reader.setMetadataStore( new OMEXMLMetadataImpl() ); detectViewsInFile( file, multiplicityMapInner,
public static void main(String[] args) { ImageReader reader = new ImageReader(); reader.setMetadataStore( new OMEXMLMetadataImpl()); try { reader.setId( new OpenDialog("pick file").getPath() ); for (int i = 0; i < reader.getSeriesCount(); i++) { reader.setSeries( i ); Arrays.asList( reader.getSeriesUsedFiles() ).forEach( s -> System.out.println( s ) ); System.out.println( ((OMEXMLMetadataImpl)reader.getMetadataStore()).dumpXML()); } reader.close(); } catch ( FormatException | IOException e ) { // TODO Auto-generated catch block e.printStackTrace(); } }
reader.setMetadataStore( new OMEXMLMetadataImpl());
reader.setOriginalMetadataPopulated(isOriginalMetadataPopulated()); reader.setNormalized(isNormalized()); reader.setMetadataStore(getMetadataStore());
reader.setOriginalMetadataPopulated(isOriginalMetadataPopulated()); reader.setNormalized(isNormalized()); reader.setMetadataStore(getMetadataStore());
@Test public void testSetId() throws FormatException, IOException { long t0 = System.currentTimeMillis(); pixelsOnly.setId(id); assertEquals(MetadataLevel.MINIMUM, pixelsOnly.getMetadataOptions().getMetadataLevel()); long t1 = System.currentTimeMillis(); all.setId(id); assertEquals(MetadataLevel.ALL, all.getMetadataOptions().getMetadataLevel()); assertFalse(0 == all.getSeriesMetadata().size() + all.getGlobalMetadata().size()); long t2 = System.currentTimeMillis(); System.err.println(String.format("Pixels only: %d -- All: %d", t1 - t0, t2 - t1)); IMetadata metadata = null; try { ServiceFactory factory = new ServiceFactory(); OMEXMLService service = factory.getInstance(OMEXMLService.class); metadata = service.createOMEXMLMetadata(); noOverlays.setMetadataStore(metadata); } catch (Exception e) { throw new FormatException("Cannot initialize OMEXML metadata store"); } noOverlays.setId(id); assertEquals(MetadataLevel.NO_OVERLAYS, noOverlays.getMetadataOptions().getMetadataLevel()); assertEquals(metadata.getROICount(), 0); }
reader.setMetadataStore( new OMEXMLMetadataImpl());
@Override protected void typedParse(final RandomAccessInputStream stream, final Metadata meta, final SCIFIOConfig config) throws IOException, FormatException { try { final ImageReader reader = createImageReader(this); meta.setReader(reader); MetadataStore store = new OMEXMLMetadataImpl(); reader.setMetadataStore(store); reader.setOriginalMetadataPopulated(config.parserIsSaveOriginalMetadata()); reader.setMetadataFiltered(config.parserIsFiltered()); reader.setGroupFiles(config.groupableIsGroupFiles()); reader.setId(stream.getFileName()); meta.setTable(new DefaultMetaTable(reader.getGlobalMetadata())); } catch (final loci.formats.FormatException e) { throw new FormatException(e); } } }