private void parseChannelData(Location dir) throws IOException {
emWave = new int[channelNames.size()];
exWave = new int[channelNames.size()];
exposure = new double[channelNames.size()];
gain = new double[channelNames.size()];
offset = new double[channelNames.size()];
for (int c = 0; c < channelNames.size(); c++) {
Location dyeFile = new Location(dir, channelNames.get(c) + ".dye");
FileInputStream stream = new FileInputStream(dyeFile.getAbsolutePath());
IniList dye =
new IniParser()
.parseINI(new BufferedReader(new InputStreamReader(stream, Constants.ENCODING)));
IniTable numerator = dye.getTable("Numerator");
String em = numerator.get("Emission");
em = em.substring(0, em.indexOf(" "));
emWave[c] = Integer.parseInt(em);
String ex = numerator.get("Excitation");
ex = ex.substring(0, ex.lastIndexOf(" "));
if (ex.indexOf(" ") != -1) {
ex = ex.substring(ex.lastIndexOf(" ") + 1);
}
exWave[c] = Integer.parseInt(ex);
exposure[c] = Double.parseDouble(numerator.get("Exposure"));
gain[c] = Double.parseDouble(numerator.get("Gain"));
offset[c] = Double.parseDouble(numerator.get("Offset"));
}
}
/* @see BaseTiffReader#initStandardMetadata() */
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
delegate = new MinimalTiffReader();
delegate.setId(currentId);
exposureTimes = new ArrayList<Double>();
String data = ifds.get(0).getComment();
// remove magic string
data = data.substring(data.indexOf("\n") + 1);
date = data.substring(0, data.indexOf("\n"));
data = data.substring(data.indexOf("\n") + 1);
data = data.replaceAll("ReadFromDoc", "");
IniParser parser = new IniParser();
parser.setCommentDelimiter(";");
IniList ini = parser.parseINI(new BufferedReader(new StringReader(data)));
String objective = ini.getTable(" MICROSCOPE ").get("Objective");
int space = objective.indexOf(" ");
if (space != -1) {
magnification = new Integer(objective.substring(0, space - 1));
immersion = objective.substring(space + 1);
}
IniTable cameraTable = ini.getTable(" CAPTURE DEVICE ");
binning = cameraTable.get("Binning") + "x" + cameraTable.get("Binning");
cameraType = cameraTable.get("Camera Type");
cameraName = cameraTable.get("Camera Name");
core[0].bitsPerPixel = Integer.parseInt(cameraTable.get("Display Depth"));
IniTable captureTable = ini.getTable(" CAPTURE ");
int index = 1;
for (int i = 0; i < getSizeC(); i++) {
if (captureTable.get("c_Filter" + index) != null) {
exposureTimes.add(new Double(captureTable.get("c_Expos" + index)));
} else i--;
index++;
}
IniTable calibrationTable = ini.getTable(" CALIBRATION ");
String units = calibrationTable.get("units");
scaling = Double.parseDouble(calibrationTable.get("factor"));
core[0].imageCount *= getSizeC();
core[0].rgb = false;
if (ifds.get(0).containsKey(CUSTOM_BITS)) {
core[0].bitsPerPixel = ifds.get(0).getIFDIntValue(CUSTOM_BITS);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
HashMap<String, String> iniMap = ini.flattenIntoHashMap();
metadata.putAll(iniMap);
}
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
// make sure we have the experiment file
id = locateExperimentFile(id);
super.initFile(id);
Location dir = new Location(id).getAbsoluteFile().getParentFile();
for (String file : dir.list(true)) {
Location f = new Location(dir, file);
if (!f.isDirectory()) {
if (checkSuffix(file, META_EXT)) {
metadataFiles.add(f.getAbsolutePath());
}
}
}
// parse Experiment metadata
IniList experiment = readMetaData(id);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
objective = experiment.getTable("Geometry").get("Name");
IniTable camera = experiment.getTable("Camera");
binning = camera.get("BinX") + "x" + camera.get("BinY");
parseChannelData(dir);
addGlobalMeta("Objective", objective);
addGlobalMeta("Camera binning", binning);
}
Vector<String> uniqueRows = new Vector<String>();
Vector<String> uniqueColumns = new Vector<String>();
for (String well : wellLabels) {
String row = well.substring(0, 1).trim();
String column = well.substring(1).trim();
if (!uniqueRows.contains(row) && row.length() > 0) uniqueRows.add(row);
