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

Example 86 with CoreMetadata

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

the class BurleighReader 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);
    m.littleEndian = true;
    in.order(isLittleEndian());
    int version = (int) in.readFloat() - 1;
    m.sizeX = in.readShort();
    m.sizeY = in.readShort();
    double xSize = 0d, ySize = 0d, zSize = 0d;
    pixelsOffset = version == 1 ? 8 : 260;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        double timePerPixel = 0d;
        int mode = 0, gain = 0, mag = 0;
        double sampleVolts = 0d, tunnelCurrent = 0d;
        if (version == 1) {
            in.seek(in.length() - 40);
            in.skipBytes(12);
            xSize = in.readInt();
            ySize = in.readInt();
            zSize = in.readInt();
            timePerPixel = in.readShort() * 50;
            mag = in.readShort();
            switch(mag) {
                case 3:
                    mag = 10;
                    break;
                case 4:
                    mag = 50;
                    break;
                case 5:
                    mag = 250;
                    break;
            }
            xSize /= mag;
            ySize /= mag;
            zSize /= mag;
            mode = in.readShort();
            gain = in.readShort();
            sampleVolts = in.readFloat() / 1000;
            tunnelCurrent = in.readFloat();
        } else if (version == 2) {
            in.skipBytes(14);
            xSize = in.readInt();
            ySize = in.readInt();
            zSize = in.readInt();
            mode = in.readShort();
            in.skipBytes(4);
            gain = in.readShort();
            timePerPixel = in.readShort() * 50;
            in.skipBytes(12);
            sampleVolts = in.readFloat();
            tunnelCurrent = in.readFloat();
            addGlobalMeta("Force", in.readFloat());
        }
        addGlobalMeta("Version", version);
        addGlobalMeta("Image mode", mode);
        addGlobalMeta("Z gain", gain);
        addGlobalMeta("Time per pixel (s)", timePerPixel);
        addGlobalMeta("Sample volts", sampleVolts);
        addGlobalMeta("Tunnel current", tunnelCurrent);
        addGlobalMeta("Magnification", mag);
    }
    m.pixelType = FormatTools.UINT16;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYZCT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        Length sizeX = FormatTools.getPhysicalSizeX(xSize / getSizeX());
        Length sizeY = FormatTools.getPhysicalSizeY(ySize / getSizeY());
        Length sizeZ = FormatTools.getPhysicalSizeZ(zSize / getSizeZ());
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, 0);
        }
    }
}

Example 87 with CoreMetadata

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

the class CellH5Reader method parseStructure.

