Examples with CoreMetadata loci.formats.CoreMetadata used on opensource projects

Example 1 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class LIFReader method translateImageNodes.

private void translateImageNodes(Element imageNode, int i) throws FormatException {
    CoreMetadata ms = core.get(i);
    ms.orderCertain = true;
    ms.metadataComplete = true;
    ms.littleEndian = true;
    ms.falseColor = true;
    NodeList channels = getChannelDescriptionNodes(imageNode);
    NodeList dimensions = getDimensionDescriptionNodes(imageNode);
    HashMap<Long, String> bytesPerAxis = new HashMap<Long, String>();
    Double physicalSizeX = null;
    Double physicalSizeY = null;
    Double physicalSizeZ = null;
    ms.sizeC = channels.getLength();
    for (int ch = 0; ch < channels.getLength(); ch++) {
        Element channel = (Element) channels.item(ch);
        lutNames.add(channel.getAttribute("LUTName"));
        String bytesInc = channel.getAttribute("BytesInc");
        long bytes = bytesInc == null || bytesInc.trim().isEmpty() ? 0 : Long.parseLong(bytesInc.trim());
        if (bytes > 0) {
            bytesPerAxis.put(bytes, "C");
        }
    }
    int extras = 1;
    for (int dim = 0; dim < dimensions.getLength(); dim++) {
        Element dimension = (Element) dimensions.item(dim);
        String v = dimension.getAttribute("DimID");
        int id = v == null || v.trim().isEmpty() ? 0 : Integer.parseInt(v.trim());
        v = dimension.getAttribute("NumberOfElements");
        int len = v == null || v.trim().isEmpty() ? 0 : Integer.parseInt(v.trim());
        v = dimension.getAttribute("BytesInc");
        long nBytes = v == null || v.trim().isEmpty() ? 0 : Long.parseLong(v.trim());
        v = dimension.getAttribute("Length");
        Double physicalLen;
        if (StringUtils.isBlank(v)) {
            physicalLen = 0d;
        } else {
            physicalLen = new Double(v.trim());
        }
        String unit = dimension.getAttribute("Unit");
        double offByOnePhysicalLen = 0d;
        if (len > 1) {
            offByOnePhysicalLen = physicalLen / len;
            physicalLen /= (len - 1);
        } else {
            physicalLen = 0d;
        }
        if (unit.equals("Ks")) {
            physicalLen /= 1000;
            offByOnePhysicalLen /= 1000;
        } else if (unit.equals("m")) {
            physicalLen *= 1000000;
            offByOnePhysicalLen *= 1000000;
        }
        boolean oldPhysicalSize = useOldPhysicalSizeCalculation();
        switch(id) {
            case // X axis
            1:
                ms.sizeX = len;
                ms.rgb = (nBytes % 3) == 0;
                if (ms.rgb)
                    nBytes /= 3;
                ms.pixelType = FormatTools.pixelTypeFromBytes((int) nBytes, false, true);
                physicalSizeX = oldPhysicalSize ? offByOnePhysicalLen : physicalLen;
                break;
            case // Y axis
            2:
                if (ms.sizeY != 0) {
                    if (ms.sizeZ == 1) {
                        ms.sizeZ = len;
                        bytesPerAxis.put(nBytes, "Z");
                        physicalSizeZ = physicalLen;
                    } else if (ms.sizeT == 1) {
                        ms.sizeT = len;
                        bytesPerAxis.put(nBytes, "T");
                    }
                } else {
                    ms.sizeY = len;
                    physicalSizeY = oldPhysicalSize ? offByOnePhysicalLen : physicalLen;
                }
                break;
            case // Z axis
            3:
                if (ms.sizeY == 0) {
                    // XZ scan - swap Y and Z
                    ms.sizeY = len;
                    ms.sizeZ = 1;
                    bytesPerAxis.put(nBytes, "Y");
                    physicalSizeY = oldPhysicalSize ? offByOnePhysicalLen : physicalLen;
                } else {
                    ms.sizeZ = len;
                    bytesPerAxis.put(nBytes, "Z");
                    physicalSizeZ = physicalLen;
                }
                break;
            case // T axis
            4:
                if (ms.sizeY == 0) {
                    // XT scan - swap Y and T
                    ms.sizeY = len;
                    ms.sizeT = 1;
                    bytesPerAxis.put(nBytes, "Y");
