Examples with MetadataStore loci.formats.meta.MetadataStore used on opensource projects

Example 91 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class LegacyQTReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    LOGGER.info("Checking for QuickTime Java");
    if (tools == null) {
        tools = new LegacyQTTools();
        r = tools.getUniverse();
    }
    tools.checkQTLibrary();
    super.initFile(id);
    LOGGER.info("Reading movie dimensions");
    try {
        r.exec("QTSession.open()");
        // open movie file
        Location file = new Location(id);
        r.setVar("path", file.getAbsolutePath());
        r.exec("qtf = new QTFile(path)");
        r.exec("openMovieFile = OpenMovieFile.asRead(qtf)");
        r.exec("m = Movie.fromFile(openMovieFile)");
        int numTracks = ((Integer) r.exec("m.getTrackCount()")).intValue();
        int trackMostLikely = 0;
        int trackNum = 0;
        while (++trackNum <= numTracks && trackMostLikely == 0) {
            r.setVar("trackNum", trackNum);
            r.exec("imageTrack = m.getTrack(trackNum)");
            r.exec("d = imageTrack.getSize()");
            Integer w = (Integer) r.exec("d.getWidth()");
            if (w.intValue() > 0)
                trackMostLikely = trackNum;
        }
        r.setVar("trackMostLikely", trackMostLikely);
        r.exec("imageTrack = m.getTrack(trackMostLikely)");
        r.exec("d = imageTrack.getSize()");
        Integer w = (Integer) r.exec("d.getWidth()");
        Integer h = (Integer) r.exec("d.getHeight()");
        r.exec("moviePlayer = new MoviePlayer(m)");
        r.setVar("dim", new Dimension(w.intValue(), h.intValue()));
        ImageProducer qtip = (ImageProducer) r.exec("qtip = new QTImageProducer(moviePlayer, dim)");
        image = Toolkit.getDefaultToolkit().createImage(qtip);
        r.setVar("zero", 0);
        r.setVar("one", 1f);
        r.exec("timeInfo = new TimeInfo(zero, zero)");
        r.exec("moviePlayer.setTime(zero)");
        Vector<Integer> v = new Vector<Integer>();
        int time = 0;
        Integer q = new Integer(time);
        do {
            v.add(q);
            r.exec("timeInfo = imageTrack.getNextInterestingTime(" + "StdQTConstants.nextTimeMediaSample, timeInfo.time, one)");
            q = (Integer) r.getVar("timeInfo.time");
            time = q.intValue();
        } while (time >= 0);
        CoreMetadata m = core.get(0);
        m.imageCount = v.size();
        times = new int[getImageCount()];
        for (int i = 0; i < times.length; i++) {
            q = v.elementAt(i);
            times[i] = q.intValue();
        }
        LOGGER.info("Populating metadata");
        BufferedImage img = AWTImageTools.makeBuffered(image);
        m.sizeX = img.getWidth();
        m.sizeY = img.getHeight();
        m.sizeZ = 1;
        m.sizeC = img.getRaster().getNumBands();
        m.sizeT = getImageCount();
        m.pixelType = AWTImageTools.getPixelType(img);
        m.dimensionOrder = "XYCTZ";
        m.rgb = true;
        m.interleaved = false;
        m.littleEndian = false;
        m.indexed = false;
        m.falseColor = false;
        MetadataStore store = makeFilterMetadata();
        MetadataTools.populatePixels(store, this);
    } catch (ReflectException e) {
        throw new FormatException("Open movie failed", e);
    }
}

Example 92 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class ChannelFiller method setId.

/* @see IFormatHandler#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    super.setId(id);
    lutLength = getLookupTableComponentCount();
    MetadataStore store = getMetadataStore();
    MetadataTools.populatePixelsOnly(store, this);
}

Example 93 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class APNGReader method initFile.