private void parseStructure() throws FormatException {
    seriesCount = 0;
    core.clear();
    // read experiment structure and collect coordinates
    String path_to_plate = CellH5Constants.PREFIX_PATH + CellH5Constants.PLATE;
    LOGGER.info("Plate :" + path_to_plate);
    for (String plate : jhdf.getMember(path_to_plate)) {
        String path_to_well = path_to_plate + plate + CellH5Constants.WELL;
        LOGGER.info("Well :" + path_to_well);
        for (String well : jhdf.getMember(path_to_well)) {
            String path_to_site = path_to_well + well + CellH5Constants.SITE;
            LOGGER.info("Site :" + path_to_site);
            for (String site : jhdf.getMember(path_to_site)) {
                CellH5PositionList.add(new CellH5Coordinate(plate, well, site));
            }
        }
    }
    if (CellH5PositionList.size() == 0) {
        throw new FormatException("No series found in file...");
    }
    List<String> seriesNames = new ArrayList<String>();
    List<String> seriesPlate = new ArrayList<String>();
    List<String> seriesWell = new ArrayList<String>();
    List<String> seriesSite = new ArrayList<String>();
    for (CellH5Coordinate coord : CellH5PositionList) {
        if (jhdf.exists(coord.pathToImageData)) {
            CoreMetadata m = new CoreMetadata();
            core.add(m);
            setSeries(seriesCount);
            LOGGER.debug(coord.pathToImageData);
            int[] ctzyx = jhdf.getShape(coord.pathToImageData);
            m.sizeC = ctzyx[0];
            m.sizeT = ctzyx[1];
            m.sizeZ = ctzyx[2];
            m.sizeY = ctzyx[3];
            m.sizeX = ctzyx[4];
            m.resolutionCount = 1;
            m.thumbnail = false;
            m.imageCount = getSizeC() * getSizeT() * getSizeZ();
            m.dimensionOrder = "XYZTC";
            m.rgb = false;
            m.thumbSizeX = 128;
            m.thumbSizeY = 128;
            m.orderCertain = false;
            m.littleEndian = true;
            m.interleaved = false;
            m.indexed = true;
            int bpp = jhdf.getElementSize(coord.pathToImageData);
            if (bpp == 1) {
                m.pixelType = FormatTools.UINT8;
            } else if (bpp == 2) {
                m.pixelType = FormatTools.UINT16;
            } else if (bpp == 4) {
                m.pixelType = FormatTools.INT32;
            } else {
                throw new FormatException("Pixel type not understood. Only 8, " + "16 and 32 bit images supported");
            }
            seriesNames.add(String.format("P_%s, W_%s_%s", coord.plate, coord.well, coord.site));
            seriesPlate.add(coord.plate);
            seriesWell.add(coord.well);
            seriesSite.add(coord.site);
            CellH5PathsToImageData.add(coord.pathToImageData);
            seriesCount++;
        }
    }
    for (CellH5Coordinate coord : CellH5PositionList) {
        if (jhdf.exists(coord.pathToSegmentationData)) {
            CoreMetadata m = new CoreMetadata();
            core.add(m);
            setSeries(seriesCount);
            LOGGER.debug(coord.pathToSegmentationData);
            int[] ctzyx = jhdf.getShape(coord.pathToSegmentationData);