                    physicalSizeY = oldPhysicalSize ? offByOnePhysicalLen : physicalLen;
                } else {
                    ms.sizeT = len;
                    bytesPerAxis.put(nBytes, "T");
                }
                break;
            case // tile axis
            10:
                tileCount[i] *= len;
                tileBytesInc[i] = nBytes;
                break;
            default:
                extras *= len;
        }
    }
    physicalSizeXs.add(physicalSizeX);
    physicalSizeYs.add(physicalSizeY);
    if (zSteps[i] == null && physicalSizeZ != null) {
        zSteps[i] = Math.abs(physicalSizeZ);
    }
    if (extras > 1) {
        if (ms.sizeZ == 1)
            ms.sizeZ = extras;
        else {
            if (ms.sizeT == 0)
                ms.sizeT = extras;
            else
                ms.sizeT *= extras;
        }
    }
    if (ms.sizeC == 0)
        ms.sizeC = 1;
    if (ms.sizeZ == 0)
        ms.sizeZ = 1;
    if (ms.sizeT == 0)
        ms.sizeT = 1;
    if (ms.sizeX == 0)
        ms.sizeX = 1;
    if (ms.sizeY == 0)
        ms.sizeY = 1;
    ms.interleaved = ms.rgb;
    ms.indexed = !ms.rgb;
    ms.imageCount = ms.sizeZ * ms.sizeT;
    if (!ms.rgb)
        ms.imageCount *= ms.sizeC;
    else {
        ms.imageCount *= (ms.sizeC / 3);
    }
    Long[] bytes = bytesPerAxis.keySet().toArray(new Long[0]);
    Arrays.sort(bytes);
    ms.dimensionOrder = "XY";
    if (getRGBChannelCount() == 1 || getRGBChannelCount() == getSizeC()) {
        if (getSizeC() > 1 && getSizeT() > 1) {
            ms.dimensionOrder += 'C';
        }
        for (Long nBytes : bytes) {
            String axis = bytesPerAxis.get(nBytes);
            if (ms.dimensionOrder.indexOf(axis) == -1) {
                ms.dimensionOrder += axis;
            }
        }
    }
    if (ms.dimensionOrder.indexOf('Z') == -1) {
        ms.dimensionOrder += 'Z';
    }
    if (ms.dimensionOrder.indexOf('C') == -1) {
        ms.dimensionOrder += 'C';
    }
    if (ms.dimensionOrder.indexOf('T') == -1) {
        ms.dimensionOrder += 'T';
    }
}

Example 2 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class LIFReader method translateMetadata.

private void translateMetadata(Element root) throws FormatException {
    Element realRoot = (Element) root.getChildNodes().item(0);
    NodeList toPrune = getNodes(realRoot, "LDM_Block_Sequential_Master");
    if (toPrune != null) {
        for (int i = 0; i < toPrune.getLength(); i++) {
            Element prune = (Element) toPrune.item(i);
            Element parent = (Element) prune.getParentNode();
            parent.removeChild(prune);
        }
    }
    NodeList images = getNodes(realRoot, "Image");
    List<Element> imageNodes = new ArrayList<Element>();
    Long[] oldOffsets = null;
    if (images.getLength() > offsets.size()) {
        oldOffsets = offsets.toArray(new Long[offsets.size()]);
        offsets.clear();
    }
    int nextOffset = 0;
    for (int i = 0; i < images.getLength(); i++) {
        Element image = (Element) images.item(i);
        Element grandparent = (Element) image.getParentNode();
        if (grandparent == null) {
            continue;
        }
        grandparent = (Element) grandparent.getParentNode();
        if (grandparent == null) {
            continue;
        }
        if (!"ProcessingHistory".equals(grandparent.getNodeName())) {
            // image is being referenced from an event list
            imageNodes.add(image);
            if (oldOffsets != null && nextOffset < oldOffsets.length) {
                offsets.add(oldOffsets[nextOffset]);
            }
        }
        grandparent = (Element) grandparent.getParentNode();
        if (grandparent == null) {
            continue;
        }
        grandparent = (Element) grandparent.getParentNode();
        if (grandparent != null) {
            if (!"Image".equals(grandparent.getNodeName())) {
                nextOffset++;
            }
        }
    }
    tileCount = new int[imageNodes.size()];
    Arrays.fill(tileCount, 1);
    tileBytesInc = new long[imageNodes.size()];
    core = new ArrayList<CoreMetadata>(imageNodes.size());
    acquiredDate = new double[imageNodes.size()];
    descriptions = new String[imageNodes.size()];
    laserWavelength = new List[imageNodes.size()];
