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

Example 26 with Time

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

the class FormatReaderTest method testExposureTimes.

@Test(groups = { "all", "fast", "automated" })
public void testExposureTimes() {
    if (config == null)
        throw new SkipException("No config tree");
    String testName = "ExposureTimes";
    if (!initFile())
        result(testName, false, "initFile");
    IMetadata retrieve = (IMetadata) reader.getMetadataStore();
    for (int i = 0; i < reader.getSeriesCount(); i++) {
        reader.setSeries(i);
        config.setSeries(i);
        if (reader.getImageCount() != retrieve.getPlaneCount(i)) {
            continue;
        }
        for (int c = 0; c < config.getChannelCount(); c++) {
            if (config.hasExposureTime(c)) {
                Time exposureTime = config.getExposureTime(c);
                for (int p = 0; p < reader.getImageCount(); p++) {
                    int[] zct = reader.getZCTCoords(p);
                    if (zct[1] == c && p < retrieve.getPlaneCount(i)) {
                        Time planeExposureTime = retrieve.getPlaneExposureTime(i, p);
                        if (exposureTime == null && planeExposureTime == null) {
                            continue;
                        }
                        if (exposureTime == null || planeExposureTime == null || !exposureTime.equals(planeExposureTime)) {
                            result(testName, false, "Series " + i + " plane " + p + " channel " + c + " (got " + planeExposureTime + ", expected " + exposureTime + ")");
                        }
                    }
                }
            }
        }
    }
    result(testName, true);
}

Example 27 with Time

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

the class MicromanagerReader method populateMetadata.

private void populateMetadata() throws FormatException, IOException {
    MetadataStore store = makeFilterMetadata();
    MetadataTools.populatePixels(store, this, true);
    String instrumentID = MetadataTools.createLSID("Instrument", 0);
    store.setInstrumentID(instrumentID, 0);
    for (int i = 0; i < positions.size(); i++) {
        Position p = positions.get(i);
        if (p.time != null) {
            String date = DateTools.formatDate(p.time, DATE_FORMAT);
            if (date != null) {
                store.setImageAcquisitionDate(new Timestamp(date), i);
            }
        }
        if (positions.size() > 1) {
            Location parent = new Location(p.metadataFile).getParentFile();
            store.setImageName(parent.getName(), i);
        }
        if (getMetadataOptions().getMetadataLevel() != MetadataLevel.MINIMUM) {
            store.setImageDescription(p.comment, i);
            // link Instrument and Image
            store.setImageInstrumentRef(instrumentID, i);
            for (int c = 0; c < p.channels.length; c++) {
                store.setChannelName(p.channels[c], i, c);
            }
            Length sizeX = FormatTools.getPhysicalSizeX(p.pixelSize);
            Length sizeY = FormatTools.getPhysicalSizeY(p.pixelSize);
            Length sizeZ = FormatTools.getPhysicalSizeZ(p.sliceThickness);
            if (sizeX != null) {
                store.setPixelsPhysicalSizeX(sizeX, i);
            }
            if (sizeY != null) {
                store.setPixelsPhysicalSizeY(sizeY, i);
            }
            if (sizeZ != null) {
                store.setPixelsPhysicalSizeZ(sizeZ, i);
            }
            int nextStamp = 0;
            for (int q = 0; q < getImageCount(); q++) {
                store.setPlaneExposureTime(p.exposureTime, i, q);
                String tiff = positions.get(getSeries()).getFile(q);
                if (tiff != null && new Location(tiff).exists() && nextStamp < p.timestamps.length && p.timestamps[nextStamp] != null) {
                    store.setPlaneDeltaT(new Time(p.timestamps[nextStamp++], UNITS.MILLISECOND), i, q);
                }
                if (p.positions != null && q < p.positions.length) {
                    if (p.positions[q][0] != null) {
                        store.setPlanePositionX(new Length(p.positions[q][0], UNITS.MICROMETER), i, q);
                    }
                    if (p.positions[q][1] != null) {
                        store.setPlanePositionY(new Length(p.positions[q][1], UNITS.MICROMETER), i, q);
                    }
                    if (p.positions[q][2] != null) {
                        store.setPlanePositionZ(new Length(p.positions[q][2], UNITS.MICROMETER), i, q);
                    }
                }
            }
            String serialNumber = p.detectorID;
            p.detectorID = MetadataTools.createLSID("Detector", 0, i);
            for (int c = 0; c < p.channels.length; c++) {
                store.setDetectorSettingsBinning(getBinning(p.binning), i, c);
                store.setDetectorSettingsGain(new Double(p.gain), i, c);
                if (c < p.voltage.size()) {
                    store.setDetectorSettingsVoltage(new ElectricPotential(p.voltage.get(c), UNITS.VOLT), i, c);
                }
                store.setDetectorSettingsID(p.detectorID, i, c);
            }
            store.setDetectorID(p.detectorID, 0, i);
            if (p.detectorModel != null) {
                store.setDetectorModel(p.detectorModel, 0, i);
            }
            if (serialNumber != null) {
                store.setDetectorSerialNumber(serialNumber, 0, i);
            }
            if (p.detectorManufacturer != null) {
                store.setDetectorManufacturer(p.detectorManufacturer, 0, i);
            }
            if (p.cameraMode == null)
                p.cameraMode = "Other";
            store.setDetectorType(getDetectorType(p.cameraMode), 0, i);
            store.setImagingEnvironmentTemperature(new Temperature(p.temperature, UNITS.CELSIUS), i);
        }
    }
}

