Examples with Timestamp ome.xml.model.primitives.Timestamp used on opensource projects

Example 16 with Timestamp

use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.

the class HISReader 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);
    in.skipBytes(14);
    int nSeries = in.readShort();
    pixelOffset = new long[nSeries];
    String[] date = new String[nSeries];
    String[] binning = new String[nSeries];
    double[] offset = new double[nSeries];
    double[] exposureTime = new double[nSeries];
    boolean adjustedBitDepth = false;
    in.seek(0);
    core.clear();
    for (int i = 0; i < nSeries; i++) {
        CoreMetadata ms = new CoreMetadata();
        core.add(ms);
        String checkString = in.readString(2);
        if (!checkString.equals("IM") && i > 0) {
            if (getBitsPerPixel() == 12) {
                core.get(i - 1).bitsPerPixel = 16;
                int prevSkip = (getSizeX() * getSizeY() * getSizeC() * 12) / 8;
                int totalBytes = FormatTools.getPlaneSize(this);
                in.skipBytes(totalBytes - prevSkip);
                adjustedBitDepth = true;
            }
        }
        setSeries(i);
        int commentBytes = in.readShort();
        ms.sizeX = in.readShort();
        ms.sizeY = in.readShort();
        in.skipBytes(4);
        int dataType = in.readShort();
        switch(dataType) {
            case 1:
                ms.pixelType = FormatTools.UINT8;
                break;
            case 2:
                ms.pixelType = FormatTools.UINT16;
                break;
            case 6:
                ms.pixelType = FormatTools.UINT16;
                ms.bitsPerPixel = adjustedBitDepth ? 16 : 12;
                break;
            case 11:
                ms.pixelType = FormatTools.UINT8;
                ms.sizeC = 3;
                break;
            case 12:
                ms.pixelType = FormatTools.UINT16;
                ms.sizeC = 3;
                break;
            case 14:
                ms.pixelType = FormatTools.UINT16;
                ms.sizeC = 3;
                ms.bitsPerPixel = adjustedBitDepth ? 16 : 12;
                break;
        }
        in.skipBytes(50);
        String comment = in.readString(commentBytes);
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            String[] data = comment.split(";");
            for (String token : data) {
                int eq = token.indexOf('=');
                if (eq != -1) {
                    String key = token.substring(0, eq);
                    String value = token.substring(eq + 1);
                    addSeriesMeta(key, value);
                    if (key.equals("vDate")) {
                        date[i] = value;
                    } else if (key.equals("vTime")) {
                        date[i] += " " + value;
                        date[i] = DateTools.formatDate(date[i], "yyyy/MM/dd HH:mm:ss");
                    } else if (key.equals("vOffset")) {
                        offset[i] = Double.parseDouble(value);
                    } else if (key.equals("vBinX")) {
                        binning[i] = value;
                    } else if (key.equals("vBinY")) {
                        binning[i] += "x" + value;
                    } else if (key.equals("vExpTim1")) {
                        exposureTime[i] = Double.parseDouble(value) * 100;
                    }
                }
            }
        }
        pixelOffset[i] = in.getFilePointer();
        ms.littleEndian = true;
        if (ms.sizeC == 0)
            ms.sizeC = 1;
        ms.sizeT = 1;
        ms.sizeZ = 1;
        ms.imageCount = 1;
        ms.rgb = ms.sizeC > 1;
        ms.interleaved = isRGB();
        ms.dimensionOrder = "XYCZT";
        in.skipBytes((getSizeX() * getSizeY() * getSizeC() * getBitsPerPixel()) / 8);
    }
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        for (int i = 0; i < nSeries; i++) {
            store.setImageInstrumentRef(instrumentID, i);
            if (date[i] != null) {
                store.setImageAcquisitionDate(new Timestamp(date[i]), i);
            }
            store.setPlaneExposureTime(new Time(exposureTime[i], UNITS.SECOND), i, 0);
            String detectorID = MetadataTools.createLSID("Detector", 0, i);
            store.setDetectorID(detectorID, 0, i);
            store.setDetectorOffset(offset[i], 0, i);
            store.setDetectorType(getDetectorType("Other"), 0, i);
            store.setDetectorSettingsID(detectorID, i, 0);
            store.setDetectorSettingsBinning(getBinning(binning[i]), i, 0);
        }
    }
}

Example 17 with Timestamp

use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.

