Example 26 with Timestamp
use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.
the class DeltavisionReader method parseLogFile.
/**
* Extract metadata from associated log file, if it exists.
*/
private boolean parseLogFile(MetadataStore store) throws FormatException, IOException {
if (logFile == null || !new Location(logFile).exists()) {
logFile = null;
return false;
}
LOGGER.info("Parsing log file");
String[] lines = DataTools.readFile(logFile).split("[\r\n]");
String key, value = "", prefix = "";
int currentImage = 0;
List<String> channelNames = new ArrayList<String>();
List<Double> filters = new ArrayList<Double>();
for (String line : lines) {
int colon = line.indexOf(':');
if (colon >= 0 && colon < line.length() - 1 && !line.startsWith("Created")) {
key = line.substring(0, colon).trim();
value = line.substring(colon + 1).trim();
if (value.equals("") && !key.equals(""))
prefix = key;
addGlobalMeta(prefix + " " + key, value);
// Objective properties
if (key.equals("Objective")) {
// assume first word is the manufacturer's name
int space = value.indexOf(' ');
if (space != -1) {
String manufacturer = value.substring(0, space);
String extra = value.substring(space + 1);
String[] tokens = extra.split(",");
store.setObjectiveManufacturer(manufacturer, 0, 0);
String magnification = "", na = "";
if (tokens.length >= 1) {
int end = tokens[0].indexOf('X');
if (end > 0)
magnification = tokens[0].substring(0, end);
int start = tokens[0].indexOf('/');
if (start >= 0)
na = tokens[0].substring(start + 1);
}
try {
Double mag = new Double(magnification);
store.setObjectiveNominalMagnification(mag, 0, 0);
} catch (NumberFormatException e) {
LOGGER.warn("Could not parse magnification '{}'", magnification);
}
try {
store.setObjectiveLensNA(new Double(na), 0, 0);
} catch (NumberFormatException e) {
LOGGER.warn("Could not parse N.A. '{}'", na);
}
if (tokens.length >= 2) {
store.setObjectiveCorrection(getCorrection(tokens[1]), 0, 0);
}
// TODO: Token #2 is the microscope model name.
if (tokens.length > 3)
store.setObjectiveModel(tokens[3], 0, 0);
}
} else if (key.equalsIgnoreCase("Lens ID")) {
if (value.indexOf(',') != -1) {
value = value.substring(0, value.indexOf(','));
}
if (value.indexOf(' ') != -1) {
value = value.substring(value.indexOf(' ') + 1);
}
if (!value.equals("null")) {
String objectiveID = "Objective:" + value;
store.setObjectiveID(objectiveID, 0, 0);
for (int series = 0; series < getSeriesCount(); series++) {
store.setObjectiveSettingsID(objectiveID, series);
}
store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
}
} else // Image properties
if (key.equals("Pixel Size")) {
String[] pixelSizes = value.split(" ");
for (int q = 0; q < pixelSizes.length; q++) {
Double size = null;
try {
size = new Double(pixelSizes[q].trim());
} catch (NumberFormatException e) {
LOGGER.warn("Could not parse pixel size '{}'", pixelSizes[q].trim());
}
if (q == 0) {
Length sizeX = FormatTools.getPhysicalSizeX(size);
if (sizeX != null) {
for (int series = 0; series < getSeriesCount(); series++) {
store.setPixelsPhysicalSizeX(sizeX, series);
}
}
}
if (q == 1) {
Length sizeY = FormatTools.getPhysicalSizeY(size);
if (sizeY != null) {
for (int series = 0; series < getSeriesCount(); series++) {
store.setPixelsPhysicalSizeY(sizeY, series);
}
}
}
if (q == 2) {
Length sizeZ = FormatTools.getPhysicalSizeZ(size);
if (sizeZ != null) {
for (int series = 0; series < getSeriesCount(); series++) {
store.setPixelsPhysicalSizeZ(sizeZ, series);
}
}
}
}
} else if (key.equals("Binning")) {
store.setDetectorType(getDetectorType("Other"), 0, 0);
String detectorID = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detectorID, 0, 0);
for (int series = 0; series < getSeriesCount(); series++) {
for (int c = 0; c < getSizeC(); c++) {
store.setDetectorSettingsBinning(getBinning(value), series, c);
// link DetectorSettings to an actual Detector
store.setDetectorSettingsID(detectorID, series, c);
}
}
} else // Camera properties
if (key.equals("Type")) {
store.setDetectorModel(value, 0, 0);
} else if (key.equals("Gain")) {
value = value.replaceAll("X", "");
try {
String detectorID = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detectorID, 0, 0);
for (int series = 0; series < getSeriesCount(); series++) {
for (int c = 0; c < getSizeC(); c++) {
store.setDetectorSettingsGain(new Double(value), series, c);
store.setDetectorSettingsID(detectorID, series, c);
}
}
} catch (NumberFormatException e) {
LOGGER.warn("Could not parse gain '{}'", value);
}
} else if (key.equals("Speed")) {
value = value.replaceAll("KHz", "");
try {
double khz = Double.parseDouble(value);
String detectorID = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detectorID, 0, 0);
for (int series = 0; series < getSeriesCount(); series++) {
for (int c = 0; c < getSizeC(); c++) {
store.setDetectorSettingsReadOutRate(new Frequency(khz, UNITS.KILOHERTZ), series, c);
store.setDetectorSettingsID(detectorID, series, c);
}
}
} catch (NumberFormatException e) {
LOGGER.warn("Could not parse read-out rate '{}'", value);
}
} else if (key.equals("Temp Setting")) {
value = value.replaceAll("C", "").trim();
try {
// this is the camera temperature, not the environment temperature
// store.setImagingEnvironmentTemperature(value, 0);
} catch (NumberFormatException e) {
LOGGER.warn("Could not parse temperature '{}'", value);
}
} else // Plane properties
if (key.equals("EM filter")) {
if (!channelNames.contains(value)) {
channelNames.add(value);
}
} else if (key.equals("ND filter")) {
value = value.replaceAll("%", "");
try {
double nd = Double.parseDouble(value) / 100;
if (!filters.contains(nd)) {
filters.add(nd);
}
} catch (NumberFormatException exc) {
// so no need to log it explicitly
if (!value.equals("BLANK")) {
LOGGER.warn("Could not parse ND filter '{}'", value);
}
filters.add(null);
} catch (IllegalArgumentException e) {
LOGGER.debug("", e);
}
} else if (key.equals("Stage coordinates")) {
if (value.length() > 1) {
value = value.substring(1, value.length() - 1);
}
String[] coords = value.split(",");
for (int i = 0; i < coords.length; i++) {
Length p = null;
try {
final Double number = Double.valueOf(coords[i]);
p = new Length(number, UNITS.REFERENCEFRAME);
} catch (NumberFormatException e) {
LOGGER.warn("Could not parse stage coordinate '{}'", coords[i]);
}
if (currentImage < getImageCount() && getSeriesCount() == 1) {
// from the extended header.