if (!uniqueColumns.contains(column) && column.length() > 0) {
uniqueColumns.add(column);
}
}
int nSlices = getSizeZ() == 0 ? 1 : getSizeZ();
int nTimepoints = getSizeT();
int nWells = wellLabels.size();
int nChannels = getSizeC() == 0 ? channelNames.size() : getSizeC();
if (nChannels == 0) nChannels = 1;
tiffs = getTiffs(dir.getAbsolutePath());
reader = new MinimalTiffReader();
reader.setId(tiffs[0][0]);
int sizeX = reader.getSizeX();
int sizeY = reader.getSizeY();
int pixelType = reader.getPixelType();
boolean rgb = reader.isRGB();
boolean interleaved = reader.isInterleaved();
boolean indexed = reader.isIndexed();
boolean littleEndian = reader.isLittleEndian();
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
IniParser parser = new IniParser();
for (String metadataFile : metadataFiles) {
String filename = new Location(metadataFile).getName();
if (!checkSuffix(metadataFile, "txt")) {
String data = DataTools.readFile(metadataFile);
IniList ini = parser.parseINI(new BufferedReader(new StringReader(data)));
HashMap<String, String> h = ini.flattenIntoHashMap();
for (String key : h.keySet()) {
addGlobalMeta(filename + " " + key, h.get(key));
}
}
}
}
for (int i = 0; i < getSeriesCount(); i++) {
core[i] = new CoreMetadata();
core[i].sizeC = nChannels;
core[i].sizeZ = nSlices;
core[i].sizeT = nTimepoints;
core[i].sizeX = sizeX / fieldCols;
core[i].sizeY = sizeY / fieldRows;
core[i].pixelType = pixelType;
core[i].rgb = rgb;
core[i].interleaved = interleaved;
core[i].indexed = indexed;
core[i].littleEndian = littleEndian;
core[i].dimensionOrder = "XYZTC";
core[i].imageCount = nSlices * nTimepoints * nChannels;
}
MetadataStore store = makeFilterMetadata();
boolean populatePlanes = getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM;
MetadataTools.populatePixels(store, this, populatePlanes);
String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
store.setPlateAcquisitionID(plateAcqID, 0, 0);
if (fieldRows * fieldCols > 0) {
store.setPlateAcquisitionMaximumFieldCount(new PositiveInteger(fieldRows * fieldCols), 0, 0);
} else {
LOGGER.warn("Expected positive value for MaximumFieldCount; got {}", fieldRows * fieldCols);
}
for (int row = 0; row < wellRows; row++) {
for (int col = 0; col < wellCols; col++) {
int index = row * wellCols + col;
store.setWellID(MetadataTools.createLSID("Well", 0, index), 0, index);
store.setWellRow(new NonNegativeInteger(row), 0, index);
store.setWellColumn(new NonNegativeInteger(col), 0, index);
}
}
for (int i = 0; i < getSeriesCount(); i++) {
int well = i / (fieldRows * fieldCols);
int field = i % (fieldRows * fieldCols);
MetadataTools.setDefaultCreationDate(store, tiffs[well][0], i);
String name = wellLabels.get(well);
String row = name.substring(0, 1);
Integer col = Integer.parseInt(name.substring(1));
int index = (row.charAt(0) - 'A') * wellCols + col - 1;
String wellSampleID = MetadataTools.createLSID("WellSample", 0, index, field);
store.setWellSampleID(wellSampleID, 0, index, field);
store.setWellSampleIndex(new NonNegativeInteger(i), 0, index, field);
String imageID = MetadataTools.createLSID("Image", i);
store.setWellSampleImageRef(imageID, 0, index, field);
store.setImageID(imageID, i);
store.setImageName(name + " Field #" + (field + 1), i);
store.setPlateAcquisitionWellSampleRef(wellSampleID, 0, 0, i);
}
MetadataLevel level = getMetadataOptions().getMetadataLevel();
if (level != MetadataLevel.MINIMUM) {
String instrumentID = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrumentID, 0);
String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
store.setObjectiveID(objectiveID, 0, 0);
if (objective != null) {
String[] tokens = objective.split(" ");
String mag = tokens[0].replaceAll("[xX]", "");
String na = null;
int naIndex = 0;
for (int i = 0; i < tokens.length; i++) {
if (tokens[i].equals("NA")) {
naIndex = i + 1;
na = tokens[naIndex];
break;
}
}
Integer magnification = new Integer(mag);
if (magnification > 0) {
store.setObjectiveNominalMagnification(new PositiveInteger(magnification), 0, 0);
} else {
