/** Parse metadata values from the Acqusition.xml file. */ private void parseXMLFile() throws IOException { Position p = positions.get(getSeries()); String xmlData = DataTools.readFile(p.xmlFile); xmlData = XMLTools.sanitizeXML(xmlData); DefaultHandler handler = new MicromanagerHandler(); XMLTools.parseXML(xmlData, handler); }
/** Parse metadata values from the Acqusition.xml file. */ private void parseXMLFile() throws IOException { Position p = positions.get(getSeries()); String xmlData = DataTools.readFile(p.xmlFile); xmlData = XMLTools.sanitizeXML(xmlData); DefaultHandler handler = new MicromanagerHandler(); XMLTools.parseXML(xmlData, handler); }
@Override protected void initStandardMetadata() throws FormatException, IOException { super.initStandardMetadata(); String xml = ifds.get(0).getIFDTextValue(NIKON_XML_TAG).trim(); if (xml.length() == 0) { xml = ifds.get(0).getIFDTextValue(NIKON_XML_TAG_2).trim(); } int open = xml.indexOf('<'); if (open >= 0) { xml = xml.substring(open); } xml = "<NIKON>" + xml + "</NIKON>"; xml = XMLTools.sanitizeXML(xml); handler = new ND2Handler(core, false, getImageCount()); try { XMLTools.parseXML(xml, handler); final Map<String, Object> globalMetadata = handler.getMetadata(); for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) { addGlobalMeta(entry.getKey(), entry.getValue()); } } catch (IOException e) { } }
@Override protected void initStandardMetadata() throws FormatException, IOException { super.initStandardMetadata(); String xml = ifds.get(0).getIFDTextValue(NIKON_XML_TAG).trim(); if (xml.length() == 0) { xml = ifds.get(0).getIFDTextValue(NIKON_XML_TAG_2).trim(); } int open = xml.indexOf('<'); if (open >= 0) { xml = xml.substring(open); } xml = "<NIKON>" + xml + "</NIKON>"; xml = XMLTools.sanitizeXML(xml); handler = new ND2Handler(core, false, getImageCount()); try { XMLTools.parseXML(xml, handler); final Map<String, Object> globalMetadata = handler.getMetadata(); for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) { addGlobalMeta(entry.getKey(), entry.getValue()); } } catch (IOException e) { } }
private void parseText(String textString, int offsetCount, boolean useDimensions) { try { ND2Handler handler = new ND2Handler(core, offsetCount); String xmlString = XMLTools.sanitizeXML(textString); int start = xmlString.indexOf('<'); int end = xmlString.lastIndexOf(">");
/** * @see OMEXMLService#createOMEXMLMetadata(java.lang.String, java.lang.String) */ @Override public OMEXMLMetadata createOMEXMLMetadata(String xml, String version) throws ServiceException { if (xml != null) { xml = XMLTools.sanitizeXML(xml); } OMEXMLMetadataRoot ome = xml == null ? null : createRoot(transformToLatestVersion(xml)); OMEXMLMetadata meta = new OMEPyramidStore(); if (ome != null) meta.setRoot(ome); return meta; }
private void parseText(String textString, int offsetCount, boolean useDimensions) { try { ND2Handler handler = new ND2Handler(core, offsetCount); String xmlString = XMLTools.sanitizeXML(textString); int start = xmlString.indexOf('<'); int end = xmlString.lastIndexOf(">");
/** * @see OMEXMLService#createOMEXMLMetadata(java.lang.String, java.lang.String) */ @Override public OMEXMLMetadata createOMEXMLMetadata(String xml, String version) throws ServiceException { if (xml != null) { xml = XMLTools.sanitizeXML(xml); } OMEXMLMetadataRoot ome = xml == null ? null : createRoot(transformToLatestVersion(xml)); OMEXMLMetadata meta = new OMEPyramidStore(); if (ome != null) meta.setRoot(ome); return meta; }
String xml = XMLTools.sanitizeXML(ifd.getIFDStringValue(FLEX));
String xml = XMLTools.sanitizeXML(ifd.getIFDStringValue(FLEX));
private void parseFile(String tiff, MetamorphHandler handler) throws IOException { try (RandomAccessInputStream s = new RandomAccessInputStream(tiff)) { TiffParser parser = new TiffParser(s); IFD firstIFD = parser.getFirstIFD(); String xml = XMLTools.sanitizeXML(firstIFD.getComment()); XMLTools.parseXML(xml, handler); } }
private void parseFile(String tiff, MetamorphHandler handler) throws IOException { try (RandomAccessInputStream s = new RandomAccessInputStream(tiff)) { TiffParser parser = new TiffParser(s); IFD firstIFD = parser.getFirstIFD(); String xml = XMLTools.sanitizeXML(firstIFD.getComment()); XMLTools.parseXML(xml, handler); } }
XMLTools.sanitizeXML(new String(buf, Constants.ENCODING));
XMLTools.sanitizeXML(new String(buf, Constants.ENCODING));
xml = XMLTools.sanitizeXML(xml);
xml = XMLTools.sanitizeXML(xml);
description = XMLTools.sanitizeXML(description);
description = XMLTools.sanitizeXML(description);
if (metadata.indexOf("xml") != -1) { metadata = metadata.substring(metadata.indexOf('<')); metadata = "<root>" + XMLTools.sanitizeXML(metadata) + "</root>"; try { Hashtable<String, String> xmlMetadata =
if (metadata.indexOf("xml") != -1) { metadata = metadata.substring(metadata.indexOf('<')); metadata = "<root>" + XMLTools.sanitizeXML(metadata) + "</root>"; try { Hashtable<String, String> xmlMetadata =