    laserIntensity = new List[imageNodes.size()];
    laserActive = new List[imageNodes.size()];
    laserFrap = new List[imageNodes.size()];
    timestamps = new Double[imageNodes.size()][];
    activeDetector = new List[imageNodes.size()];
    serialNumber = new String[imageNodes.size()];
    lensNA = new Double[imageNodes.size()];
    magnification = new Double[imageNodes.size()];
    immersions = new String[imageNodes.size()];
    corrections = new String[imageNodes.size()];
    objectiveModels = new String[imageNodes.size()];
    posX = new Length[imageNodes.size()];
    posY = new Length[imageNodes.size()];
    posZ = new Length[imageNodes.size()];
    refractiveIndex = new Double[imageNodes.size()];
    cutIns = new List[imageNodes.size()];
    cutOuts = new List[imageNodes.size()];
    filterModels = new List[imageNodes.size()];
    microscopeModels = new String[imageNodes.size()];
    detectorModels = new List[imageNodes.size()];
    detectorIndexes = new HashMap[imageNodes.size()];
    zSteps = new Double[imageNodes.size()];
    tSteps = new Double[imageNodes.size()];
    pinholes = new Double[imageNodes.size()];
    zooms = new Double[imageNodes.size()];
    expTimes = new Double[imageNodes.size()][];
    gains = new Double[imageNodes.size()][];
    detectorOffsets = new Double[imageNodes.size()][];
    channelNames = new String[imageNodes.size()][];
    exWaves = new Double[imageNodes.size()][];
    imageROIs = new ROI[imageNodes.size()][];
    imageNames = new String[imageNodes.size()];
    core.clear();
    for (int i = 0; i < imageNodes.size(); i++) {
        Element image = imageNodes.get(i);
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        int index = core.size() - 1;
        setSeries(index);
        translateImageNames(image, index);
        translateImageNodes(image, index);
        translateAttachmentNodes(image, index);
        translateScannerSettings(image, index);
        translateFilterSettings(image, index);
        translateTimestamps(image, index);
        translateLaserLines(image, index);
        translateROIs(image, index);
        translateSingleROIs(image, index);
        translateDetectors(image, index);
        final Deque<String> nameStack = new ArrayDeque<String>();
        populateOriginalMetadata(image, nameStack);
        addUserCommentMeta(image, i);
    }
    setSeries(0);
    int totalSeries = 0;
    for (int count : tileCount) {
        totalSeries += count;
    }
    ArrayList<CoreMetadata> newCore = new ArrayList<CoreMetadata>();
    for (int i = 0; i < core.size(); i++) {
        for (int tile = 0; tile < tileCount[i]; tile++) {
            newCore.add(core.get(i));
        }
    }
    core = newCore;
}

Example 3 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class LegacyND2Reader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    try {
        openFile(id);
        int numSeries = getNumSeries();
        core.clear();
        for (int i = 0; i < numSeries; i++) {
            CoreMetadata ms = new CoreMetadata();
            core.add(ms);
            ms.sizeX = getWidth(i);
            if (ms.sizeX % 2 != 0)
                ms.sizeX++;
            ms.sizeY = getHeight(i);
            ms.sizeZ = getZSlices(i);
            ms.sizeT = getTFrames(i);
            ms.sizeC = getChannels(i);
            int bytes = getBytesPerPixel(i);
            if (bytes % 3 == 0) {
                ms.sizeC *= 3;
                bytes /= 3;
                ms.rgb = true;
            } else
                ms.rgb = false;
            ms.pixelType = FormatTools.pixelTypeFromBytes(bytes, false, true);
            ms.imageCount = ms.sizeZ * ms.sizeT;
            if (!ms.rgb)
                ms.imageCount *= ms.sizeC;
            ms.interleaved = true;
            ms.littleEndian = true;
            ms.dimensionOrder = "XYCZT";
            ms.indexed = false;
            ms.falseColor = false;
        }
    } catch (UnsatisfiedLinkError e) {
        throw new MissingLibraryException(NO_NIKON_MSG, e);
    } catch (Exception e) {
        throw new MissingLibraryException(NO_NIKON_MSG, e);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName("Series " + (i + 1), i);
    }
}

Example 4 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class LeicaReader method parseFilenames.

