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; }
public String generateXml(MetadataRetrieve retrieve) throws ServiceException { IMetadata xmlMeta = convertXml(retrieve); return service.getOMEXML(xmlMeta); }
@Override public String getOMEXML(final MetadataRetrieve src) throws ServiceException { return omexmlService().getOMEXML(src); }
@Test public void getOMEXML() throws ServiceException { assertNotNull(service.getOMEXML(service.createOMEXMLMetadata(xml))); }
@Test public void testExtraMetadata() throws Exception { File fakeIni = mkIni("foo.fake.ini", "[GlobalMetadata]", "foo=bar"); reader.setId(fakeIni.getAbsolutePath()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(reader.getGlobalMetadata().get("foo"), "bar"); }
@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(); }
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); }
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); }
private void checkROIs(MetadataRetrieve m, int nImages, int nRoisPerImage, String shapeType, int nOtherRois) throws Exception { assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getImageCount(), nImages); assertEquals(m.getROICount(), nImages * nRoisPerImage + nOtherRois); for (int i = 0; i < m.getImageCount(); i++) { assertEquals(m.getImageROIRefCount(0), nRoisPerImage); } for (int i = nOtherRois; i < m.getROICount(); i++) { assertEquals(m.getShapeCount(i), 1); assertEquals(m.getShapeType(i, 0), shapeType); } }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeYIni(String value, Length length) throws Exception { mkIni("foo.fake.ini", "physicalSizeY = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeY(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeXIni(String value, Length length) throws Exception { mkIni("foo.fake.ini", "physicalSizeX = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeX(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeZIni(String value, Length length) throws Exception { mkIni("foo.fake.ini", "physicalSizeZ = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeZ(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "acquisition dates") public void testAcquisitionDateIni(String value, Timestamp date) throws Exception { mkIni("foo.fake.ini", "acquisitionDate = " + value); reader.setId(wd.resolve("foo.fake").toString()); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getImageAcquisitionDate(0), date); reader.close(); testDefaultValues(); }
@Test(dataProvider = "acquisition dates") public void testAcquisitionDateMultiSeries(String value, Timestamp date) throws Exception { reader.setId("foo&series=10&acquisitionDate=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); for (int i = 0; i < 10; i++) { assertEquals(m.getImageAcquisitionDate(i), date); } reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeZ(String value, Length length) throws Exception { reader.setId("foo&physicalSizeZ=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeZ(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeX(String value, Length length) throws Exception { reader.setId("foo&physicalSizeX=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeX(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "physical sizes") public void testPhysicalSizeY(String value, Length length) throws Exception { reader.setId("foo&physicalSizeY=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getPixelsPhysicalSizeY(0), length); reader.close(); testDefaultValues(); }
@Test(dataProvider = "acquisition dates") public void testAcquisitionDate(String value, Timestamp date) throws Exception { reader.setId("foo&acquisitionDate=" + value + ".fake"); m = service.asRetrieve(reader.getMetadataStore()); assertTrue(service.validateOMEXML(service.getOMEXML(m))); assertEquals(m.getImageAcquisitionDate(0), date); reader.close(); testDefaultValues(); }
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); }
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); }