Examples with Length ome.units.quantity.Length used on opensource projects

Example 16 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class FEITiffReader method initMetadataStore.

/* @see BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (date != null) {
        date = DateTools.formatDate(date, DATE_FORMAT);
        if (date != null) {
            store.setImageAcquisitionDate(new Timestamp(date), 0);
        }
    }
    if (imageName != null) {
        store.setImageName(imageName, 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (imageDescription != null) {
            store.setImageDescription(imageDescription, 0);
        }
        if (userName != null) {
            store.setExperimenterID(MetadataTools.createLSID("Experimenter", 0), 0);
            store.setExperimenterLastName(userName, 0);
        }
        if (microscopeModel != null) {
            String instrument = MetadataTools.createLSID("Instrument", 0);
            store.setInstrumentID(instrument, 0);
            store.setImageInstrumentRef(instrument, 0);
            store.setMicroscopeModel(microscopeModel, 0);
        }
        if (detectors != null && detectors.size() > 0) {
            String instrument = MetadataTools.createLSID("Instrument", 0);
            store.setInstrumentID(instrument, 0);
            store.setImageInstrumentRef(instrument, 0);
            for (int i = 0; i < detectors.size(); i++) {
                String detectorID = MetadataTools.createLSID("Detector", 0, i);
                store.setDetectorID(detectorID, 0, i);
                store.setDetectorModel(detectors.get(i), 0, i);
                store.setDetectorType(getDetectorType("Other"), 0, i);
            }
        }
        if (magnification != null) {
            store.setObjectiveID(MetadataTools.createLSID("Objective", 0, 0), 0, 0);
            store.setObjectiveNominalMagnification(magnification, 0, 0);
            store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
            store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
        }
        store.setStageLabelX(stageX, 0);
        store.setStageLabelY(stageY, 0);
        store.setStageLabelZ(stageZ, 0);
        store.setStageLabelName("", 0);
        boolean helios = ifds.get(0).containsKey(HELIOS_TAG);
        Unit<Length> unit = UNITS.MICROMETER;
        if (helios) {
            unit = UNITS.METER;
        }
        Length physicalSizeX = FormatTools.getPhysicalSizeX(sizeX, unit);
        Length physicalSizeY = FormatTools.getPhysicalSizeY(sizeY, unit);
        if (physicalSizeX != null) {
            store.setPixelsPhysicalSizeX(physicalSizeX, 0);
        }
        if (physicalSizeY != null) {
            store.setPixelsPhysicalSizeY(physicalSizeY, 0);
        }
        if (timeIncrement != null) {
            store.setPixelsTimeIncrement(new Time(timeIncrement, UNITS.SECOND), 0);
        }
    }
}

Example 17 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class FlexReader method populateMetadataStore.

private void populateMetadataStore(MetadataStore store) throws FormatException {
    LOGGER.info("Populating MetadataStore");
    MetadataTools.populatePixels(store, this, true);
    Location currentFile = new Location(getCurrentFile()).getAbsoluteFile();
    int[] lengths = new int[] { fieldCount, wellCount, plateCount };
    store.setPlateID(MetadataTools.createLSID("Plate", 0), 0);
    String plateAcqID = MetadataTools.createLSID("PlateAcquisition", 0, 0);
    store.setPlateAcquisitionID(plateAcqID, 0, 0);
    PositiveInteger maxFieldCount = FormatTools.getMaxFieldCount(fieldCount);
    if (maxFieldCount != null) {
        store.setPlateAcquisitionMaximumFieldCount(maxFieldCount, 0, 0);
    }
    plateAcqStartTime = DateTools.formatDate(plateAcqStartTime, "dd.MM.yyyy  HH:mm:ss");
    if (plateAcqStartTime != null) {
        store.setPlateAcquisitionStartTime(new Timestamp(plateAcqStartTime), 0, 0);
    }
    for (int row = 0; row < wellRows; row++) {
        for (int col = 0; col < wellColumns; col++) {
            int well = row * wellColumns + col;
            store.setWellID(MetadataTools.createLSID("Well", 0, well), 0, well);
            store.setWellRow(new NonNegativeInteger(row), 0, well);
            store.setWellColumn(new NonNegativeInteger(col), 0, well);
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        int[] pos = FormatTools.rasterToPosition(lengths, i);
        String imageID = MetadataTools.createLSID("Image", i);
        store.setImageID(imageID, i);
