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

Example 81 with CoreMetadata

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

the class BaseZeissReader method fillMetadataPass6.

/**
 * Read and store basic dimensions in model
 * @param store
 * @throws FormatException
 * @throws IOException
 */
protected void fillMetadataPass6(MetadataStore store) throws FormatException, IOException {
    CoreMetadata m = core.get(0);
    if (getSizeX() == 0) {
        m.sizeX = 1;
    }
    if (getSizeY() == 0) {
        m.sizeY = 1;
    }
    if (bpp == 1 || bpp == 3)
        m.pixelType = FormatTools.UINT8;
    else if (bpp == 2 || bpp == 6)
        m.pixelType = FormatTools.UINT16;
    if (isJPEG)
        m.pixelType = FormatTools.UINT8;
    m.bitsPerPixel = FormatTools.getBytesPerPixel(m.pixelType) * 8;
    m.indexed = !isRGB() && channelColors != null;
    // it's filled.
    for (int i = 1; i < core.size(); i++) {
        core.set(i, new CoreMetadata(core.get(0)));
    }
}

Example 82 with CoreMetadata

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

the class BioRadGelReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    String check = in.readString(48);
    if (check.indexOf("Intel Format") != -1) {
        in.order(true);
    }
    in.seek(START_OFFSET);
    boolean codeFound = false;
    int skip = 0;
    long baseFP = 0;
    while (!codeFound) {
        short code = in.readShort();
        if (code == 0x81)
            codeFound = true;
        short length = in.readShort();
        in.skipBytes(2 + 2 * length);
        if (codeFound) {
            baseFP = in.getFilePointer() + 2;
            if (length > 1) {
                in.seek(in.getFilePointer() - 2);
            }
            skip = in.readInt() - 32;
        } else {
            if (length == 1)
                in.skipBytes(12);
            else if (length == 2)
                in.skipBytes(10);
        }
    }
    diff = BASE_OFFSET - baseFP;
    skip += diff;
    double physicalWidth = 0d, physicalHeight = 0d;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (baseFP + skip - 8187 > 0) {
            in.seek(baseFP + skip - 8187);
            String scannerName = in.readCString();
            in.skipBytes(8);
            in.readCString();
            in.skipBytes(8);
            String imageArea = in.readCString();
            imageArea = imageArea.substring(imageArea.indexOf(':') + 1).trim();
            int xIndex = imageArea.indexOf('x');
            if (xIndex > 0) {
                int space = imageArea.indexOf(' ');
                if (space >= 0) {
                    String width = imageArea.substring(1, space);
                    int nextSpace = imageArea.indexOf(" ", xIndex + 2);
                    if (nextSpace > xIndex) {
                        String height = imageArea.substring(xIndex + 1, nextSpace);
                        physicalWidth = Double.parseDouble(width.trim()) * 1000;
                        physicalHeight = Double.parseDouble(height.trim()) * 1000;
                    }
                }
            }
        }
    }
    in.seek(baseFP + skip - 298);
    String date = in.readString(17);
    date = DateTools.formatDate(date, "dd-MMM-yyyy HH:mm");
    in.skipBytes(73);
    String scannerName = in.readCString();
    addGlobalMeta("Scanner name", scannerName);
    in.seek(baseFP + skip);
    CoreMetadata m = core.get(0);
    m.sizeX = in.readShort() & 0xffff;
    m.sizeY = in.readShort() & 0xffff;
    if (getSizeX() * getSizeY() > in.length()) {
        in.order(true);
        in.seek(in.getFilePointer() - 4);
        m.sizeX = in.readShort();
        m.sizeY = in.readShort();
    }
    in.skipBytes(2);
    int bpp = in.readShort();
    m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
    offset = in.getFilePointer();
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYCZT";
    m.rgb = false;
    m.interleaved = false;
    m.indexed = false;
    m.littleEndian = in.isLittleEndian();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(physicalWidth / getSizeX());
        Length sizeY = FormatTools.getPhysicalSizeY(physicalHeight / getSizeY());
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
    }
}

Example 83 with CoreMetadata

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

the class BioRadReader method readNotes.