            m.sizeC = ctzyx[0];
            m.sizeT = ctzyx[1];
            m.sizeZ = ctzyx[2];
            m.sizeY = ctzyx[3];
            m.sizeX = ctzyx[4];
            m.resolutionCount = 1;
            m.thumbnail = false;
            m.imageCount = getSizeC() * getSizeT() * getSizeZ();
            m.dimensionOrder = "XYZTC";
            m.rgb = false;
            m.thumbSizeX = 128;
            m.thumbSizeY = 128;
            m.orderCertain = false;
            m.littleEndian = true;
            m.interleaved = false;
            m.indexed = true;
            int bpp = jhdf.getElementSize(coord.pathToSegmentationData);
            if (bpp == 1) {
                m.pixelType = FormatTools.UINT8;
            } else if (bpp == 2) {
                m.pixelType = FormatTools.UINT16;
            } else if (bpp == 4) {
                m.pixelType = FormatTools.INT32;
            } else {
                throw new FormatException("Pixel type not understood. Only 8, " + "16 and 32 bit images supported");
            }
            seriesNames.add(String.format("P_%s, W_%s_%s label image", coord.plate, coord.well, coord.site));
            seriesPlate.add(coord.plate);
            seriesWell.add(coord.well);
            seriesSite.add(coord.site);
            CellH5PathsToImageData.add(coord.pathToSegmentationData);
            seriesCount++;
        }
    }
    if (seriesCount == 0) {
        throw new FormatException("No image data found...");
    }
    store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    for (int s = 0; s < seriesNames.size(); s++) {
        String image_id = MetadataTools.createLSID("Image", s);
        store.setImageName(seriesNames.get(s), s);
        String plate_id = MetadataTools.createLSID("Plate", 0);
        store.setPlateID(plate_id, 0);
        store.setPlateName(seriesPlate.get(s), 0);
        String well_id = MetadataTools.createLSID("Well", 0);
        store.setWellID(well_id, 0, 0);
        String cellh5WellCoord = seriesWell.get(s);
        String wellRowLetter = cellh5WellCoord.substring(0, 1);
        String wellColNumber = cellh5WellCoord.substring(1);
        int wellRowLetterIndex = "ABCDEFGHIJKLMNOP".indexOf(wellRowLetter);
        int wellColNumberIndex = -1;
        try {
            wellColNumberIndex = Integer.parseInt(wellColNumber);
        } catch (NumberFormatException e) {
        // 
        }
        if (wellRowLetterIndex > -1 && wellColNumberIndex > 0) {
            store.setWellRow(new NonNegativeInteger(wellRowLetterIndex), 0, 0);
            store.setWellColumn(new NonNegativeInteger(wellColNumberIndex - 1), 0, 0);
        } else {
            store.setWellRow(new NonNegativeInteger(0), 0, 0);
            store.setWellColumn(new NonNegativeInteger(0), 0, 0);
        }
        store.setWellExternalIdentifier(cellh5WellCoord, 0, 0);
        String site_id = MetadataTools.createLSID("WellSample", 0);
        store.setWellSampleID(site_id, 0, 0, 0);
        store.setWellSampleIndex(NonNegativeInteger.valueOf(seriesSite.get(s)), 0, 0, 0);
        store.setWellSampleImageRef(image_id, 0, 0, 0);
    }
    setSeries(0);
    parseCellObjects();
}