the class PDSReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "hdr")) {
        String headerFile = id.substring(0, id.lastIndexOf(".")) + ".hdr";
        if (!new Location(headerFile).exists()) {
            headerFile = id.substring(0, id.lastIndexOf(".")) + ".HDR";
            if (!new Location(headerFile).exists()) {
                throw new FormatException("Could not find matching .hdr file.");
            }
        }
        initFile(headerFile);
        return;
    }
    super.initFile(id);
    String[] headerData = DataTools.readFile(id).split("\r\n");
    if (headerData.length == 1) {
        headerData = headerData[0].split("\r");
    }
    Length xPos = null, yPos = null;
    Double deltaX = null, deltaY = null;
    String date = null;
    CoreMetadata m = core.get(0);
    for (String line : headerData) {
        int eq = line.indexOf('=');
        if (eq < 0)
            continue;
        int end = line.indexOf('/');
        if (end < 0)
            end = line.length();
        String key = line.substring(0, eq).trim();
        String value = line.substring(eq + 1, end).trim();
        if (key.equals("NXP")) {
            m.sizeX = Integer.parseInt(value);
        } else if (key.equals("NYP")) {
            m.sizeY = Integer.parseInt(value);
        } else if (key.equals("XPOS")) {
            final Double number = Double.valueOf(value);
            xPos = new Length(number, UNITS.REFERENCEFRAME);
            addGlobalMeta("X position for position #1", xPos);
        } else if (key.equals("YPOS")) {
            final Double number = Double.valueOf(value);
            yPos = new Length(number, UNITS.REFERENCEFRAME);
            addGlobalMeta("Y position for position #1", yPos);
        } else if (key.equals("SIGNX")) {
            reverseX = value.replaceAll("'", "").trim().equals("-");
        } else if (key.equals("SIGNY")) {
            reverseY = value.replaceAll("'", "").trim().equals("-");
        } else if (key.equals("DELTAX")) {
            deltaX = new Double(value);
        } else if (key.equals("DELTAY")) {
            deltaY = new Double(value);
        } else if (key.equals("COLOR")) {
            int color = Integer.parseInt(value);
            if (color == 4) {
                m.sizeC = 3;
                m.rgb = true;
            } else {
                m.sizeC = 1;
                m.rgb = false;
                lutIndex = color - 1;
                m.indexed = lutIndex >= 0;
            }
        } else if (key.equals("SCAN TIME")) {
            long modTime = new Location(currentId).getAbsoluteFile().lastModified();
            String year = DateTools.convertDate(modTime, DateTools.UNIX, "yyyy");
            date = value.replaceAll("'", "") + " " + year;
            date = DateTools.formatDate(date, DATE_FORMAT);
        } else if (key.equals("FILE REC LEN")) {
            recordWidth = Integer.parseInt(value) / 2;
        }
        addGlobalMeta(key, value);
    }
    m.sizeZ = 1;
    m.sizeT = 1;
    m.imageCount = 1;
    m.dimensionOrder = "XYCZT";
    m.pixelType = FormatTools.UINT16;
    m.littleEndian = true;
    String base = currentId.substring(0, currentId.lastIndexOf("."));
    pixelsFile = base + ".IMG";
    if (!new Location(pixelsFile).exists()) {
        pixelsFile = base + ".img";
    }
    boolean minimumMetadata = getMetadataOptions().getMetadataLevel() == MetadataLevel.MINIMUM;
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, !minimumMetadata);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    if (!minimumMetadata) {
        store.setPlanePositionX(xPos, 0, 0);
        store.setPlanePositionY(yPos, 0, 0);
        Length sizeX = FormatTools.getPhysicalSizeX(deltaX);
        Length sizeY = FormatTools.getPhysicalSizeY(deltaY);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
    }
}

Example 18 with Timestamp

use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.