        int well = wellNumber[pos[1]][0] * wellColumns + wellNumber[pos[1]][1];
        char wellRow = (char) ('A' + wellNumber[pos[1]][0]);
        store.setImageName("Well " + wellRow + "-" + (wellNumber[pos[1]][1] + 1) + "; Field #" + (pos[0] + 1), i);
        if (acquisitionDates.get(i) != null) {
            store.setImageAcquisitionDate(acquisitionDates.get(i), i);
        }
        if (wellRows == 0 && wellColumns == 0) {
            well = pos[1];
            NonNegativeInteger row = new NonNegativeInteger(wellNumber[pos[1]][0]);
            NonNegativeInteger col = new NonNegativeInteger(wellNumber[pos[1]][1]);
            String wellID = MetadataTools.createLSID("Well", pos[2], well);
            store.setWellID(wellID, pos[2], well);
            store.setWellRow(row, pos[2], pos[1]);
            store.setWellColumn(col, pos[2], pos[1]);
        }
        String wellSample = MetadataTools.createLSID("WellSample", pos[2], well, pos[0]);
        store.setWellSampleID(wellSample, pos[2], well, pos[0]);
        store.setWellSampleIndex(new NonNegativeInteger(i), pos[2], well, pos[0]);
        store.setWellSampleImageRef(imageID, pos[2], well, pos[0]);
        store.setPlateAcquisitionWellSampleRef(wellSample, 0, 0, i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        if (plateName == null)
            plateName = currentFile.getParentFile().getName();
        if (plateBarcode != null)
            plateName = plateBarcode + " " + plateName;
        store.setPlateName(plateName, 0);
        store.setPlateRowNamingConvention(getNamingConvention("Letter"), 0);
        store.setPlateColumnNamingConvention(getNamingConvention("Number"), 0);
        for (int i = 0; i < getSeriesCount(); i++) {
            int[] pos = FormatTools.rasterToPosition(lengths, i);
            store.setImageInstrumentRef(instrumentID, i);
            int seriesIndex = i * getImageCount();
            if (seriesIndex < objectiveRefs.size()) {
                store.setObjectiveSettingsID(objectiveRefs.get(seriesIndex), i);
            }
            for (int c = 0; c < getEffectiveSizeC(); c++) {
                int channelIndex = seriesIndex + c;
                if (seriesIndex > 0 && channelNames.length == getEffectiveSizeC() * getSeriesCount()) {
                    channelIndex = i * getEffectiveSizeC() + c;
                }
                if (channelNames != null && channelIndex >= channelNames.length) {
                    channelIndex = c;
                }
                if (channelNames != null && channelIndex < channelNames.length) {
                    store.setChannelName(channelNames[channelIndex], i, c);
                }
            }
            if (seriesIndex < lightSourceCombinationRefs.size()) {
                String lightSourceCombo = lightSourceCombinationRefs.get(seriesIndex);
                List<String> lightSources = lightSourceCombinationIDs.get(lightSourceCombo);
                for (int c = 0; c < getEffectiveSizeC(); c++) {
                    int index = seriesIndex + c;
                    if (index < cameraRefs.size()) {
                        store.setDetectorSettingsID(cameraRefs.get(index), i, c);
                        if (index < binnings.size()) {
                            store.setDetectorSettingsBinning(getBinning(binnings.get(index)), i, c);
                        }
                    }
                    if (lightSources != null && c < lightSources.size()) {
                        store.setChannelLightSourceSettingsID(lightSources.get(c), i, c);
                    } else if (c > 0 && lightSources != null && lightSources.size() == 1) {
                        lightSourceCombo = lightSourceCombinationRefs.get(seriesIndex + c);
                        lightSources = lightSourceCombinationIDs.get(lightSourceCombo);
                        store.setChannelLightSourceSettingsID(lightSources.get(0), i, c);
                    }
                    if (index < filterSets.size()) {
                        FilterGroup group = filterSetMap.get(filterSets.get(index));
                        if (group != null) {
                            if (group.emission != null) {
                                store.setLightPathEmissionFilterRef(group.emission, i, c, 0);
                            }
                            if (group.excitation != null) {
                                store.setLightPathExcitationFilterRef(group.excitation, i, c, 0);
                            }
                            if (group.dichroic != null) {