Example 88 with CoreMetadata

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

the class CellSensReader method parseETSFile.

private void parseETSFile(String file, int s) throws FormatException, IOException {
    fileMap.put(core.size() - 1, file);
    RandomAccessInputStream etsFile = new RandomAccessInputStream(file);
    etsFile.order(true);
    CoreMetadata ms = core.get(getCoreIndex());
    // read the volume header
    String magic = etsFile.readString(4).trim();
    if (!magic.equals("SIS")) {
        throw new FormatException("Unknown magic bytes: " + magic);
    }
    int headerSize = etsFile.readInt();
    int version = etsFile.readInt();
    nDimensions.add(etsFile.readInt());
    long additionalHeaderOffset = etsFile.readLong();
    int additionalHeaderSize = etsFile.readInt();
    // reserved
    etsFile.skipBytes(4);
    long usedChunkOffset = etsFile.readLong();
    int nUsedChunks = etsFile.readInt();
    // reserved
    etsFile.skipBytes(4);
    // read the additional header
    etsFile.seek(additionalHeaderOffset);
    String moreMagic = etsFile.readString(4).trim();
    if (!moreMagic.equals("ETS")) {
        throw new FormatException("Unknown magic bytes: " + moreMagic);
    }
    // extra version number
    etsFile.skipBytes(4);
    int pixelType = etsFile.readInt();
    ms.sizeC = etsFile.readInt();
    int colorspace = etsFile.readInt();
    compressionType.add(etsFile.readInt());
    int compressionQuality = etsFile.readInt();
    tileX.add(etsFile.readInt());
    tileY.add(etsFile.readInt());
    int tileZ = etsFile.readInt();
    // pixel info hints
    etsFile.skipBytes(4 * 17);
    byte[] color = new byte[ms.sizeC * FormatTools.getBytesPerPixel(convertPixelType(pixelType))];
    etsFile.read(color);
    backgroundColor.put(getCoreIndex(), color);
    // background color
    etsFile.skipBytes(4 * 10 - color.length);
    // component order
    etsFile.skipBytes(4);
    boolean usePyramid = etsFile.readInt() != 0;
    ms.rgb = ms.sizeC > 1;
    // read the used chunks
    etsFile.seek(usedChunkOffset);
    tileOffsets.add(new Long[nUsedChunks]);
    ArrayList<TileCoordinate> tmpTiles = new ArrayList<TileCoordinate>();
    for (int chunk = 0; chunk < nUsedChunks; chunk++) {
        etsFile.skipBytes(4);
        int dimensions = nDimensions.get(nDimensions.size() - 1);
        TileCoordinate t = new TileCoordinate(dimensions);
        for (int i = 0; i < dimensions; i++) {
            t.coordinate[i] = etsFile.readInt();
        }
        tileOffsets.get(tileOffsets.size() - 1)[chunk] = etsFile.readLong();
        int nBytes = etsFile.readInt();
        etsFile.skipBytes(4);
        tmpTiles.add(t);
    }
    int maxResolution = 0;
    if (usePyramid) {
        for (TileCoordinate t : tmpTiles) {
            if (t.coordinate[t.coordinate.length - 1] > maxResolution) {
                maxResolution = t.coordinate[t.coordinate.length - 1];
            }
        }
    }
    maxResolution++;
    int[] maxX = new int[maxResolution];
    int[] maxY = new int[maxResolution];
    int[] maxZ = new int[maxResolution];
    int[] maxC = new int[maxResolution];
    int[] maxT = new int[maxResolution];
    HashMap<String, Integer> dimOrder = pyramids.get(s).dimensionOrdering;
    for (TileCoordinate t : tmpTiles) {
        int resolution = usePyramid ? t.coordinate[t.coordinate.length - 1] : 0;
        Integer tv = dimOrder.get("T");
        Integer zv = dimOrder.get("Z");
        Integer cv = dimOrder.get("C");
        int tIndex = tv == null ? -1 : tv + 2;
        int zIndex = zv == null ? -1 : zv + 2;
        int cIndex = cv == null ? -1 : cv + 2;
        if (usePyramid && tIndex == t.coordinate.length - 1) {
            tv = null;
            tIndex = -1;
        }
        if (usePyramid && zIndex == t.coordinate.length - 1) {
            zv = null;
            zIndex = -1;
        }
        int upperLimit = usePyramid ? t.coordinate.length - 1 : t.coordinate.length;
        if ((tIndex < 0 || tIndex >= upperLimit) && (zIndex < 0 || zIndex >= upperLimit) && (cIndex < 0 || cIndex >= upperLimit)) {
            tIndex--;
            zIndex--;
            cIndex--;
            if (dimOrder.containsKey("T")) {
                dimOrder.put("T", tIndex - 2);
            }
            if (dimOrder.containsKey("Z")) {
                dimOrder.put("Z", zIndex - 2);
            }
            if (dimOrder.containsKey("C")) {
                dimOrder.put("C", cIndex - 2);
            }
        }
        if (tv == null && zv == null) {
            if (t.coordinate.length > 4 && cv == null) {
                cIndex = 2;
                dimOrder.put("C", cIndex - 2);
            }
            if (t.coordinate.length > 4) {