if (i == 0) {
store.setPlanePositionX(p, 0, currentImage);
}
if (i == 1) {
store.setPlanePositionY(p, 0, currentImage);
}
if (i == 2) {
store.setPlanePositionZ(p, 0, currentImage);
}
}
}
currentImage++;
}
} else if (line.startsWith("Image"))
prefix = line;
else if (line.startsWith("Created")) {
if (line.length() > 8)
line = line.substring(8).trim();
String date = DateTools.formatDate(line, DATE_FORMATS);
if (date != null) {
for (int series = 0; series < getSeriesCount(); series++) {
store.setImageAcquisitionDate(new Timestamp(date), series);
}
} else {
LOGGER.warn("Could not parse date '{}'", line);
}
} else if (line.startsWith("#KEY")) {
line = line.substring(line.indexOf(" ")).trim();
int split = line.indexOf(":");
if (split < 0) {
split = line.indexOf(" ");
}
key = line.substring(0, split).trim();
value = line.substring(split + 1).trim();
addGlobalMeta(key, value);
} else if (line.endsWith(":")) {
prefix = line.substring(0, line.length() - 1);
} else if (!line.startsWith("#") && !line.replace("-", "").isEmpty() && !prefix.isEmpty()) {
addGlobalMetaList(prefix, line);
}
}
for (int series = 0; series < getSeriesCount(); series++) {
for (int c = 0; c < getEffectiveSizeC(); c++) {
if (c < channelNames.size()) {
store.setChannelName(channelNames.get(c), series, c);
}
if (c < filters.size()) {
ndFilters[c] = filters.get(c);
}
}
}
return true;
}Example 27 with Timestamp
use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.
the class FV1000Reader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
parser.setCommentDelimiter(null);
isOIB = checkSuffix(id, OIB_SUFFIX);
if (isOIB) {
initPOIService();
}
// mappedOIF is used to distinguish between datasets that are being read
// directly (e.g. using ImageJ or showinf), and datasets that are being
// imported through omebf. In the latter case, the necessary directory
// structure is not preserved (only relative file names are stored in
// OMEIS), so we will need to use slightly different logic to build the
// list of associated files.
boolean mappedOIF = !isOIB && !new File(id).getAbsoluteFile().exists();
wavelengths = new ArrayList<Double>();
illuminations = new ArrayList<String>();
channels = new ArrayList<ChannelData>();
planes = new ArrayList<PlaneData>();
String oifName = null;
if (isOIB) {
oifName = mapOIBFiles();
} else {
// make sure we have the OIF file, not a TIFF
if (!checkSuffix(id, OIF_SUFFIX)) {
currentId = findOIFFile(id);
initFile(currentId);
}
oifName = currentId;
}
String oifPath = new Location(oifName).getAbsoluteFile().getAbsolutePath();
if (mappedOIF) {
oifPath = oifName.substring(0, oifName.lastIndexOf(File.separator) + 1);
}
String path = isOIB ? "" : oifPath.substring(0, oifPath.lastIndexOf(File.separator) + 1);
try {
RandomAccessInputStream s = getFile(oifName);
s.close();
} catch (IOException e) {
oifName = oifName.replaceAll(".oif", ".OIF");
}
// parse key/value pairs from the OIF file
code = new String[NUM_DIMENSIONS];
size = new String[NUM_DIMENSIONS];
pixelSize = new Double[NUM_DIMENSIONS];
previewNames = new ArrayList<String>();
SortedMap<Integer, String> previewFileNames = new TreeMap<Integer, String>();
boolean laserEnabled = true;
IniList f = getIniFile(oifName);
IniTable saveInfo = f.getTable("ProfileSaveInfo");
String[] saveKeys = saveInfo.keySet().toArray(new String[saveInfo.size()]);
for (String key : saveKeys) {
String value = saveInfo.get(key).toString();
value = sanitizeValue(value).trim();
if (key.startsWith("IniFileName") && key.indexOf("Thumb") == -1 && !isPreviewName(value)) {
filenames.put(new Integer(key.substring(11)), value);
} else if (key.startsWith("RoiFileName") && key.indexOf("Thumb") == -1 && !isPreviewName(value)) {
try {
roiFilenames.put(new Integer(key.substring(11)), value);
} catch (NumberFormatException e) {
}
} else if (key.equals("PtyFileNameS"))
ptyStart = value;
else if (key.equals("PtyFileNameE"))
ptyEnd = value;
else if (key.equals("PtyFileNameT2"))
ptyPattern = value;
else if (key.indexOf("Thumb") != -1) {
if (thumbId == null)
thumbId = value.trim();
} else if (key.startsWith("LutFileName")) {
lutNames.add(path + value);
} else if (isPreviewName(value)) {
try {
RandomAccessInputStream s = getFile(path + value.trim());
if (s != null) {
s.close();
Integer previewIndex = getPreviewNameIndex(key);
if (previewIndex != null) {
previewFileNames.put(previewIndex, path + value.trim());
} else {
previewNames.add(path + value.trim());
}
}
} catch (FormatException e) {
LOGGER.debug("Preview file not found", e);
} catch (IOException e) {
LOGGER.debug("Preview file not found", e);
}
}
}
// Store sorted list of preview names
previewNames.addAll(previewFileNames.values());
if (filenames.isEmpty())
addPtyFiles();
for (int i = 0; i < NUM_DIMENSIONS; i++) {
IniTable commonParams = f.getTable("Axis " + i + " Parameters Common");
code[i] = commonParams.get("AxisCode");
size[i] = commonParams.get("MaxSize");
double end = Double.parseDouble(commonParams.get("EndPosition"));
double start = Double.parseDouble(commonParams.get("StartPosition"));
pixelSize[i] = end - start;
}
IniTable referenceParams = f.getTable("Reference Image Parameter");
imageDepth = Integer.parseInt(referenceParams.get("ImageDepth"));
pixelSizeX = referenceParams.get("WidthConvertValue");
pixelSizeY = referenceParams.get("HeightConvertValue");
String ripValidBitCounts = referenceParams.get("ValidBitCounts");
if (ripValidBitCounts != null) {
validBits = Integer.parseInt(ripValidBitCounts);
}
int index = 0;
IniTable laser = f.getTable("Laser " + index + " Parameters");
while (laser != null) {
laserEnabled = laser.get("Laser Enable").equals("1");
if (laserEnabled) {
wavelengths.add(new Double(laser.get("LaserWavelength")));
}
creationDate = laser.get("ImageCaputreDate");
if (creationDate == null) {
creationDate = laser.get("ImageCaptureDate");
}
index++;