// -- Internal FormatReader 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);
    // check that this is a valid PNG file
    byte[] signature = new byte[8];
    in.read(signature);
    if (signature[0] != (byte) 0x89 || signature[1] != 0x50 || signature[2] != 0x4e || signature[3] != 0x47 || signature[4] != 0x0d || signature[5] != 0x0a || signature[6] != 0x1a || signature[7] != 0x0a) {
        throw new FormatException("Invalid PNG signature.");
    }
    // read data chunks - each chunk consists of the following:
    // 1) 32 bit length
    // 2) 4 char type
    // 3) 'length' bytes of data
    // 4) 32 bit CRC
    blocks = new Vector<PNGBlock>();
    frameCoordinates = new Vector<int[]>();
    while (in.getFilePointer() < in.length()) {
        int length = in.readInt();
        String type = in.readString(4);
        PNGBlock block = new PNGBlock();
        block.length = length;
        block.type = type;
        block.offset = in.getFilePointer();
        blocks.add(block);
        if (type.equals("acTL")) {
            // APNG-specific chunk
            m.imageCount = in.readInt();
            int loop = in.readInt();
            addGlobalMeta("Loop count", loop);
        } else if (type.equals("fcTL")) {
            in.skipBytes(4);
            int w = in.readInt();
            int h = in.readInt();
            int x = in.readInt();
            int y = in.readInt();
            frameCoordinates.add(new int[] { x, y, w, h });
            in.skipBytes(length - 20);
        } else if (type.equals("IDAT")) {
            idatCount++;
        } else if (type.equals("PLTE")) {
            // lookup table
            m.indexed = true;
            lut = new byte[3][256];
            for (int i = 0; i < length / 3; i++) {
                for (int c = 0; c < 3; c++) {
                    lut[c][i] = in.readByte();
                }
            }
        } else if (type.equals("IHDR")) {
            m.sizeX = in.readInt();
            m.sizeY = in.readInt();
            m.bitsPerPixel = in.read();
            int colorType = in.read();
            compression = in.read();
            int filter = in.read();
            interlace = in.read();
            if (filter != 0) {
                throw new FormatException("Invalid filter mode: " + filter);
            }
            switch(colorType) {
                case GRAYSCALE:
                case INDEXED:
                    m.sizeC = 1;
                    break;
                case GRAY_ALPHA:
                    m.sizeC = 2;
                    break;
                case TRUE_COLOR:
                    m.sizeC = 3;
                    break;
                case TRUE_ALPHA:
                    m.sizeC = 4;
                    break;
            }
            m.pixelType = getBitsPerPixel() <= 8 ? FormatTools.UINT8 : FormatTools.UINT16;
            m.rgb = getSizeC() > 1;
        } else if (type.equals("IEND")) {
            break;
        }
        in.seek(block.offset + length);
        if (in.getFilePointer() < in.length() - 4) {
            // skip the CRC
            in.skipBytes(4);
        }
    }
    if (m.imageCount == 0)
        m.imageCount = 1;
    m.sizeZ = 1;
    m.sizeT = getImageCount();
    m.dimensionOrder = "XYCTZ";
    m.interleaved = isRGB();
    m.falseColor = false;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 94 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class BaseTiffReader method initMetadataStore.

/**
 * Populates the metadata store using the data parsed in
 * {@link #initStandardMetadata()} along with some further parsing done in
 * the method itself.
 *
 * All calls to the active <code>MetadataStore</code> should be made in this
 * method and <b>only</b> in this method. This is especially important for
 * sub-classes that override the getters for pixel set array size, etc.
 */
protected void initMetadataStore() throws FormatException {
    LOGGER.info("Populating OME metadata");
    // the metadata store we're working with
    MetadataStore store = makeFilterMetadata();
    IFD firstIFD = ifds.get(0);
    IFD exif = null;
    if (ifds.get(0).containsKey(IFD.EXIF)) {
        try {
            IFDList exifIFDs = tiffParser.getExifIFDs();
            if (exifIFDs.size() > 0) {
                exif = exifIFDs.get(0);
            }
            tiffParser.fillInIFD(exif);
        } catch (IOException e) {
            LOGGER.debug("Could not read EXIF IFDs", e);
        }
    }
    MetadataTools.populatePixels(store, this, exif != null);
    // format the creation date to ISO 8601
    String creationDate = getImageCreationDate();
    String date = DateTools.formatDate(creationDate, DATE_FORMATS, ".");
    if (creationDate != null && date == null) {
        LOGGER.warn("unknown creation date format: {}", creationDate);
    }
    creationDate = date;
    if (creationDate != null) {
        store.setImageAcquisitionDate(new Timestamp(creationDate), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // populate Experimenter
        String artist = firstIFD.getIFDTextValue(IFD.ARTIST);
        if (artist != null) {
            String firstName = null, lastName = null;
            int ndx = artist.indexOf(' ');
            if (ndx < 0)
                lastName = artist;
            else {
                firstName = artist.substring(0, ndx);
                lastName = artist.substring(ndx + 1);
            }
            String email = firstIFD.getIFDStringValue(IFD.HOST_COMPUTER);
            store.setExperimenterFirstName(firstName, 0);
            store.setExperimenterLastName(lastName, 0);
            store.setExperimenterEmail(email, 0);
            store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
        }
        store.setImageDescription(firstIFD.getComment(), 0);
        // set the X and Y pixel dimensions
        double pixX = firstIFD.getXResolution();
        double pixY = firstIFD.getYResolution();
        String unit = getResolutionUnitFromComment(firstIFD);
        Length sizeX = FormatTools.getPhysicalSizeX(pixX, unit);
        Length sizeY = FormatTools.getPhysicalSizeY(pixY, unit);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        store.setPixelsPhysicalSizeZ(null, 0);
        if (exif != null) {
            if (exif.containsKey(IFD.EXPOSURE_TIME)) {
                Object exp = exif.get(IFD.EXPOSURE_TIME);
                if (exp instanceof TiffRational) {
                    Time exposure = new Time(((TiffRational) exp).doubleValue(), UNITS.SECOND);
                    for (int i = 0; i < getImageCount(); i++) {
                        store.setPlaneExposureTime(exposure, 0, i);
                    }
                }
            }
        }
    }
}

