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

Example 41 with Length

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

the class DeltavisionReader method parseLogFile.

/**
 * Extract metadata from associated log file, if it exists.
 */
private boolean parseLogFile(MetadataStore store) throws FormatException, IOException {
    if (logFile == null || !new Location(logFile).exists()) {
        logFile = null;
        return false;
    }
    LOGGER.info("Parsing log file");
    String[] lines = DataTools.readFile(logFile).split("[\r\n]");
    String key, value = "", prefix = "";
    int currentImage = 0;
    List<String> channelNames = new ArrayList<String>();
    List<Double> filters = new ArrayList<Double>();
    for (String line : lines) {
        int colon = line.indexOf(':');
        if (colon >= 0 && colon < line.length() - 1 && !line.startsWith("Created")) {
            key = line.substring(0, colon).trim();
            value = line.substring(colon + 1).trim();
            if (value.equals("") && !key.equals(""))
                prefix = key;
            addGlobalMeta(prefix + " " + key, value);
            // Objective properties
            if (key.equals("Objective")) {
                // assume first word is the manufacturer's name
                int space = value.indexOf(' ');
                if (space != -1) {
                    String manufacturer = value.substring(0, space);
                    String extra = value.substring(space + 1);
                    String[] tokens = extra.split(",");
                    store.setObjectiveManufacturer(manufacturer, 0, 0);
                    String magnification = "", na = "";
                    if (tokens.length >= 1) {
                        int end = tokens[0].indexOf('X');
                        if (end > 0)
                            magnification = tokens[0].substring(0, end);
                        int start = tokens[0].indexOf('/');
                        if (start >= 0)
                            na = tokens[0].substring(start + 1);
                    }
                    try {
                        Double mag = new Double(magnification);
                        store.setObjectiveNominalMagnification(mag, 0, 0);
                    } catch (NumberFormatException e) {
                        LOGGER.warn("Could not parse magnification '{}'", magnification);
                    }
                    try {
                        store.setObjectiveLensNA(new Double(na), 0, 0);
                    } catch (NumberFormatException e) {
                        LOGGER.warn("Could not parse N.A. '{}'", na);
                    }
                    if (tokens.length >= 2) {
                        store.setObjectiveCorrection(getCorrection(tokens[1]), 0, 0);
                    }
                    // TODO:  Token #2 is the microscope model name.
                    if (tokens.length > 3)
                        store.setObjectiveModel(tokens[3], 0, 0);
                }
            } else if (key.equalsIgnoreCase("Lens ID")) {
                if (value.indexOf(',') != -1) {
                    value = value.substring(0, value.indexOf(','));
                }
                if (value.indexOf(' ') != -1) {
                    value = value.substring(value.indexOf(' ') + 1);
                }
                if (!value.equals("null")) {
                    String objectiveID = "Objective:" + value;
                    store.setObjectiveID(objectiveID, 0, 0);
                    for (int series = 0; series < getSeriesCount(); series++) {
                        store.setObjectiveSettingsID(objectiveID, series);
                    }
                    store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
                    store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
                }
            } else // Image properties
            if (key.equals("Pixel Size")) {
                String[] pixelSizes = value.split(" ");
                for (int q = 0; q < pixelSizes.length; q++) {
                    Double size = null;
                    try {
                        size = new Double(pixelSizes[q].trim());
                    } catch (NumberFormatException e) {
                        LOGGER.warn("Could not parse pixel size '{}'", pixelSizes[q].trim());
                    }
                    if (q == 0) {
                        Length sizeX = FormatTools.getPhysicalSizeX(size);
                        if (sizeX != null) {
                            for (int series = 0; series < getSeriesCount(); series++) {
                                store.setPixelsPhysicalSizeX(sizeX, series);
                            }
                        }
                    }
                    if (q == 1) {
                        Length sizeY = FormatTools.getPhysicalSizeY(size);
                        if (sizeY != null) {
                            for (int series = 0; series < getSeriesCount(); series++) {
                                store.setPixelsPhysicalSizeY(sizeY, series);
                            }
                        }
                    }
                    if (q == 2) {
                        Length sizeZ = FormatTools.getPhysicalSizeZ(size);
                        if (sizeZ != null) {
                            for (int series = 0; series < getSeriesCount(); series++) {
                                store.setPixelsPhysicalSizeZ(sizeZ, series);
                            }
                        }
                    }
                }
            } else if (key.equals("Binning")) {
                store.setDetectorType(getDetectorType("Other"), 0, 0);
                String detectorID = MetadataTools.createLSID("Detector", 0, 0);
                store.setDetectorID(detectorID, 0, 0);
                for (int series = 0; series < getSeriesCount(); series++) {
                    for (int c = 0; c < getSizeC(); c++) {
                        store.setDetectorSettingsBinning(getBinning(value), series, c);
                        // link DetectorSettings to an actual Detector
