/** Populates the metadata hashtable and metadata store. */ protected void initMetadata() throws FormatException, IOException { initStandardMetadata(); initMetadataStore(); }
/** Populates the metadata hashtable and metadata store. */ protected void initMetadata() throws FormatException, IOException { initStandardMetadata(); initMetadataStore(); }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); if (description != null) { description = description.replaceAll("\n", "; "); store.setImageDescription(description, 0); } populateMetadataStoreImageJ(store); }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); if (description != null) { description = description.replaceAll("\n", "; "); store.setImageDescription(description, 0); } populateMetadataStoreImageJ(store); }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); for (int i=0; i<getSeriesCount(); i++) { store.setImageName("Series " + (i + 1), i); } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); for (int i=0; i<getSeriesCount(); i++) { store.setImageName("Series " + (i + 1), i); } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); for (int i=0; i<getSeriesCount(); i++) { store.setImageName("Series " + (i + 1), i); } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); for (int i=0; i<getSeriesCount(); i++) { store.setImageName("Series " + (i + 1), i); } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); int simsIndex = seriesTypes.get("SIMS"); String instrument = (String) simsDescription.get("mibi.instrument"); store.setInstrumentID(formatMetadata("Instrument", instrument), simsIndex); store.setImageDescription((String) simsDescription.get("mibi.description"), simsIndex); String currentFile = FilenameUtils.getName(this.getCurrentFile()); for (Map.Entry<String, Integer> entry : seriesTypes.entrySet()) { String key = entry.getKey(); if (key != null) { store.setImageID(formatMetadata("Image", entry.getKey()), entry.getValue()); store.setImageName(currentFile + " " + entry.getKey(), entry.getValue()); } } for (int j = 0; j < channelIDs.size(); j++) { store.setChannelID(formatMetadata("Channel", channelIDs.get(j)), simsIndex, j); if (channelNames.get(j) != null) { store.setChannelName(formatMetadata("Target", channelNames.get(j)), simsIndex, j); } } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); int simsIndex = seriesTypes.get("SIMS"); String instrument = (String) simsDescription.get("mibi.instrument"); store.setInstrumentID(formatMetadata("Instrument", instrument), simsIndex); store.setImageDescription((String) simsDescription.get("mibi.description"), simsIndex); String currentFile = FilenameUtils.getName(this.getCurrentFile()); for (Map.Entry<String, Integer> entry : seriesTypes.entrySet()) { String key = entry.getKey(); if (key != null) { store.setImageID(formatMetadata("Image", entry.getKey()), entry.getValue()); store.setImageName(currentFile + " " + entry.getKey(), entry.getValue()); } } for (int j = 0; j < channelIDs.size(); j++) { store.setChannelID(formatMetadata("Channel", channelIDs.get(j)), simsIndex, j); if (channelNames.get(j) != null) { store.setChannelName(formatMetadata("Target", channelNames.get(j)), simsIndex, j); } } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); for (int i=0; i<getSeriesCount(); i++) { store.setImageName("Series " + (i + 1), i); } MetadataLevel level = getMetadataOptions().getMetadataLevel(); if (level != MetadataLevel.MINIMUM) { // do not store the mask data in OME-XML MetadataStores // doing so would guarantee invalid OME-XML, since the required BinData // will not be stored with the mask dimensions if (level != MetadataLevel.NO_OVERLAYS && !(getMetadataStore() instanceof OMEXMLMetadata)) { try { parseROIs(store); } catch (IOException e) { LOGGER.debug("Could not parse ROIs", e); } } } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); for (int i=0; i<getSeriesCount(); i++) { store.setImageName("Series " + (i + 1), i); } MetadataLevel level = getMetadataOptions().getMetadataLevel(); if (level != MetadataLevel.MINIMUM) { // do not store the mask data in OME-XML MetadataStores // doing so would guarantee invalid OME-XML, since the required BinData // will not be stored with the mask dimensions if (level != MetadataLevel.NO_OVERLAYS && !(getMetadataStore() instanceof OMEXMLMetadata)) { try { parseROIs(store); } catch (IOException e) { LOGGER.debug("Could not parse ROIs", e); } } } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore();
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore();
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this);
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this);
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this, true);
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); date = DateTools.formatDate(date, "HH:mm dd-MMM-yyyy"); if (date != null) { store.setImageAcquisitionDate(new Timestamp(date), 0); } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { Length sizeX = FormatTools.getPhysicalSizeX(xSize); Length sizeY = FormatTools.getPhysicalSizeY(xSize); if (sizeX != null) { store.setPixelsPhysicalSizeX(sizeX, 0); } if (sizeY != null) { store.setPixelsPhysicalSizeY(sizeY, 0); } String instrument = MetadataTools.createLSID("Instrument", 0); store.setInstrumentID(instrument, 0); store.setImageInstrumentRef(instrument, 0); store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0); store.setObjectiveWorkingDistance(new Length(workingDistance, UNITS.MICROMETER), 0, 0); store.setObjectiveImmersion(MetadataTools.getImmersion("Other"), 0, 0); store.setObjectiveCorrection(MetadataTools.getCorrection("Other"), 0, 0); } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); date = DateTools.formatDate(date, "HH:mm dd-MMM-yyyy"); if (date != null) { store.setImageAcquisitionDate(new Timestamp(date), 0); } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { Length sizeX = FormatTools.getPhysicalSizeX(xSize); Length sizeY = FormatTools.getPhysicalSizeY(xSize); if (sizeX != null) { store.setPixelsPhysicalSizeX(sizeX, 0); } if (sizeY != null) { store.setPixelsPhysicalSizeY(sizeY, 0); } String instrument = MetadataTools.createLSID("Instrument", 0); store.setInstrumentID(instrument, 0); store.setImageInstrumentRef(instrument, 0); store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0); store.setObjectiveWorkingDistance(new Length(workingDistance, UNITS.MICROMETER), 0, 0); store.setObjectiveImmersion(MetadataTools.getImmersion("Other"), 0, 0); store.setObjectiveCorrection(MetadataTools.getCorrection("Other"), 0, 0); } }
@Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this);