the class PerkinElmerReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (currentId != null && (id.equals(currentId) || isUsedFile(id)))
        return;
    LOGGER.info("Finding HTML companion file");
    if (!checkSuffix(id, HTM_SUFFIX)) {
        Location parent = new Location(id).getAbsoluteFile().getParentFile();
        String[] ls = parent.list();
        for (String file : ls) {
            if (checkSuffix(file, HTM_SUFFIX) && !file.startsWith(".")) {
                id = new Location(parent.getAbsolutePath(), file).getAbsolutePath();
                break;
            }
        }
    }
    super.initFile(id);
    allFiles = new ArrayList<String>();
    // get the working directory
    Location tmpFile = new Location(id).getAbsoluteFile();
    Location workingDir = tmpFile.getParentFile();
    if (workingDir == null)
        workingDir = new Location(".");
    String workingDirPath = workingDir.getPath();
    if (!workingDirPath.equals(""))
        workingDirPath += File.separator;
    String[] ls = workingDir.list(true);
    if (!new Location(id).exists()) {
        ls = Location.getIdMap().keySet().toArray(new String[0]);
        workingDirPath = "";
    }
    LOGGER.info("Searching for all metadata companion files");
    // check if we have any of the required header file types
    String cfgFile = null, anoFile = null, recFile = null;
    String timFile = null, csvFile = null, zpoFile = null;
    String htmFile = null;
    final List<PixelsFile> tempFiles = new ArrayList<PixelsFile>();
    int dot = id.lastIndexOf(".");
    String check = dot < 0 ? id : id.substring(0, dot);
    check = check.substring(check.lastIndexOf(File.separator) + 1);
    // locate appropriate .tim, .csv, .zpo, .htm and .tif files
    String prefix = null;
    Arrays.sort(ls);
    for (int i = 0; i < ls.length; i++) {
        // make sure that the file has a name similar to the name of the
        // specified file
        int d = ls[i].lastIndexOf(".");
        while (d == -1 && i < ls.length - 1) {
            i++;
            d = ls[i].lastIndexOf(".");
        }
        String s = d < 0 ? ls[i] : ls[i].substring(0, d);
        if (s.startsWith(check) || check.startsWith(s) || ((prefix != null) && (s.startsWith(prefix)))) {
            prefix = ls[i].substring(0, d);
            if (cfgFile == null && checkSuffix(ls[i], CFG_SUFFIX))
                cfgFile = ls[i];
            if (anoFile == null && checkSuffix(ls[i], ANO_SUFFIX))
                anoFile = ls[i];
            if (recFile == null && checkSuffix(ls[i], REC_SUFFIX))
                recFile = ls[i];
            if (timFile == null && checkSuffix(ls[i], TIM_SUFFIX))
                timFile = ls[i];
            if (csvFile == null && checkSuffix(ls[i], CSV_SUFFIX))
                csvFile = ls[i];
            if (zpoFile == null && checkSuffix(ls[i], ZPO_SUFFIX))
                zpoFile = ls[i];
            if (htmFile == null && checkSuffix(ls[i], HTM_SUFFIX))
                htmFile = ls[i];
            dot = ls[i].lastIndexOf(".");
            PixelsFile f = new PixelsFile();
            f.path = workingDirPath + ls[i];
            if (checkSuffix(ls[i], TiffReader.TIFF_SUFFIXES)) {
                if (dot - 4 >= 0 && dot - 4 < ls[i].length() && ls[i].charAt(dot - 4) == '_') {
                    f.firstIndex = Integer.parseInt(ls[i].substring(dot - 3, dot));
                } else {
                    f.firstIndex = -1;
                }
                if (dot - 9 >= 0 && dot - 9 < ls[i].length() && ls[i].charAt(dot - 9) == '_') {
                    f.extIndex = Integer.parseInt(ls[i].substring(dot - 8, dot - 4));
                } else {
                    f.firstIndex = i;
                    f.extIndex = 0;
                }
                tempFiles.add(f);
            } else {
                try {
                    if (dot - 4 >= 0 && dot - 4 < ls[i].length() && ls[i].charAt(dot - 4) == '_') {
                        f.firstIndex = Integer.parseInt(ls[i].substring(dot - 3, dot));
                    } else {
                        f.firstIndex = -1;
                    }
                    String ext = dot + 1 < ls[i].length() ? ls[i].substring(dot + 1) : "";
                    f.extIndex = Integer.parseInt(ext, 16);
                    isTiff = false;
                    tempFiles.add(f);
                } catch (NumberFormatException exc) {
                    LOGGER.debug("Failed to parse file extension", exc);
                }
            }
        }
    }
    files = tempFiles.toArray(new PixelsFile[tempFiles.size()]);
    // determine the number of different extensions we have
    LOGGER.info("Finding image files");
    List<Integer> foundExts = new ArrayList<Integer>();
    for (PixelsFile f : files) {
        if (!foundExts.contains(f.extIndex)) {
            foundExts.add(f.extIndex);
        }