Example 28 with Time

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

the class FakeReader method parseSeriesTable.

/**
 * Translate key/value pairs from the INI table for the specified series.
 */
private void parseSeriesTable(IniTable table, MetadataStore store, int newSeries) {
    int s = getSeries();
    setSeries(newSeries);
    for (int i = 0; i < getImageCount(); i++) {
        String exposureTime = table.get("ExposureTime_" + i);
        String exposureTimeUnit = table.get("ExposureTimeUnit_" + i);
        if (exposureTime != null) {
            try {
                Double v = Double.valueOf(exposureTime);
                Time exposure = FormatTools.getTime(v, exposureTimeUnit);
                if (exposure != null) {
                    store.setPlaneExposureTime(exposure, newSeries, i);
                }
            } catch (NumberFormatException e) {
                LOGGER.trace("Could not parse ExposureTime for series #" + s + " plane #" + i, e);
            }
        }
        // TODO: could be cleaned up further when Java 8 is the minimum version
        Length x = parsePosition("X", s, i, table);
        if (x != null) {
            store.setPlanePositionX(x, newSeries, i);
        }
        Length y = parsePosition("Y", s, i, table);
        if (y != null) {
            store.setPlanePositionY(y, newSeries, i);
        }
        Length z = parsePosition("Z", s, i, table);
        if (z != null) {
            store.setPlanePositionZ(z, newSeries, i);
        }
    }
    setSeries(s);
}

Example 29 with Time

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

the class TiffReader method parseCommentImageJ.