                        store.setDetectorSettingsID(detectorID, series, c);
                    }
                }
            } else // Camera properties
            if (key.equals("Type")) {
                store.setDetectorModel(value, 0, 0);
            } else if (key.equals("Gain")) {
                value = value.replaceAll("X", "");
                try {
                    String detectorID = MetadataTools.createLSID("Detector", 0, 0);
                    store.setDetectorID(detectorID, 0, 0);
                    for (int series = 0; series < getSeriesCount(); series++) {
                        for (int c = 0; c < getSizeC(); c++) {
                            store.setDetectorSettingsGain(new Double(value), series, c);
                            store.setDetectorSettingsID(detectorID, series, c);
                        }
                    }
                } catch (NumberFormatException e) {
                    LOGGER.warn("Could not parse gain '{}'", value);
                }
            } else if (key.equals("Speed")) {
                value = value.replaceAll("KHz", "");
                try {
                    double khz = Double.parseDouble(value);
                    String detectorID = MetadataTools.createLSID("Detector", 0, 0);
                    store.setDetectorID(detectorID, 0, 0);
                    for (int series = 0; series < getSeriesCount(); series++) {
                        for (int c = 0; c < getSizeC(); c++) {
                            store.setDetectorSettingsReadOutRate(new Frequency(khz, UNITS.KILOHERTZ), series, c);
                            store.setDetectorSettingsID(detectorID, series, c);
                        }
                    }
                } catch (NumberFormatException e) {
                    LOGGER.warn("Could not parse read-out rate '{}'", value);
                }
            } else if (key.equals("Temp Setting")) {
                value = value.replaceAll("C", "").trim();
                try {
                // this is the camera temperature, not the environment temperature
                // store.setImagingEnvironmentTemperature(value, 0);
                } catch (NumberFormatException e) {
                    LOGGER.warn("Could not parse temperature '{}'", value);
                }
            } else // Plane properties
            if (key.equals("EM filter")) {
                if (!channelNames.contains(value)) {
                    channelNames.add(value);
                }
            } else if (key.equals("ND filter")) {
                value = value.replaceAll("%", "");
                try {
                    double nd = Double.parseDouble(value) / 100;
                    if (!filters.contains(nd)) {
                        filters.add(nd);
                    }
                } catch (NumberFormatException exc) {
                    // so no need to log it explicitly
                    if (!value.equals("BLANK")) {
                        LOGGER.warn("Could not parse ND filter '{}'", value);
                    }
                    filters.add(null);
                } catch (IllegalArgumentException e) {
                    LOGGER.debug("", e);
                }
            } else if (key.equals("Stage coordinates")) {
                if (value.length() > 1) {
                    value = value.substring(1, value.length() - 1);
                }
                String[] coords = value.split(",");
                for (int i = 0; i < coords.length; i++) {
                    Length p = null;
                    try {
                        final Double number = Double.valueOf(coords[i]);
                        p = new Length(number, UNITS.REFERENCEFRAME);
                    } catch (NumberFormatException e) {
                        LOGGER.warn("Could not parse stage coordinate '{}'", coords[i]);
                    }
                    if (currentImage < getImageCount() && getSeriesCount() == 1) {
                        // from the extended header.
                        if (i == 0) {
                            store.setPlanePositionX(p, 0, currentImage);
                        }
                        if (i == 1) {
                            store.setPlanePositionY(p, 0, currentImage);
                        }
                        if (i == 2) {
                            store.setPlanePositionZ(p, 0, currentImage);
                        }
                    }
                }
                currentImage++;
            }
        } else if (line.startsWith("Image"))
            prefix = line;
        else if (line.startsWith("Created")) {
            if (line.length() > 8)
                line = line.substring(8).trim();
            String date = DateTools.formatDate(line, DATE_FORMATS);
            if (date != null) {
                for (int series = 0; series < getSeriesCount(); series++) {
                    store.setImageAcquisitionDate(new Timestamp(date), series);
                }
            } else {
                LOGGER.warn("Could not parse date '{}'", line);
            }
        } else if (line.startsWith("#KEY")) {
            line = line.substring(line.indexOf(" ")).trim();
            int split = line.indexOf(":");
            if (split < 0) {
                split = line.indexOf(" ");
            }
            key = line.substring(0, split).trim();
            value = line.substring(split + 1).trim();
            addGlobalMeta(key, value);
        } else if (line.endsWith(":")) {
            prefix = line.substring(0, line.length() - 1);
        } else if (!line.startsWith("#") && !line.replace("-", "").isEmpty() && !prefix.isEmpty()) {
            addGlobalMetaList(prefix, line);
        }
    }
    for (int series = 0; series < getSeriesCount(); series++) {
        for (int c = 0; c < getEffectiveSizeC(); c++) {
            if (c < channelNames.size()) {
                store.setChannelName(channelNames.get(c), series, c);
            }
            if (c < filters.size()) {
                ndFilters[c] = filters.get(c);
            }
        }
    }
    return true;
}

