/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
Vector<String> uniqueChannels = new Vector<String>();
Vector<Double> uniqueZs = new Vector<Double>();
Vector<Double> stageX = new Vector<Double>();
Vector<Double> stageY = new Vector<Double>();
String filename = id.substring(id.lastIndexOf(File.separator) + 1);
filename = filename.substring(0, filename.indexOf("."));
boolean integerFilename = true;
try {
Integer.parseInt(filename);
} catch (NumberFormatException e) {
integerFilename = false;
}
if (integerFilename
&& ifds.size() == 1
&& ifds.get(0).getIFDIntValue(IFD.NEW_SUBFILE_TYPE) == 2) {
// look for other files in the dataset
findTIFFs();
String stageLabel = null;
for (String tiff : files) {
MetamorphHandler handler = new MetamorphHandler();
parseFile(tiff, handler);
String label = handler.getStageLabel();
if (stageLabel == null) {
stageLabel = label;
} else if (!label.equals(stageLabel)) {
break;
}
if (!uniqueChannels.contains(handler.getChannelName())) {
uniqueChannels.add(handler.getChannelName());
}
Vector<Double> zPositions = handler.getZPositions();
Double pos = Math.rint(zPositions.get(0));
if (!uniqueZs.contains(pos)) {
uniqueZs.add(pos);
}
}
MetamorphHandler handler = new MetamorphHandler();
parseFile(files[files.length - 1], handler);
String lastStageLabel = handler.getStageLabel();
int lastField = getField(lastStageLabel);
int lastWellRow = getWellRow(lastStageLabel);
int lastWellColumn = getWellColumn(lastStageLabel);
int field = getField(stageLabel);
int fieldRow = getWellRow(stageLabel);
int fieldColumn = getWellColumn(stageLabel);
wellCount = lastField - field + 1;
fieldRowCount = lastWellRow - fieldRow + 1;
fieldColumnCount = lastWellColumn - fieldColumn + 1;
core[0].sizeC = uniqueChannels.size();
core[0].sizeZ = uniqueZs.size();
} else {
files = new String[] {id};
wellCount = 1;
fieldRowCount = 1;
fieldColumnCount = 1;
core[0].sizeC = 0;
}
// parse XML comment
MetamorphHandler handler = new MetamorphHandler(getGlobalMetadata());
Vector<Double> xPositions = new Vector<Double>();
Vector<Double> yPositions = new Vector<Double>();
for (IFD ifd : ifds) {
String xml = XMLTools.sanitizeXML(ifd.getComment());
XMLTools.parseXML(xml, handler);
double x = handler.getStagePositionX();
double y = handler.getStagePositionY();
if (xPositions.size() == 0) {
xPositions.add(x);
yPositions.add(y);
} else {
double previousX = xPositions.get(xPositions.size() - 1);
double previousY = yPositions.get(yPositions.size() - 1);
if (Math.abs(previousX - x) > 0.21 || Math.abs(previousY - y) > 0.21) {
xPositions.add(x);
yPositions.add(y);
}
}
}
if (xPositions.size() > 1) {
fieldRowCount = xPositions.size();
}
Vector<Integer> wavelengths = handler.getWavelengths();
Vector<Double> zPositions = handler.getZPositions();
// calculate axis sizes
Vector<Integer> uniqueC = new Vector<Integer>();
for (Integer c : wavelengths) {
if (!uniqueC.contains(c)) {
uniqueC.add(c);
}
}
int effectiveC = uniqueC.size();
if (effectiveC == 0) effectiveC = 1;
if (getSizeC() == 0) core[0].sizeC = 1;
int samples = ifds.get(0).getSamplesPerPixel();
core[0].sizeC *= effectiveC * samples;
Vector<Double> uniqueZ = new Vector<Double>();
for (Double z : zPositions) {
if (!uniqueZ.contains(z)) uniqueZ.add(z);
}
if (getSizeZ() == 0) core[0].sizeZ = 1;
core[0].sizeZ *= uniqueZ.size();
int totalPlanes = files.length * ifds.size();
effectiveC = getSizeC() / samples;
core[0].sizeT =
totalPlanes / (wellCount * fieldRowCount * fieldColumnCount * getSizeZ() * effectiveC);
if (getSizeT() == 0) core[0].sizeT = 1;
int seriesCount = wellCount * fieldRowCount * fieldColumnCount;
if (seriesCount > 1 && getSizeZ() > totalPlanes / seriesCount) {
core[0].sizeZ = 1;
core[0].sizeT = totalPlanes / (seriesCount * getSizeT() * effectiveC);
}
core[0].imageCount = getSizeZ() * getSizeT() * effectiveC;
if (seriesCount > 1) {
CoreMetadata oldCore = core[0];
