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

Example 46 with CoreMetadata

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

the class ImagicReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "hed")) {
        id = id.substring(0, id.lastIndexOf(".")) + ".hed";
    }
    super.initFile(id);
    in = new RandomAccessInputStream(id);
    pixels = id.substring(0, id.lastIndexOf(".")) + ".img";
    pixelsFile = new RandomAccessInputStream(pixels);
    CoreMetadata m = core.get(0);
    m.littleEndian = true;
    in.order(isLittleEndian());
    pixelsFile.order(isLittleEndian());
    int nImages = (int) (in.length() / 1024);
    String imageName = null;
    double physicalXSize = 0d;
    double physicalYSize = 0d;
    double physicalZSize = 0d;
    for (int i = 0; i < nImages; i++) {
        in.seek(i * 1024);
        in.skipBytes(16);
        int month = in.readInt();
        int day = in.readInt();
        int year = in.readInt();
        int hour = in.readInt();
        int minute = in.readInt();
        int seconds = in.readInt();
        in.skipBytes(8);
        m.sizeY = in.readInt();
        m.sizeX = in.readInt();
        String type = in.readString(4);
        if (type.equals("REAL")) {
            m.pixelType = FormatTools.FLOAT;
        } else if (type.equals("INTG")) {
            m.pixelType = FormatTools.UINT16;
        } else if (type.equals("PACK")) {
            m.pixelType = FormatTools.UINT8;
        } else if (type.equals("COMP")) {
            throw new FormatException("Unsupported pixel type 'COMP'");
        } else if (type.equals("RECO")) {
            throw new FormatException("Unsupported pixel type 'RECO'");
        }
        int ixold = in.readInt();
        int iyold = in.readInt();
        float averageDensity = in.readFloat();
        float sigma = in.readFloat();
        in.skipBytes(8);
        float maxDensity = in.readFloat();
        float minDensity = in.readFloat();
        in.skipBytes(4);
        float defocus1 = in.readFloat();
        float defocus2 = in.readFloat();
        float defocusAngle = in.readFloat();
        float startAngle = in.readFloat();
        float endAngle = in.readFloat();
        imageName = in.readString(80);
        float ccc3d = in.readFloat();
        int ref3d = in.readInt();
        int micrographID = in.readInt();
        int zShift = in.readInt();
        float alpha = in.readFloat();
        float beta = in.readFloat();
        float gamma = in.readFloat();
        in.skipBytes(8);
        int nAliSum = in.readInt();
        int pointGroup = in.readInt();
        in.skipBytes(28);
        int version = in.readInt();
        int stamp = in.readInt();
        in.skipBytes(120);
        float angle = in.readFloat();
        float voltage = in.readFloat();
        float sphericalAberration = in.readFloat();
        float partialCoherence = in.readFloat();
        float ccc = in.readFloat();
        float errar = in.readFloat();
        float err3d = in.readFloat();
        int ref = in.readInt();
        float classNumber = in.readFloat();
        in.skipBytes(4);
        float representationQuality = in.readFloat();
        float eqZShift = in.readFloat();
        float xShift = in.readFloat();
        float yShift = in.readFloat();
        float numcls = in.readFloat();
        float overallQuality = in.readFloat();
        float equivalentAngle = in.readFloat();
        float eqXShift = in.readFloat();
        float eqYShift = in.readFloat();
        float cmToVar = in.readFloat();
        float informat = in.readFloat();
        int nEigenvalues = in.readInt();
        int nActiveImages = in.readInt();
        physicalXSize = in.readFloat();
        physicalYSize = in.readFloat();
        physicalZSize = in.readFloat();
        addGlobalMeta("IXOLD", ixold);
        addGlobalMeta("IYOLD", iyold);
        addGlobalMeta("Average density (AVDENS)", averageDensity);
        addGlobalMeta("SIGMA", sigma);
        addGlobalMeta("Maximum density (DENSMAX)", maxDensity);
        addGlobalMeta("Minimum density (DENSMIN)", minDensity);
        addGlobalMeta("DEFOCUS1", defocus1);
        addGlobalMeta("DEFOCUS2", defocus2);
        addGlobalMeta("Defocus angle (DEFANGLE)", defocusAngle);
        addGlobalMeta("SINOSTRT", startAngle);
        addGlobalMeta("SINOEND", endAngle);
        addGlobalMeta("Image name", imageName);
        addGlobalMeta("CCC3D", ccc3d);
        addGlobalMeta("REF3D", ref3d);
        addGlobalMeta("MIDENT", micrographID);
        addGlobalMeta("EZSHIFT", zShift);
        addGlobalMeta("EALPHA", alpha);
        addGlobalMeta("EBETA", beta);
        addGlobalMeta("EGAMMA", gamma);
        addGlobalMeta("NALISUM", nAliSum);
        addGlobalMeta("PGROUP", pointGroup);
        addGlobalMeta("IMAGIC Version (IMAVERS)", version);
        addGlobalMeta("REALTYPE", stamp);
        addGlobalMeta("ANGLE", angle);
        addGlobalMeta("VOLTAGE (in kV)", voltage);
        addGlobalMeta("SPABERR (in mm)", sphericalAberration);
        addGlobalMeta("PCOHER", partialCoherence);
        addGlobalMeta("CCC", ccc);
        addGlobalMeta("ERRAR", errar);
        addGlobalMeta("ERR3D", err3d);
        addGlobalMeta("REF", ref);
        addGlobalMeta("CLASSNO", classNumber);
        addGlobalMeta("REPQUAL", representationQuality);
        addGlobalMeta("ZSHIFT", eqZShift);
        addGlobalMeta("XSHIFT", xShift);
        addGlobalMeta("YSHIFT", yShift);
        addGlobalMeta("NUMCLS", numcls);
        addGlobalMeta("OVQUAL", overallQuality);
        addGlobalMeta("EANGLE", equivalentAngle);
        addGlobalMeta("EXSHIFT", eqXShift);
        addGlobalMeta("EYSHIFT", eqYShift);
        addGlobalMeta("CMTOTVAR", cmToVar);
        addGlobalMeta("INFORMAT", informat);
        addGlobalMeta("NUMEIGEN", nEigenvalues);
        addGlobalMeta("NIACTIVE", nActiveImages);
        addGlobalMeta("RESOLX", physicalXSize);
        addGlobalMeta("RESOLY", physicalYSize);
        addGlobalMeta("RESOLZ", physicalZSize);
    }
    m.sizeZ = nImages;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = nImages;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    store.setImageName(imageName.trim(), 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(physicalXSize * 0.0001);
        Length sizeY = FormatTools.getPhysicalSizeY(physicalYSize * 0.0001);
        Length sizeZ = FormatTools.getPhysicalSizeZ(physicalZSize * 0.0001);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
    }
}

