Examples with ServiceFactory loci.common.services.ServiceFactory used on opensource projects

Example 76 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class Upgrade200909Test method setUp.

@BeforeMethod
public void setUp() throws Exception {
    ServiceFactory sf = new ServiceFactory();
    service = sf.getInstance(OMEXMLService.class);
    InputStream s = Upgrade200909Test.class.getResourceAsStream(XML_FILE);
    byte[] b = new byte[s.available()];
    s.read(b);
    s.close();
    xml = new String(b);
    metadata = service.createOMEXMLMetadata(xml);
    ome = (OME) metadata.getRoot();
}

Example 77 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class Upgrade201106Test method setUp.

@BeforeMethod
public void setUp() throws Exception {
    ServiceFactory sf = new ServiceFactory();
    service = sf.getInstance(OMEXMLService.class);
    InputStream s = Upgrade201106Test.class.getResourceAsStream(XML_FILE);
    byte[] b = new byte[s.available()];
    s.read(b);
    s.close();
    xml = new String(b);
    metadata = service.createOMEXMLMetadata(xml);
    ome = (OME) metadata.getRoot();
}

Example 78 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class ConvertToOmeTiff method main.

public static void main(String[] args) throws Exception {
    if (args.length == 0) {
        System.out.println("Usage: java ConvertToOmeTiff file1 file2 ...");
        return;
    }
    ImageReader reader = new ImageReader();
    OMETiffWriter writer = new OMETiffWriter();
    for (int i = 0; i < args.length; i++) {
        String id = args[i];
        int dot = id.lastIndexOf(".");
        String outId = (dot >= 0 ? id.substring(0, dot) : id) + ".ome.tif";
        System.out.print("Converting " + id + " to " + outId + " ");
        // record metadata to OME-XML format
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        IMetadata omexmlMeta = service.createOMEXMLMetadata();
        reader.setMetadataStore(omexmlMeta);
        reader.setId(id);
        // configure OME-TIFF writer
        writer.setMetadataRetrieve(omexmlMeta);
        writer.setId(outId);
        // writer.setCompression("J2K");
        // write out image planes
        int seriesCount = reader.getSeriesCount();
        for (int s = 0; s < seriesCount; s++) {
            reader.setSeries(s);
            writer.setSeries(s);
            int planeCount = reader.getImageCount();
            for (int p = 0; p < planeCount; p++) {
                byte[] plane = reader.openBytes(p);
                // write plane to output file
                writer.saveBytes(p, plane);
                System.out.print(".");
            }
        }
        writer.close();
        reader.close();
        System.out.println(" [done]");
    }
}

Example 79 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class DisplayHandler method displayOMEXML.

/**
 * Displays OME-XML metadata in a tree in its own window.
 */
public XMLWindow displayOMEXML() throws FormatException, IOException {
    if (!options.isShowOMEXML())
        return null;
    XMLWindow metaWindow = null;
    metaWindow = new XMLWindow("OME Metadata - " + process.getIdName());
    Exception exc = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        metaWindow.setXML(service.getOMEXML(process.getOMEMetadata()));
        WindowTools.placeWindow(metaWindow);
        metaWindow.setVisible(true);
    } catch (DependencyException e) {
        exc = e;
    } catch (ServiceException e) {
        exc = e;
    } catch (ParserConfigurationException e) {
        exc = e;
    } catch (SAXException e) {
        exc = e;
    }
    if (exc != null)
        throw new FormatException(exc);
    // save reference to OME-XML window
    xmlWindow = metaWindow;
    return metaWindow;
}

Example 80 with ServiceFactory

use of loci.common.services.ServiceFactory in project bioformats by openmicroscopy.

the class ImportProcess method createBaseReader.

/**
 * Initializes an {@link loci.formats.IFormatReader}
 * according to the current configuration.
 */
private void createBaseReader() throws FormatException, IOException {
    if (options.isLocal() || options.isHTTP()) {
        BF.status(options.isQuiet(), "Identifying " + idName);
        imageReader = LociPrefs.makeImageReader();
        baseReader = imageReader.getReader(options.isUsingPatternIds() ? new FilePattern(options.getId()).getFiles()[0] : options.getId());
    } else if (options.isOMERO()) {
        BF.status(options.isQuiet(), "Establishing server connection");
        try {
            ReflectedUniverse r = new ReflectedUniverse();
            r.exec("import loci.ome.io.OmeroReader");
            r.exec("baseReader = new OmeroReader()");
            ClassList<IFormatReader> classes = new ClassList<IFormatReader>(IFormatReader.class);
            r.setVar("classes", classes);
            r.exec("class = baseReader.getClass()");
            r.exec("classes.addClass(class)");
            imageReader = new ImageReader(classes);
            baseReader = imageReader.getReader(options.getId());
        } catch (Exception exc) {
            WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem communicating with the server.");
            cancel();
            return;
        }
    } else {
        WindowTools.reportException(null, options.isQuiet(), "Sorry, there has been an internal error: unknown data source");
        cancel();
        return;
    }
    // attach OME-XML metadata store
    Exception exc = null;
    try {
        ServiceFactory factory = new ServiceFactory();
        OMEXMLService service = factory.getInstance(OMEXMLService.class);
        meta = service.createOMEXMLMetadata();
        omeXML = null;
    } catch (DependencyException de) {
        exc = de;
    } catch (ServiceException se) {
        exc = se;
    }
    if (exc != null) {
        WindowTools.reportException(exc, options.isQuiet(), "Sorry, there was a problem constructing the OME-XML metadata store");
        throw new FormatException(exc);
    }
    baseReader.setMetadataStore(meta);
    BF.status(options.isQuiet(), "");
    DebugTools.enableIJLogging(IJ.debugMode);
}