Examples with TiffParser loci.formats.tiff.TiffParser used on opensource projects

Example 26 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class EPSReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    LOGGER.info("Verifying EPS format");
    String line = readLine();
    if (!line.trim().startsWith("%!PS")) {
        // read the TIFF preview
        isTiff = true;
        in.order(true);
        in.seek(20);
        int offset = in.readInt();
        int len = in.readInt();
        byte[] b = new byte[len];
        in.seek(offset);
        in.read(b);
        in = new RandomAccessInputStream(b);
        TiffParser tp = new TiffParser(in);
        ifds = tp.getIFDs();
        IFD firstIFD = ifds.get(0);
        map = tp.getColorMap(firstIFD);
        m.sizeX = (int) firstIFD.getImageWidth();
        m.sizeY = (int) firstIFD.getImageLength();
        m.sizeZ = 1;
        m.sizeT = 1;
        m.sizeC = firstIFD.getSamplesPerPixel();
        if (map != null && getSizeC() == 1) {
            m.sizeC = 3;
        }
        if (getSizeC() == 2)
            m.sizeC = 4;
        m.littleEndian = firstIFD.isLittleEndian();
        m.interleaved = true;
        m.rgb = getSizeC() > 1;
        m.pixelType = firstIFD.getPixelType();
        m.imageCount = 1;
        m.dimensionOrder = "XYCZT";
        m.metadataComplete = true;
        m.indexed = false;
        m.falseColor = false;
        MetadataStore store = makeFilterMetadata();
        MetadataTools.populatePixels(store, this);
        return;
    }
    LOGGER.info("Finding image data");
    binary = false;
    String image = "image";
    int lineNum = 1;
    line = readLine().trim();
    while (line != null && !line.equals("%%EOF")) {
        if (line.endsWith(image)) {
            if (!line.startsWith(image)) {
                if (line.indexOf("colorimage") != -1)
                    m.sizeC = 3;
                String[] t = line.split(" ");
                try {
                    int newX = Integer.parseInt(t[0]);
                    int newY = Integer.parseInt(t[1]);
                    if (t.length > 2 && Integer.parseInt(t[2]) >= 8) {
                        m.sizeX = newX;
                        m.sizeY = newY;
                        start = lineNum;
                    }
                } catch (NumberFormatException exc) {
                    LOGGER.debug("Could not parse image dimensions", exc);
                    if (t.length > 3) {
                        m.sizeC = Integer.parseInt(t[3]);
                    }
                }
            }
            break;
        } else if (line.startsWith("%%")) {
            if (line.startsWith("%%BoundingBox:")) {
                line = line.substring(14).trim();
                String[] t = line.split(" ");
                try {
                    int originX = Integer.parseInt(t[0].trim());
                    int originY = Integer.parseInt(t[1].trim());
                    m.sizeX = Integer.parseInt(t[2].trim()) - originX;
                    m.sizeY = Integer.parseInt(t[3].trim()) - originY;
                    addGlobalMeta("X-coordinate of origin", originX);
                    addGlobalMeta("Y-coordinate of origin", originY);
                } catch (NumberFormatException e) {
                    throw new FormatException("Files without image data are not supported.");
                }
            } else if (line.startsWith("%%BeginBinary")) {
                binary = true;
            } else {
                // parse key/value pairs
                int ndx = line.indexOf(':');
                if (ndx != -1) {
                    String key = line.substring(0, ndx);
                    String value = line.substring(ndx + 1);
                    addGlobalMeta(key, value);
                }
            }
        } else if (line.startsWith("%ImageData:")) {
            line = line.substring(11);
            String[] t = line.split(" ");
            m.sizeX = Integer.parseInt(t[0]);
            m.sizeY = Integer.parseInt(t[1]);
            m.sizeC = Integer.parseInt(t[3]);
            for (int i = 4; i < t.length; i++) {
                image = t[i].trim();
                if (image.length() > 1) {
                    image = image.substring(1, image.length() - 1);
                }
            }
        }
        lineNum++;
        line = readLine().trim();
    }
    LOGGER.info("Populating metadata");
    if (getSizeC() == 0)
        m.sizeC = 1;
    m.sizeZ = 1;
    m.sizeT = 1;
    m.dimensionOrder = "XYCZT";
    m.pixelType = FormatTools.UINT8;
    m.rgb = getSizeC() == 3;
    m.interleaved = true;
    m.littleEndian = true;
    m.imageCount = 1;
    // Populate metadata store
    // The metadata store we're working with.
    MetadataStore store = getMetadataStore();
    MetadataTools.populatePixels(store, this);
}

