/* @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.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
experimenterName = null;
creationDate = null;
imageName = null;
}
}
/* @see BaseTiffReader#initStandardMetadata() */
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
ifds = tiffParser.getIFDs();
core.clear();
for (int i = 0; i < ifds.size(); i++) {
CoreMetadata ms = new CoreMetadata();
core.add(ms);
ms.imageCount = 1;
IFD ifd = ifds.get(i);
ifd.remove(PIXELS_TAG);
tiffParser.fillInIFD(ifd);
PhotoInterp photo = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
ms.rgb = samples > 1 || photo == PhotoInterp.RGB || photo == PhotoInterp.CFA_ARRAY;
if (photo == PhotoInterp.CFA_ARRAY) samples = 3;
ms.sizeX = (int) ifd.getImageWidth();
ms.sizeY = (int) ifd.getImageLength();
ms.sizeZ = 1;
ms.sizeC = isRGB() ? samples : 1;
ms.sizeT = 1;
ms.pixelType = ifd.getPixelType();
ms.indexed = photo == PhotoInterp.RGB_PALETTE;
ms.dimensionOrder = "XYCZT";
ms.interleaved = false;
}
IFD firstIFD = ifds.get(0);
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
String xml = firstIFD.getIFDTextValue(XML_TAG).trim();
xml = xml.substring(xml.indexOf("<"));
XMLTools.parseXML(xml, new ImaconHandler());
}
String[] creationInfo = firstIFD.getIFDTextValue(CREATOR_TAG).split("\n");
if (creationInfo.length > 4) {
experimenterName = creationInfo[4].trim();
}
if (creationInfo.length > 6) {
imageName = creationInfo[6].trim();
}
if (creationInfo.length > 8) {
creationDate = creationInfo[8].trim();
}
if (creationInfo.length > 10) {
creationDate += " " + creationInfo[10].trim();
}
}
/* @see BaseTiffReader#initMetadataStore() */
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this, true);
if (date != null) {
date = DateTools.formatDate(date, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
store.setImageDescription(MAGIC_STRING, 0);
if (scaling > 0) {
store.setPixelsPhysicalSizeX(new PositiveFloat(scaling), 0);
store.setPixelsPhysicalSizeY(new PositiveFloat(scaling), 0);
} else {
LOGGER.warn("Expected positive value for PhysicalSize; got {}", scaling);
}
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
if (magnification > 0) {
store.setObjectiveNominalMagnification(new PositiveInteger(magnification), 0, 0);
} else {
LOGGER.warn("Expected positive value for NominalMagnification; got {}", magnification);
}
store.setObjectiveImmersion(getImmersion(immersion), 0, 0);
String detector = MetadataTools.createLSID("Detector", 0, 0);
store.setDetectorID(detector, 0, 0);
store.setDetectorModel(cameraType + " " + cameraName, 0, 0);
store.setDetectorType(getDetectorType("CCD"), 0, 0);
for (int i = 0; i < getSizeC(); i++) {
store.setDetectorSettingsID(detector, 0, i);
store.setDetectorSettingsBinning(getBinning(binning), 0, i);
}
for (int i = 0; i < getImageCount(); i++) {
int[] zct = getZCTCoords(i);
store.setPlaneExposureTime(exposureTimes.get(zct[1]) / 1000000, 0, i);
}
}
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (delegate != null) delegate.close(fileOnly);
if (!fileOnly) {
delegate = null;
date = null;
magnification = null;
immersion = null;
cameraType = null;
cameraName = null;
binning = null;
exposureTimes = null;
scaling = 0d;
}
}
/* @see loci.formats.IFormatReader#close(boolean) */
@Override
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
imageName = null;
imageDescription = null;
date = null;
userName = null;
microscopeModel = null;
stageX = stageY = stageZ = null;
sizeX = sizeY = timeIncrement = null;
detectors = null;
magnification = null;
}
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
if (!checkSuffix(id, "tif")) {
Location parent = new Location(id).getAbsoluteFile().getParentFile();
String[] list = parent.list(true);
for (String f : list) {
if (checkSuffix(f, "tif")) {
String path = new Location(parent, f).getAbsolutePath();
if (isThisType(path)) {
id = path;
break;
}
}
}
}
super.initFile(id);
}
/* @see loci.formats.BaseTiffReader#initMetadataStore() */
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
for (int i = 0; i < getSeriesCount(); i++) {
store.setImageName("Series " + (i + 1), i);