LOGGER.warn("Expected positive value for NominalMagnification; got {}", magnification);
}
if (na != null) {
na = na.substring(0, 1) + "." + na.substring(1);
store.setObjectiveLensNA(new Double(na), 0, 0);
}
if (naIndex + 1 < tokens.length) {
store.setObjectiveManufacturer(tokens[naIndex + 1], 0, 0);
}
}
// populate LogicalChannel data
for (int i = 0; i < getSeriesCount(); i++) {
store.setImageInstrumentRef(instrumentID, i);
store.setObjectiveSettingsID(objectiveID, i);
for (int c = 0; c < getSizeC(); c++) {
store.setChannelName(channelNames.get(c), i, c);
if (emWave[c] > 0) {
store.setChannelEmissionWavelength(new PositiveInteger(emWave[c]), i, c);
} else {
LOGGER.warn("Expected positive value for EmissionWavelength; got {}", emWave[c]);
}
if (exWave[c] > 0) {
store.setChannelExcitationWavelength(new PositiveInteger(exWave[c]), i, c);
} else {
LOGGER.warn("Expected positive value for ExcitationWavelength; got {}", exWave[c]);
}
String detectorID = MetadataTools.createLSID("Detector", 0, c);
store.setDetectorID(detectorID, 0, c);
store.setDetectorSettingsID(detectorID, i, c);
store.setDetectorSettingsGain(gain[c], i, c);
store.setDetectorSettingsOffset(offset[c], i, c);
store.setDetectorSettingsBinning(getBinning(binning), i, c);
}
long firstPlane = 0;
for (int p = 0; p < getImageCount(); p++) {
int[] zct = getZCTCoords(p);
store.setPlaneExposureTime(exposure[zct[1]], i, p);
String file = getFilename(i, p);
if (file != null) {
long plane = getTimestamp(file);
if (p == 0) {
firstPlane = plane;
}
double timestamp = (plane - firstPlane) / 1000.0;
store.setPlaneDeltaT(timestamp, i, p);
}
}
}
store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
store.setPlateName(plateName, 0);
store.setPlateDescription(plateDescription, 0);
if (level != MetadataLevel.NO_OVERLAYS) {
parseROIs(store);
}
}
}
private IniList readMetaData(String id) throws IOException {
IniParser parser = new IniParser();
IniList exp =
parser.parseINI(
new BufferedReader(new InputStreamReader(new FileInputStream(id), Constants.ENCODING)));
IniList plate = null;
// Read Plate File
for (String filename : metadataFiles) {
if (checkSuffix(filename, "plt")) {
plate =
parser.parseINI(
new BufferedReader(
new InputStreamReader(new FileInputStream(filename), Constants.ENCODING)));
} else if (filename.endsWith("RoiSummary.txt")) {
roiFile = filename;
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
RandomAccessInputStream s = new RandomAccessInputStream(filename);
String line = s.readLine().trim();
while (!line.endsWith(".adf\"")) {
line = s.readLine().trim();
}
plateName = line.substring(line.indexOf(":")).trim();
plateName = plateName.replace('/', File.separatorChar);
plateName = plateName.replace('\\', File.separatorChar);
for (int i = 0; i < 3; i++) {
plateName = plateName.substring(0, plateName.lastIndexOf(File.separator));
}
plateName = plateName.substring(plateName.lastIndexOf(File.separator) + 1);
s.close();
}
}
}
if (plate == null) throw new IOException("No Plate File");
IniTable plateType = plate.getTable("PlateType");
if (plateName == null) {
plateName = plateType.get("Brand");
}
plateDescription = plateType.get("Brand") + " " + plateType.get("Description");
int nWells = Integer.parseInt(plateType.get("Wells"));
if (nWells == 96) {
wellRows = 8;
wellCols = 12;
} else if (nWells == 384) {
wellRows = 16;
wellCols = 24;
}
Location dir = new Location(id).getAbsoluteFile().getParentFile();
String[] wellList = dir.list();
Arrays.sort(wellList);
for (String filename : wellList) {
if (filename.startsWith("Well ")) {
wellLabels.add(filename.split("\\s|\\.")[1]);
}
}
IniTable imageTable = exp.getTable("Image");
boolean montage = imageTable.get("Montaged").equals("1");
if (montage) {
fieldRows = Integer.parseInt(imageTable.get("TilesY"));
fieldCols = Integer.parseInt(imageTable.get("TilesX"));
} else {
fieldRows = 1;
fieldCols = 1;
}
core = new CoreMetadata[wellLabels.size() * fieldRows * fieldCols];
core[0] = new CoreMetadata();
// Hack for current testing/development purposes
// Not all channels have the same Z!!! How to handle???