// -- Helper methods --
/**
 * Read all of the note strings from the given file.  If the 'add' flag is
 * set, the notes will be added to the 'noteStrings' list.
 */
private void readNotes(RandomAccessInputStream s, boolean add) throws IOException {
    s.seek(70);
    int imageLen = getSizeX() * getSizeY();
    if (picFiles == null)
        imageLen *= getImageCount();
    else {
        imageLen *= (getImageCount() / picFiles.length);
    }
    int bpp = FormatTools.getBytesPerPixel(getPixelType());
    s.skipBytes(bpp * imageLen + 6);
    boolean notes = true;
    while (notes) {
        if (s.getFilePointer() >= s.length()) {
            brokenNotes = true;
            break;
        }
        Note n = new Note();
        n.level = s.readShort();
        notes = s.readInt() != 0;
        n.num = s.readShort();
        n.status = s.readShort();
        n.type = s.readShort();
        n.x = s.readShort();
        n.y = s.readShort();
        n.p = s.readString(80);
        if (n.type < 0 || n.type >= NOTE_NAMES.length) {
            notes = false;
            brokenNotes = true;
            break;
        }
        if (!add)
            continue;
        // be sure to remove binary data from the note text
        int ndx = n.p.length();
        for (int i = 0; i < n.p.length(); i++) {
            if (n.p.charAt(i) == 0) {
                ndx = i;
                break;
            }
        }
        n.p = n.p.substring(0, ndx).trim();
        String value = n.p.replaceAll("=", "");
        final List<String> v = new ArrayList<String>();
        StringTokenizer t = new StringTokenizer(value, " ");
        while (t.hasMoreTokens()) {
            String token = t.nextToken().trim();
            if (token.length() > 0)
                v.add(token);
        }
        String[] tokens = v.toArray(new String[v.size()]);
        try {
            if (tokens.length > 1) {
                int noteType = Integer.parseInt(tokens[1]);
                if (noteType == 2 && value.indexOf("AXIS_4") != -1) {
                    CoreMetadata m = core.get(0);
                    m.sizeZ = 1;
                    m.sizeT = getImageCount();
                    m.orderCertain = true;
                }
            }
        } catch (NumberFormatException e) {
        }
        // add note to list
        noteStrings.add(n);
    }
}

Example 84 with CoreMetadata

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

the class BioRadReader method parseNotes.

