@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); } } }
private void populateMetadataStore() throws FormatException { MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this, true); for (int i=0; i<getSeriesCount(); i++) { // populate Image data if (i < imageNames.size()) { store.setImageName(imageNames.get(i), i); } String date = i < dates.size() ? dates.get(i) : ""; if (date != null && !date.equals("")) { store.setImageAcquisitionDate(new Timestamp(date), i); } } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { for (int i=0; i<getSeriesCount(); i++) { // populate PlaneTiming data for (int q=0; q<core.get(i).imageCount; q++) { if (exposureTimes.get(i) != null) { store.setPlaneExposureTime(new Time(exposureTimes.get(i), UNITS.SECOND), i, q); } } // populate Experiment data if (i < types.size()) { store.setExperimentID(MetadataTools.createLSID("Experiment", i), i); store.setExperimentType(MetadataTools.getExperimentType(types.get(i)), i); } } } }
private void populateMetadataStore() throws FormatException { MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this, true); for (int i=0; i<getSeriesCount(); i++) { // populate Image data if (i < imageNames.size()) { store.setImageName(imageNames.get(i), i); } String date = i < dates.size() ? dates.get(i) : ""; if (date != null && !date.equals("")) { store.setImageAcquisitionDate(new Timestamp(date), i); } } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { for (int i=0; i<getSeriesCount(); i++) { // populate PlaneTiming data for (int q=0; q<core.get(i).imageCount; q++) { if (exposureTimes.get(i) != null) { store.setPlaneExposureTime(new Time(exposureTimes.get(i), UNITS.SECOND), i, q); } } // populate Experiment data if (i < types.size()) { store.setExperimentID(MetadataTools.createLSID("Experiment", i), i); store.setExperimentType(MetadataTools.getExperimentType(types.get(i)), i); } } } }
/** * Populates the given {@link MetadataStore}, for the specified series, using * the provided values. * <p> * After calling this method, the metadata store will be sufficiently * populated for use with an {@link IFormatWriter} (assuming it is also a * {@link MetadataRetrieve}). * </p> */ public static void populateMetadata(MetadataStore store, String file, int series, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel) { store.setImageID(createLSID("Image", series), series); setDefaultCreationDate(store, file, series); if (imageName != null) store.setImageName(imageName, series); populatePixelsOnly(store, series, littleEndian, dimensionOrder, pixelType, sizeX, sizeY, sizeZ, sizeC, sizeT, samplesPerPixel); }
/** * Populates the given {@link MetadataStore}, for the specified series, using * the provided values. * <p> * After calling this method, the metadata store will be sufficiently * populated for use with an {@link IFormatWriter} (assuming it is also a * {@link MetadataRetrieve}). * </p> */ public static void populateMetadata(MetadataStore store, String file, int series, String imageName, boolean littleEndian, String dimensionOrder, String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel) { store.setImageID(createLSID("Image", series), series); setDefaultCreationDate(store, file, series); if (imageName != null) store.setImageName(imageName, series); populatePixelsOnly(store, series, littleEndian, dimensionOrder, pixelType, sizeX, sizeY, sizeZ, sizeC, sizeT, samplesPerPixel); }
@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); } } } }
name += " #" + (i + 1); store.setImageName(name, i); if (creationDate != null) { store.setImageAcquisitionDate(new Timestamp(creationDate), i);
timestamp = DateTools.formatDate(timestamp, DATE_FORMAT); store.setImageName(imageName, 0); if (timestamp != null) { store.setImageAcquisitionDate(new Timestamp(timestamp), 0);
name += " #" + (i + 1); store.setImageName(name, i); if (creationDate != null) { store.setImageAcquisitionDate(new Timestamp(creationDate), i);
store.setImageName(file.getParentFile().getName(), 0);
MetadataTools.populatePixels(store, this); for (int i=0; i<getSeriesCount(); i++) { store.setImageName("Series " + (i + 1), i);
store.setImageName(name, 0); store.setImageDescription(description, 0); MetadataTools.populatePixels(store, this);
MetadataTools.populatePixels(store, this); store.setImageName(imageName, 0); if (acquisitionDate != null) { store.setImageAcquisitionDate(new Timestamp(acquisitionDate), 0);
MetadataTools.populatePixels(store, this); store.setImageName(imageName, 0); if (acquisitionDate != null) { store.setImageAcquisitionDate(new Timestamp(acquisitionDate), 0);