                                store.setLightPathDichroicRef(group.dichroic, i, c);
                            }
                        }
                    }
                }
            }
            if (seriesIndex < xSizes.size()) {
                Length size = FormatTools.getPhysicalSizeX(xSizes.get(seriesIndex));
                if (size != null) {
                    store.setPixelsPhysicalSizeX(size, i);
                }
            }
            if (seriesIndex < ySizes.size()) {
                Length size = FormatTools.getPhysicalSizeY(ySizes.get(seriesIndex));
                if (size != null) {
                    store.setPixelsPhysicalSizeY(size, i);
                }
            }
            int well = wellNumber[pos[1]][0] * wellColumns + wellNumber[pos[1]][1];
            if (wellRows == 0 && wellColumns == 0) {
                well = pos[1];
            }
            if (pos[0] < xPositions.size()) {
                Length l = new Length(xPositions.get(pos[0]), UNITS.REFERENCEFRAME);
                store.setWellSamplePositionX(l, pos[2], well, pos[0]);
            }
            if (pos[0] < yPositions.size()) {
                Length l = new Length(yPositions.get(pos[0]), UNITS.REFERENCEFRAME);
                store.setWellSamplePositionY(l, pos[2], well, pos[0]);
            }
            for (int image = 0; image < getImageCount(); image++) {
                int plane = i * getImageCount() + image;
                int c = getZCTCoords(image)[1];
                if (plane < planePositionX.size()) {
                    store.setPlanePositionX(planePositionX.get(plane), i, image);
                }
                if (plane < planePositionY.size()) {
                    store.setPlanePositionY(planePositionY.get(plane), i, image);
                }
                if (plane < planePositionZ.size()) {
                    store.setPlanePositionZ(planePositionZ.get(plane), i, image);
                }
                if (plane - image + c < planeExposureTime.size()) {
                    if (planeExposureTime.get(plane - image + c) != null) {
                        store.setPlaneExposureTime(new Time(planeExposureTime.get(plane - image + c), UNITS.SECOND), i, image);
                    }
                }
                if (plane < planeDeltaT.size() && planeDeltaT.get(plane) != null) {
                    store.setPlaneDeltaT(new Time(planeDeltaT.get(plane), UNITS.SECOND), i, image);
                }
            }
        }
    }
}

Example 18 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class ImarisHDFReader 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 {
        ServiceFactory factory = new ServiceFactory();
        netcdf = factory.getInstance(NetCDFService.class);
        netcdf.setFile(id);
    } catch (DependencyException e) {
        throw new MissingLibraryException(NetCDFServiceImpl.NO_NETCDF_MSG, e);
    }
    pixelSizeX = pixelSizeY = pixelSizeZ = 1;
    emWave = new ArrayList<String>();
    exWave = new ArrayList<String>();
    channelMin = new ArrayList<String>();
    channelMax = new ArrayList<String>();
    gain = new ArrayList<String>();
    pinhole = new ArrayList<String>();
    channelName = new ArrayList<String>();
    microscopyMode = new ArrayList<String>();
    colors = new ArrayList<double[]>();
    seriesCount = 0;
    // read all of the metadata key/value pairs
    parseAttributes();
    CoreMetadata ms0 = core.get(0);
    if (seriesCount > 1) {
        for (int i = 1; i < seriesCount; i++) {
            core.add(new CoreMetadata());
        }
        for (int i = 1; i < seriesCount; i++) {
            CoreMetadata ms = core.get(i);
            String groupPath = "DataSet/ResolutionLevel_" + i + "/TimePoint_0/Channel_0";
            ms.sizeX = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeX"));
            ms.sizeY = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeY"));
            ms.sizeZ = Integer.parseInt(netcdf.getAttributeValue(groupPath + "/ImageSizeZ"));
            ms.imageCount = ms.sizeZ * getSizeC() * getSizeT();
            ms.sizeC = getSizeC();
            ms.sizeT = getSizeT();
            ms.thumbnail = true;
            if (ms.sizeZ == ms0.sizeZ && ms.sizeC == ms0.sizeC && ms.sizeT == ms0.sizeT) {
                // do not assume that all series will have the same dimensions
                // if the Z, C or T size is different, then it cannot
                // be a subresolution
                ms0.resolutionCount++;