private void parseFilenames(int seriesIndex) throws IOException {
    int maxPlanes = 0;
    final List<String> f = new ArrayList<String>();
    int tempImages = in.readInt();
    if (((long) tempImages * nameLength) > in.length()) {
        in.order(!isLittleEndian());
        tempImages = in.readInt();
        in.order(isLittleEndian());
    }
    CoreMetadata ms = core.get(seriesIndex);
    ms.sizeX = in.readInt();
    ms.sizeY = in.readInt();
    in.skipBytes(4);
    int samplesPerPixel = in.readInt();
    ms.rgb = samplesPerPixel > 1;
    ms.sizeC = samplesPerPixel;
    boolean tiffsExist = false;
    String dirPrefix = new Location(currentId).getAbsoluteFile().getParent();
    if (!dirPrefix.endsWith(File.separator))
        dirPrefix += File.separator;
    String prefix = "";
    for (int j = 0; j < tempImages; j++) {
        // read in each filename
        prefix = getString(nameLength);
        f.add(dirPrefix + prefix);
        // test to make sure the path is valid
        Location test = new Location(f.get(f.size() - 1)).getAbsoluteFile();
        LOGGER.debug("Expected to find TIFF file {}", test.getAbsolutePath());
        if (!test.exists()) {
            LOGGER.debug("  file does not exist");
        }
        if (!tiffsExist)
            tiffsExist = test.exists();
    }
    if (!tiffsExist) {
        // Strategy for handling renamed files:
        // 1) Assume that files for each series follow a pattern.
        // 2) Assign each file group to the first series with the correct count.
        LOGGER.info("Handling renamed TIFF files");
        String[] listing = getTIFFList();
        // grab the file patterns
        final List<String> filePatterns = new ArrayList<String>();
        for (String q : listing) {
            Location l = new Location(q).getAbsoluteFile();
            if (!l.exists()) {
                l = new Location(dirPrefix, q).getAbsoluteFile();
            }
            FilePattern pattern = new FilePattern(l);
            if (!pattern.isValid())
                continue;
            AxisGuesser guess = new AxisGuesser(pattern, "XYZCT", 1, 1, 1, false);
            String fp = pattern.getPattern();
            if (guess.getAxisCountS() >= 1) {
                String pre = pattern.getPrefix(guess.getAxisCountS());
                final List<String> fileList = new ArrayList<String>();
                for (int n = 0; n < listing.length; n++) {
                    Location p = new Location(dirPrefix, listing[n]);
                    if (p.getAbsolutePath().startsWith(pre)) {
                        fileList.add(listing[n]);
                    }
                }
                fp = FilePattern.findPattern(l.getAbsolutePath(), dirPrefix, fileList.toArray(new String[fileList.size()]));
            }
            if (fp != null && !filePatterns.contains(fp)) {
                filePatterns.add(fp);
            }
        }
        for (String q : filePatterns) {
            String[] pattern = new FilePattern(q).getFiles();
            if (pattern.length == tempImages) {
                // make sure that this pattern hasn't already been used
                boolean validPattern = true;
                for (int n = 0; n < seriesIndex; n++) {
                    if (files[n] == null)
                        continue;
                    if (files[n].contains(pattern[0])) {
                        validPattern = false;
                        break;
                    }
                }
                if (validPattern) {
                    files[seriesIndex] = new ArrayList<String>();
                    files[seriesIndex].addAll(Arrays.asList(pattern));
                }
            }
        }
    } else {
        files[seriesIndex] = f;
        for (int s = 0; s < seriesIndex; s++) {
            if (files[s] != null) {
                if (files[s].get(0).equals(f.get(0))) {
                    valid[s] = false;
                    files[s] = null;
                }
            }
        }
    }
    if (files[seriesIndex] == null)
        valid[seriesIndex] = false;
    else {
        ms.imageCount = files[seriesIndex].size();
        maxPlanes = (int) Math.max(maxPlanes, ms.imageCount);
    }
}

Example 5 with CoreMetadata

use of loci.formats.CoreMetadata in project bioformats by openmicroscopy.

