Examples with MetadataStore loci.formats.meta.MetadataStore used on opensource projects

Example 56 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class FEIReader 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);
    in.order(true);
    CoreMetadata m = core.get(0);
    LOGGER.info("Reading file header");
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        in.skipBytes(44);
        float magnification = in.readFloat();
        float kV = in.readFloat() / 1000;
        float wd = in.readFloat();
        in.skipBytes(12);
        float spot = in.readFloat();
        addGlobalMeta("Magnification", magnification);
        addGlobalMeta("kV", kV);
        addGlobalMeta("Working distance", wd);
        addGlobalMeta("Spot", spot);
    }
    in.seek(514);
    m.sizeX = in.readShort() - INVALID_PIXELS;
    m.sizeY = in.readShort();
    in.skipBytes(4);
    headerSize = in.readShort();
    // always one grayscale plane per file
    m.sizeZ = 1;
    m.sizeC = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.littleEndian = true;
    m.pixelType = FormatTools.UINT8;
    m.rgb = false;
    m.indexed = false;
    m.interleaved = false;
    m.dimensionOrder = "XYCZT";
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 57 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class FV1000Reader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    parser.setCommentDelimiter(null);
    isOIB = checkSuffix(id, OIB_SUFFIX);
    if (isOIB) {
        initPOIService();
    }
    // mappedOIF is used to distinguish between datasets that are being read
    // directly (e.g. using ImageJ or showinf), and datasets that are being
    // imported through omebf. In the latter case, the necessary directory
    // structure is not preserved (only relative file names are stored in
    // OMEIS), so we will need to use slightly different logic to build the
    // list of associated files.
    boolean mappedOIF = !isOIB && !new File(id).getAbsoluteFile().exists();
    wavelengths = new ArrayList<Double>();
    illuminations = new ArrayList<String>();
    channels = new ArrayList<ChannelData>();
    planes = new ArrayList<PlaneData>();
    String oifName = null;
    if (isOIB) {
        oifName = mapOIBFiles();
    } else {
        // make sure we have the OIF file, not a TIFF
        if (!checkSuffix(id, OIF_SUFFIX)) {
            currentId = findOIFFile(id);
            initFile(currentId);
        }
        oifName = currentId;
    }
    String oifPath = new Location(oifName).getAbsoluteFile().getAbsolutePath();
    if (mappedOIF) {
        oifPath = oifName.substring(0, oifName.lastIndexOf(File.separator) + 1);
    }
    String path = isOIB ? "" : oifPath.substring(0, oifPath.lastIndexOf(File.separator) + 1);
    try {
        RandomAccessInputStream s = getFile(oifName);
        s.close();
    } catch (IOException e) {
        oifName = oifName.replaceAll(".oif", ".OIF");
    }
    // parse key/value pairs from the OIF file
    code = new String[NUM_DIMENSIONS];
    size = new String[NUM_DIMENSIONS];
    pixelSize = new Double[NUM_DIMENSIONS];
    previewNames = new ArrayList<String>();
    SortedMap<Integer, String> previewFileNames = new TreeMap<Integer, String>();
    boolean laserEnabled = true;
    IniList f = getIniFile(oifName);
    IniTable saveInfo = f.getTable("ProfileSaveInfo");
    String[] saveKeys = saveInfo.keySet().toArray(new String[saveInfo.size()]);
    for (String key : saveKeys) {
        String value = saveInfo.get(key).toString();
        value = sanitizeValue(value).trim();
        if (key.startsWith("IniFileName") && key.indexOf("Thumb") == -1 && !isPreviewName(value)) {
            filenames.put(new Integer(key.substring(11)), value);
        } else if (key.startsWith("RoiFileName") && key.indexOf("Thumb") == -1 && !isPreviewName(value)) {
            try {
                roiFilenames.put(new Integer(key.substring(11)), value);
            } catch (NumberFormatException e) {
            }
        } else if (key.equals("PtyFileNameS"))
            ptyStart = value;
        else if (key.equals("PtyFileNameE"))
