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

Example 6 with TiffRational

use of loci.formats.tiff.TiffRational 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 7 with TiffRational

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

the class TiffRationalTest method testNotEqual.

@Test
public void testNotEqual() {
    TiffRational a = new TiffRational(1, 4);
    TiffRational b = new TiffRational(1, 5);
    assertTrue(!(a.equals(b)));
}

Example 8 with TiffRational

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

the class TiffRationalTest method testLessThan.

@Test
public void testLessThan() {
    TiffRational a = new TiffRational(1, 5);
    TiffRational b = new TiffRational(1, 4);
    assertEquals(-1, a.compareTo(b));
}

Example 9 with TiffRational

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

the class TiffRationalTest method testEqualObject.

@Test
public void testEqualObject() {
    TiffRational a = new TiffRational(1, 4);
    Object b = new Object();
    assertTrue(!(a.equals(b)));
}

Example 10 with TiffRational

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

the class TiffRationalTest method testGreaterThan.

@Test
public void testGreaterThan() {
    TiffRational a = new TiffRational(1, 4);
    TiffRational b = new TiffRational(1, 5);
    assertEquals(1, a.compareTo(b));
}