public OMEXMLMetadata getOmeXmlMetadata() { if (omeXmlMetadata == null) { try { omeXmlMetadata = getOmeXmlService().createOMEXMLMetadata(); } catch (ServiceException exc) { LOGGER.error("Could not create OME-XML metadata", exc); } } return omeXmlMetadata; }
@Test public void getOMEXML() throws ServiceException { assertNotNull(service.getOMEXML(service.createOMEXMLMetadata(xml))); }
@Test(groups = {"config-xml"}) public void writeXML() { setupReader(); if (!initFile(false)) return; String file = reader.getCurrentFile(); LOGGER.info("Generating XML: {}", file); try { Location l = new Location(file); File f = new File(l.getParent(), l.getName() + ".ome.xml"); OutputStreamWriter writer = new OutputStreamWriter(new FileOutputStream(f), Constants.ENCODING); MetadataStore store = reader.getMetadataStore(); MetadataRetrieve retrieve = omexmlService.asRetrieve(store); String xml = omexmlService.getOMEXML(retrieve); writer.write(xml); writer.close(); reader.close(); } catch (Throwable t) { LOGGER.info("", t); assert false; } }
public IMetadata convertXml(MetadataRetrieve retrieve) throws ServiceException { IMetadata xmlMeta = service.createOMEXMLMetadata(); xmlMeta.createRoot(); service.convertMetadata(retrieve, xmlMeta); return xmlMeta; }
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); }
@Test public void isOMEXMLMetadata() throws ServiceException { assertEquals(true, service.isOMEXMLMetadata(service.createOMEXMLMetadata())); }
@Test(dataProvider = "annotations") public void testAnnotations(String key, String methodName) throws Exception { reader.setId("foo&series=5&" + key + "=10.fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); Method method = Class.forName("loci.formats.meta.MetadataRetrieve").getMethod(methodName); assertEquals(method.invoke(m), 50); for (int i = 0; i < 5; i++) { assertEquals(m.getImageAnnotationRefCount(0), 10); } reader.close(); testDefaultValues(); }
OMEXMLService service = factory.getInstance(OMEXMLService.class); if (service.validateOMEXML(ome_xml)) { ome_meta_data = service.createOMEXMLMetadata(ome_xml); service.convertMetadata(ome_meta_data, metadataStore); = service.getOMEMetadata(service.asRetrieve(metadataStore)); for (int image = 0; image != ome_meta_data.getImageCount(); ++ image) { service.addMetadataOnly(reference, image);
final IMetadata meta = service.createOMEXMLMetadata(); r.setMetadataStore( meta ); r.setSeries( series ); final MetadataRetrieve retrieve = service.asRetrieve(r.getMetadataStore());
try { if (meta == null || !metaFile.equals(currentId)) { meta = service.createOMEXMLMetadata(xml); metaFile = currentId; meta = service.createOMEXMLMetadata(xml); service.removeChannels(meta, i, sizeC); Hashtable originalMetadata = service.getOriginalMetadata(meta); if (originalMetadata != null) metadata = originalMetadata; service.convertMetadata(meta, metadataStore); MetadataTools.populatePixels(metadataStore, this); service.convertMetadata(meta, metadataStore); Modulo z = service.getModuloAlongZ(meta, i); if (z != null) { m.moduloZ = z; Modulo c = service.getModuloAlongC(meta, i); if (c != null) { m.moduloC = c; Modulo t = service.getModuloAlongT(meta, i); if (t != null) { m.moduloT = t;
OMEXMLService service = new ServiceFactory().getInstance(OMEXMLService.class); if (service.isOMEXMLRoot(store.getRoot())) { MetadataStore baseStore = r.getMetadataStore(); if (service.isOMEXMLMetadata(baseStore)) { OMEXMLMetadata omeMeta; try { omeMeta = service.getOMEMetadata(service.asRetrieve(baseStore)); if (omeMeta.getTiffDataCount(i) == 0 && omeMeta.getPixelsBinDataCount(i) == 0) { service.addMetadataOnly(omeMeta, i, i == 0);
@Override public void close() throws IOException { if (out != null) { out.writeBytes(xmlFragments.get(xmlFragments.size() - 1)); } if (getMetadataOptions().isValidate()) { try { MetadataRetrieve r = getMetadataRetrieve(); String omexml = service.getOMEXML(r); service.validateOMEXML(omexml); } catch (ServiceException | NullPointerException e) { LOGGER.warn("OMEXMLService unable to create OME-XML metadata object.", e); } } super.close(); xmlFragments = null; service = null; }
private long getMetadataBytes(OmeroReader reader) throws DependencyException, ServiceException { String xml = service.getOMEXML(retrieve); long xmlbytes; try { xmlbytes = xml.getBytes("UTF8").length; } catch (UnsupportedEncodingException e) { throw new RuntimeException("Failed to convert to UTF-8", e); } long planebytes = reader.planes * 512; return planebytes + xmlbytes; }
service.populateOriginalMetadata((OMEXMLMetadata) store, allMetadata); String omexml = service.getOMEXML((MetadataRetrieve)store); service.validateOMEXML(omexml); } catch (ServiceException | NullPointerException e) { LOGGER.warn("OMEXMLService unable to create OME-XML metadata object.", e); getModuloT().length() > 1) service.addModuloAlong( (OMEXMLMetadata) store, getCurrentCore(), series);
try { MetadataStore store = reader.getMetadataStore(); success = omexmlService.isOMEXMLMetadata(store); if (!success) msg = TestTools.shortClassName(store); OMEXMLMetadata base = omexmlService.createOMEXMLMetadata(xml); success = omexmlService.isEqual(base, (OMEXMLMetadata) store);
@Test public void testOriginalMetadata() throws ServiceException { OMEXMLMetadata metadata = service.createOMEXMLMetadata(); service.populateOriginalMetadata(metadata, "testKey", "testValue"); Hashtable metadataTable = service.getOriginalMetadata(metadata); assertEquals(metadataTable.size(), 1); assertTrue("testValue".equals(metadataTable.get("testKey"))); OME root = (OME) metadata.getRoot(); StructuredAnnotations annotations = root.getStructuredAnnotations(); assertEquals(annotations.sizeOfXMLAnnotationList(), 1); XMLAnnotation xmlAnn = annotations.getXMLAnnotation(0); String txt = "<OriginalMetadata><Key>testKey</Key><Value>testValue</Value></OriginalMetadata>"; assertEquals(txt, xmlAnn.getValue()); OriginalMetadataAnnotation omAnn = (OriginalMetadataAnnotation) xmlAnn; assertEquals("testValue", omAnn.getValueForKey()); }
@Test public void getOMEXMLVersion() throws ServiceException { assertEquals("2008-09", service.getOMEXMLVersion(xml)); assertEquals("2016-06", service.getOMEXMLVersion(service.createOMEXMLMetadata(xml))); }
@Override public MetadataRetrieve asRetrieve(final MetadataStore meta) { return omexmlService().asRetrieve(meta); }
service.removeBinData(omeMeta); service.removeTiffData(omeMeta); service.validateOMEXML(xml);
@Override public boolean isOMEXMLMetadata(final Object o) { return omexmlService().isOMEXMLMetadata(o); }