    }
    extCount = foundExts.size();
    foundExts = null;
    CoreMetadata ms0 = core.get(0);
    ms0.imageCount = 0;
    for (PixelsFile f : files) {
        allFiles.add(f.path);
        ms0.imageCount++;
        if (f.firstIndex < 0 && files.length > extCount) {
            ms0.imageCount += ((files.length - 1) / (extCount - 1)) - 1;
        }
    }
    tiff = new MinimalTiffReader();
    // we always parse the .tim and .htm files if they exist, along with
    // either the .csv file or the .zpo file
    LOGGER.info("Parsing metadata values");
    addUsedFile(workingDirPath, cfgFile);
    addUsedFile(workingDirPath, anoFile);
    addUsedFile(workingDirPath, recFile);
    addUsedFile(workingDirPath, timFile);
    if (timFile != null)
        timFile = allFiles.get(allFiles.size() - 1);
    addUsedFile(workingDirPath, csvFile);
    if (csvFile != null)
        csvFile = allFiles.get(allFiles.size() - 1);
    addUsedFile(workingDirPath, zpoFile);
    if (zpoFile != null)
        zpoFile = allFiles.get(allFiles.size() - 1);
    addUsedFile(workingDirPath, htmFile);
    if (htmFile != null)
        htmFile = allFiles.get(allFiles.size() - 1);
    if (timFile != null)
        parseTimFile(timFile);
    if (csvFile != null)
        parseCSVFile(csvFile);
    if (zpoFile != null && csvFile == null)
        parseZpoFile(zpoFile);
    // be aggressive about parsing the HTML file, since it's the only one that
    // explicitly defines the number of wavelengths and timepoints
    final List<Double> exposureTimes = new ArrayList<Double>();
    final List<Double> zPositions = new ArrayList<Double>();
    final List<Double> emWaves = new ArrayList<Double>();
    final List<Double> exWaves = new ArrayList<Double>();
    if (htmFile != null) {
        String[] tokens = DataTools.readFile(htmFile).split(HTML_REGEX);
        for (int j = 0; j < tokens.length; j++) {
            if (tokens[j].indexOf('<') != -1)
                tokens[j] = "";
        }
        for (int j = 0; j < tokens.length - 1; j += 2) {
            if (tokens[j].indexOf("Exposure") != -1) {
                addGlobalMeta("Camera Data " + tokens[j].charAt(13), tokens[j]);
                int ndx = tokens[j].indexOf("Exposure") + 9;
                String exposure = tokens[j].substring(ndx, tokens[j].indexOf(" ", ndx)).trim();
                if (exposure.endsWith(",")) {
                    exposure = exposure.substring(0, exposure.length() - 1);
                }
                exposureTimes.add(new Double(Double.parseDouble(exposure) / 1000));
                if (tokens[j].indexOf("nm") != -1) {
                    int nmIndex = tokens[j].indexOf("nm");
                    int paren = tokens[j].lastIndexOf("(", nmIndex);
                    int slash = tokens[j].lastIndexOf("/", nmIndex);
                    if (slash == -1)
                        slash = nmIndex;
                    emWaves.add(new Double(tokens[j].substring(paren + 1, slash).trim()));
                    if (tokens[j].indexOf("nm", nmIndex + 3) != -1) {
                        nmIndex = tokens[j].indexOf("nm", nmIndex + 3);
                        paren = tokens[j].lastIndexOf(" ", nmIndex);
                        slash = tokens[j].lastIndexOf("/", nmIndex);
                        if (slash == -1)
                            slash = nmIndex + 2;
                        exWaves.add(new Double(tokens[j].substring(paren + 1, slash).trim()));
                    }
                }
                j--;
            } else if (tokens[j + 1].trim().equals("Slice Z positions")) {
                for (int q = j + 2; q < tokens.length; q++) {
                    if (!tokens[q].trim().equals("")) {
                        try {
                            zPositions.add(new Double(tokens[q].trim()));
                        } catch (NumberFormatException e) {
                        }
                    }
                }
            } else if (!tokens[j].trim().equals("")) {
                tokens[j] = tokens[j].trim();
                tokens[j + 1] = tokens[j + 1].trim();
                parseKeyValue(tokens[j], tokens[j + 1]);
            }
        }
    } else {
        throw new FormatException("Valid header files not found.");
    }
    if (details != null) {
        String[] tokens = details.split("\\s");
        int n = 0;
        for (String token : tokens) {
            if (token.equals("Wavelengths"))
                ms0.sizeC = n;
            else if (token.equals("Frames"))
                ms0.sizeT = n;
            else if (token.equals("Slices"))
                ms0.sizeZ = n;
            try {
                n = Integer.parseInt(token);
            } catch (NumberFormatException e) {
                n = 0;
            }
        }
    }
    LOGGER.info("Populating metadata");
    if (files.length == 0) {
        throw new FormatException("TIFF files not found.");