            }
        }
    }
    ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
    ms0.thumbnail = false;
    ms0.dimensionOrder = "XYZCT";
    // determine pixel type - this isn't stored in the metadata, so we need
    // to check the pixels themselves
    int type = -1;
    Object pix = getImageData(0, 0, 0, 1, 1);
    if (pix instanceof byte[][])
        type = FormatTools.UINT8;
    else if (pix instanceof short[][])
        type = FormatTools.UINT16;
    else if (pix instanceof int[][])
        type = FormatTools.UINT32;
    else if (pix instanceof float[][])
        type = FormatTools.FLOAT;
    else if (pix instanceof double[][])
        type = FormatTools.DOUBLE;
    else {
        throw new FormatException("Unknown pixel type: " + pix);
    }
    for (int i = 0; i < core.size(); i++) {
        CoreMetadata ms = core.get(i);
        ms.pixelType = type;
        ms.dimensionOrder = "XYZCT";
        ms.rgb = false;
        ms.thumbSizeX = 128;
        ms.thumbSizeY = 128;
        ms.orderCertain = true;
        ms.littleEndian = true;
        ms.interleaved = false;
        ms.indexed = colors.size() >= getSizeC();
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String imageName = new Location(getCurrentFile()).getName();
    for (int s = 0; s < getSeriesCount(); s++) {
        store.setImageName(imageName + " Resolution Level " + (s + 1), s);
    }
    if (getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM) {
        return;
    }
    int cIndex = 0;
    for (int s = 0; s < getSeriesCount(); s++) {
        setSeries(s);
        double px = pixelSizeX, py = pixelSizeY, pz = pixelSizeZ;
        if (px == 1)
            px = (maxX - minX) / getSizeX();
        if (py == 1)
            py = (maxY - minY) / getSizeY();
        if (pz == 1)
            pz = (maxZ - minZ) / getSizeZ();
        Length sizeX = FormatTools.getPhysicalSizeX(px);
        Length sizeY = FormatTools.getPhysicalSizeY(py);
        Length sizeZ = FormatTools.getPhysicalSizeZ(pz);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, s);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, s);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, s);
        }
        for (int i = 0; i < getSizeC(); i++, cIndex++) {
            Float gainValue = null;
            Integer pinholeValue = null, emWaveValue = null, exWaveValue;
            if (cIndex < gain.size()) {
                try {
                    gainValue = new Float(gain.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < pinhole.size()) {
                try {
                    pinholeValue = new Integer(pinhole.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < emWave.size()) {
                try {
                    emWaveValue = new Integer(emWave.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < exWave.size()) {
                try {
                    exWaveValue = new Integer(exWave.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            Double minValue = null, maxValue = null;
            if (cIndex < channelMin.size()) {
                try {
                    minValue = new Double(channelMin.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (cIndex < channelMax.size()) {
                try {
                    maxValue = new Double(channelMax.get(cIndex));
                } catch (NumberFormatException e) {
                }
            }
            if (i < colors.size()) {
                double[] color = colors.get(i);
                Color realColor = new Color((int) (color[0] * 255), (int) (color[1] * 255), (int) (color[2] * 255), 255);
                store.setChannelColor(realColor, s, i);
            }
        }
    }
    setSeries(0);
}

Example 19 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class FujiReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    if (checkSuffix(id, "inf")) {
        infFile = new Location(id).getAbsolutePath();
        pixelsFile = infFile.substring(0, infFile.lastIndexOf(".")) + ".img";
    } else {
        pixelsFile = new Location(id).getAbsolutePath();
        infFile = pixelsFile.substring(0, pixelsFile.lastIndexOf(".")) + ".inf";
    }
    String[] lines = DataTools.readFile(infFile).split("\r{0,1}\n");
    int bits = Integer.parseInt(lines[5]);
    CoreMetadata m = core.get(0);
    m.pixelType = FormatTools.pixelTypeFromBytes(bits / 8, false, false);
    m.sizeX = Integer.parseInt(lines[6]);
    m.sizeY = Integer.parseInt(lines[7]);
    m.sizeC = 1;
    m.sizeT = 1;