Example 47 with CoreMetadata

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

the class ImprovisionTiffReader method initStandardMetadata.

// -- Internal BaseTiffReader API methods --
/* @see BaseTiffReader#initStandardMetadata() */
@Override
protected void initStandardMetadata() throws FormatException, IOException {
    super.initStandardMetadata();
    put("Improvision", "yes");
    // parse key/value pairs in the comments
    String[] comments = new String[ifds.size()];
    String tz = null, tc = null, tt = null;
    for (int plane = 0; plane < ifds.size(); plane++) {
        String comment = ifds.get(plane).getComment();
        comments[plane] = comment;
        if (comment != null) {
            String[] lines = comment.split("\n");
            for (String line : lines) {
                int equals = line.indexOf('=');
                if (equals < 0)
                    continue;
                String key = line.substring(0, equals);
                String value = line.substring(equals + 1);
                addGlobalMeta(key, value);
                if (key.equals("TotalZPlanes"))
                    tz = value;
                else if (key.equals("TotalChannels"))
                    tc = value;
                else if (key.equals("TotalTimepoints"))
                    tt = value;
                else if (key.equals("XCalibrationMicrons")) {
                    pixelSizeX = DataTools.parseDouble(value);
                } else if (key.equals("YCalibrationMicrons")) {
                    pixelSizeY = DataTools.parseDouble(value);
                } else if (key.equals("ZCalibrationMicrons")) {
                    pixelSizeZ = DataTools.parseDouble(value);
                } else if (key.equals("WhiteColour")) {
                    String[] rgb = value.split(",");
                    if (rgb.length < 3) {
                        channelColors.add(null);
                        continue;
                    }
                    int red = 255;
                    try {
                        red = Integer.parseInt(rgb[0]);
                    } catch (NumberFormatException e) {
                    }
                    int green = 255;
                    try {
                        green = Integer.parseInt(rgb[1]);
                    } catch (NumberFormatException e) {
                    }
                    int blue = 255;
                    try {
                        blue = Integer.parseInt(rgb[2]);
                    } catch (NumberFormatException e) {
                    }
                    channelColors.add(new Color(red, green, blue, 255));
                }
            }
            metadata.remove("Comment");
        }
    }
    CoreMetadata m = core.get(0);
    m.sizeT = 1;
    if (getSizeZ() == 0)
        m.sizeZ = 1;
    if (getSizeC() == 0)
        m.sizeC = 1;
    if (tz != null)
        m.sizeZ *= Integer.parseInt(tz);
    if (tc != null)
        m.sizeC *= Integer.parseInt(tc);
    if (tt != null)
        m.sizeT *= Integer.parseInt(tt);
    if (getSizeZ() * getSizeC() * getSizeT() < getImageCount()) {
        m.sizeC *= getImageCount();
    } else
        m.imageCount = getSizeZ() * getSizeT() * Integer.parseInt(tc);
    // parse each of the comments to determine axis ordering
    long[] stamps = new long[ifds.size()];
    int[][] coords = new int[ifds.size()][3];
    cNames = new String[getSizeC()];
    boolean multipleFiles = false;
    for (int i = 0; i < ifds.size(); i++) {
        Arrays.fill(coords[i], -1);
        String comment = comments[i];
        // TODO : can use loci.common.IniParser to parse the comments
        comment = comment.replaceAll("\r\n", "\n");
        comment = comment.replaceAll("\r", "\n");
