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

Example 11 with Timestamp

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

the class FlexReader method populateMetadataStore.

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

Example 12 with Timestamp

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

the class FluoviewReader method parseComment.

private void parseComment() {
    if (comment != null) {
        // this is an INI-style comment, with one key/value pair per line
        String[] lines = comment.split("\n");
        for (String token : lines) {
            token = token.trim();
            int eq = token.indexOf('=');
            if (eq != -1) {
                String key = token.substring(0, eq);
                String value = token.substring(eq + 1);
                addGlobalMeta(key, value);
                if (key.startsWith("Gain Ch")) {
                    int index = Integer.parseInt(key.substring(7).trim());
                    if (index > 0 && index <= gains.length) {
                        gains[index - 1] = value;
                    }
                } else if (key.startsWith("PMT Voltage Ch")) {
                    int index = Integer.parseInt(key.substring(14).trim());
                    if (index > 0 && index <= voltages.length) {
                        voltages[index - 1] = value;
                    }
                } else if (key.startsWith("Offset Ch")) {
                    int index = Integer.parseInt(key.substring(9).trim());
                    if (index > 0 && index <= offsets.length) {
                        offsets[index - 1] = value;
                    }
                } else if (key.equals("Magnification"))
                    mag = value;
                else if (key.equals("System Configuration")) {
                    detectorManufacturer = value;
                } else if (key.equals("Objective Lens"))
                    objectiveManufacturer = value;
                else if (key.startsWith("Channel ") && key.endsWith("Dye")) {
                    for (int i = 0; i < channelNames.length; i++) {
                        if (channelNames[i] == null) {
                            channelNames[i] = value;
                            break;
                        }
                    }
                } else if (key.startsWith("Confocal Aperture-Ch")) {
                    int index = Integer.parseInt(key.substring(20).trim());
                    if (index > 0 && index <= lensNA.length) {
                        lensNA[index - 1] = value.substring(0, value.length() - 2);
                    }
                } else if (key.equals("Date")) {
                    date = value;
                } else if (key.equals("Time")) {
                    date += " " + value;
                } else if (key.equals("MontageOffsets")) {
                    String[] offsets = value.split("\t");
                    montageOffsets = new double[offsets.length - 1][3];
                    for (int i = 1; i < offsets.length; i++) {
                        String[] v = offsets[i].trim().split(",");
                        for (int j = 0; j < v.length; j++) {
                            montageOffsets[i - 1][j] = Double.parseDouble(v[j].trim());
                        }
                    }
                } else if (key.equals("XYFields")) {
                    String[] offsets = value.split("\t");
                    fieldOffsets = new double[offsets.length - 1][3];
                    for (int i = 1; i < offsets.length; i++) {
                        String[] v = offsets[i].trim().split(",");
                        for (int j = 0; j < v.length; j++) {
                            try {
                                fieldOffsets[i - 1][j] = Double.parseDouble(v[j].trim());
                            } catch (NumberFormatException e) {
                            }
                        }
                    }
                }
            } else if (token.startsWith("Z") && token.indexOf(" um ") != -1) {
                // looking for "Z - x um in y planes"
                String z = token.substring(token.indexOf('-') + 1);
                z = z.replaceAll("\\p{Alpha}", "").trim();
                int firstSpace = z.indexOf(' ');
                double size = Double.parseDouble(z.substring(0, firstSpace));
                double nPlanes = Double.parseDouble(z.substring(firstSpace).trim());
                voxelZ = size / nPlanes;
            }
        }
        if (date != null) {
            date = DateTools.formatDate(date.trim(), new String[] { "dd/MM/yyyy hh:mm:ss a", "MM-dd-yyyy hh:mm:ss", "dd/MM/yyyy H:mm:ss" }, true);
            Timestamp timestamp = Timestamp.valueOf(date);
            if (timeIndex >= 0 && timestamp != null) {
                long ms = timestamp.asInstant().getMillis();
                for (int i = 0; i < getImageCount(); i++) {
                    int[] zct = getZCTCoords(i);
                    String key = String.format("Timestamp for Z=%2s, C=%2s, T=%2s", zct[0], zct[1], zct[2]);
                    long stamp = ms + (long) (stamps[timeIndex][i] * 1000);
                    addGlobalMeta(key, DateTools.convertDate(stamp, DateTools.UNIX, DATE_FORMAT));
                }
            }
        }
        int start = comment.indexOf("[Version Info]");
        int end = comment.indexOf("[Version Info End]");
        if (start != -1 && end != -1 && end > start) {
            comment = comment.substring(start + 14, end).trim();
            start = comment.indexOf('=') + 1;
            end = comment.indexOf("\n");
            if (end > start)
                comment = comment.substring(start, end).trim();
            else
                comment = comment.substring(start).trim();
        } else
            comment = "";
    }
}

Example 13 with Timestamp

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

the class HitachiReader method initFile.