laser = f.getTable("Laser " + index + " Parameters");
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
index = 1;
IniTable guiChannel = f.getTable("GUI Channel " + index + " Parameters");
while (guiChannel != null) {
ChannelData channel = new ChannelData();
channel.gain = DataTools.parseDouble(guiChannel.get("AnalogPMTGain"));
channel.voltage = DataTools.parseDouble(guiChannel.get("AnalogPMTVoltage"));
channel.barrierFilter = channel.getFilter(guiChannel.get("BF Name"));
channel.active = Integer.parseInt(guiChannel.get("CH Activate")) != 0;
channel.name = guiChannel.get("CH Name");
channel.dyeName = guiChannel.get("DyeName");
channel.emissionFilter = channel.getFilter(guiChannel.get("EmissionDM Name"));
channel.emWave = DataTools.parseDouble(guiChannel.get("EmissionWavelength"));
channel.excitationFilter = channel.getFilter(guiChannel.get("ExcitationDM Name"));
channel.exWave = DataTools.parseDouble(guiChannel.get("ExcitationWavelength"));
channels.add(channel);
index++;
guiChannel = f.getTable("GUI Channel " + index + " Parameters");
}
index = 1;
IniTable channel = f.getTable("Channel " + index + " Parameters");
while (channel != null) {
String illumination = channel.get("LightType");
if (illumination != null)
illumination = illumination.toLowerCase();
if (illumination == null) {
// Ignored
} else if (illumination.indexOf("fluorescence") != -1) {
illumination = "Epifluorescence";
} else if (illumination.indexOf("transmitted") != -1) {
illumination = "Transmitted";
} else
illumination = null;
illuminations.add(illumination);
index++;
channel = f.getTable("Channel " + index + " Parameters");
}
HashMap<String, String> iniMap = f.flattenIntoHashMap();
metadata.putAll(iniMap);
}
LOGGER.info("Initializing helper readers");
if (previewNames.size() > 0) {
final List<String> v = new ArrayList<String>();
for (int i = 0; i < previewNames.size(); i++) {
String ss = previewNames.get(i);
ss = replaceExtension(ss, "pty", "tif");
if (ss.endsWith(".tif"))
v.add(ss);
}
previewNames = v;
if (previewNames.size() > 0) {
core.clear();
core.add(new CoreMetadata());
core.add(new CoreMetadata());
IFDList ifds = null;
CoreMetadata ms1 = core.get(1);
for (String previewName : previewNames) {
RandomAccessInputStream preview = getFile(previewName);
TiffParser tp = new TiffParser(preview);
ifds = tp.getIFDs();
preview.close();
tp = null;
ms1.imageCount += ifds.size();
}
ms1.sizeX = (int) ifds.get(0).getImageWidth();
ms1.sizeY = (int) ifds.get(0).getImageLength();
ms1.sizeZ = 1;
ms1.sizeT = 1;
ms1.sizeC = ms1.imageCount;
ms1.rgb = false;
int bits = ifds.get(0).getBitsPerSample()[0];
while ((bits % 8) != 0) bits++;
bits /= 8;
ms1.pixelType = FormatTools.pixelTypeFromBytes(bits, false, false);
ms1.dimensionOrder = "XYCZT";
ms1.indexed = false;
}
}
CoreMetadata ms0 = core.get(0);
ms0.imageCount = filenames.size();
tiffs = new ArrayList<String>(getImageCount());
thumbReader = new BMPReader();
if (thumbId != null) {
thumbId = replaceExtension(thumbId, "pty", "bmp");
thumbId = sanitizeFile(thumbId, path);
}
LOGGER.info("Reading additional metadata");
// open each INI file (.pty extension) and build list of TIFF files
String tiffPath = null;
ms0.dimensionOrder = "XY";
final Map<String, String> values = new HashMap<String, String>();
final List<String> baseKeys = new ArrayList<String>();
for (int i = 0, ii = 0; ii < getImageCount(); i++, ii++) {
String file = filenames.get(i);
while (file == null) file = filenames.get(++i);
file = sanitizeFile(file, path);
if (file.indexOf(File.separator) != -1) {
tiffPath = file.substring(0, file.lastIndexOf(File.separator));
} else
tiffPath = file;
Location ptyFile = new Location(file);
if (!isOIB && !ptyFile.exists()) {
LOGGER.warn("Could not find .pty file ({}); guessing at the " + "corresponding TIFF file.", file);
String tiff = replaceExtension(file, "pty", "tif");
Location tiffFile = new Location(tiff);
if (tiffFile.exists()) {
tiffs.add(ii, tiffFile.getAbsolutePath());
continue;
} else {
if (!tiffFile.getParentFile().exists()) {
String realOIFName = new Location(currentId).getName();
String basePath = tiffFile.getParentFile().getParent();
if (mappedOIF) {
tiffPath = basePath + File.separator + realOIFName + ".files";
ptyFile = new Location(tiffPath, ptyFile.getName());
file = ptyFile.getAbsolutePath();
} else {
Location newFile = new Location(basePath, realOIFName + ".files");
ptyFile = new Location(newFile, ptyFile.getName());
file = ptyFile.getAbsolutePath();
tiffPath = newFile.getAbsolutePath();
}
}
}
} else if (!isOIB) {
file = ptyFile.getAbsolutePath();
}
IniList pty = getIniFile(file);
IniTable fileInfo = pty.getTable("File Info");
file = sanitizeValue(fileInfo.get("DataName"));
if (!isPreviewName(file)) {
while (file.indexOf("GST") != -1) {
file = removeGST(file);
}
if (isOIB) {
file = tiffPath + File.separator + file;
} else
file = new Location(tiffPath, file).getAbsolutePath();
file = replaceExtension(file, "pty", "tif");
tiffs.add(ii, file);
}
PlaneData plane = new PlaneData();
for (int dim = 0; dim < NUM_DIMENSIONS; dim++) {
IniTable axis = pty.getTable("Axis " + dim + " Parameters");
if (axis == null)
break;
boolean addAxis = Integer.parseInt(axis.get("Number")) > 1;
if (dim == 2) {
if (addAxis && getDimensionOrder().indexOf('C') == -1) {
ms0.dimensionOrder += 'C';
}
} else if (dim == 3) {
if (addAxis && getDimensionOrder().indexOf('Z') == -1) {
ms0.dimensionOrder += 'Z';
}
final Double number = Double.valueOf(axis.get("AbsPositionValue"));
plane.positionZ = new Length(number, UNITS.REFERENCEFRAME);
} else if (dim == 4) {
if (addAxis && getDimensionOrder().indexOf('T') == -1) {
ms0.dimensionOrder += 'T';
}
// divide by 1000, as the position is in milliseconds
// and DeltaT is in seconds
plane.deltaT = Double.parseDouble(axis.get("AbsPositionValue")) / 1000;
} else if (dim == 7) {
try {
String xPos = axis.get("AbsPositionValueX");