Example 27 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class ZeissLSMReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    final int blockLen = 4096;
    if (!FormatTools.validStream(stream, blockLen, false))
        return false;
    TiffParser parser = new TiffParser(stream);
    if (parser.isValidHeader()) {
        return parser.getIFDOffsets().length > 1;
    }
    stream.seek(4);
    if (stream.readShort() == 0x5374) {
        String check = stream.readString((int) (blockLen - stream.getFilePointer()));
        return check.indexOf("ID") > 0;
    }
    return false;
}

Example 28 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class ZeissLSMReader 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 (getSeriesCount() > 1) {
        in.close();
        in = new RandomAccessInputStream(getLSMFileFromSeries(getSeries()));
        in.order(!isLittleEndian());
        tiffParser = new TiffParser(in);
    } else if (tiffParser == null) {
        tiffParser = new TiffParser(in);
    }
    IFDList ifds = ifdsList.get(getSeries());
    if (splitPlanes && getSizeC() > 1 && ifds.size() == getSizeZ() * getSizeT()) {
        int bpp = FormatTools.getBytesPerPixel(getPixelType());
        int plane = no / getSizeC();
        int c = no % getSizeC();
        Region region = new Region(x, y, w, h);
        if (prevPlane != plane || prevBuf == null || prevBuf.length < w * h * bpp * getSizeC() || !region.equals(prevRegion)) {
            prevBuf = new byte[w * h * bpp * getSizeC()];
            tiffParser.getSamples(ifds.get(plane), prevBuf, x, y, w, h);
            prevPlane = plane;
            prevRegion = region;
        }
        ImageTools.splitChannels(prevBuf, buf, c, getSizeC(), bpp, false, false, w * h * bpp);
        prevChannel = c;
    } else {
        tiffParser.getSamples(ifds.get(no), buf, x, y, w, h);
        prevChannel = getZCTCoords(no)[1];
    }
    if (getSeriesCount() > 1)
        in.close();
    return buf;
}

Example 29 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class ZeissLSMReader method getExtraSeries.

private int getExtraSeries(String file) throws FormatException, IOException {
    if (in != null)
        in.close();
    in = new RandomAccessInputStream(file, 16);
    boolean littleEndian = in.read() == TiffConstants.LITTLE;
    in.order(littleEndian);
    tiffParser = new TiffParser(in);
    IFD ifd = tiffParser.getFirstIFD();
    RandomAccessInputStream ras = getCZTag(ifd);
    if (ras == null)
        return 1;
    ras.order(littleEndian);
    ras.seek(264);
    dimensionP = ras.readInt();
    dimensionM = ras.readInt();
    ras.close();
    int nSeries = dimensionM * dimensionP;
    return nSeries <= 0 ? 1 : nSeries;
}

Example 30 with TiffParser

use of loci.formats.tiff.TiffParser in project bioformats by openmicroscopy.

the class TCSReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    // check for Leica TCS IFD directory entries
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    if (ifd == null) {
        stream.seek(0);
        return stream.readString(6).equals("<Data>");
    }
    String document = ifd.getIFDTextValue(IFD.DOCUMENT_NAME);
    if (document == null)
        document = "";
    String software = ifd.getIFDTextValue(IFD.SOFTWARE);
    if (software == null)
        software = "";
    software = software.trim();
    return document.startsWith("CHANNEL") || software.startsWith("TCS");
}