private String[][] getTiffs(String dir) {
Location f = new Location(dir);
Vector<Vector<String>> files = new Vector<Vector<String>>();
String[] wells = f.list(true);
Arrays.sort(wells);
for (String filename : wells) {
Location file = new Location(f, filename).getAbsoluteFile();
if (file.isDirectory() && filename.startsWith("Well ")) {
String[] list = file.list(true);
Vector<String> tiffList = new Vector<String>();
Arrays.sort(list);
for (String tiff : list) {
if (tiff.matches(".* - n\\d\\d\\d\\d\\d\\d\\.tif")) {
tiffList.add(new Location(file, tiff).getAbsolutePath());
}
}
files.add(tiffList);
}
}
String[][] tiffFiles = new String[files.size()][];
for (int i = 0; i < tiffFiles.length; i++) {
tiffFiles[i] = files.get(i).toArray(new String[0]);
}
return tiffFiles;
}
/* @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.FormatReader#initFile(String) */
public void initFile(String id) throws FormatException, IOException {
super.initFile(id);
tiffReader = new MinimalTiffReader();
positions = new Vector<Position>();
LOGGER.info("Reading metadata file");
// find metadata.txt
Location file = new Location(currentId).getAbsoluteFile();
Location parentFile = file.getParentFile();
String metadataFile = METADATA;
if (file.exists()) {
metadataFile = new Location(parentFile, METADATA).getAbsolutePath();
// look for other positions
if (parentFile.getName().indexOf("Pos_") >= 0) {
parentFile = parentFile.getParentFile();
String[] dirs = parentFile.list(true);
Arrays.sort(dirs);
for (String dir : dirs) {
if (dir.indexOf("Pos_") >= 0) {
Position pos = new Position();
Location posDir = new Location(parentFile, dir);
pos.metadataFile = new Location(posDir, METADATA).getAbsolutePath();
positions.add(pos);
}
}
} else {
Position pos = new Position();
pos.metadataFile = metadataFile;
positions.add(pos);
}
}
core = new CoreMetadata[positions.size()];
for (int i = 0; i < positions.size(); i++) {
core[i] = new CoreMetadata();
setSeries(i);
parsePosition(i);
}
setSeries(0);
populateMetadata();
}
private void buildTIFFList(int posIndex) throws FormatException {
Position p = positions.get(posIndex);
String parent = new Location(p.metadataFile).getParent();
LOGGER.info("Finding image file names");
// find the name of a TIFF file
p.tiffs = new Vector<String>();
// build list of TIFF files
buildTIFFList(posIndex, parent + File.separator + p.baseTiff);
if (p.tiffs.size() == 0) {
Vector<String> uniqueZ = new Vector<String>();
Vector<String> uniqueC = new Vector<String>();
Vector<String> uniqueT = new Vector<String>();
Location dir = new Location(p.metadataFile).getAbsoluteFile().getParentFile();
String[] files = dir.list(true);
Arrays.sort(files);
for (String f : files) {
if (checkSuffix(f, "tif") || checkSuffix(f, "tiff")) {
String[] blocks = f.split("_");
if (!uniqueT.contains(blocks[1])) uniqueT.add(blocks[1]);
if (!uniqueC.contains(blocks[2])) uniqueC.add(blocks[2]);
if (!uniqueZ.contains(blocks[3])) uniqueZ.add(blocks[3]);
p.tiffs.add(new Location(dir, f).getAbsolutePath());
}
}
core[posIndex].sizeZ = uniqueZ.size();
core[posIndex].sizeC = uniqueC.size();
core[posIndex].sizeT = uniqueT.size();
if (p.tiffs.size() == 0) {
throw new FormatException("Could not find TIFF files.");
}
}
}
/* @see loci.formats.FormatReader#initFile(String) */
protected void initFile(String id) throws FormatException, IOException {
super.initFile(id);
if (!checkSuffix(id, "vsi")) {
Location current = new Location(id).getAbsoluteFile();
Location parent = current.getParentFile();
parent = parent.getParentFile();
Location grandparent = parent.getParentFile();
String vsi = parent.getName();
vsi = vsi.substring(1, vsi.length() - 1) + ".vsi";
Location vsiFile = new Location(grandparent, vsi);
if (!vsiFile.exists()) {
throw new FormatException("Could not find .vsi file.");
} else {
id = vsiFile.getAbsolutePath();
}
}
parser = new TiffParser(id);
ifds = parser.getIFDs();
RandomAccessInputStream vsi = new RandomAccessInputStream(id);
vsi.order(parser.getStream().isLittleEndian());
vsi.seek(8);
readTags(vsi);
vsi.seek(parser.getStream().getFilePointer());
vsi.skipBytes(273);
ArrayList<String> files = new ArrayList<String>();
Location file = new Location(id).getAbsoluteFile();
Location dir = file.getParentFile();
String name = file.getName();
name = name.substring(0, name.lastIndexOf("."));
Location pixelsDir = new Location(dir, "_" + name + "_");
String[] stackDirs = pixelsDir.list(true);
if (stackDirs != null) {
for (String f : stackDirs) {
Location stackDir = new Location(pixelsDir, f);
String[] pixelsFiles = stackDir.list(true);
if (pixelsFiles != null) {
for (String pixelsFile : pixelsFiles) {
if (checkSuffix(pixelsFile, "ets")) {
files.add(new Location(stackDir, pixelsFile).getAbsolutePath());
}
}
}
}
}
files.add(file.getAbsolutePath());
usedFiles = files.toArray(new String[files.size()]);
core = new CoreMetadata[files.size() - 1 + ifds.size()];
tileOffsets = new Long[files.size() - 1][];
rows = new int[files.size() - 1];
cols = new int[files.size() - 1];
nDimensions = new int[core.length];
IFDList exifs = parser.getExifIFDs();
compressionType = new int[core.length];
tileX = new int[core.length];
tileY = new int[core.length];
tileMap = new HashMap[core.length];
for (int s = 0; s < core.length; s++) {
core[s] = new CoreMetadata();
}
for (int s = 0; s < core.length; s++) {
tileMap[s] = new HashMap<TileCoordinate, Integer>();
if (s == 0 && !hasFlattenedResolutions()) {
core[s].resolutionCount = ifds.size() + (files.size() == 1 ? 0 : 1);
}
if (s < files.size() - 1) {
setSeries(s);
parseETSFile(files.get(s), s);
core[s].littleEndian = compressionType[s] == RAW;
core[s].interleaved = core[s].rgb;
if (s == 0 && exifs.size() > 0) {
IFD exif = exifs.get(0);
int newX = exif.getIFDIntValue(IFD.PIXEL_X_DIMENSION);
int newY = exif.getIFDIntValue(IFD.PIXEL_Y_DIMENSION);
if (getSizeX() > newX || getSizeY() > newY) {
core[s].sizeX = newX;
core[s].sizeY = newY;
}
}
setSeries(0);
} else {
IFD ifd = ifds.get(s - files.size() + 1);
PhotoInterp p = ifd.getPhotometricInterpretation();
int samples = ifd.getSamplesPerPixel();
core[s].rgb = samples > 1 || p == PhotoInterp.RGB;
core[s].sizeX = (int) ifd.getImageWidth();
core[s].sizeY = (int) ifd.getImageLength();
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].interleaved = false;
core[s].falseColor = false;
core[s].thumbnail = s != 0;
}
core[s].metadataComplete = true;
core[s].dimensionOrder = "XYCZT";
}
vsi.close();
MetadataStore store = makeFilterMetadata();
MetadataTools.populatePixels(store, this);
}
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 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.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());
}
}
}