private boolean parseNotes(MetadataStore store) throws FormatException {
    boolean multipleFiles = false;
    int nextDetector = 0, nLasers = 0;
    for (Note n : noteStrings) {
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            switch(n.type) {
                case NOTE_TYPE_USER:
                    // TODO : this should be an overlay
                    addGlobalMetaList("Note", n.toString());
                    break;
                case NOTE_TYPE_SCALEBAR:
                    // TODO : this should be an overlay
                    // the format of the text is:
                    // SCALEBAR = <length> <angle>
                    // where <length> is the length of the scalebar in microns,
                    // and <angle> is the angle in degrees
                    addGlobalMetaList("Note", n.toString());
                    break;
                case NOTE_TYPE_ARROW:
                    // TODO : this should be an overlay
                    // the format of the text is:
                    // ARROW = <lx> <ly> <angle> <fill>
                    // where <lx> and <ly> define the arrow's bounding box,
                    // <angle> is the angle in degrees and <fill> is either "Fill" or
                    // "Outline"
                    addGlobalMetaList("Note", n.toString());
                    break;
                case NOTE_TYPE_VARIABLE:
                    if (n.p.indexOf('=') >= 0) {
                        String key = n.p.substring(0, n.p.indexOf('=')).trim();
                        String value = n.p.substring(n.p.indexOf('=') + 1).trim();
                        addGlobalMeta(key, value);
                        if (key.equals("INFO_OBJECTIVE_NAME")) {
                            store.setObjectiveModel(value, 0, 0);
                        } else if (key.equals("INFO_OBJECTIVE_MAGNIFICATION")) {
                            Double mag = Double.parseDouble(value);
                            store.setObjectiveNominalMagnification(mag, 0, 0);
                        } else if (key.equals("LENS_MAGNIFICATION")) {
                            Double magnification = Double.parseDouble(value);
                            store.setObjectiveNominalMagnification(magnification, 0, 0);
                        } else if (key.startsWith("SETTING")) {
                            if (key.indexOf("_DET_") != -1) {
                                int index = key.indexOf("_DET_") + 5;
                                if (key.lastIndexOf("_") > index) {
                                    String detectorID = MetadataTools.createLSID("Detector", 0, nextDetector);
                                    store.setDetectorID(detectorID, 0, nextDetector);
                                    store.setDetectorType(getDetectorType("Other"), 0, nextDetector);
                                    if (key.endsWith("OFFSET")) {
                                        if (nextDetector < offset.size()) {
                                            offset.set(nextDetector, Double.parseDouble(value));
                                        } else {
                                            while (nextDetector > offset.size()) {
                                                offset.add(null);
                                            }
                                            offset.add(new Double(value));
                                        }
                                    } else if (key.endsWith("GAIN")) {
                                        if (nextDetector < gain.size()) {
                                            gain.set(nextDetector, Double.parseDouble(value));
                                        } else {
                                            while (nextDetector > gain.size()) {
                                                gain.add(null);
                                            }
                                            gain.add(new Double(value));
                                        }
                                    }
                                    nextDetector++;
                                }
                            }
                        } else {
                            String[] values = value.split(" ");
                            if (values.length > 1) {
                                try {
                                    int type = Integer.parseInt(values[0]);
                                    if (type == 257 && values.length >= 3) {
                                        // found length of axis in um
                                        Double pixelSize = new Double(values[2]);
                                        if (key.equals("AXIS_2")) {
                                            Length size = FormatTools.getPhysicalSizeX(pixelSize);
                                            if (size != null) {
                                                store.setPixelsPhysicalSizeX(size, 0);
                                            }
                                        } else if (key.equals("AXIS_3")) {
                                            Length size = FormatTools.getPhysicalSizeY(pixelSize);
                                            if (size != null) {
                                                store.setPixelsPhysicalSizeY(size, 0);
                                            }
                                        }
                                    }
                                } catch (NumberFormatException e) {
                                }
                            }
                        }
                    } else if (n.p.startsWith("AXIS_2")) {
                        String[] values = n.p.split(" ");
                        Double pixelSize = new Double(values[3]);
                        Length size = FormatTools.getPhysicalSizeX(pixelSize);
                        if (size != null) {
                            store.setPixelsPhysicalSizeX(size, 0);
                        }
                    } else if (n.p.startsWith("AXIS_3")) {
                        String[] values = n.p.split(" ");
                        Double pixelSize = new Double(values[3]);
                        Length size = FormatTools.getPhysicalSizeY(pixelSize);
                        if (size != null) {
                            store.setPixelsPhysicalSizeY(size, 0);
                        }
                    } else {
                        addGlobalMetaList("Note", n.toString());
                    }
                    break;
                case NOTE_TYPE_STRUCTURE:
                    int structureType = (n.x & 0xff00) >> 8;
                    int version = (n.x & 0xff);
                    String[] values = n.p.split(" ");
                    if (structureType == 1) {
                        switch(n.y) {
                            case 1:
                                for (int i = 0; i < STRUCTURE_LABELS_1.length; i++) {
                                    addGlobalMeta(STRUCTURE_LABELS_1[i], values[i]);
                                }
                                Double mag = Double.parseDouble(values[11]);
                                store.setObjectiveNominalMagnification(mag, 0, 0);
                                Double sizeZ = new Double(values[14]);
                                Length size = FormatTools.getPhysicalSizeZ(sizeZ);
                                if (size != null) {
                                    store.setPixelsPhysicalSizeZ(size, 0);
                                }
                                break;
