private void fillPhysicalSizes(MetadataStore store) { if (physicalSizeX == null && physicalSizeY == null && physicalSizeZ == null) return; for (int s=0; s<getSeriesCount(); s++) { store.setPixelsPhysicalSizeX(physicalSizeX, s); store.setPixelsPhysicalSizeY(physicalSizeY, s); store.setPixelsPhysicalSizeZ(physicalSizeZ, s); } }
@Override public void characters(char[] ch, int start, int length) { if (currentQName.equals("UserComment")) { String value = new String(ch, start, length); store.setImageDescription(value, 0); } }
/** * Set the value of this annotation using the given Modulo object * @param meta the associated OMEXMLMetadata * @param m the Modulo object from which to retrieve dimension information */ public void setModulo(OMEXMLMetadata meta, Modulo m) { modulo = m; setNamespace(MODULO_NS); Document doc = XMLTools.createDocument(); Element r = makeModuloElement(doc); setValue(XMLTools.dumpXML(null, doc, r, false)); }
/** * Create an empty ROI and link it to the Image. * @param store MetadataStore in which to create the ROI * @param index ROI index * @return corresponding Shape ID to be used with the new ROI */ private String createROI(MetadataStore store, int index) { String roi = MetadataTools.createLSID("ROI", index); store.setROIID(roi, index); store.setImageROIRef(roi, 0, index); return MetadataTools.createLSID("Shape", index, 0); }
@Override public Object getMetadataStoreRoot() { FormatTools.assertId(currentId, true, 1); return getMetadataStore().getRoot(); }
@Override public void setSeries(int series) throws FormatException { if (series < 0) throw new FormatException("Series must be > 0."); if (series >= metadataRetrieve.getImageCount()) { throw new FormatException("Series is '" + series + "' but MetadataRetrieve only defines " + metadataRetrieve.getImageCount() + " series."); } this.series = series; resolution = 0; }
public void getSeriesName(String[] seriesName) { MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); seriesName[0] = retrieve.getImageName(r.getSeries()); }
private void fillAcquisitionDate(MetadataStore store, String date, int imageIndex) { if (date == null) return; if(DateTools.getTime(date, DateTools.FILENAME_FORMAT) != -1) { Timestamp stamp = new Timestamp( DateTools.formatDate(date, DateTools.FILENAME_FORMAT)); store.setImageAcquisitionDate(stamp, imageIndex); } }
private void fillExposureTime(MetadataStore store) { if (exposureTime == null) return; int oldSeries = getSeries(); for (int s=0; s<getSeriesCount(); s++) { setSeries(s); for (int i=0; i<getImageCount(); i++) { store.setPlaneExposureTime(exposureTime, s, i); } } setSeries(oldSeries); }
/** Return a properly configured loci.formats.meta.FilterMetadata. */ protected MetadataStore makeFilterMetadata() { return new FilterMetadata(getMetadataStore(), isMetadataFiltered()); }
public IMetadata convertXml(MetadataRetrieve retrieve) throws ServiceException { IMetadata xmlMeta = service.createOMEXMLMetadata(); xmlMeta.createRoot(); service.convertMetadata(retrieve, xmlMeta); return xmlMeta; }
@Override public int getResolutionCount() { if (hasResolutions()) { return resolutionData.get(getSeries()).size() + 1; } MetadataRetrieve r = getMetadataRetrieve(); if (r instanceof IPyramidStore) { return ((IPyramidStore) r).getResolutionCount(getSeries()); } return 1; }
private void readWavelength(int channel, MetadataStore store) throws FormatException, IOException { float min = in.readFloat(); float max = in.readFloat(); addGlobalMeta("Wavelength " + (channel + 1) + " min. intensity", min); addGlobalMeta("Wavelength " + (channel + 1) + " max. intensity", max); if (store instanceof IMinMaxStore) { ((IMinMaxStore) store).setChannelGlobalMinMax(channel, min, max, 0); } }
private void fillPhysicalSizes(MetadataStore store) { if (physicalSizeX == null && physicalSizeY == null && physicalSizeZ == null) return; for (int s=0; s<getSeriesCount(); s++) { store.setPixelsPhysicalSizeX(physicalSizeX, s); store.setPixelsPhysicalSizeY(physicalSizeY, s); store.setPixelsPhysicalSizeZ(physicalSizeZ, s); } }
@Override public void setSeries(int series) throws FormatException { if (series < 0) throw new FormatException("Series must be > 0."); if (series >= metadataRetrieve.getImageCount()) { throw new FormatException("Series is '" + series + "' but MetadataRetrieve only defines " + metadataRetrieve.getImageCount() + " series."); } this.series = series; resolution = 0; }
public void getSeriesName(String[] seriesName) { MetadataRetrieve retrieve = (MetadataRetrieve) r.getMetadataStore(); seriesName[0] = retrieve.getImageName(r.getSeries()); }
/** * Set the value of this annotation using the given Modulo object * @param meta the associated OMEXMLMetadata * @param m the Modulo object from which to retrieve dimension information */ public void setModulo(OMEXMLMetadata meta, Modulo m) { modulo = m; setNamespace(MODULO_NS); Document doc = XMLTools.createDocument(); Element r = makeModuloElement(doc); setValue(XMLTools.dumpXML(null, doc, r, false)); }
@Override public void characters(char[] ch, int start, int length) { if (currentQName.equals("UserComment")) { String value = new String(ch, start, length); store.setImageDescription(value, 0); } }
private void fillExposureTime(MetadataStore store) { if (exposureTime == null) return; int oldSeries = getSeries(); for (int s=0; s<getSeriesCount(); s++) { setSeries(s); for (int i=0; i<getImageCount(); i++) { store.setPlaneExposureTime(exposureTime, s, i); } } setSeries(oldSeries); }
/** Return a properly configured loci.formats.meta.FilterMetadata. */ protected MetadataStore makeFilterMetadata() { return new FilterMetadata(getMetadataStore(), isMetadataFiltered()); }