if (xPos != null) {
final Double number = Double.valueOf(xPos);
plane.positionX = new Length(number, UNITS.REFERENCEFRAME);
}
} catch (NumberFormatException e) {
}
try {
String yPos = axis.get("AbsPositionValueY");
if (yPos != null) {
final Double number = Double.valueOf(yPos);
plane.positionY = new Length(number, UNITS.REFERENCEFRAME);
}
} catch (NumberFormatException e) {
}
}
}
ms0.bitsPerPixel = validBits;
planes.add(plane);
IniTable acquisition = pty.getTable("Acquisition Parameters Common");
if (acquisition != null) {
magnification = acquisition.get("Magnification");
lensNA = acquisition.get("ObjectiveLens NAValue");
objectiveName = acquisition.get("ObjectiveLens Name");
workingDistance = acquisition.get("ObjectiveLens WDValue");
pinholeSize = acquisition.get("PinholeDiameter");
String validBitCounts = acquisition.get("ValidBitCounts");
if (validBitCounts != null) {
ms0.bitsPerPixel = Integer.parseInt(validBitCounts);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
for (IniTable table : pty) {
String[] keys = table.keySet().toArray(new String[table.size()]);
for (String key : keys) {
values.put("Image " + ii + " : " + key, table.get(key));
if (!baseKeys.contains(key))
baseKeys.add(key);
}
}
}
}
for (String key : baseKeys) {
if (key.equals("DataName") || key.indexOf("FileName") >= 0)
break;
boolean equal = true;
String first = values.get("Image 0 : " + key);
for (int i = 1; i < getImageCount(); i++) {
if (!first.equals(values.get("Image " + i + " : " + key))) {
equal = false;
break;
}
}
if (equal) {
addGlobalMeta(key, first);
} else {
for (int i = 0; i < getImageCount(); i++) {
String k = "Image " + i + " : " + key;
addGlobalMeta(k, values.get(k));
}
}
}
if (tiffs.size() != getImageCount()) {
ms0.imageCount = tiffs.size();
}
usedFiles = new ArrayList<String>();
if (tiffPath != null) {
usedFiles.add(isOIB ? id : oifName);
if (!isOIB) {
Location dir = new Location(tiffPath);
if (!mappedOIF && !dir.exists()) {
throw new FormatException("Required directory " + tiffPath + " was not found.");
}
String[] list = mappedOIF ? Location.getIdMap().keySet().toArray(new String[0]) : dir.list(true);
for (int i = 0; i < list.length; i++) {
if (mappedOIF)
usedFiles.add(list[i]);
else {
String p = new Location(tiffPath, list[i]).getAbsolutePath();
String check = p.toLowerCase();
if (!check.endsWith(".tif") && !check.endsWith(".pty") && !check.endsWith(".roi") && !check.endsWith(".lut") && !check.endsWith(".bmp")) {
continue;
}
usedFiles.add(p);
}
}
}
}
LOGGER.info("Populating metadata");
// calculate axis sizes
int realChannels = 0;
for (int i = 0; i < NUM_DIMENSIONS; i++) {
int ss = Integer.parseInt(size[i]);
if (pixelSize[i] == null)
pixelSize[i] = 1.0;
if (code[i].equals("X"))
ms0.sizeX = ss;
else if (code[i].equals("Y") && ss > 1)
ms0.sizeY = ss;
else if (code[i].equals("Z")) {
if (getSizeY() == 0) {
ms0.sizeY = ss;
} else {
ms0.sizeZ = ss;
// Z size stored in nm
pixelSizeZ = Math.abs((pixelSize[i].doubleValue() / (getSizeZ() - 1)) / 1000);
}
} else if (code[i].equals("T")) {
if (getSizeY() == 0) {
ms0.sizeY = ss;
} else {
ms0.sizeT = ss;
pixelSizeT = Math.abs((pixelSize[i].doubleValue() / (getSizeT() - 1)) / 1000);
}
} else if (ss > 0) {
if (getSizeC() == 0)
ms0.sizeC = ss;
else
ms0.sizeC *= ss;
if (code[i].equals("C"))
realChannels = ss;
}
}
if (getSizeZ() == 0)
ms0.sizeZ = 1;
if (getSizeC() == 0)
ms0.sizeC = 1;
if (getSizeT() == 0)
ms0.sizeT = 1;
if (getImageCount() == getSizeC() && getSizeY() == 1) {
ms0.imageCount *= getSizeZ() * getSizeT();
} else if (getImageCount() == getSizeC()) {
ms0.sizeZ = 1;
ms0.sizeT = 1;
}
if (getSizeZ() * getSizeT() * getSizeC() != getImageCount()) {
int diff = (getSizeZ() * getSizeC() * getSizeT()) - getImageCount();
if (diff == previewNames.size() || diff < 0) {
diff /= getSizeC();
if (getSizeT() > 1 && getSizeZ() == 1)
ms0.sizeT -= diff;
else if (getSizeZ() > 1 && getSizeT() == 1)
ms0.sizeZ -= diff;
} else
ms0.imageCount += diff;
}
if (getSizeC() > 1 && getSizeZ() == 1 && getSizeT() == 1) {
if (getDimensionOrder().indexOf('C') == -1)
ms0.dimensionOrder += 'C';
}
if (getDimensionOrder().indexOf('Z') == -1)
ms0.dimensionOrder += 'Z';
if (getDimensionOrder().indexOf('C') == -1)
ms0.dimensionOrder += 'C';
if (getDimensionOrder().indexOf('T') == -1)
ms0.dimensionOrder += 'T';
ms0.pixelType = FormatTools.pixelTypeFromBytes(imageDepth, false, false);
try {
RandomAccessInputStream thumb = getFile(thumbId);
byte[] b = new byte[(int) thumb.length()];
thumb.read(b);
thumb.close();
Location.mapFile("thumbnail.bmp", new ByteArrayHandle(b));
thumbReader.setId("thumbnail.bmp");
for (int i = 0; i < getSeriesCount(); i++) {
core.get(i).thumbSizeX = thumbReader.getSizeX();
core.get(i).thumbSizeY = thumbReader.getSizeY();
}
thumbReader.close();
Location.mapFile("thumbnail.bmp", null);
} catch (IOException e) {
LOGGER.debug("Could not read thumbnail", e);
} catch (FormatException e) {
LOGGER.debug("Could not read thumbnail", e);
}
// initialize lookup table
lut = new short[getSizeC()][3][65536];
byte[] buffer = new byte[65536 * 4];
int count = (int) Math.min(getSizeC(), lutNames.size());
for (int c = 0; c < count; c++) {
Exception exc = null;
try {
RandomAccessInputStream stream = getFile(lutNames.get(c));
stream.seek(stream.length() - 65536 * 4);
stream.read(buffer);
stream.close();
for (int q = 0; q < buffer.length; q += 4) {
lut[c][0][q / 4] = (short) ((buffer[q + 2] & 0xff) * 257);
lut[c][1][q / 4] = (short) ((buffer[q + 1] & 0xff) * 257);
lut[c][2][q / 4] = (short) ((buffer[q] & 0xff) * 257);
}
} catch (IOException e) {
exc = e;
} catch (FormatException e) {
exc = e;
}
if (exc != null) {
LOGGER.debug("Could not read LUT", exc);
lut = null;
break;
}
}
for (int i = 0; i < getSeriesCount(); i++) {
CoreMetadata ms = core.get(i);
ms.rgb = false;
ms.littleEndian = true;
ms.interleaved = false;