}
MetadataLevel level = getMetadataOptions().getMetadataLevel();
if (level != MetadataLevel.MINIMUM) {
if (level != MetadataLevel.NO_OVERLAYS) {
try {
parseROIs(store);
} catch (IOException e) {
LOGGER.debug("Could not parse ROIs", e);
}
}
}
}
/* @see BaseTiffReader#initMetadataStore() */
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
if (creationDate != null) {
creationDate = DateTools.formatDate(creationDate, "yyyyMMdd HHmmSSZ");
}
for (int i = 0; i < getSeriesCount(); i++) {
String name = imageName;
if (imageName.length() == 0) {
name = "#" + (i + 1);
} else {
name += " #" + (i + 1);
}
store.setImageName(name, i);
if (creationDate != null) {
store.setImageAcquisitionDate(new Timestamp(creationDate), i);
}
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (experimenterName == null) experimenterName = "";
int nameSpace = experimenterName.indexOf(" ");
String firstName = nameSpace == -1 ? "" : experimenterName.substring(0, nameSpace);
String lastName =
nameSpace == -1 ? experimenterName : experimenterName.substring(nameSpace + 1);
String experimenter = MetadataTools.createLSID("Experimenter", 0);
store.setExperimenterID(experimenter, 0);
store.setExperimenterFirstName(firstName, 0);
store.setExperimenterLastName(lastName, 0);
for (int i = 0; i < getSeriesCount(); i++) {
store.setImageExperimenterRef(experimenter, i);
}
}
}
/* @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 BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
CoreMetadata m = core.get(0);
m.sizeZ = 0;
m.sizeT = 0;
MetadataLevel level = getMetadataOptions().getMetadataLevel();
for (IFD ifd : ifds) {
if (level != MetadataLevel.MINIMUM) {
short[] tag1 = (short[]) ifd.getIFDValue(IMAGE_PRO_TAG_1);
if (tag1 != null) {
String seqId = "";
for (int i = 0; i < tag1.length; i++) seqId = seqId + tag1[i];
addGlobalMeta("Image-Pro SEQ ID", seqId);
}
}
int tag2 = ifds.get(0).getIFDIntValue(IMAGE_PRO_TAG_2);
if (tag2 != -1) {
// should be one of these for every image plane
m.sizeZ++;
addGlobalMeta("Frame Rate", tag2);
}
addGlobalMeta("Number of images", getSizeZ());
}
if (getSizeZ() == 0) m.sizeZ = 1;
if (getSizeT() == 0) m.sizeT = 1;
if (getSizeZ() == 1 && getSizeT() == 1) {
m.sizeZ = ifds.size();
}
// default values
addGlobalMeta("frames", getSizeZ());
addGlobalMeta("channels", super.getSizeC());
addGlobalMeta("slices", getSizeT());
// parse the description to get channels, slices and times where applicable
String descr = ifds.get(0).getComment();
metadata.remove("Comment");
if (descr != null) {
String[] lines = descr.split("\n");
for (String token : lines) {
token = token.trim();
int eq = token.indexOf("=");
if (eq == -1) eq = token.indexOf(":");
if (eq != -1) {
String label = token.substring(0, eq);
String data = token.substring(eq + 1);
addGlobalMeta(label, data);
if (label.equals("channels")) m.sizeC = Integer.parseInt(data);
else if (label.equals("frames")) {
m.sizeT = Integer.parseInt(data);
} else if (label.equals("slices")) {
m.sizeZ = Integer.parseInt(data);
}
}
}
}
if (isRGB() && getSizeC() != 3) m.sizeC *= 3;
m.dimensionOrder = "XY";
int maxNdx = 0, max = 0;
int[] dims = {getSizeZ(), getSizeC(), getSizeT()};
String[] axes = {"Z", "C", "T"};
for (int i = 0; i < dims.length; i++) {
if (dims[i] > max) {
max = dims[i];
maxNdx = i;
}
}
m.dimensionOrder += axes[maxNdx];
if (maxNdx != 1) {
if (getSizeC() > 1) {
m.dimensionOrder += "C";
m.dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]);
} else m.dimensionOrder += (maxNdx == 0 ? axes[2] : axes[0]) + "C";
} else {
if (getSizeZ() > getSizeT()) m.dimensionOrder += "ZT";
else m.dimensionOrder += "TZ";
}
}
/* @see loci.formats.in.BaseTiffReader#initStandardMetadata() */
protected void initStandardMetadata() throws FormatException, IOException {
super.initStandardMetadata();
ifds = tiffParser.getIFDs();
for (IFD ifd : ifds) {
tiffParser.fillInIFD(ifd);
}
String comment = ifds.get(0).getComment();
String[] values = comment.split(";");
for (String v : values) {
int eq = v.indexOf("=");
if (eq < 0) continue;
String key = v.substring(0, eq).trim();
String value = v.substring(eq + 1).trim();
