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('<'); xmlString = null; textString = null; core = handler.getCoreMetadataList(); if (backupHandler == null || backupHandler.getChannelNames().size() == 0) final Map<String, Object> globalMetadata = handler.getMetadata(); for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) { addGlobalMeta(entry.getKey(), entry.getValue()); ND2Handler handler = new ND2Handler(core, offsetCount); for (String line : lines) { int separator = line.indexOf(':'); handler.parseKeyAndValue(key, value, null); if (handler.isDimensions(key)) { textData = true; core = handler.getCoreMetadataList(); if (backupHandler == null || backupHandler.getChannelNames().size() == 0)
@Test(dataProvider="pixelsSizeKey") public void testParsePixelsSizeZ(String key, String value, double pixelSizeZ) { handler.parseKeyAndValue(key, value, ""); assertEquals(handler.getPixelSizeZ(), pixelSizeZ); } }
@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) { } }
String date = handler.getDate(); if (date != null) { store.setImageAcquisitionDate(new Timestamp(date), 0); Length sizeX = FormatTools.getPhysicalSizeX(handler.getPixelSizeX()); Length sizeY = FormatTools.getPhysicalSizeY(handler.getPixelSizeY()); Length sizeZ = FormatTools.getPhysicalSizeZ(handler.getPixelSizeZ()); if (sizeX != null) { store.setPixelsPhysicalSizeX(sizeX, 0); ArrayList<Double> exposureTimes = handler.getExposureTimes(); ArrayList<Length> posX = handler.getXPositions(); ArrayList<Length> posY = handler.getYPositions(); ArrayList<Length> posZ = handler.getZPositions(); store.setDetectorModel(handler.getCameraModel(), 0, 0); store.setDetectorType(MetadataTools.getDetectorType("Other"), 0, 0); ArrayList<String> channelNames = handler.getChannelNames(); ArrayList<String> modality = handler.getModalities(); ArrayList<String> binning = handler.getBinnings(); ArrayList<Double> speed = handler.getSpeeds(); ArrayList<Double> gain = handler.getGains(); ArrayList<Double> temperature = handler.getTemperatures(); ArrayList<Double> exWave = handler.getExcitationWavelengths(); ArrayList<Double> emWave = handler.getEmissionWavelengths(); ArrayList<Integer> power = handler.getPowers(); ArrayList<Hashtable<String, String>> rois = handler.getROIs(); Double pinholeSize = handler.getPinholeSize();
new ND2Handler(core, imageOffsets.size()); XMLTools.parseXML(xmlString, handler); xmlString = null; core = handler.getCoreMetadataList(); if (backupHandler == null) { backupHandler = handler; new ND2Handler(core, getSizeX() == 0, imageOffsets.size()); XMLTools.parseXML(xmlString, handler); xmlString = null; if (handler.getChannelColors().size() > 0) { channelColors = handler.getChannelColors(); isLossless = handler.isLossless(); fieldIndex = handler.getFieldIndex(); core = handler.getCoreMetadataList(); final Map<String, Object> globalMetadata = handler.getMetadata(); nXFields = handler.getXFields(); if (nXFields > 6) { nXFields = 0; core.add(handler.getCoreMetadataList().get(0, 0)); if (positionCount != getSeriesCount() && (getSizeZ() == imageOffsets.size() || (extraZDataCount > 1 && getSizeZ() == 1 && (extraZDataCount == getSizeC())) || (handler.getXPositions().size() == 0 && (xOffset == 0 && getSizeZ() != getSeriesCount()))) && getSeriesCount() > 1) { CoreMetadata ms0 = core.get(0, 0); if (getSeriesCount() > ms0.sizeZ) {