    m.sizeZ = 1;
    m.imageCount = getSizeZ() * getSizeC() * getSizeT();
    m.dimensionOrder = "XYCZT";
    for (String line : lines) {
        addGlobalMetaList("Line", line);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    String imageName = lines[1];
    String timestamp = lines[10];
    timestamp = DateTools.formatDate(timestamp, DATE_FORMAT);
    store.setImageName(imageName, 0);
    if (timestamp != null) {
        store.setImageAcquisitionDate(new Timestamp(timestamp), 0);
    }
    double physicalWidth = Double.parseDouble(lines[3]);
    double physicalHeight = Double.parseDouble(lines[4]);
    Length sizeX = FormatTools.getPhysicalSizeX(physicalWidth);
    Length sizeY = FormatTools.getPhysicalSizeY(physicalHeight);
    if (sizeX != null) {
        store.setPixelsPhysicalSizeX(sizeX, 0);
    }
    if (sizeY != null) {
        store.setPixelsPhysicalSizeY(sizeY, 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        String instrument = lines[13];
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setMicroscopeModel(instrument, 0);
    }
}

Example 20 with Length

use of ome.units.quantity.Length in project bioformats by openmicroscopy.

the class GatanReader method parseTags.

// -- Helper methods --
/**
 * Parses Gatan DM3 tags.
 * Information on the DM3 structure found at:
 * http://rsb.info.nih.gov/ij/plugins/DM3Format.gj.html and
 * http://www-hrem.msm.cam.ac.uk/~cbb/info/dmformat/
 *
 * The basic structure is this: the file is comprised of a list of tags.
 * Each tag is either a data tag or a group tag.  Group tags are simply
 * containers for more group and data tags, where data tags contain actual
 * metadata.  Each data tag is comprised of a type (byte, short, etc.),
 * a label, and a value.
 */
private void parseTags(int numTags, String parent, String indent) throws FormatException, IOException, ParseException {
    for (int i = 0; i < numTags; i++) {
        if (in.getFilePointer() + 3 >= in.length())
            break;
        // can be 21 (data) or 20 (tag group)
        byte type = in.readByte();
        int length = in.readShort();
        // image data is in tag with type 21 and label 'Data'
        // image dimensions are in type 20 tag with 2 type 15 tags
        // bytes per pixel is in type 21 tag with label 'PixelDepth'
        String labelString = null;
        String value = null;
        if (type == VALUE) {
            labelString = in.readByteToString(length);
            skipPadding();
            skipPadding();
            // equal to '%%%%' / 623191333
            int skip = in.readInt();
            skipPadding();
            int n = in.readInt();
            skipPadding();
            int dataType = in.readInt();
            String sb = labelString;
            if (sb.length() > 32) {
                sb = sb.substring(0, 20) + "... (" + sb.length() + ")";
            }
            LOGGER.debug("{}{}: n={}, dataType={}, label={}", new Object[] { indent, i, n, dataType, sb });
            if (skip != 623191333)
                LOGGER.warn("Skip mismatch: {}", skip);
            if (n == 1) {
                if ("Dimensions".equals(parent) && labelString.length() == 0) {
                    if (adjustEndianness)
                        in.order(!in.isLittleEndian());
                    if (i == 0) {
                        core.get(0).sizeX = in.readInt();
                    } else if (i == 1)
                        core.get(0).sizeY = in.readInt();
                    else if (i == 2) {
                        core.get(0).sizeZ = in.readInt();
                    }
                    if (adjustEndianness)
                        in.order(!in.isLittleEndian());
                } else
                    value = String.valueOf(readValue(dataType));
            } else if (n == 2) {
                if (dataType == 18) {
                    // this should always be true
                    length = in.readInt();
                } else
                    LOGGER.warn("dataType mismatch: {}", dataType);
                value = in.readString(length);
            } else if (n == 3) {
                if (dataType == GROUP) {
                    // this should always be true
                    skipPadding();
                    dataType = in.readInt();
                    long dataLength = 0;
                    if (version == 4) {
                        dataLength = in.readLong();
                    } else {
                        dataLength = in.readInt();
                    }