private void parseCommentImageJ(String comment) throws FormatException, IOException {
    int nl = comment.indexOf("\n");
    put("ImageJ", nl < 0 ? comment.substring(7) : comment.substring(7, nl));
    metadata.remove("Comment");
    description = "";
    int z = 1, t = 1;
    int c = getSizeC();
    int images = 1;
    CoreMetadata m = core.get(0);
    if (ifds.get(0).containsKey(IMAGEJ_TAG)) {
        comment += "\n" + ifds.get(0).getIFDTextValue(IMAGEJ_TAG);
    }
    // parse ImageJ metadata (ZCT sizes, calibration units, etc.)
    StringTokenizer st = new StringTokenizer(comment, "\n");
    while (st.hasMoreTokens()) {
        String token = st.nextToken();
        String value = null;
        int eq = token.indexOf('=');
        if (eq >= 0)
            value = token.substring(eq + 1);
        if (token.startsWith("channels="))
            c = parseInt(value);
        else if (token.startsWith("slices="))
            z = parseInt(value);
        else if (token.startsWith("frames="))
            t = parseInt(value);
        else if (token.startsWith("images=")) {
            images = parseInt(value);
        } else if (token.startsWith("mode=")) {
            put("Color mode", value);
        } else if (token.startsWith("unit=")) {
            calibrationUnit = value;
            put("Unit", calibrationUnit);
        } else if (token.startsWith("finterval=")) {
            Double valueDouble = parseDouble(value);
            if (valueDouble != null) {
                timeIncrement = new Time(valueDouble, UNITS.SECOND);
                put("Frame Interval", timeIncrement);
            }
        } else if (token.startsWith("spacing=")) {
            physicalSizeZ = parseDouble(value);
            put("Spacing", physicalSizeZ);
        } else if (token.startsWith("xorigin=")) {
            xOrigin = parseInt(value);
            put("X Origin", xOrigin);
        } else if (token.startsWith("yorigin=")) {
            yOrigin = parseInt(value);
            put("Y Origin", yOrigin);
        } else if (eq > 0) {
            put(token.substring(0, eq).trim(), value);
        }
    }
    if (z * c * t == c && isRGB()) {
        t = getImageCount();
    }
    m.dimensionOrder = "XYCZT";
    if (z * t * (isRGB() ? 1 : c) == ifds.size()) {
        m.sizeZ = z;
        m.sizeT = t;
        m.sizeC = isRGB() ? getSizeC() : c;
    } else if (z * c * t == ifds.size() && isRGB()) {
        m.sizeZ = z;
        m.sizeT = t;
        m.sizeC *= c;
    } else if (ifds.size() == 1 && images > ifds.size() && ifds.get(0).getCompression() == TiffCompression.UNCOMPRESSED) {
        // file is likely corrupt or larger than 4GB (missing end IFDs)
        // 
        // ImageJ writes TIFF files like this:
        // IFD #0
        // comment
        // all pixel data
        // IFD #1
        // IFD #2
        // ...
        // 
        // since we know where the pixel data is, we can create fake
        // IFDs in an attempt to read the rest of the pixels
        IFD firstIFD = ifds.get(0);
        int planeSize = getSizeX() * getSizeY() * getRGBChannelCount() * FormatTools.getBytesPerPixel(getPixelType());
        long[] stripOffsets = firstIFD.getStripOffsets();
        long[] stripByteCounts = firstIFD.getStripByteCounts();
        long endOfFirstPlane = stripOffsets[stripOffsets.length - 1] + stripByteCounts[stripByteCounts.length - 1];
        long totalBytes = in.length() - endOfFirstPlane;
        int totalPlanes = (int) (totalBytes / planeSize) + 1;
        ifds = new IFDList();
        ifds.add(firstIFD);
        for (int i = 1; i < totalPlanes; i++) {
            IFD ifd = new IFD(firstIFD);
            ifds.add(ifd);
            long[] prevOffsets = ifds.get(i - 1).getStripOffsets();
            long[] offsets = new long[stripOffsets.length];
            offsets[0] = prevOffsets[prevOffsets.length - 1] + stripByteCounts[stripByteCounts.length - 1];
            for (int j = 1; j < offsets.length; j++) {
                offsets[j] = offsets[j - 1] + stripByteCounts[j - 1];
            }
            ifd.putIFDValue(IFD.STRIP_OFFSETS, offsets);
        }
        if (z * c * t == ifds.size()) {
            m.sizeZ = z;
            m.sizeT = t;
            m.sizeC = c;
        } else if (z * t == ifds.size()) {
            m.sizeZ = z;
            m.sizeT = t;
        } else
            m.sizeZ = ifds.size();
        m.imageCount = ifds.size();
    } else {
        m.sizeT = ifds.size();
        m.imageCount = ifds.size();
    }
}

Example 30 with Time

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

the class ICSWriter method setId.