                            case 2:
                                for (int i = 0; i < STRUCTURE_LABELS_2.length; i++) {
                                    addGlobalMeta(STRUCTURE_LABELS_2[i], values[i]);
                                }
                                double x1 = Double.parseDouble(values[2]);
                                double x2 = Double.parseDouble(values[4]);
                                double width = x2 - x1;
                                width /= getSizeX();
                                double y1 = Double.parseDouble(values[3]);
                                double y2 = Double.parseDouble(values[5]);
                                double height = y2 - y1;
                                height /= getSizeY();
                                Length sizeX = FormatTools.getPhysicalSizeX(width);
                                Length sizeY = FormatTools.getPhysicalSizeY(height);
                                if (sizeX != null) {
                                    store.setPixelsPhysicalSizeX(sizeX, 0);
                                }
                                if (sizeY != null) {
                                    store.setPixelsPhysicalSizeY(sizeY, 0);
                                }
                                break;
                            case 3:
                                for (int i = 0; i < 3; i++) {
                                    for (int j = 0; j < STRUCTURE_LABELS_3.length; j++) {
                                        String v = j == STRUCTURE_LABELS_3.length - 1 ? values[12 + i] : values[i * 4 + j];
                                        addGlobalMetaList(STRUCTURE_LABELS_3[j], v);
                                    }
                                }
                                break;
                            case 4:
                                nLasers = Integer.parseInt(values[0]);
                                addGlobalMeta("Number of lasers", values[0]);
                                addGlobalMeta("Number of transmission detectors", values[1]);
                                addGlobalMeta("Number of PMTs", values[2]);
                                for (int i = 1; i <= 3; i++) {
                                    int idx = (i + 1) * 3;
                                    addGlobalMetaList("Shutter present for laser", values[i + 2]);
                                    addGlobalMetaList("Neutral density filter for laser", values[idx]);
                                    addGlobalMetaList("Excitation filter for laser", values[idx + 1]);
                                    addGlobalMetaList("Use laser", values[idx + 2]);
                                }
                                for (int i = 0; i < nLasers; i++) {
                                    addGlobalMetaList("Neutral density filter name - laser", values[15 + i]);
                                }
                                break;
                            case 5:
                                String prefix = "Excitation filter name - laser";
                                for (int i = 0; i < nLasers; i++) {
                                    addGlobalMetaList(prefix, values[i]);
                                }
                                break;
                            case 6:
                                prefix = "Emission filter name - laser";
                                for (int i = 0; i < nLasers; i++) {
                                    addGlobalMeta(prefix, values[i]);
                                }
                                break;
                            case 7:
                                for (int i = 0; i < 2; i++) {
                                    prefix = "Mixer " + i + " - ";
                                    for (int j = 0; j < STRUCTURE_LABELS_4.length; j++) {
                                        addGlobalMeta(prefix + STRUCTURE_LABELS_4[j], values[i * 7 + j]);
                                    }
                                }
                                addGlobalMeta("Mixer 0 - low signal on", values[14]);
                                addGlobalMeta("Mixer 1 - low signal on", values[15]);
                                break;
                            case 8:
                            case 9:
                            case 10:
                                addGlobalMeta("Laser name - laser " + (n.y - 7), values[0]);
                                break;
                            case 11:
                                for (int i = 0; i < 3; i++) {
                                    prefix = "Transmission detector " + (i + 1) + " - ";
                                    addGlobalMeta(prefix + "offset", values[i * 3]);
                                    addGlobalMeta(prefix + "gain", values[i * 3 + 1]);
                                    addGlobalMeta(prefix + "black level", values[i * 3 + 2]);
                                    String detectorID = MetadataTools.createLSID("Detector", 0, i);
                                    store.setDetectorID(detectorID, 0, i);
                                    store.setDetectorOffset(new Double(values[i * 3]), 0, i);
                                    store.setDetectorGain(new Double(values[i * 3 + 1]), 0, i);
                                    store.setDetectorType(getDetectorType("Other"), 0, i);
                                }
                                break;
                            case 12:
                                for (int i = 0; i < 2; i++) {
                                    prefix = "Part number for ";
                                    for (int j = 0; j < STRUCTURE_LABELS_5.length; j++) {
                                        addGlobalMetaList(prefix + STRUCTURE_LABELS_5[j], values[i * 4 + j]);
                                    }
                                }
                                break;
                            case 13:
                                for (int i = 0; i < STRUCTURE_LABELS_6.length; i++) {
                                    addGlobalMeta(STRUCTURE_LABELS_6[i], values[i]);
                                }
                                break;
                            case 14:
                                prefix = "Filter Block Name - filter block ";
                                addGlobalMetaList(prefix, values[0]);
                                addGlobalMetaList(prefix, values[1]);
                                break;
                            case 15:
                                for (int i = 0; i < 5; i++) {
                                    addGlobalMetaList("Image bands status - band", values[i * 3]);
                                    addGlobalMetaList("Image bands min - band", values[i * 3 + 1]);
                                    addGlobalMetaList("Image bands max - band", values[i * 3 + 2]);
                                    if (store instanceof IMinMaxStore) {
                                        ((IMinMaxStore) store).setChannelGlobalMinMax(i, Double.parseDouble(values[i * 3 + 1]), Double.parseDouble(values[i * 3 + 2]), 0);
                                    }
                                }
                                break;
                            case 17:
                                int year = Integer.parseInt(values[5]) + 1900;
                                for (int i = 0; i < 5; i++) {
                                    if (values[i].length() == 1)
                                        values[i] = "0" + values[i];
                                }
