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

Example 46 with IMetadata

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

the class Calibrator method applyCalibration.

// -- Calibrator methods --
/**
 * Applies spatial calibrations to an image stack.
 */
public void applyCalibration(ImagePlus imp) {
    final IMetadata meta = process.getOMEMetadata();
    final int series = (Integer) imp.getProperty(ImagePlusReader.PROP_SERIES);
    double xcal = Double.NaN, ycal = Double.NaN;
    double zcal = Double.NaN, tcal = Double.NaN;
    Length xd = meta.getPixelsPhysicalSizeX(series);
    if (xd != null && xd.unit().isConvertible(UNITS.MICROMETER))
        xcal = xd.value(UNITS.MICROMETER).doubleValue();
    Length yd = meta.getPixelsPhysicalSizeY(series);
    if (yd != null && yd.unit().isConvertible(UNITS.MICROMETER))
        ycal = yd.value(UNITS.MICROMETER).doubleValue();
    Length zd = meta.getPixelsPhysicalSizeZ(series);
    if (zd != null && zd.unit().isConvertible(UNITS.MICROMETER))
        zcal = zd.value(UNITS.MICROMETER).doubleValue();
    Time td = meta.getPixelsTimeIncrement(series);
    if (td != null)
        tcal = td.value(UNITS.SECOND).doubleValue();
    boolean xcalPresent = !Double.isNaN(xcal);
    boolean ycalPresent = !Double.isNaN(ycal);
    boolean zcalPresent = !Double.isNaN(zcal);
    boolean tcalPresent = !Double.isNaN(tcal) && tcal != 0;
    // assume that the width and height are equal.
    if (xcalPresent && !ycalPresent)
        ycal = xcal;
    else if (ycalPresent && !xcalPresent)
        xcal = ycal;
    // average any variable time interval values.
    if (!tcalPresent)
        tcal = computeVariableTimeInterval(meta, series);
    xcalPresent = !Double.isNaN(xcal);
    ycalPresent = !Double.isNaN(ycal);
    zcalPresent = !Double.isNaN(zcal);
    tcalPresent = !Double.isNaN(tcal);
    final boolean hasSpatial = xcalPresent || ycalPresent || zcalPresent;
    final boolean hasCalibration = hasSpatial || ycalPresent;
    if (hasCalibration) {
        // set calibration only if at least one value is present
        Calibration cal = new Calibration();
        if (hasSpatial)
            cal.setUnit("micron");
        if (xcalPresent)
            cal.pixelWidth = xcal == 0 ? 1 : xcal;
        if (ycalPresent)
            cal.pixelHeight = ycal == 0 ? 1 : ycal;
        if (zcalPresent)
            cal.pixelDepth = zcal == 0 ? 1 : zcal;
        if (tcalPresent)
            cal.frameInterval = tcal == 0 ? 1 : tcal;
        imp.setCalibration(cal);
    }
    String type = meta.getPixelsType(series).toString();
    int pixelType = FormatTools.pixelTypeFromString(type);
    // NB: INT32 is represented with FloatProcessor, so no need to calibrate.
    boolean signed = pixelType == FormatTools.INT8 || // || pixelType == FormatTools.INT32;
    pixelType == FormatTools.INT16;
    // values are shown
    if (signed) {
        int bitsPerPixel = FormatTools.getBytesPerPixel(pixelType) * 8;
        double min = -1 * Math.pow(2, bitsPerPixel - 1);
        imp.getLocalCalibration().setFunction(Calibration.STRAIGHT_LINE, new double[] { min, 1.0 }, "gray value");
    }
}

Example 47 with IMetadata

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

the class EightBitLosslessJPEG2000Test method setUp.

@BeforeMethod
public void setUp() throws Exception {
    for (byte v = Byte.MIN_VALUE; v < Byte.MAX_VALUE; v++) {
        int index = v + Byte.MAX_VALUE + 1;
        pixels[index][0] = v;
        String file = index + ".jp2";
        File tempFile = File.createTempFile("test", ".jp2");
        tempFile.deleteOnExit();
        Location.mapId(file, tempFile.getAbsolutePath());
        files.add(file);
        IMetadata metadata;
        try {
            ServiceFactory factory = new ServiceFactory();
            OMEXMLService service = factory.getInstance(OMEXMLService.class);
            metadata = service.createOMEXMLMetadata();
        } catch (DependencyException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        } catch (ServiceException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        }
        MetadataTools.populateMetadata(metadata, 0, "foo", false, "XYCZT", "uint8", 1, 1, 1, 1, 1, 1);
        IFormatWriter writer = new JPEG2000Writer();
        writer.setMetadataRetrieve(metadata);
        writer.setId(file);
        writer.saveBytes(0, pixels[index]);
        writer.close();
    }
}

Example 48 with IMetadata

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

the class FormatReaderTest method testPhysicalSizeZ.

@Test(groups = { "all", "fast", "automated" })
public void testPhysicalSizeZ() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "PhysicalSizeZ";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        Length expectedSize = config.getPhysicalSizeZ();
        Length realSize = retrieve.getPixelsPhysicalSizeZ(i);
        if (!isAlmostEqual(realSize, expectedSize)) {
            result(testName, false, "Series " + i + " (expected " + expectedSize + ", actual " + realSize + ")");
        }
    }
    result(testName, true);
}

Example 49 with IMetadata

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

the class FormatReaderTest method testImageDescriptions.

@Test(groups = { "all", "fast", "automated" })
public void testImageDescriptions() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "ImageDescriptions";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        String realDescription = retrieve.getImageDescription(i);
        if (realDescription != null) {
            realDescription = realDescription.trim();
        }
        if (config.hasImageDescription()) {
            String expectedDescription = config.getImageDescription();
            if (expectedDescription != null) {
                expectedDescription = expectedDescription.trim();
            }
            if (!expectedDescription.equals(realDescription) && !(realDescription == null && expectedDescription.equals("null"))) {
                result(testName, false, "Series " + i + " (got '" + realDescription + "', expected '" + expectedDescription + "')");
            }
        }
    }
    result(testName, true);
}

Example 50 with IMetadata

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

the class FormatReaderTest method testTimeIncrement.

@Test(groups = { "all", "fast", "automated" })
public void testTimeIncrement() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "TimeIncrement";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        Time expectedIncrement = config.getTimeIncrement();
        Time realIncrement = retrieve.getPixelsTimeIncrement(i);
        if (!isAlmostEqual(expectedIncrement, realIncrement)) {
            result(testName, false, "Series " + i + " (expected " + expectedIncrement + ", actual " + realIncrement + ")");
        }
    }
    result(testName, true);
}