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

Example 16 with ByteArrayHandle

use of loci.common.ByteArrayHandle 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 17 with ByteArrayHandle

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

the class SixteenBitLosslessJPEG2000Test method testLosslessPixels.

@Test
public void testLosslessPixels() throws Exception {
    int failureCount = 0;
    for (int v = Short.MIN_VALUE; v < Short.MAX_VALUE; v += increment) {
        int index = v + Short.MAX_VALUE + 1;
        byte[] pixels = DataTools.shortToBytes((short) v, false);
        String file = index + ".jp2";
        ByteArrayHandle tmpFile = new ByteArrayHandle(1);
        Location.mapFile(file, tmpFile);
        IMetadata metadata16;
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            metadata16 = service.createOMEXMLMetadata();
        } catch (DependencyException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        } catch (ServiceException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        }
        MetadataTools.populateMetadata(metadata16, 0, "foo", false, "XYCZT", "uint16", 1, 1, 1, 1, 1, 1);
        IFormatWriter writer16 = new JPEG2000Writer();
        writer16.setMetadataRetrieve(metadata16);
        writer16.setId(file);
        writer16.saveBytes(0, pixels);
        writer16.close();
        byte[] buf = tmpFile.getBytes();
        byte[] realData = new byte[(int) tmpFile.length()];
        System.arraycopy(buf, 0, realData, 0, realData.length);
        tmpFile.close();
        tmpFile = new ByteArrayHandle(realData);
        Location.mapFile(file, tmpFile);
        ImageReader reader = new ImageReader();
        reader.setId(file);
        byte[] plane = reader.openBytes(0);
        for (int q = 0; q < plane.length; q++) {
            if (plane[q] != pixels[q]) {
                LOGGER.debug("FAILED on {}", DataTools.bytesToShort(pixels, false));
                failureCount++;
                break;
            }
        }
        reader.close();
        tmpFile.close();
        Location.mapFile(file, null);
    }
    assertEquals(failureCount, 0);
}

Example 18 with ByteArrayHandle

use of loci.common.ByteArrayHandle 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 19 with ByteArrayHandle

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

the class ZeissCZIReader method readAttachments.

private void readAttachments() throws FormatException, IOException {
    if (!canReadAttachments()) {
        return;
    }
    boolean foundLabel = false;
    boolean foundPreview = false;
    for (Segment segment : segments) {
        if (segment instanceof Attachment) {
            AttachmentEntry entry = ((Attachment) segment).attachment;
            String name = entry.name.trim();
            if ((name.equals("Label") && !foundLabel) || (name.equals("SlidePreview") && !foundPreview)) {
                if (!foundLabel) {
                    foundLabel = name.equals("Label");
                }
                if (!foundPreview) {
                    foundPreview = name.equals("SlidePreview");
                }
                segment.fillInData();
                // label and preview are CZI files embedded as attachments
                ZeissCZIReader thumbReader = new ZeissCZIReader();
                thumbReader.setMetadataOptions(getMetadataOptions());
                ByteArrayHandle stream = new ByteArrayHandle(((Attachment) segment).attachmentData);
                Location.mapFile("image.czi", stream);
                thumbReader.setId("image.czi");
                CoreMetadata c = thumbReader.getCoreMetadataList().get(0);
                if (c.sizeZ > 1 || c.sizeT > 1) {
                    continue;
                }
                core.add(new CoreMetadata(c));
                core.get(core.size() - 1).thumbnail = true;
                ((Attachment) segment).attachmentData = thumbReader.openBytes(0);
                thumbReader.close();
                stream.close();
                Location.mapFile("image.czi", null);
                extraImages.add((Attachment) segment);
            }
        }
        segment.close();
    }
}

Example 20 with ByteArrayHandle

use of loci.common.ByteArrayHandle 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;
}