the class LeicaReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    close();
    String leiFile = findLEIFile(id);
    if (leiFile == null || leiFile.trim().length() == 0 || new Location(leiFile).isDirectory()) {
        if (checkSuffix(id, TiffReader.TIFF_SUFFIXES)) {
            super.initFile(id);
            TiffReader r = new TiffReader();
            r.setMetadataStore(getMetadataStore());
            r.setId(id);
            core = new ArrayList<CoreMetadata>(r.getCoreMetadataList());
            metadataStore = r.getMetadataStore();
            final Map<String, Object> globalMetadata = r.getGlobalMetadata();
            for (final Map.Entry<String, Object> entry : globalMetadata.entrySet()) {
                addGlobalMeta(entry.getKey(), entry.getValue());
            }
            r.close();
            files = new List[] { new ArrayList<String>() };
            files[0].add(id);
            tiff = new MinimalTiffReader();
            return;
        } else {
            throw new FormatException("LEI file not found.");
        }
    }
    // parse the LEI file
    super.initFile(leiFile);
    leiFilename = new File(leiFile).exists() ? new Location(leiFile).getAbsolutePath() : id;
    in = new RandomAccessInputStream(leiFile);
    byte[] data = null;
    try {
        data = new byte[(int) in.length()];
        in.read(data);
    } finally {
        in.close();
    }
    in = new RandomAccessInputStream(data);
    MetadataLevel metadataLevel = metadataOptions.getMetadataLevel();
    seriesNames = new ArrayList<String>();
    byte[] fourBytes = new byte[4];
    in.read(fourBytes);
    core.get(0).littleEndian = (fourBytes[0] == TiffConstants.LITTLE && fourBytes[1] == TiffConstants.LITTLE && fourBytes[2] == TiffConstants.LITTLE && fourBytes[3] == TiffConstants.LITTLE);
    boolean realLittleEndian = isLittleEndian();
    in.order(isLittleEndian());
    LOGGER.info("Reading metadata blocks");
    in.skipBytes(8);
    int addr = in.readInt();
    headerIFDs = new IFDList();
    while (addr != 0) {
        IFD ifd = new IFD();
        headerIFDs.add(ifd);
        in.seek(addr + 4);
        int tag = in.readInt();
        while (tag != 0) {
            // create the IFD structure
            int offset = in.readInt();
            long pos = in.getFilePointer();
            in.seek(offset + 12);
            int size = in.readInt();
            ifd.putIFDValue(tag, in.getFilePointer());
            in.seek(pos);
            tag = in.readInt();
        }
        addr = in.readInt();
    }
    numSeries = headerIFDs.size();
    tileWidth = new int[numSeries];
    tileHeight = new int[numSeries];
    core.clear();
    for (int i = 0; i < numSeries; i++) {
        core.add(new CoreMetadata());
    }
    files = new List[numSeries];
    channelNames = new List[getSeriesCount()];
    emWaves = new List[getSeriesCount()];
    exWaves = new List[getSeriesCount()];
    cutInPopulated = new boolean[getSeriesCount()][];
    cutOutPopulated = new boolean[getSeriesCount()][];
    filterRefPopulated = new boolean[getSeriesCount()][];
    for (int i = 0; i < getSeriesCount(); i++) {
        channelNames[i] = new ArrayList();
        emWaves[i] = new ArrayList();
        exWaves[i] = new ArrayList();
    }
    // determine the length of a filename
    LOGGER.info("Parsing metadata blocks");
    core.get(0).littleEndian = !isLittleEndian();
    int seriesIndex = 0;
    int invalidCount = 0;
    valid = new boolean[numSeries];
    timestamps = new String[headerIFDs.size()][];
    for (int i = 0; i < headerIFDs.size(); i++) {
        IFD ifd = headerIFDs.get(i);
        valid[i] = true;
        if (ifd.get(SERIES) != null) {
            long offset = ((Long) ifd.get(SERIES)).longValue();
            in.seek(offset + 8);
            nameLength = in.readInt() * 2;
        }
        in.seek(((Long) ifd.get(IMAGES)).longValue());
        parseFilenames(i);
        if (!valid[i])
            invalidCount++;
    }
    numSeries -= invalidCount;
    if (numSeries <= 0) {
        throw new FormatException("TIFF files not found");
    }
    int[] count = new int[getSeriesCount()];
    for (int i = 0; i < getSeriesCount(); i++) {
        count[i] = core.get(i).imageCount;
    }
    final List<String>[] tempFiles = files;
    IFDList tempIFDs = headerIFDs;
    core = new ArrayList<CoreMetadata>(numSeries);
    files = new List[numSeries];
    headerIFDs = new IFDList();
    int index = 0;