parseKeyAndValue(v[0].trim(), v[1].trim(), runtype); parseKeyAndValue(v[0], t.substring(t.indexOf(':') + 1).trim(), runtype); else if (isDimensions(key)) { String[] dims = value.split(" x "); Double step = parsePixelsSizeZFromKey(key); if (step != null) pixelSizeZ = step; String nextKey = values[q].substring(0, colon).trim(); String nextValue = values[q].substring(colon + 1).trim(); parseKeyAndValue(nextKey, nextValue, runtype);
parseKeyAndValue(qName, value, prevRuntype); parseKeyAndValue(qName, attributes.getValue("Text"), prevRuntype); parseKeyAndValue(qName, value, prevRuntype); parseKeyAndValue(qName, value, prevRuntype); parseKeyAndValue(sb.toString(), value, prevRuntype);
@BeforeMethod public void setUp() { coreList = new CoreMetadataList(); coreList.add(new CoreMetadata()); handler = new ND2Handler(coreList, 1); }
String date = handler.getDate(); if (date != null) { store.setImageAcquisitionDate(new Timestamp(date), 0); Length sizeX = FormatTools.getPhysicalSizeX(handler.getPixelSizeX()); Length sizeY = FormatTools.getPhysicalSizeY(handler.getPixelSizeY()); Length sizeZ = FormatTools.getPhysicalSizeZ(handler.getPixelSizeZ()); if (sizeX != null) { store.setPixelsPhysicalSizeX(sizeX, 0); ArrayList<Double> exposureTimes = handler.getExposureTimes(); ArrayList<Length> posX = handler.getXPositions(); ArrayList<Length> posY = handler.getYPositions(); ArrayList<Length> posZ = handler.getZPositions(); store.setDetectorModel(handler.getCameraModel(), 0, 0); store.setDetectorType(MetadataTools.getDetectorType("Other"), 0, 0); ArrayList<String> channelNames = handler.getChannelNames(); ArrayList<String> modality = handler.getModalities(); ArrayList<String> binning = handler.getBinnings(); ArrayList<Double> speed = handler.getSpeeds(); ArrayList<Double> gain = handler.getGains(); ArrayList<Double> temperature = handler.getTemperatures(); ArrayList<Double> exWave = handler.getExcitationWavelengths(); ArrayList<Double> emWave = handler.getEmissionWavelengths(); ArrayList<Integer> power = handler.getPowers(); ArrayList<Hashtable<String, String>> rois = handler.getROIs(); Double pinholeSize = handler.getPinholeSize();
new ND2Handler(core, imageOffsets.size()); XMLTools.parseXML(xmlString, handler); xmlString = null; core = handler.getCoreMetadataList(); if (backupHandler == null) { backupHandler = handler; new ND2Handler(core, getSizeX() == 0, imageOffsets.size()); XMLTools.parseXML(xmlString, handler); xmlString = null; if (handler.getChannelColors().size() > 0) { channelColors = handler.getChannelColors(); isLossless = handler.isLossless(); fieldIndex = handler.getFieldIndex(); core = handler.getCoreMetadataList(); final Map<String, Object> globalMetadata = handler.getMetadata(); nXFields = handler.getXFields(); if (nXFields > 6) { nXFields = 0; core.add(handler.getCoreMetadataList().get(0, 0)); if (positionCount != getSeriesCount() && (getSizeZ() == imageOffsets.size() || (extraZDataCount > 1 && getSizeZ() == 1 && (extraZDataCount == getSizeC())) || (handler.getXPositions().size() == 0 && (xOffset == 0 && getSizeZ() != getSeriesCount()))) && getSeriesCount() > 1) { CoreMetadata ms0 = core.get(0, 0); if (getSeriesCount() > ms0.sizeZ) {
parseKeyAndValue(v[0].trim(), v[1].trim(), runtype); parseKeyAndValue(v[0], t.substring(t.indexOf(':') + 1).trim(), runtype); else if (isDimensions(key)) { String[] dims = value.split(" x "); Double step = parsePixelsSizeZFromKey(key); if (step != null) pixelSizeZ = step; String nextKey = values[q].substring(0, colon).trim(); String nextValue = values[q].substring(colon + 1).trim(); parseKeyAndValue(nextKey, nextValue, runtype);
@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) { } }