                    length = (int) (dataLength & 0xffffffff);
                    if (labelString.equals("Data")) {
                        if (dataLength > 0) {
                            pixelOffset = in.getFilePointer();
                            in.seek(in.getFilePointer() + getNumBytes(dataType) * dataLength);
                            numPixelBytes = in.getFilePointer() - pixelOffset;
                        }
                    } else {
                        if (dataType == 10)
                            in.skipBytes(length);
                        else
                            value = in.readByteToString(length * 2);
                    }
                } else
                    LOGGER.warn("dataType mismatch: {}", dataType);
            } else {
                // this is a normal struct of simple types
                if (dataType == ARRAY) {
                    in.skipBytes(4);
                    skipPadding();
                    skipPadding();
                    int numFields = in.readInt();
                    long startFP = in.getFilePointer();
                    final StringBuilder s = new StringBuilder();
                    in.skipBytes(4);
                    skipPadding();
                    long baseFP = in.getFilePointer();
                    if (version == 4) {
                        baseFP += 4;
                    }
                    int width = version == 4 ? 16 : 8;
                    for (int j = 0; j < numFields; j++) {
                        in.seek(baseFP + j * width);
                        dataType = in.readInt();
                        in.seek(startFP + numFields * width + j * getNumBytes(dataType));
                        s.append(readValue(dataType));
                        if (j < numFields - 1)
                            s.append(", ");
                    }
                    value = s.toString();
                } else if (dataType == GROUP) {
                    // this is an array of structs
                    skipPadding();
                    dataType = in.readInt();
                    if (dataType == ARRAY) {
                        // should always be true
                        in.skipBytes(4);
                        skipPadding();
                        skipPadding();
                        int numFields = in.readInt();
                        int[] dataTypes = new int[numFields];
                        long baseFP = in.getFilePointer() + 12;
                        for (int j = 0; j < numFields; j++) {
                            in.skipBytes(4);
                            if (version == 4) {
                                in.seek(baseFP + j * 16);
                            }
                            dataTypes[j] = in.readInt();
                        }
                        skipPadding();
                        int len = in.readInt();
                        double[][] values = new double[numFields][len];
                        for (int k = 0; k < len; k++) {
                            for (int q = 0; q < numFields; q++) {
                                values[q][k] = readValue(dataTypes[q]);
                            }
                        }
                    } else
                        LOGGER.warn("dataType mismatch: {}", dataType);
                }
            }
        } else if (type == GROUP) {
            labelString = in.readByteToString(length);
            in.skipBytes(2);
            skipPadding();
            skipPadding();
            skipPadding();
            int num = in.readInt();
            LOGGER.debug("{}{}: group({}) {} {", new Object[] { indent, i, num, labelString });
            parseTags(num, labelString.isEmpty() ? parent : labelString, indent + "  ");
            LOGGER.debug("{}}", indent);
        } else {
            LOGGER.debug("{}{}: unknown type: {}", new Object[] { indent, i, type });
        }
        NumberFormat f = NumberFormat.getInstance(Locale.ENGLISH);
        if (value != null) {
            addGlobalMeta(labelString, value);
            if (parent != null && parent.equals("AnnotationGroupList")) {
                // ROI found
                ROIShape shape = new ROIShape();
                if (labelString.equals("AnnotationType")) {
                    shape.type = DataTools.parseDouble(value).intValue();
                    shapes.add(shape);
                } else if (shapes.size() > 0) {
                    shape = shapes.get(shapes.size() - 1);
                }