            ptyEnd = value;
        else if (key.equals("PtyFileNameT2"))
            ptyPattern = value;
        else if (key.indexOf("Thumb") != -1) {
            if (thumbId == null)
                thumbId = value.trim();
        } else if (key.startsWith("LutFileName")) {
            lutNames.add(path + value);
        } else if (isPreviewName(value)) {
            try {
                RandomAccessInputStream s = getFile(path + value.trim());
                if (s != null) {
                    s.close();
                    Integer previewIndex = getPreviewNameIndex(key);
                    if (previewIndex != null) {
                        previewFileNames.put(previewIndex, path + value.trim());
                    } else {
                        previewNames.add(path + value.trim());
                    }
                }
            } catch (FormatException e) {
                LOGGER.debug("Preview file not found", e);
            } catch (IOException e) {
                LOGGER.debug("Preview file not found", e);
            }
        }
    }
    // Store sorted list of preview names
    previewNames.addAll(previewFileNames.values());
    if (filenames.isEmpty())
        addPtyFiles();
    for (int i = 0; i < NUM_DIMENSIONS; i++) {
        IniTable commonParams = f.getTable("Axis " + i + " Parameters Common");
        code[i] = commonParams.get("AxisCode");
        size[i] = commonParams.get("MaxSize");
        double end = Double.parseDouble(commonParams.get("EndPosition"));
        double start = Double.parseDouble(commonParams.get("StartPosition"));
        pixelSize[i] = end - start;
    }
    IniTable referenceParams = f.getTable("Reference Image Parameter");
    imageDepth = Integer.parseInt(referenceParams.get("ImageDepth"));
    pixelSizeX = referenceParams.get("WidthConvertValue");
    pixelSizeY = referenceParams.get("HeightConvertValue");
    String ripValidBitCounts = referenceParams.get("ValidBitCounts");
    if (ripValidBitCounts != null) {
        validBits = Integer.parseInt(ripValidBitCounts);
    }
    int index = 0;
    IniTable laser = f.getTable("Laser " + index + " Parameters");
    while (laser != null) {
        laserEnabled = laser.get("Laser Enable").equals("1");
        if (laserEnabled) {
            wavelengths.add(new Double(laser.get("LaserWavelength")));
        }
        creationDate = laser.get("ImageCaputreDate");
        if (creationDate == null) {
            creationDate = laser.get("ImageCaptureDate");
        }
        index++;
        laser = f.getTable("Laser " + index + " Parameters");
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        index = 1;
        IniTable guiChannel = f.getTable("GUI Channel " + index + " Parameters");
        while (guiChannel != null) {
            ChannelData channel = new ChannelData();
            channel.gain = DataTools.parseDouble(guiChannel.get("AnalogPMTGain"));
            channel.voltage = DataTools.parseDouble(guiChannel.get("AnalogPMTVoltage"));
            channel.barrierFilter = channel.getFilter(guiChannel.get("BF Name"));
            channel.active = Integer.parseInt(guiChannel.get("CH Activate")) != 0;
            channel.name = guiChannel.get("CH Name");
            channel.dyeName = guiChannel.get("DyeName");
            channel.emissionFilter = channel.getFilter(guiChannel.get("EmissionDM Name"));
            channel.emWave = DataTools.parseDouble(guiChannel.get("EmissionWavelength"));
            channel.excitationFilter = channel.getFilter(guiChannel.get("ExcitationDM Name"));
            channel.exWave = DataTools.parseDouble(guiChannel.get("ExcitationWavelength"));
            channels.add(channel);
            index++;
            guiChannel = f.getTable("GUI Channel " + index + " Parameters");
        }
        index = 1;
        IniTable channel = f.getTable("Channel " + index + " Parameters");
        while (channel != null) {
            String illumination = channel.get("LightType");
            if (illumination != null)
                illumination = illumination.toLowerCase();