        String channelName = null;
        String[] lines = comment.split("\n");
        for (String line : lines) {
            int equals = line.indexOf('=');
            if (equals < 0)
                continue;
            String key = line.substring(0, equals);
            String value = line.substring(equals + 1);
            if (key.equals("TimeStampMicroSeconds")) {
                stamps[i] = Long.parseLong(value);
            } else if (key.equals("ZPlane"))
                coords[i][0] = Integer.parseInt(value);
            else if (key.equals("ChannelNo")) {
                coords[i][1] = Integer.parseInt(value);
                int ndx = Integer.parseInt(value) - 1;
                if (cNames[ndx] == null)
                    cNames[ndx] = channelName;
            } else if (key.equals("TimepointName")) {
                coords[i][2] = Integer.parseInt(value);
            } else if (key.equals("ChannelName")) {
                channelName = value;
            } else if (key.equals("MultiFileTIFF")) {
                multipleFiles = value.equalsIgnoreCase("yes");
            }
            if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM && coords[i][0] >= 0 && coords[i][1] >= 0 && coords[i][2] >= 0) {
                break;
            }
        }
    }
    if (multipleFiles) {
        // look for other TIFF files that belong to this dataset
        String currentUUID = getUUID(currentId);
        Location parent = new Location(currentId).getAbsoluteFile().getParentFile();
        String[] list = parent.list(true);
        Arrays.sort(list);
        ArrayList<String> matchingFiles = new ArrayList<String>();
        for (String f : list) {
            String path = new Location(parent, f).getAbsolutePath();
            if (isThisType(path) && getUUID(path).equals(currentUUID)) {
                matchingFiles.add(path);
            }
        }
        files = matchingFiles.toArray(new String[matchingFiles.size()]);
    } else {
        files = new String[] { currentId };
    }
    if (files.length * ifds.size() < getImageCount()) {
        files = new String[] { currentId };
        m.imageCount = ifds.size();
        m.sizeZ = ifds.size();
        m.sizeT = 1;
        if (!isRGB()) {
            m.sizeC = 1;
        }
    }
    readers = new MinimalTiffReader[files.length];
    for (int i = 0; i < readers.length; i++) {
        readers[i] = new MinimalTiffReader();
        readers[i].setId(files[i]);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // determine average time per plane
        long sum = 0;
        for (int i = 1; i < stamps.length; i++) {
            long diff = stamps[i] - stamps[i - 1];
            if (diff > 0)
                sum += diff;
        }
        pixelSizeT = (int) (sum / getSizeT());
    }
    // determine dimension order
    m.dimensionOrder = "XY";
    if (isRGB())
        m.dimensionOrder += 'C';
    for (int i = 1; i < coords.length; i++) {
        int zDiff = coords[i][0] - coords[i - 1][0];
        int cDiff = coords[i][1] - coords[i - 1][1];
        int tDiff = coords[i][2] - coords[i - 1][2];
        if (zDiff > 0 && getDimensionOrder().indexOf('Z') < 0) {
            m.dimensionOrder += 'Z';
        }
        if (cDiff > 0 && getDimensionOrder().indexOf('C') < 0) {
            m.dimensionOrder += 'C';
        }
        if (tDiff > 0 && getDimensionOrder().indexOf('T') < 0) {
            m.dimensionOrder += 'T';
        }
        if (m.dimensionOrder.length() == 5)
            break;
    }
    if (getDimensionOrder().indexOf('Z') < 0)
        m.dimensionOrder += 'Z';
    if (getDimensionOrder().indexOf('C') < 0)
        m.dimensionOrder += 'C';
    if (getDimensionOrder().indexOf('T') < 0)
        m.dimensionOrder += 'T';
}

