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

Example 6 with TiffParser

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

the class NDPIReader 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 (x == 0 && y == 0 && w == 1 && h == 1) {
        return buf;
    } else if (getSizeX() <= MAX_SIZE || getSizeY() <= MAX_SIZE) {
        int ifdIndex = getIFDIndex(getCoreIndex(), no);
        in = new RandomAccessInputStream(currentId);
        tiffParser = new TiffParser(in);
        tiffParser.setUse64BitOffsets(true);
        tiffParser.setYCbCrCorrection(false);
        byte[] b = tiffParser.getSamples(ifds.get(ifdIndex), buf, x, y, w, h);
        in.close();
        tiffParser.getStream().close();
        return b;
    }
    if (initializedSeries != getCoreIndex() || initializedPlane != no) {
        IFD ifd = ifds.get(getIFDIndex(getCoreIndex(), no));
        long offset = ifd.getStripOffsets()[0];
        long byteCount = ifd.getStripByteCounts()[0];
        if (in != null) {
            in.close();
        }
        in = new RandomAccessInputStream(currentId);
        in.seek(offset);
        in.setLength(offset + byteCount);
        try {
            service.close();
            long[] markers = ifd.getIFDLongArray(MARKER_TAG);
            if (!use64Bit) {
                for (int i = 0; i < markers.length; i++) {
                    markers[i] = markers[i] & 0xffffffffL;
                }
            }
            if (markers != null) {
                service.setRestartMarkers(markers);
            }
            service.initialize(in, getSizeX(), getSizeY());
        } catch (ServiceException e) {
            throw new FormatException(e);
        }
        initializedSeries = getCoreIndex();
        initializedPlane = no;
    }
    service.getTile(buf, x, y, w, h);
    return buf;
}

Example 7 with TiffParser

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

the class NikonElementsTiffReader method isThisType.

// -- IFormatReader API methods --
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    if (ifd == null)
        return false;
    return ifd.containsKey(NIKON_XML_TAG);
}

Example 8 with TiffParser

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

the class NikonReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser tp = new TiffParser(stream);
    IFD ifd = tp.getFirstIFD();
    if (ifd == null)
        return false;
    if (ifd.containsKey(TIFF_EPS_STANDARD))
        return true;
    String make = ifd.getIFDTextValue(IFD.MAKE);
    return make != null && make.indexOf("Nikon") != -1;
}

Example 9 with TiffParser

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

the class NikonReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    // reset image dimensions
    // the actual image data is stored in IFDs referenced by the SubIFD tag
    // in the 'real' IFD
    CoreMetadata m = core.get(0);
    m.imageCount = ifds.size();
    IFD firstIFD = ifds.get(0);
    PhotoInterp photo = firstIFD.getPhotometricInterpretation();
    int samples = firstIFD.getSamplesPerPixel();
    m.rgb = samples > 1 || photo == PhotoInterp.RGB || photo == PhotoInterp.CFA_ARRAY;
    if (photo == PhotoInterp.CFA_ARRAY)
        samples = 3;
    m.sizeX = (int) firstIFD.getImageWidth();
    m.sizeY = (int) firstIFD.getImageLength();
    m.sizeZ = 1;
    m.sizeC = isRGB() ? samples : 1;
    m.sizeT = ifds.size();
    m.pixelType = firstIFD.getPixelType();
    m.indexed = false;
    // now look for the EXIF IFD pointer
    IFDList exifIFDs = tiffParser.getExifIFDs();
    if (exifIFDs.size() > 0) {
        IFD exifIFD = exifIFDs.get(0);
        tiffParser.fillInIFD(exifIFD);
        for (Integer key : exifIFD.keySet()) {
            int tag = key.intValue();
            String name = IFD.getIFDTagName(tag);
            if (tag == IFD.CFA_PATTERN) {
                byte[] cfa = (byte[]) exifIFD.get(key);
                int[] colorMap = new int[cfa.length];
                for (int i = 0; i < cfa.length; i++) colorMap[i] = (int) cfa[i];
                addGlobalMeta(name, colorMap);
                cfaPattern = colorMap;
            } else {
                addGlobalMeta(name, exifIFD.get(key));
                if (name.equals("MAKER_NOTE")) {
                    byte[] b = (byte[]) exifIFD.get(key);
                    int extra = new String(b, 0, 10, Constants.ENCODING).startsWith("Nikon") ? 10 : 0;
                    byte[] buf = new byte[b.length];
                    System.arraycopy(b, extra, buf, 0, buf.length - extra);
                    RandomAccessInputStream makerNote = new RandomAccessInputStream(buf);
                    TiffParser tp = new TiffParser(makerNote);
                    IFD note = null;
                    try {
                        note = tp.getFirstIFD();
                    } catch (Exception e) {
                        LOGGER.debug("Failed to parse first IFD", e);
                    }
                    if (note != null) {
                        for (Integer nextKey : note.keySet()) {
                            int nextTag = nextKey.intValue();
                            addGlobalMeta(name, note.get(nextKey));
                            if (nextTag == 150) {
                                b = (byte[]) note.get(nextKey);
                                RandomAccessInputStream s = new RandomAccessInputStream(b);
                                byte check1 = s.readByte();
                                byte check2 = s.readByte();
                                lossyCompression = check1 != 0x46;
                                vPredictor = new int[4];
                                for (int q = 0; q < vPredictor.length; q++) {
                                    vPredictor[q] = s.readShort();
                                }
                                curve = new int[16385];
                                int bps = ifds.get(0).getBitsPerSample()[0];
                                int max = 1 << bps & 0x7fff;
                                int step = 0;
                                int csize = s.readShort();
                                if (csize > 1) {
                                    step = max / (csize - 1);
                                }
                                if (check1 == 0x44 && check2 == 0x20 && step > 0) {
                                    for (int i = 0; i < csize; i++) {
                                        curve[i * step] = s.readShort();
                                    }
                                    for (int i = 0; i < max; i++) {
                                        int n = i % step;
                                        curve[i] = (curve[i - n] * (step - n) + curve[i - n + step] * n) / step;
                                    }
                                    s.seek(562);
                                    split = s.readShort();
                                } else {
                                    int maxValue = (int) Math.pow(2, bps) - 1;
                                    Arrays.fill(curve, maxValue);
                                    int nElements = (int) (s.length() - s.getFilePointer()) / 2;
                                    if (nElements < 100) {
                                        for (int i = 0; i < curve.length; i++) {
                                            curve[i] = (short) i;
                                        }
                                    } else {
                                        for (int q = 0; q < nElements; q++) {
                                            curve[q] = s.readShort();
                                        }
                                    }
                                }
                                s.close();
                            } else if (nextTag == WHITE_BALANCE_RGB_COEFFS) {
                                whiteBalance = (TiffRational[]) note.get(nextKey);
                            }
                        }
                    }
                    makerNote.close();
                }
            }
        }
    }
}

Example 10 with TiffParser

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

the class OperettaReader method isThisType.

/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
@Override
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
    TiffParser p = new TiffParser(stream);
    IFD ifd = p.getFirstIFD();
    if (ifd == null)
        return false;
    Object s = ifd.getIFDValue(XML_TAG);
    if (s == null)
        return false;
    String xml = s instanceof String[] ? ((String[]) s)[0] : s.toString();
    return xml.indexOf("Operetta") < 1024;
}