// -- Internal FormatReader API methods --
/* @see loci.formats.FormatReader#initFile(String) */
@Override
protected void initFile(String id) throws FormatException, IOException {
    if (!checkSuffix(id, "txt")) {
        String base = id;
        if (base.indexOf('.') >= 0) {
            base = base.substring(0, base.lastIndexOf("."));
        }
        id = base + ".txt";
        initFile(id);
        return;
    }
    super.initFile(id);
    String data = DataTools.readFile(id);
    IniParser parser = new IniParser();
    parser.setBackslashContinuesLine(false);
    IniList ini = parser.parseINI(new BufferedReader(new StringReader(data)));
    IniTable image = ini.getTable("SemImageFile");
    if (image == null) {
        throw new FormatException("Could not find 'SemImageFile' table.");
    }
    for (String key : image.keySet()) {
        addGlobalMeta(key, image.get(key));
    }
    String imageName = image.get("SampleName");
    String pixelsFile = image.get("ImageName");
    String date = image.get("Date");
    String time = image.get("Time");
    Location parent = new Location(id).getAbsoluteFile().getParentFile();
    pixelsFile = new Location(parent, pixelsFile).getAbsolutePath();
    ClassList<IFormatReader> classes = ImageReader.getDefaultReaderClasses();
    Class<? extends IFormatReader>[] classArray = classes.getClasses();
    ClassList<IFormatReader> newClasses = new ClassList<IFormatReader>(IFormatReader.class);
    for (Class<? extends IFormatReader> c : classArray) {
        if (!c.equals(HitachiReader.class)) {
            newClasses.addClass(c);
        }
    }
    helperReader = new ImageReader(newClasses);
    helperReader.setId(pixelsFile);
    core = new ArrayList<CoreMetadata>(helperReader.getCoreMetadataList());
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM);
    store.setImageName(imageName, 0);
    date = DateTools.formatDate(date + " " + time, DATE_FORMAT);
    if (date != null) {
        store.setImageAcquisitionDate(new Timestamp(date), 0);
    }
    populateOMEMetadata(image, store);
}

Example 14 with Timestamp

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

the class ImaconReader method initMetadataStore.

/* @see BaseTiffReader#initMetadataStore() */
@Override
protected void initMetadataStore() throws FormatException {
    super.initMetadataStore();
    MetadataStore store = makeFilterMetadata();
    if (creationDate != null) {
        creationDate = DateTools.formatDate(creationDate, "yyyyMMdd HHmmSSZ");
    }
    for (int i = 0; i < getSeriesCount(); i++) {
        String name = imageName;
        if (imageName.length() == 0) {
            name = "#" + (i + 1);
        } else {
            name += " #" + (i + 1);
        }
        store.setImageName(name, i);
        if (creationDate != null) {
            store.setImageAcquisitionDate(new Timestamp(creationDate), i);
        }
    }
    if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
        if (experimenterName == null)
            experimenterName = "";
        int nameSpace = experimenterName.indexOf(' ');
        String firstName = nameSpace == -1 ? "" : experimenterName.substring(0, nameSpace);
        String lastName = nameSpace == -1 ? experimenterName : experimenterName.substring(nameSpace + 1);
        String experimenter = MetadataTools.createLSID("Experimenter", 0);
        store.setExperimenterID(experimenter, 0);
        store.setExperimenterFirstName(firstName, 0);
        store.setExperimenterLastName(lastName, 0);
        for (int i = 0; i < getSeriesCount(); i++) {
            store.setImageExperimenterRef(experimenter, i);
        }
    }
}

Example 15 with Timestamp

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

the class FujiReader method initFile.

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