Examples with OMEXMLMetadata loci.formats.ome.OMEXMLMetadata used on opensource projects

Example 21 with OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata in project bioformats by openmicroscopy.

the class OMEXMLWriter method setId.

// -- FormatWriter API methods --
/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    if (id.equals(currentId)) {
        return;
    }
    super.setId(id);
    MetadataRetrieve retrieve = getMetadataRetrieve();
    String xml;
    try {
        ServiceFactory factory = new ServiceFactory();
        service = factory.getInstance(OMEXMLService.class);
        xml = service.getOMEXML(retrieve);
        OMEXMLMetadata noBin = service.createOMEXMLMetadata(xml);
        service.removeBinData(noBin);
        OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) noBin.getRoot();
        root.setCreator(FormatTools.CREATOR);
        xml = service.getOMEXML(noBin);
    } catch (DependencyException de) {
        throw new MissingLibraryException(OMEXMLServiceImpl.NO_OME_XML_MSG, de);
    } catch (ServiceException se) {
        throw new FormatException(se);
    }
    xmlFragments = new ArrayList<String>();
    currentFragment = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>";
    XMLTools.parseXML(xml, new OMEHandler());
    xmlFragments.add(currentFragment);
}

Example 22 with OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata in project bioformats by openmicroscopy.

the class OMETiffWriter method getBinaryOnlyOMEXML.

private String getBinaryOnlyOMEXML(String file, String companion, String companionUUID) throws FormatException, IOException, DependencyException, ServiceException {
    ServiceFactory factory = new ServiceFactory();
    OMEXMLService service = factory.getInstance(OMEXMLService.class);
    OMEXMLMetadata meta = service.createOMEXMLMetadata();
    String uuid = "urn:uuid:" + getUUID(new Location(file).getName());
    meta.setUUID(uuid);
    meta.setBinaryOnlyMetadataFile(new Location(companion).getName());
    meta.setBinaryOnlyUUID(companionUUID);
    OMEXMLMetadataRoot root = (OMEXMLMetadataRoot) meta.getRoot();
    root.setCreator(FormatTools.CREATOR);
    return service.getOMEXML(meta);
}

Example 23 with OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata in project bioformats by openmicroscopy.

the class OMETiffWriter method setupServiceAndMetadata.

private void setupServiceAndMetadata() throws DependencyException, ServiceException {
    // extract OME-XML string from metadata object
    MetadataRetrieve retrieve = getMetadataRetrieve();
    ServiceFactory factory = new ServiceFactory();
    service = factory.getInstance(OMEXMLService.class);
    OMEXMLMetadata originalOMEMeta = service.getOMEMetadata(retrieve);
    originalOMEMeta.resolveReferences();
    String omexml = service.getOMEXML(originalOMEMeta);
    omeMeta = service.createOMEXMLMetadata(omexml);
}

Example 24 with OMEXMLMetadata

use of loci.formats.ome.OMEXMLMetadata in project bioformats by openmicroscopy.

the class FormatReaderTest method testEqualOMEXML.

@Test(groups = { "all", "xml", "automated" })
public void testEqualOMEXML() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "testEqualOMEXML";
    if (!initFile())
        result(testName, false, "initFile");
    boolean success = true;
    String msg = null;
    try {
        MetadataStore store = reader.getMetadataStore();
        success = omexmlService.isOMEXMLMetadata(store);
        if (!success)
            msg = TestTools.shortClassName(store);
        String file = reader.getCurrentFile() + ".ome.xml";
        if (success) {
            if (!new File(file).exists() && omexmlDir != null && new File(omexmlDir).exists()) {
                String dir = System.getProperty("testng.directory");
                if (dir != null) {
                    file = reader.getCurrentFile().replace(dir, omexmlDir) + ".ome.xml";
                    if (!new File(file).exists()) {
                        file = reader.getCurrentFile().replace(dir, omexmlDir);
                        file = file.substring(0, file.lastIndexOf(".")) + ".ome.xml";
                    }
                }
            }
            if (new File(file).exists()) {
                String xml = DataTools.readFile(file);
                OMEXMLMetadata base = omexmlService.createOMEXMLMetadata(xml);
                success = omexmlService.isEqual(base, (OMEXMLMetadata) store);
            }
        }
    } catch (Throwable t) {
        LOGGER.info("", t);
        msg = t.getMessage();
    }
    result(testName, success, msg);
}