            if (illumination == null) {
            // Ignored
            } else if (illumination.indexOf("fluorescence") != -1) {
                illumination = "Epifluorescence";
            } else if (illumination.indexOf("transmitted") != -1) {
                illumination = "Transmitted";
            } else
                illumination = null;
            illuminations.add(illumination);
            index++;
            channel = f.getTable("Channel " + index + " Parameters");
        }
        HashMap<String, String> iniMap = f.flattenIntoHashMap();
        metadata.putAll(iniMap);
    }
    LOGGER.info("Initializing helper readers");
    if (previewNames.size() > 0) {
        final List<String> v = new ArrayList<String>();
        for (int i = 0; i < previewNames.size(); i++) {
            String ss = previewNames.get(i);
            ss = replaceExtension(ss, "pty", "tif");
            if (ss.endsWith(".tif"))
                v.add(ss);
        }
        previewNames = v;
        if (previewNames.size() > 0) {
            core.clear();
            core.add(new CoreMetadata());
            core.add(new CoreMetadata());
            IFDList ifds = null;
            CoreMetadata ms1 = core.get(1);
            for (String previewName : previewNames) {
                RandomAccessInputStream preview = getFile(previewName);
                TiffParser tp = new TiffParser(preview);
                ifds = tp.getIFDs();
                preview.close();
                tp = null;
                ms1.imageCount += ifds.size();
            }
            ms1.sizeX = (int) ifds.get(0).getImageWidth();
            ms1.sizeY = (int) ifds.get(0).getImageLength();
            ms1.sizeZ = 1;
            ms1.sizeT = 1;
            ms1.sizeC = ms1.imageCount;
            ms1.rgb = false;
            int bits = ifds.get(0).getBitsPerSample()[0];
            while ((bits % 8) != 0) bits++;
            bits /= 8;
            ms1.pixelType = FormatTools.pixelTypeFromBytes(bits, false, false);
            ms1.dimensionOrder = "XYCZT";
            ms1.indexed = false;
        }
    }
    CoreMetadata ms0 = core.get(0);
    ms0.imageCount = filenames.size();
    tiffs = new ArrayList<String>(getImageCount());
    thumbReader = new BMPReader();
    if (thumbId != null) {
        thumbId = replaceExtension(thumbId, "pty", "bmp");
        thumbId = sanitizeFile(thumbId, path);
    }
    LOGGER.info("Reading additional metadata");
    // open each INI file (.pty extension) and build list of TIFF files
    String tiffPath = null;
    ms0.dimensionOrder = "XY";
    final Map<String, String> values = new HashMap<String, String>();
    final List<String> baseKeys = new ArrayList<String>();
    for (int i = 0, ii = 0; ii < getImageCount(); i++, ii++) {
        String file = filenames.get(i);
        while (file == null) file = filenames.get(++i);
        file = sanitizeFile(file, path);
        if (file.indexOf(File.separator) != -1) {
            tiffPath = file.substring(0, file.lastIndexOf(File.separator));
        } else
            tiffPath = file;
        Location ptyFile = new Location(file);
        if (!isOIB && !ptyFile.exists()) {
            LOGGER.warn("Could not find .pty file ({}); guessing at the " + "corresponding TIFF file.", file);
            String tiff = replaceExtension(file, "pty", "tif");
            Location tiffFile = new Location(tiff);
            if (tiffFile.exists()) {
                tiffs.add(ii, tiffFile.getAbsolutePath());
                continue;
            } else {
                if (!tiffFile.getParentFile().exists()) {
                    String realOIFName = new Location(currentId).getName();
                    String basePath = tiffFile.getParentFile().getParent();
                    if (mappedOIF) {
                        tiffPath = basePath + File.separator + realOIFName + ".files";
                        ptyFile = new Location(tiffPath, ptyFile.getName());
                        file = ptyFile.getAbsolutePath();
                    } else {
                        Location newFile = new Location(basePath, realOIFName + ".files");