parseKeyAndValue(qName, value, prevRuntype); parseKeyAndValue(qName, attributes.getValue("Text"), prevRuntype); parseKeyAndValue(qName, value, prevRuntype); parseKeyAndValue(qName, value, prevRuntype); parseKeyAndValue(sb.toString(), value, prevRuntype);
ArrayList<String> posNames = handler.getPositionNames(); int nameWidth = String.valueOf(getSeriesCount()).length(); for (int i=0; i<getSeriesCount(); i++) { channelNames = handler.getChannelNames(); if (channelNames.size() < getEffectiveSizeC() && backupHandler != null) { channelNames = backupHandler.getChannelNames(); double sizeX = handler.getPixelSizeX(); double sizeY = handler.getPixelSizeY(); double sizeZ = handler.getPixelSizeZ(); if (handler != null && handler.getExposureTimes().size() > 0) { for (Double time : handler.getExposureTimes()) { addGlobalMetaList("Exposure time (primary XML)", time); for (Double time : backupHandler.getExposureTimes()) { addGlobalMetaList("Exposure time (secondary XML)", time); if (exposureTime.size() == 0 || handler.getExposureTimes().size() == 1 || exposureTime.size() % getSizeC() != 0) { exposureTime = handler.getExposureTimes(); if (backupHandler != null && backupHandler.getExposureTimes().size() > exposureTime.size()) { exposureTime = backupHandler.getExposureTimes(); else if (backupHandler == null || backupHandler.getExposureTimes().size() == 0) { exposureTime = handler.getExposureTimes(); else if (backupHandler != null && backupHandler.getExposureTimes().size() == exposureTime.size()) { exposureTime = backupHandler.getExposureTimes();
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('<'); xmlString = null; textString = null; core = handler.getCoreMetadataList(); if (backupHandler == null || backupHandler.getChannelNames().size() == 0) final Map<String, Object> globalMetadata = handler.getMetadata(); for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) { addGlobalMeta(entry.getKey(), entry.getValue()); ND2Handler handler = new ND2Handler(core, offsetCount); for (String line : lines) { int separator = line.indexOf(':'); handler.parseKeyAndValue(key, value, null); if (handler.isDimensions(key)) { textData = true; core = handler.getCoreMetadataList(); if (backupHandler == null || backupHandler.getChannelNames().size() == 0)
ArrayList<String> posNames = handler.getPositionNames(); int nameWidth = String.valueOf(getSeriesCount()).length(); for (int i=0; i<getSeriesCount(); i++) { channelNames = handler.getChannelNames(); if (channelNames.size() < getEffectiveSizeC() && backupHandler != null) { channelNames = backupHandler.getChannelNames(); double sizeX = handler.getPixelSizeX(); double sizeY = handler.getPixelSizeY(); double sizeZ = handler.getPixelSizeZ(); if (handler != null && handler.getExposureTimes().size() > 0) { for (Double time : handler.getExposureTimes()) { addGlobalMetaList("Exposure time (primary XML)", time); for (Double time : backupHandler.getExposureTimes()) { addGlobalMetaList("Exposure time (secondary XML)", time); if (exposureTime.size() == 0 || handler.getExposureTimes().size() == 1 || exposureTime.size() % getSizeC() != 0) { exposureTime = handler.getExposureTimes(); if (backupHandler != null && backupHandler.getExposureTimes().size() > exposureTime.size()) { exposureTime = backupHandler.getExposureTimes(); else if (backupHandler == null || backupHandler.getExposureTimes().size() == 0) { exposureTime = handler.getExposureTimes(); else if (backupHandler != null && backupHandler.getExposureTimes().size() == exposureTime.size()) { exposureTime = backupHandler.getExposureTimes();