Examples with DynamicMetadataOptions loci.formats.in.DynamicMetadataOptions used on opensource projects

Example 1 with DynamicMetadataOptions

use of loci.formats.in.DynamicMetadataOptions in project bioformats by openmicroscopy.

the class DynamicMetadataOptionsTest method testMetadataLevel.

// -- MetadataOptions tests --
@Test
public void testMetadataLevel() {
    assertEquals(opt.getMetadataLevel(), DynamicMetadataOptions.METADATA_LEVEL_DEFAULT);
    for (MetadataLevel level : MetadataLevel.values()) {
        opt.setMetadataLevel(level);
        assertEquals(opt.getMetadataLevel(), level);
        assertEquals((new DynamicMetadataOptions(level)).getMetadataLevel(), level);
    }
}

Example 2 with DynamicMetadataOptions

use of loci.formats.in.DynamicMetadataOptions in project bioformats by openmicroscopy.

the class OMETiffWriterTest method testCompanion.

@Test
public void testCompanion() throws Exception {
    Path wd = Files.createTempDirectory(this.getClass().getName());
    File outFile = wd.resolve("test.ome.tif").toFile();
    File cFile = wd.resolve("test.companion.ome").toFile();
    String companion = cFile.getAbsolutePath();
    DynamicMetadataOptions options = new DynamicMetadataOptions();
    options.set(OMETiffWriter.COMPANION_KEY, companion);
    int planeCount = WriterUtilities.SIZE_Z * WriterUtilities.SIZE_C * WriterUtilities.SIZE_T;
    OMETiffWriter cwriter = new OMETiffWriter();
    cwriter.setMetadataOptions(options);
    cwriter.setMetadataRetrieve(metadata);
    cwriter.setId(outFile.getAbsolutePath());
    cwriter.setSeries(0);
    byte[] img = new byte[WriterUtilities.SIZE_X * WriterUtilities.SIZE_Y];
    for (int i = 0; i < planeCount; i++) {
        cwriter.saveBytes(i, img);
    }
    cwriter.close();
    assertTrue(cFile.exists());
    OMETiffReader reader = new OMETiffReader();
    reader.setId(companion);
    assertEquals(reader.getSizeX(), WriterUtilities.SIZE_X);
    assertEquals(reader.getSizeY(), WriterUtilities.SIZE_Y);
    assertEquals(reader.getSizeZ(), WriterUtilities.SIZE_Z);
    assertEquals(reader.getSizeC(), WriterUtilities.SIZE_C);
    assertEquals(reader.getSizeT(), WriterUtilities.SIZE_T);
    reader.close();
    outFile.deleteOnExit();
    cFile.deleteOnExit();
    wd.toFile().deleteOnExit();
}

Example 3 with DynamicMetadataOptions

use of loci.formats.in.DynamicMetadataOptions in project bioformats by openmicroscopy.

the class FileStitcherTest method checkKV.

public static void checkKV(IFormatReader r, String k, String expv) {
    MetadataOptions rOpt = r.getMetadataOptions();
    assertTrue(rOpt instanceof DynamicMetadataOptions);
    String v = ((DynamicMetadataOptions) rOpt).get(k);
    assertNotNull(v);
    assertEquals(v, expv);
}

Example 4 with DynamicMetadataOptions

use of loci.formats.in.DynamicMetadataOptions in project bioformats by openmicroscopy.

the class LociPrefs method makeImageReader.

// -- Utility methods --
/**
 * Creates an image reader according to the current configuration settings,
 * including which format readers are currently enabled, as well as
 * format-specific configuration settings.
 */
public static ImageReader makeImageReader() {
    ClassList<IFormatReader> defaultClasses = ImageReader.getDefaultReaderClasses();
    Class<? extends IFormatReader>[] c = defaultClasses.getClasses();
    // include only enabled classes
    ClassList<IFormatReader> enabledClasses = new ClassList<IFormatReader>(IFormatReader.class);
    for (int i = 0; i < c.length; i++) {
        boolean on = LociPrefs.isReaderEnabled(c[i]);
        if (on)
            enabledClasses.addClass(c[i]);
    }
    ImageReader reader = new ImageReader(enabledClasses);
    MetadataOptions options = reader.getMetadataOptions();
    if (options instanceof DynamicMetadataOptions) {
        ((DynamicMetadataOptions) options).setBoolean(ZeissCZIReader.ALLOW_AUTOSTITCHING_KEY, allowCZIAutostitch());
        ((DynamicMetadataOptions) options).setBoolean(ZeissCZIReader.INCLUDE_ATTACHMENTS_KEY, includeCZIAttachments());
        ((DynamicMetadataOptions) options).setBoolean(NativeND2Reader.USE_CHUNKMAP_KEY, useND2Chunkmap());
        ((DynamicMetadataOptions) options).setBoolean(LIFReader.OLD_PHYSICAL_SIZE_KEY, isLeicaLIFPhysicalSizeBackwardsCompatible());
        ((DynamicMetadataOptions) options).setBoolean(CellSensReader.FAIL_ON_MISSING_KEY, isCellsensFailOnMissing());
        reader.setMetadataOptions(options);
    }
    // toggle reader-specific options
    boolean nd2Nikon = LociPrefs.isND2Nikon();
    boolean pictQTJava = LociPrefs.isPictQTJava();
    boolean qtQTJava = LociPrefs.isQTQTJava();
    boolean sdtIntensity = LociPrefs.isSDTIntensity();
    boolean tiffImageIO = LociPrefs.isTiffImageIO();
    IFormatReader[] r = reader.getReaders();
    for (int i = 0; i < r.length; i++) {
        if (r[i] instanceof ND2Reader) {
            ND2Reader nd2 = (ND2Reader) r[i];
            nd2.setLegacy(nd2Nikon);
        } else if (r[i] instanceof PictReader) {
            PictReader pict = (PictReader) r[i];
            pict.setLegacy(pictQTJava);
        } else if (r[i] instanceof QTReader) {
            QTReader qt = (QTReader) r[i];
            qt.setLegacy(qtQTJava);
        } else if (r[i] instanceof SDTReader) {
            SDTReader sdt = (SDTReader) r[i];
            sdt.setIntensity(sdtIntensity);
        } else if (r[i] instanceof TiffDelegateReader) {
            TiffDelegateReader tiff = (TiffDelegateReader) r[i];
            tiff.setLegacy(tiffImageIO);
        }
    }
    return reader;
}

Example 5 with DynamicMetadataOptions

use of loci.formats.in.DynamicMetadataOptions in project bioformats by openmicroscopy.

the class FileStitcherTest method testOptionsExplicit.

@Test
public void testOptionsExplicit() throws IOException, FormatException {
    DynamicMetadataOptions opt = new DynamicMetadataOptions();
    opt.set(KEY, VALUE);
    FileStitcher fs = new FileStitcher();
    fs.setMetadataOptions(opt);
    fs.setId("test_z<0-2>.fake");
    checkKV(fs.getUnderlyingReaders(), KEY, VALUE);
    DynamicMetadataOptions newOpt = new DynamicMetadataOptions();
    String newValue = VALUE + "_";
    newOpt.set(KEY, newValue);
    fs.setMetadataOptions(newOpt);
    checkKV(fs.getUnderlyingReaders(), KEY, newValue);
    fs.close();
}