/** @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
String file = getFilename(getSeries(), no);
int field = getSeries() % (fieldRows * fieldCols);
int fieldRow = field / fieldCols;
int fieldCol = field % fieldCols;
if (file != null) {
try {
reader.setId(file);
if (fieldRows * fieldCols == 1) {
reader.openBytes(0, buf, x, y, w, h);
} else {
// fields are stored together in a single image,
// so we need to split them up
int fx = x + (fieldCol * getSizeX());
int fy = y + (fieldRow * getSizeY());
reader.openBytes(0, buf, fx, fy, w, h);
}
} catch (FormatException e) {
LOGGER.debug("Could not read file " + file, e);
return buf;
} catch (IOException e) {
LOGGER.debug("Could not read file " + file, e);
return buf;
}
}
return buf;
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
if (tiffReader.getCurrentFile() == null) {
setupReader();
}
return tiffReader.getOptimalTileHeight();
}
/** @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
String file = positions.get(getSeries()).getFile(no);
if (file != null && new Location(file).exists()) {
tiffReader.setId(file);
return tiffReader.openBytes(0, buf, x, y, w, h);
}
LOGGER.warn("File for image #{} ({}) is missing.", no, file);
return buf;
}
/* @see loci.formats.IFormatReader#close(boolean) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (tiffReader != null) tiffReader.close(fileOnly);
if (!fileOnly) {
positions = null;
}
}
/* @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);
}
}
/** Initialize the TIFF reader with the first file in the current series. */
private void setupReader() {
try {
String file = positions.get(getSeries()).getFile(0);
tiffReader.setId(file);
} catch (Exception e) {
LOGGER.debug("", e);
}
}
/** @see loci.formats.IFormatReader#openBytes(int, byte[], int, int, int, int) */
public byte[] openBytes(int no, byte[] buf, int x, int y, int w, int h)
throws FormatException, IOException {
FormatTools.checkPlaneParameters(this, no, buf.length, x, y, w, h);
if (getSizeC() == 1) {
return super.openBytes(no, buf, x, y, w, h);
}
byte[] b = delegate.openBytes(no / getSizeC(), x, y, w, h);
int bpp = FormatTools.getBytesPerPixel(getPixelType());
int c = getZCTCoords(no)[1];
ImageTools.splitChannels(b, buf, c, getSizeC(), bpp, false, isInterleaved(), w * h * bpp);
return buf;
}
/* @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) */
public void close(boolean fileOnly) throws IOException {
super.close(fileOnly);
if (!fileOnly) {
if (reader != null) reader.close();
reader = null;
tiffs = null;
plateName = null;
plateDescription = null;
channelNames.clear();
metadataFiles.clear();
wellLabels.clear();
wellRows = 0;
wellCols = 0;
fieldRows = 0;
fieldCols = 0;
}
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
initMetadata();
}
/* @see loci.formats.IFormatReader#isThisType(RandomAccessInputStream) */
public boolean isThisType(RandomAccessInputStream stream) throws IOException {
if (tiffReader == null) tiffReader = new MinimalTiffReader();
return tiffReader.isThisType(stream);
}
/* @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);
}
}
}
/* @see loci.formats.IFormatReader#getOptimalTileHeight() */
public int getOptimalTileHeight() {
FormatTools.assertId(currentId, true, 1);
return reader.getOptimalTileHeight();
}