Example 42 with Length

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

the class FV1000Reader method populateMetadataStore.

private void populateMetadataStore(MetadataStore store, String path) throws FormatException, IOException {
    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);
    for (int i = 0; i < getSeriesCount(); i++) {
        // link Instrument and Image
        store.setImageInstrumentRef(instrumentID, i);
        if (pixelSizeX != null) {
            Double sizeX = new Double(pixelSizeX);
            Length size = FormatTools.getPhysicalSizeX(sizeX);
            if (size != null) {
                store.setPixelsPhysicalSizeX(size, i);
            }
        }
        if (pixelSizeY != null) {
            Double sizeY = new Double(pixelSizeY);
            Length size = FormatTools.getPhysicalSizeY(sizeY);
            if (size != null) {
                store.setPixelsPhysicalSizeY(size, i);
            }
        }
        if (pixelSizeZ == Double.NEGATIVE_INFINITY || pixelSizeZ == Double.POSITIVE_INFINITY || getSizeZ() == 1) {
            pixelSizeZ = 1d;
        }
        if (pixelSizeT == Double.NEGATIVE_INFINITY || pixelSizeT == Double.POSITIVE_INFINITY || getSizeT() == 1) {
            pixelSizeT = 1d;
        }
        Length sizeZ = FormatTools.getPhysicalSizeZ(pixelSizeZ);
        if (sizeZ != null) {
            store.setPixelsPhysicalSizeZ(sizeZ, i);
        }
        store.setPixelsTimeIncrement(new Time(pixelSizeT, UNITS.SECOND), i);
        for (int p = 0; p < core.get(i).imageCount; p++) {
            store.setPlaneDeltaT(new Time(pixelSizeT * p, UNITS.SECOND), i, p);
        }
        for (int c = 0; c < core.get(i).sizeC; c++) {
            if (c < illuminations.size()) {
                store.setChannelIlluminationType(getIlluminationType(illuminations.get(c)), i, c);
            }
        }
    }
    int channelIndex = 0;
    for (ChannelData channel : channels) {
        if (!channel.active)
            continue;
        if (channelIndex >= getEffectiveSizeC())
            break;
        // populate Detector data
        String detectorID = MetadataTools.createLSID("Detector", 0, channelIndex);
        store.setDetectorID(detectorID, 0, channelIndex);
        store.setDetectorSettingsID(detectorID, 0, channelIndex);
        store.setDetectorGain(channel.gain, 0, channelIndex);
        ElectricPotential theVoltage = FormatTools.createElectricPotential(channel.voltage, UNITS.VOLT);
        if (theVoltage != null) {
            store.setDetectorVoltage(theVoltage, 0, channelIndex);
        }
        store.setDetectorType(getDetectorType("PMT"), 0, channelIndex);
        // populate LogicalChannel data
        store.setChannelName(channel.name, 0, channelIndex);
        String lightSourceID = MetadataTools.createLSID("LightSource", 0, channelIndex);
        store.setChannelLightSourceSettingsID(lightSourceID, 0, channelIndex);
        Length wavelength = FormatTools.getWavelength(channel.exWave);
        Length emission = FormatTools.getEmissionWavelength(channel.emWave);
        Length excitation = FormatTools.getExcitationWavelength(channel.exWave);
        if (emission != null) {
            store.setChannelEmissionWavelength(emission, 0, channelIndex);
        }
        if (excitation != null) {
            store.setChannelExcitationWavelength(excitation, 0, channelIndex);
        }
        if (wavelength != null) {
            store.setChannelLightSourceSettingsWavelength(wavelength, 0, channelIndex);
        }
        // populate Filter data
        if (channel.barrierFilter != null) {
            String filterID = MetadataTools.createLSID("Filter", 0, channelIndex);
            store.setFilterID(filterID, 0, channelIndex);
            store.setFilterModel(channel.barrierFilter, 0, channelIndex);
            if (channel.barrierFilter.indexOf('-') != -1) {
                String[] emValues = channel.barrierFilter.split("-");