core = new CoreMetadata[seriesCount];
for (int i = 0; i < seriesCount; i++) {
core[i] = oldCore;
}
}
for (int s = 0; s < wellCount * fieldRowCount * fieldColumnCount; s++) {
if (files.length > 1) {
int[] lengths =
new int[] {
getSizeZ(),
getEffectiveSizeC(),
fieldColumnCount,
fieldRowCount,
wellCount,
getSizeT()
};
Well well = getWell(s);
int[] position = new int[] {0, 0, well.fieldCol, well.fieldRow, well.well, 0};
int fileIndex = FormatTools.positionToRaster(lengths, position);
parseFile(files[fileIndex], handler);
stageX.add(handler.getStagePositionX());
stageY.add(handler.getStagePositionY());
} else {
stageX.add(xPositions.get(s));
stageY.add(yPositions.get(s));
}
}
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
store.setPlateRowNamingConvention(NamingConvention.LETTER, 0);
store.setPlateColumnNamingConvention(NamingConvention.NUMBER, 0);
for (int well = 0; well < wellCount; well++) {
store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
store.setWellRow(new NonNegativeInteger(0), 0, well);
store.setWellColumn(new NonNegativeInteger(well), 0, well);
for (int row = 0; row < fieldRowCount; row++) {
for (int col = 0; col < fieldColumnCount; col++) {
int field = row * fieldColumnCount + col;
String wellSampleID = MetadataTools.createLSID("WellSample", 0, well, field);
store.setWellSampleID(wellSampleID, 0, well, field);
int seriesIndex = getSeriesIndex(row, col, well);
String imageID = MetadataTools.createLSID("Image", seriesIndex);
store.setImageID(imageID, seriesIndex);
store.setWellSampleImageRef(imageID, 0, well, field);
store.setWellSampleIndex(new NonNegativeInteger(seriesIndex), 0, well, field);
}
}
}
for (int s = 0; s < seriesCount; s++) {
setSeries(s);
Well well = getWell(s);
String name = handler.getImageName();
if (seriesCount > 1) {
name =
"Field "
+ (char) (well.fieldRow + 'A')
+ (well.fieldCol + 1)
+ ", Well "
+ (well.well + 1)
+ ": "
+ name;
}
store.setImageName(name, s);
String date = DateTools.formatDate(handler.getDate(), DateTools.ISO8601_FORMAT);
store.setImageAcquiredDate(date, s);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
Vector<String> timestamps = handler.getTimestamps();
Vector<Double> exposures = handler.getExposures();
for (int i = 0; i < timestamps.size(); i++) {
long timestamp = DateTools.getTime(timestamps.get(i), DATE_FORMAT);
addSeriesMeta("timestamp " + i, timestamp);
}
for (int i = 0; i < exposures.size(); i++) {
addSeriesMeta("exposure time " + i + " (ms)", exposures.get(i).floatValue() * 1000);
}
long startDate = 0;
if (timestamps.size() > 0) {
startDate = DateTools.getTime(timestamps.get(0), DATE_FORMAT);
}
store.setImageDescription("", s);
int image = 0;
for (int c = 0; c < getEffectiveSizeC(); c++) {
for (int t = 0; t < getSizeT(); t++) {
store.setPlaneTheZ(new NonNegativeInteger(0), s, image);
store.setPlaneTheC(new NonNegativeInteger(c), s, image);
store.setPlaneTheT(new NonNegativeInteger(t), s, image);
if (t < timestamps.size()) {
String stamp = timestamps.get(t);
long ms = DateTools.getTime(stamp, DATE_FORMAT);
store.setPlaneDeltaT((ms - startDate) / 1000.0, s, image);
}
if (image < exposures.size()) {
store.setPlaneExposureTime(exposures.get(image), s, image);
}
if (s < stageX.size()) {
store.setPlanePositionX(stageX.get(s), s, image);
}
if (s < stageY.size()) {
store.setPlanePositionY(stageY.get(s), s, image);
}
image++;
}
}
store.setImagingEnvironmentTemperature(handler.getTemperature(), s);
store.setPixelsPhysicalSizeX(new PositiveFloat(handler.getPixelSizeX()), s);
store.setPixelsPhysicalSizeY(new PositiveFloat(handler.getPixelSizeY()), s);
for (int c = 0; c < getEffectiveSizeC(); c++) {
if (uniqueChannels.size() > c) {
store.setChannelName(uniqueChannels.get(c), s, c);
} else store.setChannelName(handler.getChannelName(), s, c);
}
}
}
}
/* @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);
}
}
}