ms.metadataComplete = true;
ms.indexed = lut != null;
ms.falseColor = true;
int nFiles = i == 0 ? tiffs.size() : previewNames.size();
for (int file = 0; file < nFiles; file++) {
RandomAccessInputStream plane = getFile(i == 0 ? tiffs.get(file) : previewNames.get(file));
if (plane == null) {
ifds.add(null);
continue;
}
try {
TiffParser tp = new TiffParser(plane);
IFDList ifd = tp.getIFDs();
ifds.add(ifd);
} finally {
plane.close();
}
}
}
// populate MetadataStore
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
if (creationDate != null) {
creationDate = creationDate.replaceAll("'", "");
creationDate = DateTools.formatDate(creationDate, DATE_FORMAT);
}
for (int i = 0; i < getSeriesCount(); i++) {
// populate Image data
store.setImageName("Series " + (i + 1), i);
if (creationDate != null)
store.setImageAcquisitionDate(new Timestamp(creationDate), i);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
populateMetadataStore(store, path);
}
}
Also used :
IniList(loci.common.IniList)
HashMap(java.util.HashMap)
ArrayList(java.util.ArrayList)
Timestamp(ome.xml.model.primitives.Timestamp)
IOException(java.io.IOException)
TreeMap(java.util.TreeMap)
CoreMetadata(loci.formats.CoreMetadata)
FormatException(loci.formats.FormatException)
DependencyException(loci.common.services.DependencyException)
FormatException(loci.formats.FormatException)
IOException(java.io.IOException)
NonNegativeInteger(ome.xml.model.primitives.NonNegativeInteger)
MetadataStore(loci.formats.meta.MetadataStore)
Length(ome.units.quantity.Length)
IniTable(loci.common.IniTable)
IFDList(loci.formats.tiff.IFDList)
TiffParser(loci.formats.tiff.TiffParser)
RandomAccessInputStream(loci.common.RandomAccessInputStream)
ByteArrayHandle(loci.common.ByteArrayHandle)
File(java.io.File)
Location(loci.common.Location)
Example 28 with Timestamp
use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.
the class BaseZeissReader method fillMetadataPass7.
/**
* Store basic dimensions in model
* @param store
* @throws FormatException
* @throws IOException
*/
protected void fillMetadataPass7(MetadataStore store) throws FormatException, IOException {
for (int i = 0; i < getSeriesCount(); i++) {
long firstStamp = 0;
if (timestamps.size() > 0) {
String timestamp = timestamps.get(0);
store.setImageAcquisitionDate(new Timestamp(timestamp), i);
} else if (acquisitionDate != null) {
store.setImageAcquisitionDate(acquisitionDate, i);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
// link Instrument and Image
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
store.setObjectiveID(objectiveID, 0, 0);
store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
Integer[] channelKeys = channelName.keySet().toArray(new Integer[channelName.size()]);
Arrays.sort(channelKeys);
// link DetectorSettings to an actual Detector
for (int i = 0; i < getEffectiveSizeC(); i++) {
String detectorID = MetadataTools.createLSID("Detector", 0, i);
store.setDetectorID(detectorID, 0, i);
store.setDetectorType(getDetectorType("Other"), 0, i);
for (int s = 0; s < getSeriesCount(); s++) {
int c = i;
if (i < channelKeys.length) {
c = channelKeys[i];
}
store.setDetectorSettingsID(detectorID, s, i);
store.setDetectorSettingsGain(detectorGain.get(c), s, i);
store.setDetectorSettingsOffset(detectorOffset.get(c), s, i);
store.setChannelName(channelName.get(c), s, i);
store.setChannelEmissionWavelength(emWavelength.get(c), s, i);
store.setChannelExcitationWavelength(exWavelength.get(c), s, i);
if (channelColors != null && i < channelColors.length) {
int color = channelColors[i];
int red = color & 0xff;
int green = (color & 0xff00) >> 8;
int blue = (color & 0xff0000) >> 16;
store.setChannelColor(new Color(red, green, blue, 255), s, i);
}
}
}
for (int i = 0; i < getSeriesCount(); i++) {
store.setImageInstrumentRef(instrumentID, i);
store.setObjectiveSettingsID(objectiveID, i);
if (imageDescription != null) {
store.setImageDescription(imageDescription, i);
}
if (getSeriesCount() > 1) {
store.setImageName("Tile #" + (i + 1), i);
}
Length sizeX = FormatTools.getPhysicalSizeX(physicalSizeX);
Length sizeY = FormatTools.getPhysicalSizeY(physicalSizeY);
Length sizeZ = FormatTools.getPhysicalSizeZ(physicalSizeZ);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, i);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, i);
}
if (sizeZ != null) {
store.setPixelsPhysicalSizeZ(sizeZ, i);
}
Timestamp firstStamp = null;
if (timestamps.get(0) != null) {
firstStamp = new Timestamp(timestamps.get(0));
}
for (int plane = 0; plane < getImageCount(); plane++) {
int[] zct = getZCTCoords(plane);
int expIndex = zct[1];
if (channelKeys.length > 0) {
expIndex += channelKeys[0];
}
String exposure = exposureTime.get(expIndex);
if (exposure == null && exposureTime.size() == 1) {
exposure = exposureTime.values().iterator().next();
}
Double exp = 0d;
try {
exp = new Double(exposure);
} catch (NumberFormatException e) {
} catch (NullPointerException e) {
}
store.setPlaneExposureTime(new Time(exp, UNITS.SECOND), i, plane);
int posIndex = i * getImageCount() + plane;
if (posIndex < timestamps.size() && firstStamp != null) {
Timestamp timestamp = new Timestamp(timestamps.get(posIndex));
long difference = timestamp.asInstant().getMillis() - firstStamp.asInstant().getMillis();
double delta = (double) difference;
store.setPlaneDeltaT(new Time(delta, UNITS.MILLISECOND), i, plane);
}
if (stageX.get(posIndex) != null) {
store.setPlanePositionX(stageX.get(posIndex), i, plane);
}
if (stageY.get(posIndex) != null) {
store.setPlanePositionY(stageY.get(posIndex), i, plane);
}
}
}
for (int i = 0; i < getSeriesCount(); i++) {
for (int roi = 0; roi < roiIDs.size(); roi++) {
store.setImageROIRef(roiIDs.get(roi), i, roi);
}
}
}
}Example 29 with Timestamp
use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.
the class BioRadGelReader method initFile.
// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
in = new RandomAccessInputStream(id);
String check = in.readString(48);
if (check.indexOf("Intel Format") != -1) {
in.order(true);
}
in.seek(START_OFFSET);
boolean codeFound = false;
int skip = 0;
long baseFP = 0;
while (!codeFound) {
short code = in.readShort();
if (code == 0x81)
codeFound = true;
short length = in.readShort();
in.skipBytes(2 + 2 * length);
if (codeFound) {
baseFP = in.getFilePointer() + 2;
if (length > 1) {
in.seek(in.getFilePointer() - 2);
}
skip = in.readInt() - 32;
} else {
if (length == 1)
in.skipBytes(12);
else if (length == 2)
in.skipBytes(10);
}
}
diff = BASE_OFFSET - baseFP;
skip += diff;
double physicalWidth = 0d, physicalHeight = 0d;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (baseFP + skip - 8187 > 0) {
in.seek(baseFP + skip - 8187);
String scannerName = in.readCString();
in.skipBytes(8);
in.readCString();
in.skipBytes(8);
String imageArea = in.readCString();
imageArea = imageArea.substring(imageArea.indexOf(':') + 1).trim();
int xIndex = imageArea.indexOf('x');
if (xIndex > 0) {
int space = imageArea.indexOf(' ');
if (space >= 0) {
String width = imageArea.substring(1, space);
int nextSpace = imageArea.indexOf(" ", xIndex + 2);
if (nextSpace > xIndex) {
String height = imageArea.substring(xIndex + 1, nextSpace);
physicalWidth = Double.parseDouble(width.trim()) * 1000;
physicalHeight = Double.parseDouble(height.trim()) * 1000;
}
}
}
}
}
in.seek(baseFP + skip - 298);
String date = in.readString(17);
date = DateTools.formatDate(date, "dd-MMM-yyyy HH:mm");
in.skipBytes(73);
String scannerName = in.readCString();
addGlobalMeta("Scanner name", scannerName);
in.seek(baseFP + skip);
CoreMetadata m = core.get(0);
m.sizeX = in.readShort() & 0xffff;
m.sizeY = in.readShort() & 0xffff;
if (getSizeX() * getSizeY() > in.length()) {
in.order(true);
in.seek(in.getFilePointer() - 4);
m.sizeX = in.readShort();
m.sizeY = in.readShort();
}
in.skipBytes(2);
int bpp = in.readShort();
m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
offset = in.getFilePointer();
m.sizeZ = 1;
m.sizeC = 1;
m.sizeT = 1;
m.imageCount = 1;
m.dimensionOrder = "XYCZT";
m.rgb = false;
m.interleaved = false;
m.indexed = false;
m.littleEndian = in.isLittleEndian();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Length sizeX = FormatTools.getPhysicalSizeX(physicalWidth / getSizeX());
Length sizeY = FormatTools.getPhysicalSizeY(physicalHeight / getSizeY());
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
}
}
Also used :
MetadataStore(loci.formats.meta.MetadataStore)
Length(ome.units.quantity.Length)
RandomAccessInputStream(loci.common.RandomAccessInputStream)
CoreMetadata(loci.formats.CoreMetadata)
Timestamp(ome.xml.model.primitives.Timestamp)
Example 30 with Timestamp
use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.
the class BioRadReader method parseNotes.
private boolean parseNotes(MetadataStore store) throws FormatException {
boolean multipleFiles = false;
int nextDetector = 0, nLasers = 0;
for (Note n : noteStrings) {
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
switch(n.type) {
case NOTE_TYPE_USER:
// TODO : this should be an overlay
addGlobalMetaList("Note", n.toString());
break;
case NOTE_TYPE_SCALEBAR:
// TODO : this should be an overlay
// the format of the text is:
// SCALEBAR = <length> <angle>
// where <length> is the length of the scalebar in microns,
// and <angle> is the angle in degrees
addGlobalMetaList("Note", n.toString());
break;
case NOTE_TYPE_ARROW:
// TODO : this should be an overlay
// the format of the text is:
// ARROW = <lx> <ly> <angle> <fill>
// where <lx> and <ly> define the arrow's bounding box,
// <angle> is the angle in degrees and <fill> is either "Fill" or
// "Outline"
addGlobalMetaList("Note", n.toString());
break;
case NOTE_TYPE_VARIABLE:
if (n.p.indexOf('=') >= 0) {
String key = n.p.substring(0, n.p.indexOf('=')).trim();
String value = n.p.substring(n.p.indexOf('=') + 1).trim();
addGlobalMeta(key, value);
if (key.equals("INFO_OBJECTIVE_NAME")) {
store.setObjectiveModel(value, 0, 0);
} else if (key.equals("INFO_OBJECTIVE_MAGNIFICATION")) {
Double mag = Double.parseDouble(value);
store.setObjectiveNominalMagnification(mag, 0, 0);
} else if (key.equals("LENS_MAGNIFICATION")) {
Double magnification = Double.parseDouble(value);
store.setObjectiveNominalMagnification(magnification, 0, 0);
} else if (key.startsWith("SETTING")) {
if (key.indexOf("_DET_") != -1) {
int index = key.indexOf("_DET_") + 5;
if (key.lastIndexOf("_") > index) {
String detectorID = MetadataTools.createLSID("Detector", 0, nextDetector);
store.setDetectorID(detectorID, 0, nextDetector);
store.setDetectorType(getDetectorType("Other"), 0, nextDetector);
if (key.endsWith("OFFSET")) {
if (nextDetector < offset.size()) {
offset.set(nextDetector, Double.parseDouble(value));
} else {
while (nextDetector > offset.size()) {
offset.add(null);
}
offset.add(new Double(value));
}
} else if (key.endsWith("GAIN")) {
if (nextDetector < gain.size()) {
gain.set(nextDetector, Double.parseDouble(value));
} else {
while (nextDetector > gain.size()) {
gain.add(null);
}
gain.add(new Double(value));
}
}
nextDetector++;
}
}
} else {
String[] values = value.split(" ");
if (values.length > 1) {
try {
int type = Integer.parseInt(values[0]);
if (type == 257 && values.length >= 3) {
// found length of axis in um