    core.clear();
    for (int i = 0; i < numSeries; i++) {
        CoreMetadata ms = new CoreMetadata();
        while (index < valid.length && !valid[index]) index++;
        if (index >= valid.length) {
            break;
        }
        ms.imageCount = count[index];
        files[i] = tempFiles[index];
        Collections.sort(files[i]);
        headerIFDs.add(tempIFDs.get(index));
        index++;
        core.add(ms);
    }
    tiff = new MinimalTiffReader();
    LOGGER.info("Populating metadata");
    if (headerIFDs == null)
        headerIFDs = ifds;
    seriesDescriptions = new ArrayList<String>();
    physicalSizes = new double[headerIFDs.size()][5];
    pinhole = new double[headerIFDs.size()];
    exposureTime = new double[headerIFDs.size()];
    channelColor = new Color[headerIFDs.size()][];
    for (int i = 0; i < headerIFDs.size(); i++) {
        IFD ifd = headerIFDs.get(i);
        CoreMetadata ms = core.get(i);
        ms.littleEndian = isLittleEndian();
        setSeries(i);
        Integer[] keys = ifd.keySet().toArray(new Integer[ifd.size()]);
        Arrays.sort(keys);
        for (Integer key : keys) {
            long offset = ((Long) ifd.get(key)).longValue();
            in.seek(offset);
            if (key.equals(SERIES)) {
                parseSeriesTag();
            } else if (key.equals(IMAGES)) {
                parseImageTag(i);
            } else if (key.equals(DIMDESCR)) {
                parseDimensionTag(i);
            } else if (key.equals(TIMEINFO) && metadataLevel != MetadataLevel.MINIMUM) {
                parseTimeTag(i);
            } else if (key.equals(EXPERIMENT) && metadataLevel != MetadataLevel.MINIMUM) {
                parseExperimentTag();
            } else if (key.equals(LUTDESC)) {
                parseLUT(i);
            } else if (key.equals(CHANDESC) && metadataLevel != MetadataLevel.MINIMUM) {
                parseChannelTag();
            }
        }
        ms.orderCertain = true;
        ms.littleEndian = isLittleEndian();
        ms.falseColor = true;
        ms.metadataComplete = true;
        ms.interleaved = false;
        String filename = (String) files[i].get(0);
        if (checkSuffix(filename, TiffReader.TIFF_SUFFIXES)) {
            RandomAccessInputStream s = new RandomAccessInputStream(filename, 16);
            try {
                TiffParser parser = new TiffParser(s);
                parser.setDoCaching(false);
                IFD firstIFD = parser.getFirstIFD();
                parser.fillInIFD(firstIFD);
                ms.sizeX = (int) firstIFD.getImageWidth();
                ms.sizeY = (int) firstIFD.getImageLength();
                // override the .lei pixel type, in case a TIFF file was overwritten
                ms.pixelType = firstIFD.getPixelType();
                // won't affect the pixel data
                if (FormatTools.getBytesPerPixel(ms.pixelType) > 1) {
                    ms.littleEndian = firstIFD.isLittleEndian();
                } else {
                    ms.littleEndian = realLittleEndian;
                }
                tileWidth[i] = (int) firstIFD.getTileWidth();
                tileHeight[i] = (int) firstIFD.getTileLength();
            } finally {
                s.close();
            }
        } else {
            ms.littleEndian = realLittleEndian;
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        setSeries(i);
        CoreMetadata ms = core.get(i);
        if (getSizeZ() == 0)
            ms.sizeZ = 1;
        if (getSizeT() == 0)
            ms.sizeT = 1;
        if (getSizeC() == 0)
            ms.sizeC = 1;
        if (getImageCount() == 0)
            ms.imageCount = 1;
        if (getImageCount() == 1 && getSizeZ() * getSizeT() > 1) {
            ms.sizeZ = 1;
            ms.sizeT = 1;
        }
        if (getSizeY() == 1 || getSizeY() == getSizeZ() || getSizeY() == getSizeT()) {
            // XZ or XT scan
            if (getSizeZ() > 1 && getImageCount() == getSizeC() * getSizeT()) {
                ms.sizeY = getSizeZ();
                ms.sizeZ = 1;
            } else if (getSizeT() > 1 && getImageCount() == getSizeC() * getSizeZ()) {
                ms.sizeY = getSizeT();
                ms.sizeT = 1;
            }
        }
        if (isRGB())
            ms.indexed = false;
        ms.dimensionOrder = MetadataTools.makeSaneDimensionOrder(getDimensionOrder());
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    // minimum metadata level.
