public FlexHandler(List<String> names, List<String> factors, MetadataStore store, boolean populateCore, int well, int thisField) { this.names = names; this.factors = factors; this.store = store; this.populateCore = populateCore; this.well = well; level = getMetadataOptions().getMetadataLevel(); this.thisField = thisField; }
@Test public void testMetadataLevel() { assertEquals(opt.getMetadataLevel(), MetadataLevel.ALL); for (MetadataLevel level: MetadataLevel.values()) { opt.setMetadataLevel(level); assertEquals(opt.getMetadataLevel(), level); assertEquals( (new DefaultMetadataOptions(level)).getMetadataLevel(), level ); } }
@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; }
@Test public void testIsValidate() { assertFalse(opt.isValidate()); opt.setValidate(true); assertTrue(opt.isValidate()); opt.setValidate(false); assertFalse(opt.isValidate()); }
@BeforeClass public void setUp() { pixelsOnly = new DeltavisionReader(); pixelsOnly.getMetadataOptions().setMetadataLevel(MetadataLevel.MINIMUM); all = new DeltavisionReader(); all.getMetadataOptions().setMetadataLevel(MetadataLevel.ALL); }
/** Performed following ImportStep.FILE notification. */ private void initializeFile() throws FormatException, IOException { saveDefaults(); BF.status(options.isQuiet(), "Analyzing " + getIdName()); baseReader.setMetadataFiltered(true); baseReader.setGroupFiles(!options.isUngroupFiles() || options.isGroupFiles()); if(options != null && !options.showROIs()){ baseReader.getMetadataOptions().setMetadataLevel( MetadataLevel.NO_OVERLAYS); } baseReader.setId(options.isUsingPatternIds() ? new FilePattern(options.getId()).getFiles()[0] : options.getId()); boolean mustGroup = baseReader.fileGroupOption(options.getId()) == FormatTools.MUST_GROUP; options.setMustGroup(mustGroup); }
public FlexHandler(List<String> names, List<String> factors, MetadataStore store, boolean populateCore, int well, int thisField) { this.names = names; this.factors = factors; this.store = store; this.populateCore = populateCore; this.well = well; level = getMetadataOptions().getMetadataLevel(); this.thisField = thisField; }
@Test(dataProvider = "levels") public void testOptionsImplicit(MetadataLevel level) throws Exception { ImageReader reader = new ImageReader(); reader.getMetadataOptions().setMetadataLevel(level); reader.setId("test.fake"); MetadataLevel rLevel = reader.getReader().getMetadataOptions().getMetadataLevel(); assertEquals(rLevel, level); reader.close(); }
/** Performed following ImportStep.FILE notification. */ private void initializeFile() throws FormatException, IOException { saveDefaults(); BF.status(options.isQuiet(), "Analyzing " + getIdName()); baseReader.setMetadataFiltered(true); baseReader.setGroupFiles(!options.isUngroupFiles() || options.isGroupFiles()); if(options != null && !options.showROIs()){ baseReader.getMetadataOptions().setMetadataLevel( MetadataLevel.NO_OVERLAYS); } baseReader.setId(options.isUsingPatternIds() ? new FilePattern(options.getId()).getFiles()[0] : options.getId()); boolean mustGroup = baseReader.fileGroupOption(options.getId()) == FormatTools.MUST_GROUP; options.setMustGroup(mustGroup); }
@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; }
/** Gets whether to populate only the minimum required metadata. */ private boolean isMinimumMetadata() { return getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM; }
@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(); }
reader = new ImageProcessorReader(r); if(options != null && !options.showROIs()){ baseReader.getMetadataOptions().setMetadataLevel( MetadataLevel.NO_OVERLAYS);
if (getMetadataOptions().isValidate()) { service.validateOMEXML(xml);
/** Gets whether to populate only the minimum required metadata. */ private boolean isMinimumMetadata() { return getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM; }
reader = new ImageProcessorReader(r); if(options != null && !options.showROIs()){ baseReader.getMetadataOptions().setMetadataLevel( MetadataLevel.NO_OVERLAYS);
if (getMetadataOptions().isValidate()) { service.validateOMEXML(xml);
private void parseZpoFile(String zpoFile) throws IOException { if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) { return; } String[] tokens = DataTools.readFile(zpoFile).split("\\s"); for (int t=0; t<tokens.length; t++) { addGlobalMetaList("Z slice position", tokens[t]); } }
setupService(); if (getMetadataOptions().isValidate()) { try { String omexml = service.getOMEXML((MetadataRetrieve)store);
private void parseZpoFile(String zpoFile) throws IOException { if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) { return; } String[] tokens = DataTools.readFile(zpoFile).split("\\s"); for (int t=0; t<tokens.length; t++) { addGlobalMetaList("Z slice position", tokens[t]); } }