Double pixelSize = new Double(values[2]);
if (key.equals("AXIS_2")) {
Length size = FormatTools.getPhysicalSizeX(pixelSize);
if (size != null) {
store.setPixelsPhysicalSizeX(size, 0);
}
} else if (key.equals("AXIS_3")) {
Length size = FormatTools.getPhysicalSizeY(pixelSize);
if (size != null) {
store.setPixelsPhysicalSizeY(size, 0);
}
}
}
} catch (NumberFormatException e) {
}
}
}
} else if (n.p.startsWith("AXIS_2")) {
String[] values = n.p.split(" ");
Double pixelSize = new Double(values[3]);
Length size = FormatTools.getPhysicalSizeX(pixelSize);
if (size != null) {
store.setPixelsPhysicalSizeX(size, 0);
}
} else if (n.p.startsWith("AXIS_3")) {
String[] values = n.p.split(" ");
Double pixelSize = new Double(values[3]);
Length size = FormatTools.getPhysicalSizeY(pixelSize);
if (size != null) {
store.setPixelsPhysicalSizeY(size, 0);
}
} else {
addGlobalMetaList("Note", n.toString());
}
break;
case NOTE_TYPE_STRUCTURE:
int structureType = (n.x & 0xff00) >> 8;
int version = (n.x & 0xff);
String[] values = n.p.split(" ");
if (structureType == 1) {
switch(n.y) {
case 1:
for (int i = 0; i < STRUCTURE_LABELS_1.length; i++) {
addGlobalMeta(STRUCTURE_LABELS_1[i], values[i]);
}
Double mag = Double.parseDouble(values[11]);
store.setObjectiveNominalMagnification(mag, 0, 0);
Double sizeZ = new Double(values[14]);
Length size = FormatTools.getPhysicalSizeZ(sizeZ);
if (size != null) {
store.setPixelsPhysicalSizeZ(size, 0);
}
break;
case 2:
for (int i = 0; i < STRUCTURE_LABELS_2.length; i++) {
addGlobalMeta(STRUCTURE_LABELS_2[i], values[i]);
}
double x1 = Double.parseDouble(values[2]);
double x2 = Double.parseDouble(values[4]);
double width = x2 - x1;
width /= getSizeX();
double y1 = Double.parseDouble(values[3]);
double y2 = Double.parseDouble(values[5]);
double height = y2 - y1;
height /= getSizeY();
Length sizeX = FormatTools.getPhysicalSizeX(width);
Length sizeY = FormatTools.getPhysicalSizeY(height);
if (sizeX != null) {
store.setPixelsPhysicalSizeX(sizeX, 0);
}
if (sizeY != null) {
store.setPixelsPhysicalSizeY(sizeY, 0);
}
break;
case 3:
for (int i = 0; i < 3; i++) {
for (int j = 0; j < STRUCTURE_LABELS_3.length; j++) {
String v = j == STRUCTURE_LABELS_3.length - 1 ? values[12 + i] : values[i * 4 + j];
addGlobalMetaList(STRUCTURE_LABELS_3[j], v);
}
}
break;
case 4:
nLasers = Integer.parseInt(values[0]);
addGlobalMeta("Number of lasers", values[0]);
addGlobalMeta("Number of transmission detectors", values[1]);
addGlobalMeta("Number of PMTs", values[2]);
for (int i = 1; i <= 3; i++) {
int idx = (i + 1) * 3;
addGlobalMetaList("Shutter present for laser", values[i + 2]);
addGlobalMetaList("Neutral density filter for laser", values[idx]);
addGlobalMetaList("Excitation filter for laser", values[idx + 1]);
addGlobalMetaList("Use laser", values[idx + 2]);
}
for (int i = 0; i < nLasers; i++) {
addGlobalMetaList("Neutral density filter name - laser", values[15 + i]);
}
break;
case 5:
String prefix = "Excitation filter name - laser";
for (int i = 0; i < nLasers; i++) {
addGlobalMetaList(prefix, values[i]);
}
break;
case 6:
prefix = "Emission filter name - laser";
for (int i = 0; i < nLasers; i++) {
addGlobalMeta(prefix, values[i]);
}
break;
case 7:
for (int i = 0; i < 2; i++) {
prefix = "Mixer " + i + " - ";
for (int j = 0; j < STRUCTURE_LABELS_4.length; j++) {
addGlobalMeta(prefix + STRUCTURE_LABELS_4[j], values[i * 7 + j]);
}
}
addGlobalMeta("Mixer 0 - low signal on", values[14]);
addGlobalMeta("Mixer 1 - low signal on", values[15]);
break;
case 8:
case 9:
case 10:
addGlobalMeta("Laser name - laser " + (n.y - 7), values[0]);
break;
case 11:
for (int i = 0; i < 3; i++) {
prefix = "Transmission detector " + (i + 1) + " - ";
addGlobalMeta(prefix + "offset", values[i * 3]);
addGlobalMeta(prefix + "gain", values[i * 3 + 1]);
addGlobalMeta(prefix + "black level", values[i * 3 + 2]);
String detectorID = MetadataTools.createLSID("Detector", 0, i);
store.setDetectorID(detectorID, 0, i);
store.setDetectorOffset(new Double(values[i * 3]), 0, i);
store.setDetectorGain(new Double(values[i * 3 + 1]), 0, i);
store.setDetectorType(getDetectorType("Other"), 0, i);
}
break;
case 12:
for (int i = 0; i < 2; i++) {
prefix = "Part number for ";
for (int j = 0; j < STRUCTURE_LABELS_5.length; j++) {
addGlobalMetaList(prefix + STRUCTURE_LABELS_5[j], values[i * 4 + j]);
}
}
break;
case 13:
for (int i = 0; i < STRUCTURE_LABELS_6.length; i++) {
addGlobalMeta(STRUCTURE_LABELS_6[i], values[i]);
}
break;
case 14:
prefix = "Filter Block Name - filter block ";
addGlobalMetaList(prefix, values[0]);
addGlobalMetaList(prefix, values[1]);
break;
case 15:
for (int i = 0; i < 5; i++) {
addGlobalMetaList("Image bands status - band", values[i * 3]);
addGlobalMetaList("Image bands min - band", values[i * 3 + 1]);
addGlobalMetaList("Image bands max - band", values[i * 3 + 2]);
if (store instanceof IMinMaxStore) {
((IMinMaxStore) store).setChannelGlobalMinMax(i, Double.parseDouble(values[i * 3 + 1]), Double.parseDouble(values[i * 3 + 2]), 0);
}
}
break;
case 17:
int year = Integer.parseInt(values[5]) + 1900;
for (int i = 0; i < 5; i++) {
if (values[i].length() == 1)
values[i] = "0" + values[i];
}
// date is in yyyy-MM-dd'T'HH:mm:ss
String date = year + "-" + values[4] + "-" + values[3] + "T" + values[2] + ":" + values[1] + ":" + values[0];
addGlobalMeta("Acquisition date", date);
try {