    for (int i = 0; i < getSeriesCount(); i++) {
        store.setImageName(seriesNames.get(i), i);
    }
    if (metadataLevel == MetadataLevel.MINIMUM)
        return;
    for (int i = 0; i < getSeriesCount(); i++) {
        CoreMetadata ms = core.get(i);
        IFD ifd = headerIFDs.get(i);
        long firstPlane = 0;
        if (i < timestamps.length && timestamps[i] != null && timestamps[i].length > 0) {
            firstPlane = DateTools.getTime(timestamps[i][0], DATE_FORMAT, ":");
            String date = DateTools.formatDate(timestamps[i][0], DATE_FORMAT);
            if (date != null) {
                store.setImageAcquisitionDate(new Timestamp(date), i);
            }
        }
        store.setImageDescription(seriesDescriptions.get(i), i);
        String instrumentID = MetadataTools.createLSID("Instrument", i);
        store.setInstrumentID(instrumentID, i);
        // parse instrument data
        nextDetector = 0;
        nextChannel = 0;
        detectors.clear();
        cutInPopulated[i] = new boolean[ms.sizeC];
        cutOutPopulated[i] = new boolean[ms.sizeC];
        filterRefPopulated[i] = new boolean[ms.sizeC];
        Integer[] keys = ifd.keySet().toArray(new Integer[ifd.size()]);
        Arrays.sort(keys);
        int nextInstrumentBlock = 1;
        sequential = DataTools.indexOf(keys, SEQ_SCANNERSET) != -1;
        for (Integer key : keys) {
            if (key.equals(FILTERSET) || key.equals(SCANNERSET) || key.equals(SEQ_SCANNERSET) || key.equals(SEQ_FILTERSET) || (key > SEQ_SCANNERSET && key < SEQ_SCANNERSET_END) || (key > SEQ_FILTERSET && key < SEQ_FILTERSET_END)) {
                if (sequential && (key.equals(FILTERSET) || key.equals(SCANNERSET))) {
                    continue;
                }
                long offset = ((Long) ifd.get(key)).longValue();
                in.seek(offset);
                setSeries(i);
                parseInstrumentData(store, nextInstrumentBlock++);
            }
        }
        activeChannelIndices.clear();
        // link Instrument and Image
        store.setImageInstrumentRef(instrumentID, i);
        Length sizeX = FormatTools.getPhysicalSizeX(physicalSizes[i][0]);
        Length sizeY = FormatTools.getPhysicalSizeY(physicalSizes[i][1]);
        Length sizeZ = FormatTools.getPhysicalSizeZ(physicalSizes[i][2]);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, i);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, i);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, i);
        }
        if ((int) physicalSizes[i][4] > 0) {
            store.setPixelsTimeIncrement(new Time(physicalSizes[i][4], UNITS.SECOND), i);
        }
        for (int j = 0; j < ms.imageCount; j++) {
            if (timestamps[i] != null && j < timestamps[i].length) {
                long time = DateTools.getTime(timestamps[i][j], DATE_FORMAT, ":");
                double elapsedTime = (double) (time - firstPlane) / 1000;
                store.setPlaneDeltaT(new Time(elapsedTime, UNITS.SECOND), i, j);
                if (exposureTime[i] > 0) {
                    store.setPlaneExposureTime(new Time(exposureTime[i], UNITS.SECOND), i, j);
                }
            }
        }
    }
    setSeries(0);
}