
                // rows of the matrix - they should correspond to the first two rows
                // of an identity matrix.
                // TODO : adapt to use the value of flip
                flip = matrix[0][0] == 0 && matrix[1][0] != 0;
                if (getSizeX() == 0)
                    core.get(0).sizeX = in.readInt();
                if (getSizeY() == 0)
                    core.get(0).sizeY = in.readInt();
            } else if (atomType.equals("cmov")) {
                in.skipBytes(8);
                if ("zlib".equals(in.readString(4))) {
                    atomSize = in.readInt();
                    in.skipBytes(4);
                    int uncompressedSize = in.readInt();
                    byte[] b = new byte[(int) (atomSize - 12)];
                    in.read(b);
                    byte[] output = new ZlibCodec().decompress(b, null);
                    RandomAccessInputStream oldIn = in;
                    in = new RandomAccessInputStream(output);
                    parse(0, 0, output.length);
                    in.close();
                    in = oldIn;
                } else {
                    throw new UnsupportedCompressionException("Compressed header not supported.");
                }
            } else if (atomType.equals("stco")) {
                if (offsets.size() > 0)
                    break;
                separatedFork = false;
                in.skipBytes(4);
                int numPlanes = in.readInt();
                if (numPlanes != getImageCount()) {
                    in.seek(in.getFilePointer() - 4);
                    int off = in.readInt();
                    offsets.add(new Integer(off));
                    for (int i = 1; i < getImageCount(); i++) {
                        if ((chunkSizes.size() > 0) && (i < chunkSizes.size())) {
                            rawSize = chunkSizes.get(i).intValue();
                        } else
                            i = getImageCount();
                        off += rawSize;
                        offsets.add(new Integer(off));
                    }
                } else {
                    for (int i = 0; i < numPlanes; i++) {
                        offsets.add(new Integer(in.readInt()));
                    }
                }
            } else if (atomType.equals("stsd")) {
                // found video codec and pixel depth information
                in.skipBytes(4);
                int numEntries = in.readInt();
                in.skipBytes(4);
                for (int i = 0; i < numEntries; i++) {
                    if (i == 0) {
                        codec = in.readString(4);
                        if (!codec.equals("raw ") && !codec.equals("rle ") && !codec.equals("rpza") && !codec.equals("mjpb") && !codec.equals("jpeg")) {
                            throw new UnsupportedCompressionException("Unsupported codec: " + codec);
                        }
                        in.skipBytes(16);
                        if (in.readShort() == 0) {
                            in.skipBytes(56);
                            bitsPerPixel = in.readShort();
                            if (codec.equals("rpza"))
                                bitsPerPixel = 8;
                            in.skipBytes(10);
                            interlaced = in.read() == 2;
                            addGlobalMeta("Codec", codec);
                            addGlobalMeta("Bits per pixel", bitsPerPixel);
                            in.skipBytes(9);
                        }
                    } else {
                        altCodec = in.readString(4);
                        addGlobalMeta("Second codec", altCodec);
                    }
                }
            } else if (atomType.equals("stsz")) {
                // found the number of planes
                in.skipBytes(4);
                rawSize = in.readInt();
                core.get(0).imageCount = in.readInt();
                if (rawSize == 0) {
                    in.seek(in.getFilePointer() - 4);
                    for (int b = 0; b < getImageCount(); b++) {
                        chunkSizes.add(new Integer(in.readInt()));
                    }
                }
            } else if (atomType.equals("stsc")) {
                in.skipBytes(4);
                int numChunks = in.readInt();
                if (altCodec != null) {
                    int prevChunk = 0;
                    for (int i = 0; i < numChunks; i++) {
                        int chunk = in.readInt();
                        int planesPerChunk = in.readInt();
                        int id = in.readInt();
                        if (id == 2)
                            altPlanes += planesPerChunk * (chunk - prevChunk);
                        prevChunk = chunk;
                    }
                }
            } else if (atomType.equals("stts")) {
                in.skipBytes(12);
                int fps = in.readInt();
                addGlobalMeta("Frames per second", fps);
            }
            if (oldpos + atomSize < in.length()) {
                in.seek(oldpos + atomSize);
            } else
                break;
        }
        if (atomSize == 0)
            offset = in.length();
        else
            offset += atomSize;
        // if a 'udta' atom, skip ahead 4 bytes
        if (atomType.equals("udta"))
            offset += 4;
        print(depth, atomSize, atomType);
    }
}

Example 4 with ZlibCodec

use of loci.formats.codec.ZlibCodec 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 5 with ZlibCodec

use of loci.formats.codec.ZlibCodec 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;
}