Example 95 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class DimensionSwapper method swapDimensions.

// -- DimensionSwapper API methods --
/**
 * Sets the input dimension order according to the given string (e.g.,
 * "XYZCT"). This string indicates the planar rasterization order from the
 * source, overriding the detected order. It may result in the dimensional
 * axis sizes changing.
 *
 * If the given order is identical to the file's native order, then
 * nothing happens. Note that this method will throw an exception if X and Y
 * do not appear in positions 0 and 1 (although X and Y can be reversed).
 */
public void swapDimensions(String order) {
    FormatTools.assertId(getCurrentFile(), true, 2);
    if (order == null)
        throw new IllegalArgumentException("order is null");
    String oldOrder = getInputOrder();
    if (order.equals(oldOrder))
        return;
    if (order.length() != 5) {
        throw new IllegalArgumentException("order is unexpected length (" + order.length() + ")");
    }
    int newX = order.indexOf('X');
    int newY = order.indexOf('Y');
    int newZ = order.indexOf('Z');
    int newC = order.indexOf('C');
    int newT = order.indexOf('T');
    if (newX < 0)
        throw new IllegalArgumentException("X does not appear");
    if (newY < 0)
        throw new IllegalArgumentException("Y does not appear");
    if (newZ < 0)
        throw new IllegalArgumentException("Z does not appear");
    if (newC < 0)
        throw new IllegalArgumentException("C does not appear");
    if (newT < 0)
        throw new IllegalArgumentException("T does not appear");
    if (newX > 1) {
        throw new IllegalArgumentException("X in unexpected position (" + newX + ")");
    }
    if (newY > 1) {
        throw new IllegalArgumentException("Y in unexpected position (" + newY + ")");
    }
    int[] dims = new int[5];
    int oldX = oldOrder.indexOf('X');
    int oldY = oldOrder.indexOf('Y');
    int oldZ = oldOrder.indexOf('Z');
    int oldC = oldOrder.indexOf('C');
    int oldT = oldOrder.indexOf('T');
    if (oldC != newC && reader.getRGBChannelCount() > 1) {
        throw new IllegalArgumentException("Cannot swap C dimension when RGB channel count > 1");
    }
    dims[oldX] = getSizeX();
    dims[oldY] = getSizeY();
    dims[oldZ] = getSizeZ();
    dims[oldC] = getSizeC();
    dims[oldT] = getSizeT();
    Modulo[] moduli = new Modulo[3];
    moduli[oldZ - 2] = getModuloZ();
    moduli[oldC - 2] = getModuloC();
    moduli[oldT - 2] = getModuloT();
    SwappableMetadata ms = (SwappableMetadata) core.get(getCoreIndex());
    ms.sizeX = dims[newX];
    ms.sizeY = dims[newY];
    ms.sizeZ = dims[newZ];
    ms.sizeC = dims[newC];
    ms.sizeT = dims[newT];
    ms.moduloZ = moduli[newZ - 2];
    ms.moduloC = moduli[newC - 2];
    ms.moduloT = moduli[newT - 2];
    ms.inputOrder = order;
    MetadataStore store = getMetadataStore();
    MetadataTools.populatePixels(store, this);
}