// FIXME FIXME FIXME
core[0].sizeZ = 1;
// FIXME FIXME FIXME
// END OF HACK
core[0].sizeC = Integer.parseInt(exp.getTable("General").get("Dyes"));
core[0].bitsPerPixel = Integer.parseInt(exp.getTable("Camera").get("BitdepthUsed"));
IniTable dyeTable = exp.getTable("Dyes");
for (int i = 1; i <= getSizeC(); i++) {
channelNames.add(dyeTable.get(Integer.toString(i)));
}
// Count Images
core[0].sizeT = 0;
Location well = new Location(dir.getAbsolutePath(), "Well " + wellLabels.get(1));
for (String channelName : channelNames) {
int timepoints = 0;
for (String filename : well.list()) {
if (filename.startsWith(channelName) && filename.endsWith(".tif")) {
timepoints++;
}
}
if (timepoints > getSizeT()) {
core[0].sizeT = timepoints;
}
}
return exp;
}
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
boolean helios = ifds.get(0).containsKey(HELIOS_TAG);
boolean titan = ifds.get(0).containsKey(TITAN_TAG);
// Helios etc data might have a stray Titan tag
if (titan && ifds.get(0).getIFDTextValue(TITAN_TAG).trim().isEmpty()) {
titan = false;
}
// Titan data (always?) has an empty Helios tag as well, so the Titan tag is checked first
String software = "S-FEG";
if (titan) {
software = "Titan";
} else if (helios) {
software = "Helios NanoLab";
}
addGlobalMeta("Software", software);
int tagKey = SFEG_TAG;
if (titan) {
tagKey = TITAN_TAG;
} else if (helios) {
tagKey = HELIOS_TAG;
}
String tag = ifds.get(0).getIFDTextValue(tagKey);
if (tag == null) {
return;
}
tag = tag.trim();
if (tag.isEmpty()) {
return; // fall back to regular reader
}
// store metadata for later conversion to OME-XML
if (tag.startsWith("<")) {
XMLTools.parseXML(tag, new FEIHandler());
} else {
IniParser parser = new IniParser();
IniList ini = parser.parseINI(new BufferedReader(new StringReader(tag)));
detectors = new ArrayList<String>();
if (helios) {
IniTable userTable = ini.getTable("User");
date = userTable.get("Date") + " " + userTable.get("Time");
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
userName = userTable.get("User");
IniTable systemTable = ini.getTable("System");
if (systemTable == null) {
systemTable = ini.getTable("SYSTEM");
}
if (systemTable != null) {
microscopeModel = systemTable.get("SystemType");
}
IniTable beamTable = ini.getTable("Beam");
if (beamTable != null) {
String beamTableName = beamTable.get("Beam");
if (beamTableName != null) {
beamTable = ini.getTable(beamTableName);
}
}
if (beamTable != null) {
String beamX = beamTable.get("StageX");
String beamY = beamTable.get("StageY");
String beamZ = beamTable.get("StageZ");
IniTable stageTable = ini.getTable("Stage");
if (beamX != null) {
final Double number = Double.valueOf(beamX);
stageX = new Length(number, UNITS.REFERENCEFRAME);
} else if (stageTable != null) {
final Double number = Double.valueOf(stageTable.get("StageX"));
stageX = new Length(number, UNITS.REFERENCEFRAME);
}
if (beamY != null) {
final Double number = Double.valueOf(beamY);
stageY = new Length(number, UNITS.REFERENCEFRAME);
} else if (stageTable != null) {
final Double number = Double.valueOf(stageTable.get("StageY"));
stageY = new Length(number, UNITS.REFERENCEFRAME);
}
if (beamZ != null) {
final Double number = Double.valueOf(beamZ);
stageZ = new Length(number, UNITS.REFERENCEFRAME);
} else if (stageTable != null) {
final Double number = Double.valueOf(stageTable.get("StageZ"));
stageZ = new Length(number, UNITS.REFERENCEFRAME);
}
}
IniTable scanTable = ini.getTable("Scan");
// physical sizes are stored in meters
sizeX = new Double(scanTable.get("PixelWidth")) * 1000000;
sizeY = new Double(scanTable.get("PixelHeight")) * 1000000;
timeIncrement = new Double(scanTable.get("FrameTime"));
}
} else {
IniTable dataTable = ini.getTable("DatabarData");
imageName = dataTable.get("ImageName");
imageDescription = dataTable.get("szUserText");
String magnification = ini.getTable("Vector").get("Magnification");
sizeX = new Double(magnification) * MAG_MULTIPLIER;
sizeY = new Double(magnification) * MAG_MULTIPLIER;
IniTable scanTable = ini.getTable("Vector.Sysscan");
final Double posX = Double.valueOf(scanTable.get("PositionX"));
final Double posY = Double.valueOf(scanTable.get("PositionY"));
stageX = new Length(posX, UNITS.REFERENCEFRAME);
stageY = new Length(posY, UNITS.REFERENCEFRAME);
IniTable detectorTable = ini.getTable("Vector.Video.Detectors");
int detectorCount = Integer.parseInt(detectorTable.get("NrDetectorsConnected"));
for (int i = 0; i < detectorCount; i++) {
detectors.add(detectorTable.get("Detector_" + i + "_Name"));
}
}
// store everything else in the metadata hashtable
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
HashMap<String, String> iniMap = ini.flattenIntoHashMap();
metadata.putAll(iniMap);
}
}
}