                        ptyFile = new Location(newFile, ptyFile.getName());
                        file = ptyFile.getAbsolutePath();
                        tiffPath = newFile.getAbsolutePath();
                    }
                }
            }
        } else if (!isOIB) {
            file = ptyFile.getAbsolutePath();
        }
        IniList pty = getIniFile(file);
        IniTable fileInfo = pty.getTable("File Info");
        file = sanitizeValue(fileInfo.get("DataName"));
        if (!isPreviewName(file)) {
            while (file.indexOf("GST") != -1) {
                file = removeGST(file);
            }
            if (isOIB) {
                file = tiffPath + File.separator + file;
            } else
                file = new Location(tiffPath, file).getAbsolutePath();
            file = replaceExtension(file, "pty", "tif");
            tiffs.add(ii, file);
        }
        PlaneData plane = new PlaneData();
        for (int dim = 0; dim < NUM_DIMENSIONS; dim++) {
            IniTable axis = pty.getTable("Axis " + dim + " Parameters");
            if (axis == null)
                break;
            boolean addAxis = Integer.parseInt(axis.get("Number")) > 1;
            if (dim == 2) {
                if (addAxis && getDimensionOrder().indexOf('C') == -1) {
                    ms0.dimensionOrder += 'C';
                }
            } else if (dim == 3) {
                if (addAxis && getDimensionOrder().indexOf('Z') == -1) {
                    ms0.dimensionOrder += 'Z';
                }
                final Double number = Double.valueOf(axis.get("AbsPositionValue"));
                plane.positionZ = new Length(number, UNITS.REFERENCEFRAME);
            } else if (dim == 4) {
                if (addAxis && getDimensionOrder().indexOf('T') == -1) {
                    ms0.dimensionOrder += 'T';
                }
                // divide by 1000, as the position is in milliseconds
                // and DeltaT is in seconds
                plane.deltaT = Double.parseDouble(axis.get("AbsPositionValue")) / 1000;
            } else if (dim == 7) {
                try {
                    String xPos = axis.get("AbsPositionValueX");
                    if (xPos != null) {
                        final Double number = Double.valueOf(xPos);
                        plane.positionX = new Length(number, UNITS.REFERENCEFRAME);
                    }
                } catch (NumberFormatException e) {
                }
                try {
                    String yPos = axis.get("AbsPositionValueY");
                    if (yPos != null) {
                        final Double number = Double.valueOf(yPos);
                        plane.positionY = new Length(number, UNITS.REFERENCEFRAME);
                    }
                } catch (NumberFormatException e) {
                }
            }
        }
        ms0.bitsPerPixel = validBits;
        planes.add(plane);
        IniTable acquisition = pty.getTable("Acquisition Parameters Common");
        if (acquisition != null) {
            magnification = acquisition.get("Magnification");
            lensNA = acquisition.get("ObjectiveLens NAValue");
            objectiveName = acquisition.get("ObjectiveLens Name");
            workingDistance = acquisition.get("ObjectiveLens WDValue");
            pinholeSize = acquisition.get("PinholeDiameter");
            String validBitCounts = acquisition.get("ValidBitCounts");
            if (validBitCounts != null) {
                ms0.bitsPerPixel = Integer.parseInt(validBitCounts);
            }
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            for (IniTable table : pty) {
                String[] keys = table.keySet().toArray(new String[table.size()]);
                for (String key : keys) {
                    values.put("Image " + ii + " : " + key, table.get(key));
                    if (!baseKeys.contains(key))
                        baseKeys.add(key);
                }
            }
        }
    }
    for (String key : baseKeys) {
        if (key.equals("DataName") || key.indexOf("FileName") >= 0)