Example 48 with CoreMetadata

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

the class InveonReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "hdr")) {
        id += ".hdr";
    }
    super.initFile(id);
    String headerData = DataTools.readFile(id);
    String[] lines = headerData.split("\n");
    String date = null;
    String institution = null, investigator = null;
    String model = null;
    String description = null;
    Double pixelSizeX = null;
    Double pixelSizeY = null;
    Double pixelSizeZ = null;
    int frames = 0;
    for (String line : lines) {
        line = line.trim();
        if (!line.startsWith("#")) {
            int space = line.indexOf(' ');
            if (space < 0) {
                continue;
            }
            String key = line.substring(0, space);
            String value = line.substring(space + 1);
            if (key.equals("institution")) {
                institution = value;
            } else if (key.equals("investigator")) {
                investigator = value;
            } else if (key.equals("study")) {
                description = value;
            } else if (key.equals("model")) {
                value = transformModel(value);
                model = value;
            } else if (key.equals("modality")) {
                value = transformModality(value);
            } else if (key.equals("modality_configuration")) {
                value = transformModalityConfiguration(value);
            } else if (key.equals("file_type")) {
                value = transformFileType(value);
            } else if (key.equals("acquisition_mode")) {
                value = transformAcquisitionMode(value);
            } else if (key.equals("bed_control")) {
                value = transformBedControl(value);
            } else if (key.equals("bed_motion")) {
                value = transformBedMotion(value);
            } else if (key.equals("registration_available")) {
                value = transformRegistrationAvailable(value);
            } else if (key.equals("normalization_applied")) {
                value = transformNormalizationApplied(value);
            } else if (key.equals("recon_algorithm")) {
                value = transformReconAlgorithm(value);
            } else if (key.equals("x_filter")) {
                value = transformFilter(value);
            } else if (key.equals("y_filter")) {
                value = transformFilter(value);
            } else if (key.equals("z_filter")) {
                value = transformFilter(value);
            } else if (key.equals("subject_orientation")) {
                value = transformSubjectOrientation(value);
            } else if (key.equals("subject_length_units")) {
                value = transformSubjectLengthUnits(value);
            } else if (key.equals("subject_weight_units")) {
                value = transformSubjectWeightUnits(value);
            } else if (key.equals("gantry_rotation")) {
                value = transformGantryRotation(value);
            } else if (key.equals("rotation_direction")) {
                value = transformRotationDirection(value);
            } else if (key.equals("ct_warping")) {
                value = transformCTWarping(value);
            } else if (key.equals("ct_projection_interpolation")) {
                value = transformCTProjectionInterpolation(value);
            } else if (key.equals("event_type")) {
                value = transformEventType(value);
            } else if (key.equals("projection") || key.equals("ct_projection_center_offset") || key.equals("ct_projection_horizontal_bed_offset")) {
                space = value.indexOf(' ');
                int index = Integer.parseInt(value.substring(0, space));
                value = value.substring(space + 1);
                key += " " + index;
            } else if (key.equals("user")) {
                space = value.indexOf(' ');
                key = value.substring(0, space);
                value = value.substring(space + 1);
            } else if (key.equals("file_name")) {
                // remove path from stored file name, if present
                value = value.replace('/', File.separatorChar);
                value = value.replace('\\', File.separatorChar);
                value = value.substring(value.lastIndexOf(File.separator) + 1);
                Location header = new Location(currentId).getAbsoluteFile();
                datFile = new Location(header.getParent(), value).getAbsolutePath();
            } else if (key.equals("time_frames")) {
                int sizeT = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeT = sizeT;
                }
            } else if (key.equals("total_frames")) {
                frames = Integer.parseInt(value);
            } else if (key.equals("number_of_bed_positions")) {