                for (int i = 0; i < emValues.length; i++) {
                    emValues[i] = emValues[i].replaceAll("\\D", "");
                }
                try {
                    Double cutIn = new Double(emValues[0]);
                    Double cutOut = new Double(emValues[1]);
                    Length in = FormatTools.getCutIn(cutIn);
                    Length out = FormatTools.getCutOut(cutOut);
                    if (in != null) {
                        store.setTransmittanceRangeCutIn(in, 0, channelIndex);
                    }
                    if (out != null) {
                        store.setTransmittanceRangeCutOut(out, 0, channelIndex);
                    }
                } catch (NumberFormatException e) {
                }
            }
            store.setLightPathEmissionFilterRef(filterID, 0, channelIndex, 0);
        }
        // populate FilterSet data
        int emIndex = channelIndex * 2;
        int exIndex = channelIndex * 2 + 1;
        String emFilter = MetadataTools.createLSID("Dichroic", 0, emIndex);
        String exFilter = MetadataTools.createLSID("Dichroic", 0, exIndex);
        // populate Dichroic data
        store.setDichroicID(emFilter, 0, emIndex);
        store.setDichroicModel(channel.emissionFilter, 0, emIndex);
        store.setDichroicID(exFilter, 0, exIndex);
        store.setDichroicModel(channel.excitationFilter, 0, exIndex);
        store.setLightPathDichroicRef(exFilter, 0, channelIndex);
        // populate Laser data
        store.setLaserID(lightSourceID, 0, channelIndex);
        store.setLaserLaserMedium(getLaserMedium(channel.dyeName), 0, channelIndex);
        if (channelIndex < wavelengths.size()) {
            Length wave = FormatTools.getWavelength(wavelengths.get(channelIndex));
            if (wave != null) {
                store.setLaserWavelength(wave, 0, channelIndex);
            }
        }
        store.setLaserType(getLaserType("Other"), 0, channelIndex);
        channelIndex++;
    }
    if (lensNA != null)
        store.setObjectiveLensNA(new Double(lensNA), 0, 0);
    store.setObjectiveModel(objectiveName, 0, 0);
    if (magnification != null) {
        Double mag = Double.parseDouble(magnification);
        store.setObjectiveNominalMagnification(mag, 0, 0);
    }
    if (workingDistance != null) {
        store.setObjectiveWorkingDistance(new Length(new Double(workingDistance), UNITS.MICROMETER), 0, 0);
    }
    store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
    store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
    // link Objective to Image using ObjectiveSettings
    String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
    store.setObjectiveID(objectiveID, 0, 0);
    store.setObjectiveSettingsID(objectiveID, 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.NO_OVERLAYS) {
        int nextROI = -1;
        // populate ROI data - there is one ROI file per plane
        for (int i = 0; i < roiFilenames.size(); i++) {
            if (i >= getImageCount())
                break;
            String filename = roiFilenames.get(i);
            filename = sanitizeFile(filename, path);
            nextROI = parseROIFile(filename, store, nextROI, i);
        }
    }
    // Populate metadata for the planes
    for (int i = 0; i < planes.size(); i++) {
        PlaneData plane = planes.get(i);
        if (plane.deltaT != null) {
            store.setPlaneDeltaT(new Time(plane.deltaT, UNITS.SECOND), 0, i);
        }
        store.setPlanePositionX(plane.positionX, 0, i);
        store.setPlanePositionY(plane.positionY, 0, i);
        store.setPlanePositionZ(plane.positionZ, 0, i);
    }
}

Example 43 with Length

use of ome.units.quantity.Length 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 44 with Length

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

the class BaseZeissReader method fillMetadataPass7.