                if (labelString.equals("Rectangle")) {
                    String[] points = value.split(",");
                    shape.y1 = DataTools.parseDouble(points[0].trim());
                    shape.x1 = DataTools.parseDouble(points[1].trim());
                    shape.y2 = DataTools.parseDouble(points[2].trim());
                    shape.x2 = DataTools.parseDouble(points[3].trim());
                } else if (labelString.equals("Text")) {
                    shape.text = value;
                } else if (labelString.equals("ForegroundColor")) {
                    String[] colors = value.split(",");
                    int red = DataTools.parseDouble(colors[0].trim()).intValue() & 0xff;
                    int green = DataTools.parseDouble(colors[1].trim()).intValue() & 0xff;
                    int blue = DataTools.parseDouble(colors[2].trim()).intValue() & 0xff;
                    shape.strokeColor = new Color(red, green, blue, 255);
                }
            } else if (parent != null && parent.equals("TextFormat")) {
                if (labelString.equals("FontSize")) {
                    ROIShape shape = shapes.get(shapes.size() - 1);
                    shape.fontSize = FormatTools.getFontSize(DataTools.parseDouble(value).intValue());
                }
            }
            boolean validPhysicalSize = parent != null && (parent.equals("Dimension") || ((pixelSizes.size() == 4 || units.size() == 4) && parent.equals("2")));
            if (labelString.equals("Scale") && validPhysicalSize) {
                if (value.indexOf(',') == -1) {
                    pixelSizes.add(f.parse(value).doubleValue());
                }
            } else if (labelString.equals("Units") && validPhysicalSize) {
                // make sure that we don't add more units than sizes
                if (pixelSizes.size() == units.size() + 1) {
                    units.add(value);
                }
            } else if (labelString.equals("LowLimit")) {
                signed = f.parse(value).doubleValue() < 0;
            } else if (labelString.equals("Acquisition Start Time (epoch)")) {
                timestamp = f.parse(value).longValue();
            } else if (labelString.equals("Voltage")) {
                voltage = f.parse(value).doubleValue();
            } else if (labelString.equals("Microscope Info"))
                info = value;
            else if (labelString.equals("Indicated Magnification")) {
                mag = f.parse(value).doubleValue();
            } else if (labelString.equals("Gamma")) {
                gamma = f.parse(value).doubleValue();
            } else if (labelString.startsWith("xPos")) {
                final Double number = f.parse(value).doubleValue();
                posX = new Length(number, UNITS.REFERENCEFRAME);
            } else if (labelString.startsWith("yPos")) {
                final Double number = f.parse(value).doubleValue();
                posY = new Length(number, UNITS.REFERENCEFRAME);
            } else if (labelString.startsWith("Specimen position")) {
                final Double number = f.parse(value).doubleValue();
                posZ = new Length(number, UNITS.REFERENCEFRAME);
            } else if (labelString.equals("Sample Time")) {
                sampleTime = f.parse(value).doubleValue();
            } else if (labelString.equals("DataType")) {
                int pixelType = f.parse(value).intValue();
                switch(pixelType) {
                    case 1:
                        core.get(0).pixelType = FormatTools.INT16;
                        break;
                    case 10:
                        core.get(0).pixelType = FormatTools.UINT16;
                        break;
                    case 2:
                        core.get(0).pixelType = FormatTools.FLOAT;
                        break;
                    case 12:
                        core.get(0).pixelType = FormatTools.DOUBLE;
                        break;
                    case 9:
                        core.get(0).pixelType = FormatTools.INT8;
                        break;
                    case 6:
                        core.get(0).pixelType = FormatTools.UINT8;
                        break;
                    case 7:
                        core.get(0).pixelType = FormatTools.INT32;
                        break;
                    case 11:
                        core.get(0).pixelType = FormatTools.UINT32;
                }
            }
            value = null;
        }
    }
}