                                // date is in yyyy-MM-dd'T'HH:mm:ss
                                String date = year + "-" + values[4] + "-" + values[3] + "T" + values[2] + ":" + values[1] + ":" + values[0];
                                addGlobalMeta("Acquisition date", date);
                                try {
                                    store.setImageAcquisitionDate(new Timestamp(date), 0);
                                } catch (Exception e) {
                                    LOGGER.debug("Failed to parse acquisition date", e);
                                }
                                break;
                            case 18:
                                addGlobalMeta("Mixer 3 - enhanced", values[0]);
                                for (int i = 1; i <= 3; i++) {
                                    addGlobalMetaList("Mixer 3 - PMT percentage", values[i]);
                                    addGlobalMetaList("Mixer 3 - Transmission percentage", values[i + 3]);
                                    addGlobalMetaList("Mixer 3 - photon counting", values[i + 7]);
                                }
                                addGlobalMeta("Mixer 3 - low signal on", values[7]);
                                addGlobalMeta("Mixer 3 - mode", values[11]);
                                break;
                            case 19:
                                for (int i = 1; i <= 2; i++) {
                                    prefix = "Mixer " + i + " - ";
                                    String photon = prefix + "photon counting ";
                                    addGlobalMetaList(photon, values[i * 4 - 4]);
                                    addGlobalMetaList(photon, values[i * 4 - 3]);
                                    addGlobalMetaList(photon, values[i * 4 - 2]);
                                    addGlobalMeta(prefix + "mode", values[i * 4 - 1]);
                                }
                                break;
                            case 20:
                                addGlobalMeta("Display mode", values[0]);
                                addGlobalMeta("Course", values[1]);
                                addGlobalMeta("Time Course - experiment type", values[2]);
                                addGlobalMeta("Time Course - kd factor", values[3]);
                                String experimentID = MetadataTools.createLSID("Experiment", 0);
                                store.setExperimentID(experimentID, 0);
                                store.setExperimentType(getExperimentType(values[2]), 0);
                                break;
                            case 21:
                                addGlobalMeta("Time Course - ion name", values[0]);
                                break;
                            case 22:
                                addGlobalMeta("PIC file generated on Isoscan (lite)", values[0]);
                                for (int i = 1; i <= 3; i++) {
                                    addGlobalMetaList("Photon counting used - PMT", values[i]);
                                    addGlobalMetaList("Hot spot filter used - PMT", values[i + 3]);
                                    addGlobalMetaList("Tx Selector used - TX", values[i + 6]);
                                }
                                break;
                        }
                    }
                    break;
                default:
                    // notes for display only
                    addGlobalMetaList("Note", n.toString());
            }
        }
        if (n.p.indexOf("AXIS") != -1) {
            n.p = n.p.replaceAll("=", "");
            final List<String> v = new ArrayList<String>();
            StringTokenizer tokens = new StringTokenizer(n.p, " ");
            while (tokens.hasMoreTokens()) {
                String token = tokens.nextToken().trim();
                if (token.length() > 0)
                    v.add(token);
            }
            String[] values = v.toArray(new String[v.size()]);
            String key = values[0];
            String noteType = values[1];
            int axisType = Integer.parseInt(noteType);
            if (axisType == 11 && values.length > 2) {
                addGlobalMeta(key + " RGB type (X)", values[2]);
                addGlobalMeta(key + " RGB type (Y)", values[3]);
                CoreMetadata m = core.get(0);
                if (key.equals("AXIS_4")) {
                    // this is a single section multi-channel dataset
                    m.sizeC = getImageCount();
                    m.sizeZ = 1;
                    m.sizeT = 1;
                } else if (key.equals("AXIS_9")) {
                    multipleFiles = true;
                    m.sizeC = (int) Double.parseDouble(values[3]);
                }
            }
            if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM && values.length > 2) {
                switch(axisType) {
                    case 1:
                        addGlobalMeta(key + " distance (X) in microns", values[2]);
                        addGlobalMeta(key + " distance (Y) in microns", values[3]);
                        break;
                    case 3:
                        addGlobalMeta(key + " angle (X) in degrees", values[2]);
                        addGlobalMeta(key + " angle (Y) in degrees", values[3]);
                        break;
                    case 4:
                        addGlobalMeta(key + " intensity (X)", values[2]);
                        addGlobalMeta(key + " intensity (Y)", values[3]);
                        break;
                    case 6:
                        addGlobalMeta(key + " ratio (X)", values[2]);
                        addGlobalMeta(key + " ratio (Y)", values[3]);
                        break;
                    case 7:
                        addGlobalMeta(key + " log ratio (X)", values[2]);
                        addGlobalMeta(key + " log ratio (Y)", values[3]);
                        break;
                    case 9:
                        addGlobalMeta(key + " noncalibrated intensity min", values[2]);
                        addGlobalMeta(key + " noncalibrated intensity max", values[3]);
                        addGlobalMeta(key + " calibrated intensity min", values[4]);
                        addGlobalMeta(key + " calibrated intensity max", values[5]);
                        break;
                    case 14:
                        addGlobalMeta(key + " time course type (X)", values[2]);
                        addGlobalMeta(key + " time course type (Y)", values[3]);
                        break;
                    case 15:
                        String prefix = " inverse sigmoid calibrated intensity ";
                        addGlobalMeta(key + prefix + "(min)", values[2]);
                        addGlobalMeta(key + prefix + "(max)", values[3]);
                        addGlobalMeta(key + prefix + "(beta)", values[4]);
                        addGlobalMeta(key + prefix + "(Kd)", values[5]);
                        break;
                    case 16:
                        prefix = " log inverse sigmoid calibrated intensity ";
                        addGlobalMeta(key + prefix + "(min)", values[2]);
                        addGlobalMeta(key + prefix + "(max)", values[3]);
                        addGlobalMeta(key + prefix + "(beta)", values[4]);
                        addGlobalMeta(key + prefix + "(Kd)", values[5]);
                        break;
                }
            }
        }
    }
    return multipleFiles;
}