    }
    if (isTiff) {
        tiff.setId(getFile(0));
        ms0.pixelType = tiff.getPixelType();
    } else {
        RandomAccessInputStream tmp = new RandomAccessInputStream(getFile(0));
        int bpp = (int) (tmp.length() - 6) / (getSizeX() * getSizeY());
        tmp.close();
        if (bpp % 3 == 0)
            bpp /= 3;
        ms0.pixelType = FormatTools.pixelTypeFromBytes(bpp, false, false);
    }
    if (getSizeZ() <= 0)
        ms0.sizeZ = 1;
    if (getSizeC() <= 0)
        ms0.sizeC = 1;
    if (getSizeT() <= 0 || getImageCount() % (getSizeZ() * getSizeC()) == 0) {
        ms0.sizeT = getImageCount() / (getSizeZ() * getSizeC());
    } else {
        ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
        if (getImageCount() > files.length) {
            ms0.imageCount = files.length;
            ms0.sizeT = getImageCount() / (getSizeZ() * getSizeC());
        }
    }
    ms0.dimensionOrder = "XYCTZ";
    ms0.rgb = isTiff ? tiff.isRGB() : false;
    ms0.interleaved = false;
    ms0.littleEndian = isTiff ? tiff.isLittleEndian() : true;
    ms0.metadataComplete = true;
    ms0.indexed = isTiff ? tiff.isIndexed() : false;
    ms0.falseColor = false;
    if (getImageCount() != getSizeZ() * getSizeC() * getSizeT()) {
        ms0.imageCount = getSizeZ() * getSizeC() * getSizeT();
    }
    if (!isTiff && extCount > getSizeT()) {
        extCount = getSizeT() * getSizeC();
    }
    // Populate metadata store
    // The metadata store we're working with.
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    // populate Image element
    if (finishTime != null) {
        Timestamp timestamp = Timestamp.valueOf(DateTools.formatDate(finishTime, DATE_FORMAT));
        if (timestamp != null)
            store.setImageAcquisitionDate(timestamp, 0);
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        // populate Dimensions element
        Length sizeX = FormatTools.getPhysicalSizeX(pixelSizeX);
        Length sizeY = FormatTools.getPhysicalSizeY(pixelSizeY);
        if (sizeX != null) {
            store.setPixelsPhysicalSizeX(sizeX, 0);
        }
        if (sizeY != null) {
            store.setPixelsPhysicalSizeY(sizeY, 0);
        }
        // link Instrument and Image
        String instrumentID = MetadataTools.createLSID("Instrument", 0);
        store.setInstrumentID(instrumentID, 0);
        store.setImageInstrumentRef(instrumentID, 0);
        // populate LogicalChannel element
        for (int i = 0; i < getEffectiveSizeC(); i++) {
            if (i < emWaves.size()) {
                Length em = FormatTools.getEmissionWavelength(emWaves.get(i));
                if (em != null) {
                    store.setChannelEmissionWavelength(em, 0, i);
                }
            }
            if (i < exWaves.size()) {
                Length ex = FormatTools.getExcitationWavelength(exWaves.get(i));
                if (ex != null) {
                    store.setChannelExcitationWavelength(ex, 0, i);
                }
            }
        }
        // populate PlaneTiming and StagePosition
        long start = 0, end = 0;
        if (startTime != null) {
            start = DateTools.getTime(startTime, DATE_FORMAT);
        }
        if (finishTime != null) {
            end = DateTools.getTime(finishTime, DateTools.ISO8601_FORMAT);
        }
        double secondsPerPlane = (double) (end - start) / getImageCount() / 1000;
        for (int i = 0; i < getImageCount(); i++) {
            int[] zct = getZCTCoords(i);
            store.setPlaneDeltaT(new Time(i * secondsPerPlane, UNITS.SECOND), 0, i);
            if (zct[1] < exposureTimes.size() && exposureTimes.get(zct[1]) != null) {
                store.setPlaneExposureTime(new Time(exposureTimes.get(zct[1]), UNITS.SECOND), 0, i);
            }
            if (zct[0] < zPositions.size()) {
                final Double zPosition = zPositions.get(zct[0]);
                final Length xl = new Length(0d, UNITS.REFERENCEFRAME);
                final Length yl = new Length(0d, UNITS.REFERENCEFRAME);
                final Length zl;
                if (zPosition == null) {
                    zl = null;
                } else {
                    zl = new Length(zPosition, UNITS.REFERENCEFRAME);
                }
                store.setPlanePositionX(xl, 0, i);
                store.setPlanePositionY(yl, 0, i);
                store.setPlanePositionZ(zl, 0, i);
            }
        }
    }
}

Example 19 with Timestamp

use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.

the class InveonReader method initFile.

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

Example 20 with Timestamp

use of ome.xml.model.primitives.Timestamp in project bioformats by openmicroscopy.

the class IvisionReader method initFile.

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