            break;
        boolean equal = true;
        String first = values.get("Image 0 : " + key);
        for (int i = 1; i < getImageCount(); i++) {
            if (!first.equals(values.get("Image " + i + " : " + key))) {
                equal = false;
                break;
            }
        }
        if (equal) {
            addGlobalMeta(key, first);
        } else {
            for (int i = 0; i < getImageCount(); i++) {
                String k = "Image " + i + " : " + key;
                addGlobalMeta(k, values.get(k));
            }
        }
    }
    if (tiffs.size() != getImageCount()) {
        ms0.imageCount = tiffs.size();
    }
    usedFiles = new ArrayList<String>();
    if (tiffPath != null) {
        usedFiles.add(isOIB ? id : oifName);
        if (!isOIB) {
            Location dir = new Location(tiffPath);
            if (!mappedOIF && !dir.exists()) {
                throw new FormatException("Required directory " + tiffPath + " was not found.");
            }
            String[] list = mappedOIF ? Location.getIdMap().keySet().toArray(new String[0]) : dir.list(true);
            for (int i = 0; i < list.length; i++) {
                if (mappedOIF)
                    usedFiles.add(list[i]);
                else {
                    String p = new Location(tiffPath, list[i]).getAbsolutePath();
                    String check = p.toLowerCase();
                    if (!check.endsWith(".tif") && !check.endsWith(".pty") && !check.endsWith(".roi") && !check.endsWith(".lut") && !check.endsWith(".bmp")) {
                        continue;
                    }
                    usedFiles.add(p);
                }
            }
        }
    }
    LOGGER.info("Populating metadata");
    // calculate axis sizes
    int realChannels = 0;
    for (int i = 0; i < NUM_DIMENSIONS; i++) {
        int ss = Integer.parseInt(size[i]);
        if (pixelSize[i] == null)
            pixelSize[i] = 1.0;
        if (code[i].equals("X"))
            ms0.sizeX = ss;
        else if (code[i].equals("Y") && ss > 1)
            ms0.sizeY = ss;
        else if (code[i].equals("Z")) {
            if (getSizeY() == 0) {
                ms0.sizeY = ss;
            } else {
                ms0.sizeZ = ss;
                // Z size stored in nm
                pixelSizeZ = Math.abs((pixelSize[i].doubleValue() / (getSizeZ() - 1)) / 1000);
            }
        } else if (code[i].equals("T")) {
            if (getSizeY() == 0) {
                ms0.sizeY = ss;
            } else {
                ms0.sizeT = ss;
                pixelSizeT = Math.abs((pixelSize[i].doubleValue() / (getSizeT() - 1)) / 1000);
            }
        } else if (ss > 0) {
            if (getSizeC() == 0)
                ms0.sizeC = ss;
            else
                ms0.sizeC *= ss;
            if (code[i].equals("C"))
                realChannels = ss;
        }
    }
    if (getSizeZ() == 0)
        ms0.sizeZ = 1;
    if (getSizeC() == 0)
        ms0.sizeC = 1;
    if (getSizeT() == 0)
        ms0.sizeT = 1;
    if (getImageCount() == getSizeC() && getSizeY() == 1) {
        ms0.imageCount *= getSizeZ() * getSizeT();
    } else if (getImageCount() == getSizeC()) {
        ms0.sizeZ = 1;
        ms0.sizeT = 1;
    }
    if (getSizeZ() * getSizeT() * getSizeC() != getImageCount()) {
        int diff = (getSizeZ() * getSizeC() * getSizeT()) - getImageCount();
        if (diff == previewNames.size() || diff < 0) {
            diff /= getSizeC();
            if (getSizeT() > 1 && getSizeZ() == 1)
                ms0.sizeT -= diff;
            else if (getSizeZ() > 1 && getSizeT() == 1)
                ms0.sizeZ -= diff;
        } else
            ms0.imageCount += diff;
    }
    if (getSizeC() > 1 && getSizeZ() == 1 && getSizeT() == 1) {
        if (getDimensionOrder().indexOf('C') == -1)
            ms0.dimensionOrder += 'C';
    }
    if (getDimensionOrder().indexOf('Z') == -1)
        ms0.dimensionOrder += 'Z';
    if (getDimensionOrder().indexOf('C') == -1)
        ms0.dimensionOrder += 'C';
    if (getDimensionOrder().indexOf('T') == -1)
