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

Example 6 with IFD

use of loci.formats.tiff.IFD 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 IFD

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

the class NDPIReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see loci.formats.BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    ifds = tiffParser.getIFDs();
    // fix the offsets for > 4 GB files
    RandomAccessInputStream stream = new RandomAccessInputStream(currentId);
    for (int i = 0; i < ifds.size(); i++) {
        IFD ifd = ifds.get(i);
        long[] stripOffsets = ifd.getStripOffsets();
        boolean neededAdjustment = false;
        for (int j = 0; j < stripOffsets.length; j++) {
            long prevOffset = i == 0 ? 0 : ifds.get(i - 1).getStripOffsets()[0];
            long prevByteCount = i == 0 ? 0 : ifds.get(i - 1).getStripByteCounts()[0];
            long currentOffset = (int) stripOffsets[j];
            while (currentOffset < prevOffset || currentOffset < prevOffset + prevByteCount) {
                long newOffset = currentOffset + 0x100000000L;
                if (newOffset < stream.length() && ((j > 0 && (currentOffset < stripOffsets[j - 1])) || (i > 0 && currentOffset < prevOffset + prevByteCount))) {
                    stripOffsets[j] = newOffset;
                    currentOffset = stripOffsets[j];
                    neededAdjustment = true;
                }
            }
        }
        if (neededAdjustment) {
            ifd.putIFDValue(IFD.STRIP_OFFSETS, stripOffsets);
        }
        neededAdjustment = false;
        long[] stripByteCounts = ifd.getStripByteCounts();
        for (int j = 0; j < stripByteCounts.length; j++) {
            long currentCount = (int) stripByteCounts[j];
            long newByteCount = currentCount + 0x100000000L;
            if (currentCount < 0 || neededAdjustment || newByteCount + stripOffsets[j] < in.length()) {
                if (newByteCount < ifd.getImageWidth() * ifd.getImageLength()) {
                    stripByteCounts[j] = newByteCount;
                    neededAdjustment = true;
                }
            }
        }
        if (neededAdjustment) {
            ifd.putIFDValue(IFD.STRIP_BYTE_COUNTS, stripByteCounts);
        }
    }
    stream.close();
    for (int i = 1; i < ifds.size(); i++) {
        IFD ifd = ifds.get(i);
        if (ifd.getImageWidth() == ifds.get(0).getImageWidth() && ifd.getImageLength() == ifds.get(0).getImageLength()) {
            sizeZ++;
        } else if (sizeZ == 1) {
            boolean isPyramid;
            Object source_lens_value = ifd.getIFDValue(SOURCE_LENS);
            if (source_lens_value != null) {
                float source_lens = (Float) source_lens_value;
                // A value of -1 correspond to the macro image and a value of -2
                // correspond to the map image
                isPyramid = (source_lens != -1 && source_lens != -2);
            } else {
                // Assume the last IFD is the macro image
                isPyramid = i < ifds.size() - 1;
            }
            if (isPyramid)
                pyramidHeight++;
        }
    }
    // repopulate core metadata
    int seriesCount = pyramidHeight + (ifds.size() - pyramidHeight * sizeZ);
    for (int i = 0; i < ifds.size(); i++) {
        IFD ifd = ifds.get(i);
        ifd.remove(THUMB_TAG_2);
        ifds.set(i, ifd);
        TiffIFDEntry markerTag = (TiffIFDEntry) ifd.get(MARKER_TAG);
        if (markerTag != null) {
            if (markerTag.getValueOffset() > in.length()) {
                // can't rely upon the MARKER_TAG to be detected correctly
                ifds.get(i).remove(MARKER_TAG);
            } else {
                Object value = tiffParser.getIFDValue(markerTag);
                ifds.get(i).putIFDValue(MARKER_TAG, value);
            }
        }
        tiffParser.fillInIFD(ifds.get(i));
        int[] bpp = ifds.get(i).getBitsPerSample();
        for (int q = 0; q < bpp.length; q++) {
            if (bpp[q] < 8) {
                bpp[q] = 8;
            }
        }
        ifds.get(i).putIFDValue(IFD.BITS_PER_SAMPLE, bpp);
    }
    core.clear();
    for (int s = 0; s < seriesCount; s++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        if (s == 0) {
            ms.resolutionCount = pyramidHeight;
        }
    }
    for (int s = 0; s < core.size(); s++) {
        IFD ifd = ifds.get(getIFDIndex(s, 0));
        PhotoInterp p = ifd.getPhotometricInterpretation();
        int samples = ifd.getSamplesPerPixel();
        CoreMetadata ms = core.get(s);
        ms.rgb = samples > 1 || p == PhotoInterp.RGB;
        ms.sizeX = (int) ifd.getImageWidth();
        ms.sizeY = (int) ifd.getImageLength();
        ms.sizeZ = s < pyramidHeight ? sizeZ : 1;
        ms.sizeT = 1;
        ms.sizeC = ms.rgb ? samples : 1;
        ms.littleEndian = ifd.isLittleEndian();
        ms.indexed = p == PhotoInterp.RGB_PALETTE && (get8BitLookupTable() != null || get16BitLookupTable() != null);
        ms.imageCount = ms.sizeZ * ms.sizeT;
        ms.pixelType = ifd.getPixelType();
        ms.metadataComplete = true;
        ms.interleaved = ms.sizeX > MAX_SIZE && ms.sizeY > MAX_SIZE;
        ms.falseColor = false;
        ms.dimensionOrder = "XYCZT";
        ms.thumbnail = s != 0;
    }
    String metadataTag = ifds.get(0).getIFDStringValue(METADATA_TAG);
    if (metadataTag != null) {
        String[] entries = metadataTag.split("\n");
        for (String entry : entries) {
            int eq = entry.indexOf('=');
            if (eq < 0) {
                continue;
            }
            String key = entry.substring(0, eq).trim();
            String value = entry.substring(eq + 1).trim();
            addGlobalMeta(key, value);
            if (key.equals("Objective.Lens.Magnificant")) {
                // not a typo
                magnification = new Double(value);
            } else if (key.equals("NDP.S/N")) {
                serialNumber = value;
            } else if (key.equals("Product")) {
                instrumentModel = value;
            }
        }
    }
}

Example 8 with IFD

use of loci.formats.tiff.IFD 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 9 with IFD

use of loci.formats.tiff.IFD 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 10 with IFD

use of loci.formats.tiff.IFD 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();
                }
            }
        }
    }
}