@Override public MetadataStore getMetadataStore() { if (this.userMetadataStore != null) { return this.userMetadataStore; } return reader.getMetadataStore(); }
@Override public MetadataStore getMetadataStore() { if (this.userMetadataStore != null) { return this.userMetadataStore; } return reader.getMetadataStore(); }
@Override public MetadataStore getMetadataStore() { return reader.getMetadataStore(); }
@Override public MetadataStore getMetadataStore() { return reader.getMetadataStore(); }
@Override public MetadataStore getMetadataStore() { return getReader().getMetadataStore(); }
@Override public MetadataStore getMetadataStore() { return getReader().getMetadataStore(); }
@Override public MetadataStore getMetadataStore() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.getMetadataStore() : store; }
/** * @throws FormatException Never actually thrown. * @throws IOException Never actually thrown. */ public static String getFilename(int series, int image, IFormatReader r, String pattern, boolean padded) throws FormatException, IOException { MetadataStore store = r.getMetadataStore(); MetadataRetrieve retrieve = store instanceof MetadataRetrieve ? (MetadataRetrieve) store : new DummyMetadata(); return getFilename(series, image, retrieve, pattern, padded); }
@Override protected void translateFormatMetadata(final BioFormatsFormat.Metadata source, final OMEMetadata dest) { // Just copy the root over Object root = source.getReader().getMetadataStore(); if (root != null && root instanceof ome.xml.meta.OMEXMLMetadata) { dest.setRoot((OMEXMLMetadata) root); } } }
@Override public MetadataStore getMetadataStore() { FormatTools.assertId(getCurrentFile(), true, 2); return noStitch ? reader.getMetadataStore() : store; }
/** * @throws FormatException Never actually thrown. * @throws IOException Never actually thrown. */ public static String getFilename(int series, int image, IFormatReader r, String pattern, boolean padded) throws FormatException, IOException { MetadataStore store = r.getMetadataStore(); MetadataRetrieve retrieve = store instanceof MetadataRetrieve ? (MetadataRetrieve) store : new DummyMetadata(); return getFilename(series, image, retrieve, pattern, padded); }
@Override public void setId(String id) throws FormatException, IOException { if (isLegacy()) { super.setId(id); } nativeReader.setId(id); nativeReaderInitialized = true; currentId = nativeReader.getCurrentFile(); core = new ArrayList<CoreMetadata>(nativeReader.getCoreMetadataList()); metadata = nativeReader.getGlobalMetadata(); metadataStore = nativeReader.getMetadataStore(); }
@Override public void setId(String id) throws FormatException, IOException { if (isLegacy()) { super.setId(id); } nativeReader.setId(id); nativeReaderInitialized = true; currentId = nativeReader.getCurrentFile(); core = new ArrayList<CoreMetadata>(nativeReader.getCoreMetadataList()); metadata = nativeReader.getGlobalMetadata(); metadataStore = nativeReader.getMetadataStore(); }
public void printOMEXML() throws MissingLibraryException, ServiceException { LOGGER.info(""); MetadataStore ms = reader.getMetadataStore();
/** Finds the Plane index corresponding to the given image plane number. */ private static int getPlaneIndex(IFormatReader r, int no) { MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); int imageIndex = r.getSeries(); int planeCount = retrieve.getPlaneCount(imageIndex); int[] zct = r.getZCTCoords(no); for (int i=0; i<planeCount; i++) { Integer theC = retrieve.getPlaneTheC(imageIndex, i).getValue(); Integer theT = retrieve.getPlaneTheT(imageIndex, i).getValue(); Integer theZ = retrieve.getPlaneTheZ(imageIndex, i).getValue(); if (zct[0] == theZ.intValue() && zct[1] == theC.intValue() && zct[2] == theT.intValue()) { return i; } } return -1; }
/** Finds the Plane index corresponding to the given image plane number. */ private static int getPlaneIndex(IFormatReader r, int no) { MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); int imageIndex = r.getSeries(); int planeCount = retrieve.getPlaneCount(imageIndex); int[] zct = r.getZCTCoords(no); for (int i=0; i<planeCount; i++) { Integer theC = retrieve.getPlaneTheC(imageIndex, i).getValue(); Integer theT = retrieve.getPlaneTheT(imageIndex, i).getValue(); Integer theZ = retrieve.getPlaneTheZ(imageIndex, i).getValue(); if (zct[0] == theZ.intValue() && zct[1] == theC.intValue() && zct[2] == theT.intValue()) { return i; } } return -1; }
/** * @return true if min-max is set * @throws FormatException * @throws IOException */ @SuppressWarnings("unchecked") public boolean isMinMaxSet() throws FormatException, IOException { if (minMaxSet == null) { MetadataStore store = reader.getMetadataStore(); int series = reader.getSeries(); List<Pixels> pixels = (List<Pixels>) store.getRoot(); if (pixels == null) { return minMaxSet = true; } Pixels p = pixels.get(series); Channel c = p.getChannel(p.getSizeC().getValue() - 1); minMaxSet = c.getStatsInfo() != null; } return minMaxSet; }
final MetadataRetrieve retrieve = (MetadataRetrieve)r.getMetadataStore(); double[] loc = new double[3];
final int cModStep = hasModulo ? (int) cMod.step : r.getSizeC(); final MetadataRetrieve mr = (MetadataRetrieve) r.getMetadataStore();
throws FormatException, IOException MetadataStore store = input.getMetadataStore(); MetadataRetrieve meta = null; try {