                int nPos = (int) Math.min(frames, Integer.parseInt(value));
                if (nPos > 1) {
                    CoreMetadata original = core.get(0);
                    core.clear();
                    for (int i = 0; i < nPos; i++) {
                        core.add(original);
                    }
                }
            } else if (key.equals("data_type")) {
                setDataType(value);
            } else if (key.equals("x_dimension")) {
                int sizeX = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeX = sizeX;
                }
            } else if (key.equals("y_dimension")) {
                int sizeY = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeY = sizeY;
                }
            } else if (key.equals("z_dimension")) {
                int sizeZ = Integer.parseInt(value);
                for (int i = 0; i < core.size(); i++) {
                    core.get(i).sizeZ = sizeZ;
                }
            } else if (key.equals("scan_time")) {
                date = value;
            } else if (key.equals("data_file_pointer")) {
                String[] values = value.split(" ");
                int[] ints = new int[values.length];
                for (int i = 0; i < ints.length; i++) {
                    ints[i] = Integer.parseInt(values[i]);
                }
                byte[] b = DataTools.intsToBytes(ints, false);
                dataPointers.add(DataTools.bytesToLong(b, false));
            } else // pixel sizes stored in mm
            if (key.equals("pixel_size_x")) {
                pixelSizeX = new Double(value) * 1000;
            } else if (key.equals("pixel_size_y")) {
                pixelSizeY = new Double(value) * 1000;
            } else if (key.equals("pixel_size_z")) {
                pixelSizeZ = new Double(value) * 1000;
            }
            addGlobalMeta(key, value);
        }
    }
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        if (ms.sizeZ == 0) {
            ms.sizeZ = 1;
        }
        if (ms.sizeT == 0) {
            ms.sizeT = 1;
        }
        ms.sizeC = 1;
        ms.rgb = false;
        ms.interleaved = false;
        ms.indexed = false;
        ms.dimensionOrder = "XYZCT";
        ms.imageCount = ms.sizeZ * ms.sizeC * ms.sizeT;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String experimenter = null, instrument = null;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        experimenter = MetadataTools.createLSID("Experimenter", 0);
        store.setExperimenterID(experimenter, 0);
        store.setExperimenterUserName(investigator, 0);
        store.setExperimenterInstitution(institution, 0);
        instrument = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrument, 0);
        store.setMicroscopeModel(model, 0);
    }
    for (int i = 0; i < core.size(); i++) {
        if (date != null) {
            String newDate = DateTools.formatDate(date, "EEE MMM dd HH:mm:ss yyyy");
            if (newDate != null) {
                store.setImageAcquisitionDate(new Timestamp(newDate), i);
            }
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            if (experimenter != null) {
                store.setImageExperimenterRef(experimenter, i);
            }
            if (instrument != null) {
                store.setImageInstrumentRef(instrument, i);
            }
            store.setImageDescription(description, i);
            Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
            Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
            Length sizeZ = FormatTools.getPhysicalSizeZ(pixelSizeZ);
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, i);
            }
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, i);
            }
            if (sizeZ != null) {
                store.setPixelsPhysicalSizeZ(sizeZ, i);
            }
        }
    }
}

Example 49 with CoreMetadata

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

the class InveonReader method setDataType.

private void setDataType(String value) {
    int type = Integer.parseInt(value);
    int pixelType = FormatTools.INT8;
    boolean littleEndian = true;
    switch(type) {
        case 2:
            pixelType = FormatTools.INT16;
            break;
        case 3:
            pixelType = FormatTools.INT32;
            break;
        case 4:
            pixelType = FormatTools.FLOAT;
            break;
        case 5:
            pixelType = FormatTools.FLOAT;
            littleEndian = false;
            break;
        case 6:
            pixelType = FormatTools.INT16;
            littleEndian = false;
            break;
        case 7:
            pixelType = FormatTools.INT32;
            littleEndian = false;
            break;
    }
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        ms.pixelType = pixelType;
        ms.littleEndian = littleEndian;
    }
}

