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

Example 21 with IMetadata

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

the class Jpeg2000GrindTest method initializeWriter.

/**
 * Initializes the writer.
 * @param output The file where to write the compressed data.
 * @param compression The compression to use.
 * @param bigTiff Pass <code>true</code> to set the <code>bigTiff</code>
 * flag, <code>false</code> otherwise.
 * @throws Exception Thrown if an error occurred.
 */
private void initializeWriter(String output, String compression, boolean bigTiff) throws Exception {
    ServiceFactory sf = new ServiceFactory();
    OMEXMLService service = sf.getInstance(OMEXMLService.class);
    IMetadata metadata = service.createOMEXMLMetadata();
    metadata.setImageID("Image:0", 0);
    metadata.setPixelsID("Pixels:0", 0);
    metadata.setPixelsBinDataBigEndian(true, 0, 0);
    metadata.setPixelsDimensionOrder(DimensionOrder.XYZCT, 0);
    metadata.setPixelsType(ome.xml.model.enums.PixelType.fromString(PIXEL_TYPE), 0);
    metadata.setPixelsSizeX(new PositiveInteger(SIZE_X), 0);
    metadata.setPixelsSizeY(new PositiveInteger(SIZE_Y), 0);
    metadata.setPixelsSizeZ(new PositiveInteger(1), 0);
    metadata.setPixelsSizeC(new PositiveInteger(1), 0);
    metadata.setPixelsSizeT(new PositiveInteger(SIZE_Z * SIZE_C * SIZE_T), 0);
    metadata.setChannelID("Channel:0", 0, 0);
    metadata.setChannelSamplesPerPixel(new PositiveInteger(1), 0, 0);
    writer = new TiffWriter();
    writer.setMetadataRetrieve(metadata);
    writer.setCompression(compression);
    writer.setWriteSequentially(false);
    writer.setInterleaved(true);
    writer.setBigTiff(bigTiff);
    writer.setId(output);
    bytesPerPixel = FormatTools.getBytesPerPixel(PIXEL_TYPE);
}

Example 22 with IMetadata

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

the class MetadataConfigurableTest method testSetId.

@Test
public void testSetId() throws FormatException, IOException {
    long t0 = System.currentTimeMillis();
    pixelsOnly.setId(id);
    assertEquals(MetadataLevel.MINIMUM, pixelsOnly.getMetadataOptions().getMetadataLevel());
    long t1 = System.currentTimeMillis();
    all.setId(id);
    assertEquals(MetadataLevel.ALL, all.getMetadataOptions().getMetadataLevel());
    assertFalse(0 == all.getSeriesMetadata().size() + all.getGlobalMetadata().size());
    long t2 = System.currentTimeMillis();
    System.err.println(String.format("Pixels only: %d -- All: %d", t1 - t0, t2 - t1));
    IMetadata metadata = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        metadata = service.createOMEXMLMetadata();
        noOverlays.setMetadataStore(metadata);
    } catch (Exception e) {
        throw new FormatException("Cannot initialize OMEXML metadata store");
    }
    noOverlays.setId(id);
    assertEquals(MetadataLevel.NO_OVERLAYS, noOverlays.getMetadataOptions().getMetadataLevel());
    assertEquals(metadata.getROICount(), 0);
}

Example 23 with IMetadata

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

the class FormatReaderTest method testExposureTimes.

@Test(groups = { "all", "fast", "automated" })
public void testExposureTimes() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "ExposureTimes";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        reader.setSeries(i);
        config.setSeries(i);
        if (reader.getImageCount() != retrieve.getPlaneCount(i)) {
            continue;
        }
        for (int c = 0; c < config.getChannelCount(); c++) {
            if (config.hasExposureTime(c)) {
                Time exposureTime = config.getExposureTime(c);
                for (int p = 0; p < reader.getImageCount(); p++) {
                    int[] zct = reader.getZCTCoords(p);
                    if (zct[1] == c && p < retrieve.getPlaneCount(i)) {
                        Time planeExposureTime = retrieve.getPlaneExposureTime(i, p);
                        if (exposureTime == null && planeExposureTime == null) {
                            continue;
                        }
                        if (exposureTime == null || planeExposureTime == null || !exposureTime.equals(planeExposureTime)) {
                            result(testName, false, "Series " + i + " plane " + p + " channel " + c + " (got " + planeExposureTime + ", expected " + exposureTime + ")");
                        }
                    }
                }
            }
        }
    }
    result(testName, true);
}

Example 24 with IMetadata

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

the class FormatReaderTest method testDetectors.

@Test(groups = { "all", "fast", "automated" })
public void testDetectors() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "Detectors";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        config.setSeries(i);
        for (int c = 0; c < config.getChannelCount(); c++) {
            String expectedDetector = config.getDetector(c);
            String realDetector = null;
            try {
                realDetector = retrieve.getDetectorSettingsID(i, c);
            } catch (NullPointerException e) {
            }
            if (!(expectedDetector == null && realDetector == null)) {
                if ((expectedDetector == null || !expectedDetector.equals(realDetector)) && (realDetector == null || !realDetector.equals(expectedDetector))) {
                    result(testName, false, "Series " + i + " channel " + c + " (expected " + expectedDetector + ", actual " + realDetector + ")");
                }
            }
        }
    }
    result(testName, true);
}

Example 25 with IMetadata

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

the class FormatReaderTest method testImageNames.

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