Examples with IFormatReader loci.formats.IFormatReader used on opensource projects

Example 6 with IFormatReader

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

the class CellWorxReader method getReader.

private IFormatReader getReader(String file, boolean omexml) throws FormatException, IOException {
    IFormatReader pnl = new DeltavisionReader();
    if (checkSuffix(file, "tif")) {
        pnl = new MetamorphReader();
    }
    if (omexml) {
        IMetadata metadata;
        try {
            metadata = service.createOMEXMLMetadata();
        } catch (ServiceException exc) {
            throw new FormatException("Could not create OME-XML store.", exc);
        }
        pnl.setMetadataStore(metadata);
    }
    pnl.setId(file);
    return pnl;
}

Example 7 with IFormatReader

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

the class FileStitcherTest method testOptionsImplicit.

@Test(dataProvider = "levels")
public void testOptionsImplicit(MetadataLevel level) throws IOException, FormatException {
    FileStitcher fs = new FileStitcher();
    fs.getMetadataOptions().setMetadataLevel(level);
    fs.setId("test_z<0-2>.fake");
    for (IFormatReader r : fs.getUnderlyingReaders()) {
        assertEquals(r.getMetadataOptions().getMetadataLevel(), level);
    }
    fs.close();
}

Example 8 with IFormatReader

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

the class PrintDomains method main.

public static void main(String[] args) {
    // get a list of all available readers
    IFormatReader[] readers = new ImageReader().getReaders();
    final TreeMultimap<String, String> domains = TreeMultimap.create();
    for (IFormatReader reader : readers) {
        try {
            String[] readerDomains = reader.getPossibleDomains("");
            for (String domain : readerDomains) {
                domains.put(domain, reader.getFormat());
            }
        } catch (FormatException e) {
            e.printStackTrace();
        } catch (IOException e) {
            e.printStackTrace();
        }
    }
    for (final Map.Entry<String, Collection<String>> domain : domains.asMap().entrySet()) {
        System.out.println(domain.getKey() + ":");
        for (final String readerFormat : domain.getValue()) {
            System.out.println("  " + readerFormat);
        }
    }
}

Example 9 with IFormatReader

use of loci.formats.IFormatReader 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 10 with IFormatReader

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

the class FormatReaderTest method testConsistentReader.

@Test(groups = { "all", "fast", "automated" })
public void testConsistentReader() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "testConsistentReader";
    if (!initFile())
        result(testName, false, "initFile");
    String format = config.getReader();
    IFormatReader r = reader;
    if (r instanceof ImageReader) {
        r = ((ImageReader) r).getReader();
    } else if (r instanceof ReaderWrapper) {
        try {
            r = ((ReaderWrapper) r).unwrap();
        } catch (FormatException e) {
        } catch (IOException e) {
        }
    }
    String realFormat = TestTools.shortClassName(r);
    result(testName, realFormat.equals(format), realFormat);
}