Examples with RandomAccessOutputStream loci.common.RandomAccessOutputStream used on opensource projects

Example 11 with RandomAccessOutputStream

use of loci.common.RandomAccessOutputStream in project bioformats by openmicroscopy.

the class TiffSaverTest method setUp.

@BeforeMethod
public void setUp() throws IOException {
    ByteArrayHandle handle = new ByteArrayHandle(INITIAL_CAPACITY);
    out = new RandomAccessOutputStream(handle);
    in = new RandomAccessInputStream(handle);
    tiffSaver = new TiffSaver(out, handle);
    tiffParser = new TiffParser(in);
    ifd = new IFD();
    ifd.putIFDValue(IFD.IMAGE_WIDTH, 512);
    ifd.putIFDValue(IFD.IMAGE_DESCRIPTION, "comment");
}

Example 12 with RandomAccessOutputStream

use of loci.common.RandomAccessOutputStream in project bioformats by openmicroscopy.

the class PGMReader 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);
    if (rawBits) {
        readPlane(in, x, y, w, h, buf);
    } else {
        ByteArrayHandle handle = new ByteArrayHandle();
        RandomAccessOutputStream out = new RandomAccessOutputStream(handle);
        out.order(isLittleEndian());
        while (in.getFilePointer() < in.length()) {
            String line = in.readLine().trim();
            line = line.replaceAll("[^0-9]", " ");
            StringTokenizer t = new StringTokenizer(line, " ");
            while (t.hasMoreTokens()) {
                int q = Integer.parseInt(t.nextToken().trim());
                if (getPixelType() == FormatTools.UINT16) {
                    out.writeShort(q);
                } else
                    out.writeByte(q);
            }
        }
        out.close();
        RandomAccessInputStream s = new RandomAccessInputStream(handle);
        s.seek(0);
        readPlane(s, x, y, w, h, buf);
        s.close();
    }
    return buf;
}

Example 13 with RandomAccessOutputStream

use of loci.common.RandomAccessOutputStream in project bioformats by openmicroscopy.

the class ICSWriter method saveBytes.

// -- IFormatWriter API methods --
/**
 * @see loci.formats.IFormatWriter#saveBytes(int, byte[], int, int, int, int)
 */
@Override
public void saveBytes(int no, byte[] buf, int x, int y, int w, int h) throws FormatException, IOException {
    checkParams(no, buf, x, y, w, h);
    if (pixels == null) {
        pixels = new RandomAccessOutputStream(currentId);
    }
    MetadataRetrieve meta = getMetadataRetrieve();
    int rgbChannels = getSamplesPerPixel();
    String order = meta.getPixelsDimensionOrder(series).getValue();
    int sizeZ = meta.getPixelsSizeZ(series).getValue().intValue();
    int sizeC = meta.getChannelCount(series);
    if (rgbChannels <= sizeC) {
        sizeC /= rgbChannels;
    }
    int sizeT = meta.getPixelsSizeT(series).getValue().intValue();
    int planes = sizeZ * sizeC * sizeT;
    int[] coords = FormatTools.getZCTCoords(order, sizeZ, sizeC, sizeT, planes, no);
    int realIndex = FormatTools.getIndex(outputOrder, sizeZ, sizeC, sizeT, planes, coords[0], coords[1], coords[2]);
    if (uniqueFiles.size() > 1) {
        realIndex = no;
    }
    int sizeX = meta.getPixelsSizeX(series).getValue().intValue();
    int sizeY = meta.getPixelsSizeY(series).getValue().intValue();
    int pixelType = FormatTools.pixelTypeFromString(meta.getPixelsType(series).toString());
    int bytesPerPixel = FormatTools.getBytesPerPixel(pixelType);
    long planeSize = sizeX * sizeY * rgbChannels * bytesPerPixel;
    if (!initialized[series][realIndex]) {
        initialized[series][realIndex] = true;
        if (!isFullPlane(x, y, w, h)) {
            // write a dummy plane that will be overwritten in sections
            pixels.seek(pixelOffset + (realIndex + 1) * planeSize);
        }
    }
    pixels.seek(pixelOffset + realIndex * planeSize);
    if (isFullPlane(x, y, w, h) && (interleaved || rgbChannels == 1)) {
        pixels.write(buf);
    } else {
        pixels.skipBytes(bytesPerPixel * rgbChannels * sizeX * y);
        for (int row = 0; row < h; row++) {
            ByteArrayOutputStream strip = new ByteArrayOutputStream();
            for (int col = 0; col < w; col++) {
                for (int c = 0; c < rgbChannels; c++) {
                    int index = interleaved ? rgbChannels * (row * w + col) + c : w * (c * h + row) + col;
                    strip.write(buf, index * bytesPerPixel, bytesPerPixel);
                }
            }
            pixels.skipBytes(bytesPerPixel * rgbChannels * x);
            pixels.write(strip.toByteArray());
            pixels.skipBytes(bytesPerPixel * rgbChannels * (sizeX - w - x));
        }
    }
    lastPlane = realIndex;
    overwriteDimensions(getMetadataRetrieve());
    pixels.close();
    pixels = null;
}