Example 85 with CoreMetadata

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

the class BioRadSCNReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    CoreMetadata m = core.get(0);
    String line = in.readLine();
    String currentBoundary = "";
    String currentType = "";
    int currentLength = 0;
    ArrayList<String> xml = new ArrayList<String>();
    while (in.getFilePointer() < in.length() && line != null) {
        line = line.trim();
        if (line.startsWith("Content-Type")) {
            currentType = line.substring(line.indexOf(' ') + 1);
            int boundary = currentType.indexOf("boundary");
            if (boundary > 0) {
                currentBoundary = currentType.substring(boundary + 10, currentType.length() - 1);
            }
            if (currentType.indexOf(';') > 0) {
                currentType = currentType.substring(0, currentType.indexOf(';'));
            }
        } else if (line.equals("--" + currentBoundary)) {
            currentLength = 0;
        } else if (line.startsWith("Content-Length")) {
            currentLength = Integer.parseInt(line.substring(line.indexOf(' ') + 1));
        } else if (line.length() == 0) {
            if (currentType.equals("application/octet-stream")) {
                pixelsOffset = in.getFilePointer();
                in.skipBytes(currentLength);
            } else if (currentType.equals("text/xml")) {
                String xmlBlock = in.readString(currentLength);
                xml.add(xmlBlock);
            }
        }
        line = in.readLine();
    }
    SCNHandler handler = new SCNHandler();
    for (String block : xml) {
        XMLTools.parseXML(block, handler);
    }
    m.sizeZ = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYCZT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, exposureTime != null);
    store.setInstrumentID(MetadataTools.createLSID("Instrument", 0), 0);
    if (serialNumber != null) {
        store.setMicroscopeSerialNumber(serialNumber, 0);
    }
    if (model != null) {
        store.setMicroscopeModel(model, 0);
    }
    if (imageName != null) {
        store.setImageName(imageName, 0);
    }
    if (acquisitionDate != null) {
        store.setImageAcquisitionDate(new Timestamp(acquisitionDate), 0);
    }
    if (gain != null || binning != null) {
        String detector = MetadataTools.createLSID("Detector", 0, 0);
        store.setDetectorID(detector, 0, 0);
        store.setDetectorSettingsID(detector, 0, 0);
    }
    if (gain != null) {
        store.setDetectorSettingsGain(gain, 0, 0);
    }
    if (binning != null) {
        store.setDetectorSettingsBinning(getBinning(binning), 0, 0);
    }
    if (exposureTime != null) {
        store.setPlaneExposureTime(new Time(exposureTime, UNITS.SECOND), 0, 0);
    }
    if (physicalSizeX != null) {
        store.setPixelsPhysicalSizeX(FormatTools.createLength(physicalSizeX, UNITS.MICROMETER), 0);
    }
    if (physicalSizeY != null) {
        store.setPixelsPhysicalSizeY(FormatTools.createLength(physicalSizeY, UNITS.MICROMETER), 0);
    }
}