                if (cv == null) {
                    tIndex = 3;
                } else {
                    tIndex = cIndex + 2;
                }
                if (tIndex < t.coordinate.length) {
                    dimOrder.put("T", tIndex - 2);
                } else {
                    tIndex = -1;
                }
            }
            if (t.coordinate.length > 5) {
                if (cv == null) {
                    zIndex = 4;
                } else {
                    zIndex = cIndex + 1;
                }
                if (zIndex < t.coordinate.length) {
                    dimOrder.put("Z", zIndex - 2);
                } else {
                    zIndex = -1;
                }
            }
        }
        if (t.coordinate[0] > maxX[resolution]) {
            maxX[resolution] = t.coordinate[0];
        }
        if (t.coordinate[1] > maxY[resolution]) {
            maxY[resolution] = t.coordinate[1];
        }
        if (tIndex >= 0 && t.coordinate[tIndex] > maxT[resolution]) {
            maxT[resolution] = t.coordinate[tIndex];
        }
        if (zIndex >= 0 && t.coordinate[zIndex] > maxZ[resolution]) {
            maxZ[resolution] = t.coordinate[zIndex];
        }
        if (cIndex >= 0 && t.coordinate[cIndex] > maxC[resolution]) {
            maxC[resolution] = t.coordinate[cIndex];
        }
    }
    if (pyramids.get(s).width != null) {
        ms.sizeX = pyramids.get(s).width;
    }
    if (pyramids.get(s).height != null) {
        ms.sizeY = pyramids.get(s).height;
    }
    ms.sizeZ = maxZ[0] + 1;
    if (maxC[0] > 0) {
        ms.sizeC *= (maxC[0] + 1);
    }
    ms.sizeT = maxT[0] + 1;
    if (ms.sizeZ == 0) {
        ms.sizeZ = 1;
    }
    ms.imageCount = ms.sizeZ * ms.sizeT;
    if (maxC[0] > 0) {
        ms.imageCount *= (maxC[0] + 1);
    }
    if (maxY[0] >= 1) {
        rows.add(maxY[0] + 1);
    } else {
        rows.add(1);
    }
    if (maxX[0] >= 1) {
        cols.add(maxX[0] + 1);
    } else {
        cols.add(1);
    }
    ArrayList<TileCoordinate> map = new ArrayList<TileCoordinate>();
    for (int i = 0; i < tmpTiles.size(); i++) {
        map.add(tmpTiles.get(i));
    }
    tileMap.add(map);
    ms.pixelType = convertPixelType(pixelType);
    if (usePyramid) {
        int finalResolution = 1;
        int initialCoreSize = core.size();
        for (int i = 1; i < maxResolution; i++) {
            CoreMetadata newResolution = new CoreMetadata(ms);
            int previousX = core.get(core.size() - 1).sizeX;
            int previousY = core.get(core.size() - 1).sizeY;
            int maxSizeX = tileX.get(tileX.size() - 1) * (maxX[i] < 1 ? 1 : maxX[i] + 1);
            int maxSizeY = tileY.get(tileY.size() - 1) * (maxY[i] < 1 ? 1 : maxY[i] + 1);
            newResolution.sizeX = previousX / 2;
            if (previousX % 2 == 1 && newResolution.sizeX < maxSizeX) {
                newResolution.sizeX++;
            } else if (newResolution.sizeX > maxSizeX) {
                newResolution.sizeX = maxSizeX;
            }
            newResolution.sizeY = previousY / 2;
            if (previousY % 2 == 1 && newResolution.sizeY < maxSizeY) {
                newResolution.sizeY++;
            } else if (newResolution.sizeY > maxSizeY) {
                newResolution.sizeY = maxSizeY;
            }
            newResolution.sizeZ = maxZ[i] + 1;
            if (maxC[i] > 0 && newResolution.sizeC != (maxC[i] + 1)) {
                newResolution.sizeC *= (maxC[i] + 1);
            }
            newResolution.sizeT = maxT[i] + 1;
            if (newResolution.sizeZ == 0) {
                newResolution.sizeZ = 1;
            }
            newResolution.imageCount = newResolution.sizeZ * newResolution.sizeT;
            if (maxC[i] > 0) {
                newResolution.imageCount *= (maxC[i] + 1);
            }
            newResolution.metadataComplete = true;
            newResolution.dimensionOrder = "XYCZT";
            core.add(newResolution);
            rows.add(maxY[i] >= 1 ? maxY[i] + 1 : 1);
            cols.add(maxX[i] >= 1 ? maxX[i] + 1 : 1);
            fileMap.put(core.size() - 1, file);
            finalResolution = core.size() - initialCoreSize + 1;
            tileX.add(tileX.get(tileX.size() - 1));
            tileY.add(tileY.get(tileY.size() - 1));
            compressionType.add(compressionType.get(compressionType.size() - 1));
            tileMap.add(map);
            nDimensions.add(nDimensions.get(nDimensions.size() - 1));
            tileOffsets.add(tileOffsets.get(tileOffsets.size() - 1));
            backgroundColor.put(core.size() - 1, color);
        }
        ms.resolutionCount = finalResolution;
    }
    etsFile.close();
}