Example 50 with CoreMetadata

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

the class IvisionReader 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);
    LOGGER.info("Populating metadata");
    String version = in.readString(4);
    addGlobalMeta("Version", version);
    int fileFormat = in.read();
    int dataType = in.read();
    CoreMetadata m = core.get(0);
    m.sizeC = 1;
    switch(dataType) {
        case 0:
            m.pixelType = FormatTools.UINT8;
            break;
        case 1:
            m.pixelType = FormatTools.INT16;
            break;
        case 2:
            m.pixelType = FormatTools.INT32;
            break;
        case 3:
            m.pixelType = FormatTools.FLOAT;
            break;
        case 4:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 3;
            color16 = true;
            break;
        case 5:
            m.pixelType = FormatTools.UINT8;
            m.sizeC = 3;
            hasPaddingByte = true;
            break;
        case 6:
            m.pixelType = FormatTools.UINT16;
            break;
        case 7:
            m.pixelType = FormatTools.FLOAT;
            squareRoot = true;
            break;
        case 8:
            m.pixelType = FormatTools.UINT16;
            m.sizeC = 3;
            break;
    }
    m.sizeX = in.readInt();
    m.sizeY = in.readInt();
    in.skipBytes(6);
    m.sizeZ = in.readShort();
    in.skipBytes(50);
    m.sizeT = 1;
    if (getSizeX() > 1 && getSizeY() > 1) {
        lut = new byte[2048];
        in.read(lut);
    }
    imageOffset = in.getFilePointer();
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        in.skipBytes(getSizeZ() * getSizeC() * getSizeT() * getSizeX() * getSizeY() * FormatTools.getBytesPerPixel(getPixelType()));
        // look for block of XML data
        LOGGER.info("Looking for XML metadata");
        in.findString(false, "<?xml");
        if (in.getFilePointer() < in.length()) {
            in.seek(in.getFilePointer() - 5);
            String xml = in.readString((int) (in.length() - in.getFilePointer()));
            xml = xml.substring(xml.indexOf('<'), xml.lastIndexOf("plist>") + 6);
            IvisionHandler handler = new IvisionHandler();
            try {
                XMLTools.parseXML(xml, handler);
            } catch (IOException e) {
                LOGGER.debug("", e);
            }
        } else
            LOGGER.debug("XML metadata not found");
    }
    LOGGER.info("Populating core metadata");
    m.rgb = getSizeC() > 1;
    m.dimensionOrder = "XYCZT";
    m.littleEndian = false;
    m.interleaved = true;
    m.indexed = false;
    m.imageCount = getSizeZ() * getSizeT();
    LOGGER.info("Populating MetadataStore");
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (creationDate != null) {
        String date = DateTools.formatDate(creationDate, DATE_FORMAT);
        if (date != null) {
            store.setImageAcquisitionDate(new Timestamp(date), 0);
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        if (deltaT != null) {
            Double increment = 0d;
            try {
                increment = new Double(deltaT);
            } catch (NumberFormatException e) {
                LOGGER.debug("Failed to parse time increment", e);
            }
            if (increment != null) {
                store.setPixelsTimeIncrement(new Time(increment, UNITS.SECOND), 0);
            }
        }
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        store.setObjectiveSettingsID(objectiveID, 0);
        store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
        store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
        if (lensNA != null)
            store.setObjectiveLensNA(lensNA, 0, 0);
        if (magnification != null) {
            store.setObjectiveNominalMagnification(magnification, 0, 0);
        }
        if (refractiveIndex != null) {
            store.setObjectiveSettingsRefractiveIndex(refractiveIndex, 0);
        }
        String detectorID = MetadataTools.createLSID("Detector", 0, 0);
        store.setDetectorID(detectorID, 0, 0);
        store.setDetectorSettingsID(detectorID, 0, 0);
        store.setDetectorType(getDetectorType("Other"), 0, 0);
        store.setDetectorSettingsBinning(getBinning(binX + "x" + binY), 0, 0);
        if (gain != null) {
            try {
                store.setDetectorSettingsGain(new Double(gain), 0, 0);
            } catch (NumberFormatException e) {
                LOGGER.debug("Failed to parse detector gain", e);
            }
        }
    }
}