Example 14 with RandomAccessOutputStream

use of loci.common.RandomAccessOutputStream in project bioformats by openmicroscopy.

the class TiffSaver method writeIFD.

public void writeIFD(IFD ifd, long nextOffset) throws FormatException, IOException {
    TreeSet<Integer> keys = new TreeSet<Integer>(ifd.keySet());
    int keyCount = keys.size();
    if (ifd.containsKey(new Integer(IFD.LITTLE_ENDIAN)))
        keyCount--;
    if (ifd.containsKey(new Integer(IFD.BIG_TIFF)))
        keyCount--;
    if (ifd.containsKey(new Integer(IFD.REUSE)))
        keyCount--;
    long fp = out.getFilePointer();
    int bytesPerEntry = bigTiff ? TiffConstants.BIG_TIFF_BYTES_PER_ENTRY : TiffConstants.BYTES_PER_ENTRY;
    int ifdBytes = (bigTiff ? 16 : 6) + bytesPerEntry * keyCount;
    if (bigTiff)
        out.writeLong(keyCount);
    else
        out.writeShort(keyCount);
    ByteArrayHandle extra = new ByteArrayHandle();
    RandomAccessOutputStream extraStream = new RandomAccessOutputStream(extra);
    for (Integer key : keys) {
        if (key.equals(IFD.LITTLE_ENDIAN) || key.equals(IFD.BIG_TIFF) || key.equals(IFD.REUSE))
            continue;
        Object value = ifd.get(key);
        writeIFDValue(extraStream, ifdBytes + fp, key.intValue(), value);
    }
    if (bigTiff)
        out.seek(out.getFilePointer());
    writeIntValue(out, nextOffset);
    out.write(extra.getBytes(), 0, (int) extra.length());
    extraStream.close();
}

Example 15 with RandomAccessOutputStream

use of loci.common.RandomAccessOutputStream in project bioformats by openmicroscopy.

the class OMETiffWriter method saveComment.

private void saveComment(String file, String xml) throws IOException {
    if (out != null)
        out.close();
    out = new RandomAccessOutputStream(file);
    RandomAccessInputStream in = null;
    try {
        TiffSaver saver = new TiffSaver(out, file);
        saver.setBigTiff(isBigTiff);
        in = new RandomAccessInputStream(file);
        saver.overwriteLastIFDOffset(in);
        saver.overwriteComment(in, xml);
    } catch (FormatException exc) {
        IOException io = new IOException("Unable to append OME-XML comment");
        io.initCause(exc);
        throw io;
    } finally {
        if (out != null)
            out.close();
        if (in != null)
            in.close();
    }
}