Example 89 with CoreMetadata

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

the class AIMReader 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);
    m.littleEndian = true;
    in.order(isLittleEndian());
    // check for newer version of AIM format with wider offsets
    String version = in.readString(16);
    boolean widerOffsets = version.startsWith("AIMDATA_V030");
    if (widerOffsets) {
        in.seek(96);
        m.sizeX = (int) in.readLong();
        m.sizeY = (int) in.readLong();
        m.sizeZ = (int) in.readLong();
        in.seek(280);
    } else {
        in.seek(56);
        m.sizeX = in.readInt();
        m.sizeY = in.readInt();
        m.sizeZ = in.readInt();
        in.seek(160);
    }
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = getSizeZ();
    m.pixelType = FormatTools.INT16;
    m.dimensionOrder = "XYZCT";
    String processingLog = in.readCString();
    pixelOffset = in.getFilePointer();
    String date = null;
    Double xSize = null, xLength = null;
    Double ySize = null, yLength = null;
    Double zSize = null, zLength = null;
    String[] lines = processingLog.split("\n");
    for (String line : lines) {
        line = line.trim();
        int split = line.indexOf("  ");
        if (split > 0) {
            String key = line.substring(0, split).trim();
            String value = line.substring(split).trim();
            addGlobalMeta(key, value);
            if (key.equals("Original Creation-Date")) {
                date = DateTools.formatDate(value, "dd-MMM-yyyy HH:mm:ss", ".");
            } else if (key.equals("Orig-ISQ-Dim-p")) {
                String[] tokens = value.split(" ");
                for (String token : tokens) {
                    token = token.trim();
                    if (token.length() > 0) {
                        if (xSize == null) {
                            xSize = new Double(token);
                        } else if (ySize == null) {
                            ySize = new Double(token);
                        } else if (zSize == null) {
                            zSize = new Double(token);
                        }
                    }
                }
            } else if (key.equals("Orig-ISQ-Dim-um")) {
                String[] tokens = value.split(" ");
                for (String token : tokens) {
                    token = token.trim();
                    if (token.length() > 0) {
                        if (xLength == null) {
                            xLength = new Double(token);
                        } else if (yLength == null) {
                            yLength = new Double(token);
                        } else if (zLength == null) {
                            zLength = new Double(token);
                        }
                    }
                }
            }
        }
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (xSize != null && xLength != null) {
            Double size = xLength / xSize;
            Length physicalSize = FormatTools.getPhysicalSizeX(size);
            if (physicalSize != null) {
                store.setPixelsPhysicalSizeX(physicalSize, 0);
            }
        }
        if (ySize != null && yLength != null) {
            Double size = yLength / ySize;
            Length physicalSize = FormatTools.getPhysicalSizeY(size);
            if (physicalSize != null) {
                store.setPixelsPhysicalSizeY(physicalSize, 0);
            }
        }
        if (zSize != null && zLength != null) {
            Double size = zLength / zSize;
            Length physicalSize = FormatTools.getPhysicalSizeZ(size);
            if (physicalSize != null) {
                store.setPixelsPhysicalSizeZ(physicalSize, 0);
            }
        }
    }
}

Example 90 with CoreMetadata

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

the class ARFReader 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);
    // parse file header
    LOGGER.info("Reading file header");
    byte endian1 = in.readByte();
    byte endian2 = in.readByte();
    boolean little;
    if (endian1 == 1 && endian2 == 0)
        little = true;
    else if (endian1 == 0 && endian2 == 1)
        little = false;
    else
        throw new FormatException("Undefined endianness");
    in.order(little);
    // 'AR' signature
    in.skipBytes(2);
    int version = in.readUnsignedShort();
    int width = in.readUnsignedShort();
    int height = in.readUnsignedShort();
    int bitsPerPixel = in.readUnsignedShort();
    int numImages = version == 2 ? in.readUnsignedShort() : 1;
    // NB: The next 510 bytes are unused 'application dependent' data,
    // followed by raw image data with no padding.
    // populate core metadata
    CoreMetadata m = core.get(0);
    m.sizeX = width;
    m.sizeY = height;
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = numImages;
    int bpp = bitsPerPixel / 8;
    if ((bitsPerPixel % 8) != 0)
        bpp++;
    m.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
    m.bitsPerPixel = bitsPerPixel;
    m.imageCount = numImages;
    m.dimensionOrder = "XYCZT";
    m.orderCertain = true;
    m.littleEndian = little;
    m.rgb = false;
    m.interleaved = false;
    m.indexed = false;
    m.metadataComplete = true;
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // populate original metadata
        addGlobalMeta("Endianness", little ? "little" : "big");
        addGlobalMeta("Version", version);
        addGlobalMeta("Width", width);
        addGlobalMeta("Height", height);
        addGlobalMeta("Bits per pixel", bitsPerPixel);
        addGlobalMeta("Image count", numImages);
    }
    // populate OME metadata
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}