addGlobalMeta(key, value);
if (key.equals("OverlapsXY")) {
String[] overlapValues = value.split(" ");
overlaps = new int[ifds.size() * 2];
for (int i = 0; i < overlapValues.length; i++) {
overlaps[i] = Integer.parseInt(overlapValues[i]);
}
}
}
core = new CoreMetadata[ifds.size()];
for (int i = 0; i < core.length; i++) {
setSeries(i);
core[i] = new CoreMetadata();
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {}
}
setSeries(0);
// repopulate core metadata
for (int s = 0; s < core.length; s++) {
IFD ifd = ifds.get(s);
PhotoInterp p = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
core[s].rgb = samples > 1 || p == PhotoInterp.RGB;
long numTileRows = ifd.getTilesPerColumn() - 1;
long numTileCols = ifd.getTilesPerRow() - 1;
int overlapX = overlaps[s * 2];
int overlapY = overlaps[s * 2 + 1];
core[s].sizeX = (int) (ifd.getImageWidth() - (numTileCols * overlapX));
core[s].sizeY = (int) (ifd.getImageLength() - (numTileRows * overlapY));
core[s].sizeZ = 1;
core[s].sizeT = 1;
core[s].sizeC = core[s].rgb ? samples : 1;
core[s].littleEndian = ifd.isLittleEndian();
core[s].indexed =
p == PhotoInterp.RGB_PALETTE
&& (get8BitLookupTable() != null || get16BitLookupTable() != null);
core[s].imageCount = 1;
core[s].pixelType = ifd.getPixelType();
core[s].metadataComplete = true;
core[s].interleaved = false;
core[s].falseColor = false;
core[s].dimensionOrder = "XYCZT";
core[s].thumbnail = s > 0;
}
// look for all of the other associated metadata files
files = new ArrayList<String>();
Location baseFile = new Location(currentId).getAbsoluteFile();
Location parent = baseFile.getParentFile();
String name = baseFile.getName();
if (name.indexOf(".") >= 0) {
name = name.substring(0, name.indexOf(".") + 1);
}
roiFile = new Location(parent, name + "ROI").getAbsolutePath();
roiDrawFile = new Location(parent, name + "ROI-draw").getAbsolutePath();
String[] list = parent.list(true);
for (String f : list) {
if (!f.equals(baseFile.getName())) {
files.add(new Location(parent, f).getAbsolutePath());
}
}
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
files = null;
}
}
/* @see BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
super.initMetadataStore();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
if (date != null) {
date = DateTools.formatDate(date, DATE_FORMAT);
if (date != null) {
store.setImageAcquisitionDate(new Timestamp(date), 0);
}
}
if (imageName != null) {
store.setImageName(imageName, 0);
}
if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
if (imageDescription != null) {
store.setImageDescription(imageDescription, 0);
}
if (userName != null) {
store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
store.setExperimenterLastName(userName, 0);
}
if (microscopeModel != null) {
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
store.setMicroscopeModel(microscopeModel, 0);
}
if (detectors != null && detectors.size() > 0) {
String instrument = MetadataTools.createLSID("Instrument", 0);
store.setInstrumentID(instrument, 0);
store.setImageInstrumentRef(instrument, 0);
for (int i = 0; i < detectors.size(); i++) {
String detectorID = MetadataTools.createLSID("Detector", 0, i);
store.setDetectorID(detectorID, 0, i);
store.setDetectorModel(detectors.get(i), 0, i);
store.setDetectorType(getDetectorType("Other"), 0, i);
}
}
if (magnification != null) {
store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
store.setObjectiveNominalMagnification(magnification, 0, 0);
store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
}
store.setStageLabelX(stageX, 0);
store.setStageLabelY(stageY, 0);
store.setStageLabelZ(stageZ, 0);
store.setStageLabelName("", 0);
Length physicalSizeX = FormatTools.getPhysicalSizeX(sizeX);
Length physicalSizeY = FormatTools.getPhysicalSizeY(sizeY);
if (physicalSizeX != null) {
store.setPixelsPhysicalSizeX(physicalSizeX, 0);
}
if (physicalSizeY != null) {
store.setPixelsPhysicalSizeY(physicalSizeY, 0);
}
if (timeIncrement != null) {
store.setPixelsTimeIncrement(new Time(timeIncrement, UNITS.S), 0);
}
}
}
/* @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);
}
}
}