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

Example 41 with IFD

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

the class ExtractFlexMetadata method main.

public static void main(String[] args) throws Exception {
    File dir;
    if (args.length != 1 || !(dir = new File(args[0])).canRead()) {
        System.out.println("Usage: java ExtractFlexMetadata dir");
        return;
    }
    for (File file : dir.listFiles()) {
        if (file.getName().endsWith(".flex")) {
            String id = file.getPath();
            int dot = id.lastIndexOf(".");
            String outId = (dot >= 0 ? id.substring(0, dot) : id) + ".xml";
            RandomAccessInputStream in = new RandomAccessInputStream(id);
            TiffParser parser = new TiffParser(in);
            IFD firstIFD = parser.getIFDs().get(0);
            String xml = firstIFD.getIFDTextValue(FlexReader.FLEX);
            in.close();
            FileWriter writer = new FileWriter(new File(outId));
            writer.write(xml);
            writer.close();
            System.out.println("Writing header of: " + id);
        }
    }
    System.out.println("Done");
}

Example 42 with IFD

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

the class FV1000Reader 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);
    int nFiles = getSeries() == 0 ? tiffs.size() : previewNames.size();
    int image = no % (getImageCount() / nFiles);
    int file = no / (getImageCount() / nFiles);
    int[] coords = getZCTCoords(image);
    lastChannel = coords[1];
    RandomAccessInputStream plane = getPlane(getSeries(), no);
    if (plane == null)
        return buf;
    TiffParser tp = new TiffParser(plane);
    int index = getSeries() == 0 ? file : tiffs.size() + file;
    IFDList ifdList = ifds.get(index);
    if (image >= ifdList.size())
        return buf;
    IFD ifd = ifdList.get(image);
    if (getSizeY() != ifd.getImageLength()) {
        tp.getSamples(ifd, buf, x, getIndex(coords[0], 0, coords[2]), w, 1);
    } else
        tp.getSamples(ifd, buf, x, y, w, h);
    plane.close();
    plane = null;
    tp = null;
    return buf;
}

Example 43 with IFD

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

the class DNGReader 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;
    boolean hasEPSTag = ifd.containsKey(TIFF_EPS_STANDARD);
    if (!hasEPSTag) {
        hasEPSTag = ifd.containsKey(CANON_TAG);
    }
    String make = ifd.getIFDTextValue(IFD.MAKE);
    String model = ifd.getIFDTextValue(IFD.MODEL);
    String software = ifd.getIFDTextValue(IFD.SOFTWARE);
    return make != null && make.indexOf("Canon") != -1 && hasEPSTag && (model == null || !model.endsWith("S1 IS")) && (software == null || software.indexOf("Canon") != -1);
}

Example 44 with IFD

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

the class DNGReader 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 = FormatTools.UINT16;
    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 offset = DataTools.bytesToInt(b, b.length - 4, isLittleEndian());
                    byte[] buf = new byte[b.length + offset - 8];
                    System.arraycopy(b, b.length - 8, buf, 0, 8);
                    System.arraycopy(b, 0, buf, offset, b.length - 8);
                    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 == WHITE_BALANCE_RGB_COEFFS) {
                                if (note.get(nextTag) instanceof TiffRational[]) {
                                    TiffRational[] wb = (TiffRational[]) note.get(nextTag);
                                    whiteBalance = new double[wb.length];
                                    for (int i = 0; i < wb.length; i++) {
                                        whiteBalance[i] = wb[i].doubleValue();
                                    }
                                } else {
                                    // use a default white balance table
                                    whiteBalance = new double[3];
                                    whiteBalance[0] = 2.391381;
                                    whiteBalance[1] = 0.929156;
                                    whiteBalance[2] = 1.298254;
                                }
                            }
                        }
                    }
                    makerNote.close();
                }
            }
        }
    }
}

Example 45 with IFD

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

the class APLReader 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 (parser == null) {
        parser = new TiffParser[getSeriesCount()];
    }
    if (parser[getSeries()] == null) {
        parser[getSeries()] = new TiffParser(tiffFiles[getSeries()]);
        parser[getSeries()].setDoCaching(false);
    }
    IFD ifd = ifds[getSeries()].get(no);
    return parser[getSeries()].getSamples(ifd, buf, x, y, w, h);
}