        ms0.dimensionOrder += 'T';
    ms0.pixelType = FormatTools.pixelTypeFromBytes(imageDepth, false, false);
    try {
        RandomAccessInputStream thumb = getFile(thumbId);
        byte[] b = new byte[(int) thumb.length()];
        thumb.read(b);
        thumb.close();
        Location.mapFile("thumbnail.bmp", new ByteArrayHandle(b));
        thumbReader.setId("thumbnail.bmp");
        for (int i = 0; i < getSeriesCount(); i++) {
            core.get(i).thumbSizeX = thumbReader.getSizeX();
            core.get(i).thumbSizeY = thumbReader.getSizeY();
        }
        thumbReader.close();
        Location.mapFile("thumbnail.bmp", null);
    } catch (IOException e) {
        LOGGER.debug("Could not read thumbnail", e);
    } catch (FormatException e) {
        LOGGER.debug("Could not read thumbnail", e);
    }
    // initialize lookup table
    lut = new short[getSizeC()][3][65536];
    byte[] buffer = new byte[65536 * 4];
    int count = (int) Math.min(getSizeC(), lutNames.size());
    for (int c = 0; c < count; c++) {
        Exception exc = null;
        try {
            RandomAccessInputStream stream = getFile(lutNames.get(c));
            stream.seek(stream.length() - 65536 * 4);
            stream.read(buffer);
            stream.close();
            for (int q = 0; q < buffer.length; q += 4) {
                lut[c][0][q / 4] = (short) ((buffer[q + 2] & 0xff) * 257);
                lut[c][1][q / 4] = (short) ((buffer[q + 1] & 0xff) * 257);
                lut[c][2][q / 4] = (short) ((buffer[q] & 0xff) * 257);
            }
        } catch (IOException e) {
            exc = e;
        } catch (FormatException e) {
            exc = e;
        }
        if (exc != null) {
            LOGGER.debug("Could not read LUT", exc);
            lut = null;
            break;
        }
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        CoreMetadata ms = core.get(i);
        ms.rgb = false;
        ms.littleEndian = true;
        ms.interleaved = false;
        ms.metadataComplete = true;
        ms.indexed = lut != null;
        ms.falseColor = true;
        int nFiles = i == 0 ? tiffs.size() : previewNames.size();
        for (int file = 0; file < nFiles; file++) {
            RandomAccessInputStream plane = getFile(i == 0 ? tiffs.get(file) : previewNames.get(file));
            if (plane == null) {
                ifds.add(null);
                continue;
            }
            try {
                TiffParser tp = new TiffParser(plane);
                IFDList ifd = tp.getIFDs();
                ifds.add(ifd);
            } finally {
                plane.close();
            }
        }
    }
    // populate MetadataStore
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    if (creationDate != null) {
        creationDate = creationDate.replaceAll("'", "");
        creationDate = DateTools.formatDate(creationDate, DATE_FORMAT);
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        // populate Image data
        store.setImageName("Series " + (i + 1), i);
        if (creationDate != null)
            store.setImageAcquisitionDate(new Timestamp(creationDate), i);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        populateMetadataStore(store, path);
    }
}

Example 58 with MetadataStore

use of loci.formats.meta.MetadataStore in project bioformats by openmicroscopy.

the class DNGReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    super.initFile(id);
    original = ifds.get(0);
    if (cfaPattern != null) {
        original.putIFDValue(IFD.COLOR_MAP, (int[]) cfaPattern);
    }
    ifds.set(0, original);
    CoreMetadata m = core.get(0);
    m.imageCount = 1;
    m.sizeT = 1;
    if (ifds.get(0).getSamplesPerPixel() == 1) {
        m.interleaved = true;
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this);
}

Example 59 with MetadataStore

use of loci.formats.meta.MetadataStore 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 60 with MetadataStore

use of loci.formats.meta.MetadataStore 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);
    }
}