store.setImageAcquisitionDate(new Timestamp(date), 0);
} catch (Exception e) {
LOGGER.debug("Failed to parse acquisition date", e);
}
break;
case 18:
addGlobalMeta("Mixer 3 - enhanced", values[0]);
for (int i = 1; i <= 3; i++) {
addGlobalMetaList("Mixer 3 - PMT percentage", values[i]);
addGlobalMetaList("Mixer 3 - Transmission percentage", values[i + 3]);
addGlobalMetaList("Mixer 3 - photon counting", values[i + 7]);
}
addGlobalMeta("Mixer 3 - low signal on", values[7]);
addGlobalMeta("Mixer 3 - mode", values[11]);
break;
case 19:
for (int i = 1; i <= 2; i++) {
prefix = "Mixer " + i + " - ";
String photon = prefix + "photon counting ";
addGlobalMetaList(photon, values[i * 4 - 4]);
addGlobalMetaList(photon, values[i * 4 - 3]);
addGlobalMetaList(photon, values[i * 4 - 2]);
addGlobalMeta(prefix + "mode", values[i * 4 - 1]);
}
break;
case 20:
addGlobalMeta("Display mode", values[0]);
addGlobalMeta("Course", values[1]);
addGlobalMeta("Time Course - experiment type", values[2]);
addGlobalMeta("Time Course - kd factor", values[3]);
String experimentID = MetadataTools.createLSID("Experiment", 0);
store.setExperimentID(experimentID, 0);
store.setExperimentType(getExperimentType(values[2]), 0);
break;
case 21:
addGlobalMeta("Time Course - ion name", values[0]);
break;
case 22:
addGlobalMeta("PIC file generated on Isoscan (lite)", values[0]);
for (int i = 1; i <= 3; i++) {
addGlobalMetaList("Photon counting used - PMT", values[i]);
addGlobalMetaList("Hot spot filter used - PMT", values[i + 3]);
addGlobalMetaList("Tx Selector used - TX", values[i + 6]);
}
break;
}
}
break;
default:
// notes for display only
addGlobalMetaList("Note", n.toString());
}
}
if (n.p.indexOf("AXIS") != -1) {
n.p = n.p.replaceAll("=", "");
final List<String> v = new ArrayList<String>();
StringTokenizer tokens = new StringTokenizer(n.p, " ");
while (tokens.hasMoreTokens()) {
String token = tokens.nextToken().trim();
if (token.length() > 0)
v.add(token);
}
String[] values = v.toArray(new String[v.size()]);
String key = values[0];
String noteType = values[1];
int axisType = Integer.parseInt(noteType);
if (axisType == 11 && values.length > 2) {
addGlobalMeta(key + " RGB type (X)", values[2]);
addGlobalMeta(key + " RGB type (Y)", values[3]);
CoreMetadata m = core.get(0);
if (key.equals("AXIS_4")) {
// this is a single section multi-channel dataset
m.sizeC = getImageCount();
m.sizeZ = 1;
m.sizeT = 1;
} else if (key.equals("AXIS_9")) {
multipleFiles = true;
m.sizeC = (int) Double.parseDouble(values[3]);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM && values.length > 2) {
switch(axisType) {
case 1:
addGlobalMeta(key + " distance (X) in microns", values[2]);
addGlobalMeta(key + " distance (Y) in microns", values[3]);
break;
case 3:
addGlobalMeta(key + " angle (X) in degrees", values[2]);
addGlobalMeta(key + " angle (Y) in degrees", values[3]);
break;
case 4:
addGlobalMeta(key + " intensity (X)", values[2]);
addGlobalMeta(key + " intensity (Y)", values[3]);
break;
case 6:
addGlobalMeta(key + " ratio (X)", values[2]);
addGlobalMeta(key + " ratio (Y)", values[3]);
break;
case 7:
addGlobalMeta(key + " log ratio (X)", values[2]);
addGlobalMeta(key + " log ratio (Y)", values[3]);
break;
case 9:
addGlobalMeta(key + " noncalibrated intensity min", values[2]);
addGlobalMeta(key + " noncalibrated intensity max", values[3]);
addGlobalMeta(key + " calibrated intensity min", values[4]);
addGlobalMeta(key + " calibrated intensity max", values[5]);
break;
case 14:
addGlobalMeta(key + " time course type (X)", values[2]);
addGlobalMeta(key + " time course type (Y)", values[3]);
break;
case 15:
String prefix = " inverse sigmoid calibrated intensity ";
addGlobalMeta(key + prefix + "(min)", values[2]);
addGlobalMeta(key + prefix + "(max)", values[3]);
addGlobalMeta(key + prefix + "(beta)", values[4]);
addGlobalMeta(key + prefix + "(Kd)", values[5]);
break;
case 16:
prefix = " log inverse sigmoid calibrated intensity ";
addGlobalMeta(key + prefix + "(min)", values[2]);
addGlobalMeta(key + prefix + "(max)", values[3]);
addGlobalMeta(key + prefix + "(beta)", values[4]);
addGlobalMeta(key + prefix + "(Kd)", values[5]);
break;
}
}
}
}
return multipleFiles;
}
Also used :
ArrayList(java.util.ArrayList)
Timestamp(ome.xml.model.primitives.Timestamp)
CoreMetadata(loci.formats.CoreMetadata)
FormatException(loci.formats.FormatException)
IOException(java.io.IOException)
StringTokenizer(java.util.StringTokenizer)
Length(ome.units.quantity.Length)
IMinMaxStore(loci.formats.meta.IMinMaxStore)
Aggregations
Timestamp (ome.xml.model.primitives.Timestamp)76
MetadataStore (loci.formats.meta.MetadataStore)54
Length (ome.units.quantity.Length)52
CoreMetadata (loci.formats.CoreMetadata)44
Time (ome.units.quantity.Time)33
Location (loci.common.Location)28
RandomAccessInputStream (loci.common.RandomAccessInputStream)28
FormatException (loci.formats.FormatException)23
ArrayList (java.util.ArrayList)20
IFD (loci.formats.tiff.IFD)11
NonNegativeInteger (ome.xml.model.primitives.NonNegativeInteger)10
TiffParser (loci.formats.tiff.TiffParser)9
IOException (java.io.IOException)8
IFDList (loci.formats.tiff.IFDList)8
PositiveInteger (ome.xml.model.primitives.PositiveInteger)8
Temperature (ome.units.quantity.Temperature)7
Hashtable (java.util.Hashtable)4
StringTokenizer (java.util.StringTokenizer)4
Frequency (ome.units.quantity.Frequency)4
File (java.io.File)3
