/* @see BaseTiffReader#initMetadataStore() */ protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); if (creationDate != null) { creationDate = DateTools.formatDate(creationDate, "yyyyMMdd HHmmSSZ"); } for (int i = 0; i < getSeriesCount(); i++) { String name = imageName; if (imageName.length() == 0) { name = "#" + (i + 1); } else { name += " #" + (i + 1); } store.setImageName(name, i); if (creationDate != null) { store.setImageAcquisitionDate(new Timestamp(creationDate), i); } } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { if (experimenterName == null) experimenterName = ""; int nameSpace = experimenterName.indexOf(" "); String firstName = nameSpace == -1 ? "" : experimenterName.substring(0, nameSpace); String lastName = nameSpace == -1 ? experimenterName : experimenterName.substring(nameSpace + 1); String experimenter = MetadataTools.createLSID("Experimenter", 0); store.setExperimenterID(experimenter, 0); store.setExperimenterFirstName(firstName, 0); store.setExperimenterLastName(lastName, 0); for (int i = 0; i < getSeriesCount(); i++) { store.setImageExperimenterRef(experimenter, i); } } }
/** * Populates the metadata store using the data parsed in {@link #initStandardMetadata()} along * with some further parsing done in the method itself. * * <p>All calls to the active <code>MetadataStore</code> should be made in this method and * <b>only</b> in this method. This is especially important for sub-classes that override the * getters for pixel set array size, etc. */ protected void initMetadataStore() throws FormatException { LOGGER.info("Populating OME metadata"); // the metadata store we're working with MetadataStore store = makeFilterMetadata(); IFD firstIFD = ifds.get(0); IFD exif = null; if (ifds.get(0).containsKey(IFD.EXIF)) { try { IFDList exifIFDs = tiffParser.getExifIFDs(); if (exifIFDs.size() > 0) { exif = exifIFDs.get(0); } tiffParser.fillInIFD(exif); } catch (IOException e) { LOGGER.debug("Could not read EXIF IFDs", e); } } MetadataTools.populatePixels(store, this, exif != null); // format the creation date to ISO 8601 String creationDate = getImageCreationDate(); String date = DateTools.formatDate(creationDate, DATE_FORMATS); if (creationDate != null && date == null) { LOGGER.warn("unknown creation date format: {}", creationDate); } creationDate = date; // populate Image if (creationDate != null) { store.setImageAcquisitionDate(new Timestamp(creationDate), 0); } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { // populate Experimenter String artist = firstIFD.getIFDTextValue(IFD.ARTIST); if (artist != null) { String firstName = null, lastName = null; int ndx = artist.indexOf(" "); if (ndx < 0) lastName = artist; else { firstName = artist.substring(0, ndx); lastName = artist.substring(ndx + 1); } String email = firstIFD.getIFDStringValue(IFD.HOST_COMPUTER); store.setExperimenterFirstName(firstName, 0); store.setExperimenterLastName(lastName, 0); store.setExperimenterEmail(email, 0); store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0); } store.setImageDescription(firstIFD.getComment(), 0); // set the X and Y pixel dimensions double pixX = firstIFD.getXResolution(); double pixY = firstIFD.getYResolution(); PositiveFloat sizeX = FormatTools.getPhysicalSizeX(pixX); PositiveFloat sizeY = FormatTools.getPhysicalSizeY(pixY); if (sizeX != null) { store.setPixelsPhysicalSizeX(sizeX, 0); } if (sizeY != null) { store.setPixelsPhysicalSizeY(sizeY, 0); } store.setPixelsPhysicalSizeZ(null, 0); if (exif != null) { if (exif.containsKey(IFD.EXPOSURE_TIME)) { Object exp = exif.get(IFD.EXPOSURE_TIME); if (exp instanceof TiffRational) { Double exposure = ((TiffRational) exp).doubleValue(); for (int i = 0; i < getImageCount(); i++) { store.setPlaneExposureTime(exposure, 0, i); } } } } } }
/* @see BaseTiffReader#initMetadataStore() */ @Override protected void initMetadataStore() throws FormatException { super.initMetadataStore(); MetadataStore store = makeFilterMetadata(); MetadataTools.populatePixels(store, this); if (date != null) { date = DateTools.formatDate(date, DATE_FORMAT); if (date != null) { store.setImageAcquisitionDate(new Timestamp(date), 0); } } if (imageName != null) { store.setImageName(imageName, 0); } if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) { if (imageDescription != null) { store.setImageDescription(imageDescription, 0); } if (userName != null) { store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0); store.setExperimenterLastName(userName, 0); } if (microscopeModel != null) { String instrument = MetadataTools.createLSID("Instrument", 0); store.setInstrumentID(instrument, 0); store.setImageInstrumentRef(instrument, 0); store.setMicroscopeModel(microscopeModel, 0); } if (detectors != null && detectors.size() > 0) { String instrument = MetadataTools.createLSID("Instrument", 0); store.setInstrumentID(instrument, 0); store.setImageInstrumentRef(instrument, 0); for (int i = 0; i < detectors.size(); i++) { String detectorID = MetadataTools.createLSID("Detector", 0, i); store.setDetectorID(detectorID, 0, i); store.setDetectorModel(detectors.get(i), 0, i); store.setDetectorType(getDetectorType("Other"), 0, i); } } if (magnification != null) { store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0); store.setObjectiveNominalMagnification(magnification, 0, 0); store.setObjectiveCorrection(getCorrection("Other"), 0, 0); store.setObjectiveImmersion(getImmersion("Other"), 0, 0); } store.setStageLabelX(stageX, 0); store.setStageLabelY(stageY, 0); store.setStageLabelZ(stageZ, 0); store.setStageLabelName("", 0); Length physicalSizeX = FormatTools.getPhysicalSizeX(sizeX); Length physicalSizeY = FormatTools.getPhysicalSizeY(sizeY); if (physicalSizeX != null) { store.setPixelsPhysicalSizeX(physicalSizeX, 0); } if (physicalSizeY != null) { store.setPixelsPhysicalSizeY(physicalSizeY, 0); } if (timeIncrement != null) { store.setPixelsTimeIncrement(new Time(timeIncrement, UNITS.S), 0); } } }