/**
 * Store basic dimensions in model
 * @param store
 * @throws FormatException
 * @throws IOException
 */
protected void fillMetadataPass7(MetadataStore store) throws FormatException, IOException {
    for (int i = 0; i < getSeriesCount(); i++) {
        long firstStamp = 0;
        if (timestamps.size() > 0) {
            String timestamp = timestamps.get(0);
            store.setImageAcquisitionDate(new Timestamp(timestamp), i);
        } else if (acquisitionDate != null) {
            store.setImageAcquisitionDate(acquisitionDate, i);
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // link Instrument and Image
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        String objectiveID = MetadataTools.createLSID("Objective", 0, 0);
        store.setObjectiveID(objectiveID, 0, 0);
        store.setObjectiveCorrection(getCorrection("Other"), 0, 0);
        store.setObjectiveImmersion(getImmersion("Other"), 0, 0);
        Integer[] channelKeys = channelName.keySet().toArray(new Integer[channelName.size()]);
        Arrays.sort(channelKeys);
        // link DetectorSettings to an actual Detector
        for (int i = 0; i < getEffectiveSizeC(); i++) {
            String detectorID = MetadataTools.createLSID("Detector", 0, i);
            store.setDetectorID(detectorID, 0, i);
            store.setDetectorType(getDetectorType("Other"), 0, i);
            for (int s = 0; s < getSeriesCount(); s++) {
                int c = i;
                if (i < channelKeys.length) {
                    c = channelKeys[i];
                }
                store.setDetectorSettingsID(detectorID, s, i);
                store.setDetectorSettingsGain(detectorGain.get(c), s, i);
                store.setDetectorSettingsOffset(detectorOffset.get(c), s, i);
                store.setChannelName(channelName.get(c), s, i);
                store.setChannelEmissionWavelength(emWavelength.get(c), s, i);
                store.setChannelExcitationWavelength(exWavelength.get(c), s, i);
                if (channelColors != null && i < channelColors.length) {
                    int color = channelColors[i];
                    int red = color & 0xff;
                    int green = (color & 0xff00) >> 8;
                    int blue = (color & 0xff0000) >> 16;
                    store.setChannelColor(new Color(red, green, blue, 255), s, i);
                }
            }
        }
        for (int i = 0; i < getSeriesCount(); i++) {
            store.setImageInstrumentRef(instrumentID, i);
            store.setObjectiveSettingsID(objectiveID, i);
            if (imageDescription != null) {
                store.setImageDescription(imageDescription, i);
            }
            if (getSeriesCount() > 1) {
                store.setImageName("Tile #" + (i + 1), i);
            }
            Length sizeX = FormatTools.getPhysicalSizeX(physicalSizeX);
            Length sizeY = FormatTools.getPhysicalSizeY(physicalSizeY);
            Length sizeZ = FormatTools.getPhysicalSizeZ(physicalSizeZ);
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, i);
            }
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, i);
            }
            if (sizeZ != null) {
                store.setPixelsPhysicalSizeZ(sizeZ, i);
            }
            Timestamp firstStamp = null;
            if (timestamps.get(0) != null) {
                firstStamp = new Timestamp(timestamps.get(0));
            }
            for (int plane = 0; plane < getImageCount(); plane++) {
                int[] zct = getZCTCoords(plane);
                int expIndex = zct[1];
                if (channelKeys.length > 0) {
                    expIndex += channelKeys[0];
                }
                String exposure = exposureTime.get(expIndex);
                if (exposure == null && exposureTime.size() == 1) {
                    exposure = exposureTime.values().iterator().next();
                }
                Double exp = 0d;
                try {
                    exp = new Double(exposure);
                } catch (NumberFormatException e) {
                } catch (NullPointerException e) {
                }
                store.setPlaneExposureTime(new Time(exp, UNITS.SECOND), i, plane);
                int posIndex = i * getImageCount() + plane;
                if (posIndex < timestamps.size() && firstStamp != null) {
                    Timestamp timestamp = new Timestamp(timestamps.get(posIndex));
                    long difference = timestamp.asInstant().getMillis() - firstStamp.asInstant().getMillis();
                    double delta = (double) difference;
                    store.setPlaneDeltaT(new Time(delta, UNITS.MILLISECOND), i, plane);
                }
                if (stageX.get(posIndex) != null) {
                    store.setPlanePositionX(stageX.get(posIndex), i, plane);
                }
                if (stageY.get(posIndex) != null) {
                    store.setPlanePositionY(stageY.get(posIndex), i, plane);
                }
            }
        }
        for (int i = 0; i < getSeriesCount(); i++) {
            for (int roi = 0; roi < roiIDs.size(); roi++) {
                store.setImageROIRef(roiIDs.get(roi), i, roi);
            }
        }
    }
}

Example 45 with Length

use of ome.units.quantity.Length 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);
        }
    }
}