// -- IFormatHandler API methods --
/* @see loci.formats.FormatWriter#setId(String) */
@Override
public void setId(String id) throws FormatException, IOException {
    super.setId(id);
    if (!uniqueFiles.contains(id)) {
        uniqueFiles.add(id);
    }
    if (checkSuffix(currentId, "ids")) {
        String metadataFile = currentId.substring(0, currentId.lastIndexOf("."));
        metadataFile += ".ics";
        out.close();
        out = new RandomAccessOutputStream(metadataFile);
    }
    if (out.length() == 0) {
        out.writeBytes("\t\n");
        if (checkSuffix(id, "ids")) {
            out.writeBytes("ics_version\t1.0\n");
        } else {
            out.writeBytes("ics_version\t2.0\n");
        }
        out.writeBytes("filename\t" + currentId + "\n");
        out.writeBytes("layout\tparameters\t6\n");
        MetadataRetrieve meta = getMetadataRetrieve();
        MetadataTools.verifyMinimumPopulated(meta, series);
        int pixelType = FormatTools.pixelTypeFromString(meta.getPixelsType(series).toString());
        dimensionOffset = out.getFilePointer();
        int[] sizes = overwriteDimensions(meta);
        dimensionLength = (int) (out.getFilePointer() - dimensionOffset);
        if (validBits != 0) {
            out.writeBytes("layout\tsignificant_bits\t" + validBits + "\n");
        }
        boolean signed = FormatTools.isSigned(pixelType);
        boolean littleEndian = false;
        if (meta.getPixelsBigEndian(series) != null) {
            littleEndian = !meta.getPixelsBigEndian(series).booleanValue();
        } else if (meta.getPixelsBinDataCount(series) == 0) {
            littleEndian = !meta.getPixelsBinDataBigEndian(series, 0).booleanValue();
        }
        out.writeBytes("representation\tformat\t" + (pixelType == FormatTools.FLOAT ? "real\n" : "integer\n"));
        out.writeBytes("representation\tsign\t" + (signed ? "signed\n" : "unsigned\n"));
        out.writeBytes("representation\tcompression\tuncompressed\n");
        out.writeBytes("representation\tbyte_order\t");
        for (int i = 0; i < sizes[0] / 8; i++) {
            if ((littleEndian && (sizes[0] < 32 || pixelType == FormatTools.FLOAT)) || (!littleEndian && sizes[0] >= 32 && pixelType != FormatTools.FLOAT)) {
                out.writeBytes((i + 1) + "\t");
            } else {
                out.writeBytes(((sizes[0] / 8) - i) + "\t");
            }
        }
        out.writeBytes("\nparameter\tscale\t1.000000\t");
        final StringBuilder units = new StringBuilder();
        for (int i = 0; i < outputOrder.length(); i++) {
            char dim = outputOrder.charAt(i);
            Number value = 1.0;
            if (dim == 'X') {
                if (meta.getPixelsPhysicalSizeX(0) != null) {
                    value = meta.getPixelsPhysicalSizeX(0).value(UNITS.MICROMETER).doubleValue();
                }
                units.append("micrometers\t");
            } else if (dim == 'Y') {
                if (meta.getPixelsPhysicalSizeY(0) != null) {
                    value = meta.getPixelsPhysicalSizeY(0).value(UNITS.MICROMETER).doubleValue();
                }
                units.append("micrometers\t");
            } else if (dim == 'Z') {
                if (meta.getPixelsPhysicalSizeZ(0) != null) {
                    value = meta.getPixelsPhysicalSizeZ(0).value(UNITS.MICROMETER).doubleValue();
                }
                units.append("micrometers\t");
            } else if (dim == 'T') {
                Time valueTime = meta.getPixelsTimeIncrement(0);
                if (valueTime != null) {
                    value = valueTime.value(UNITS.SECOND);
                    units.append("seconds\t");
                }
            }
            out.writeBytes(value + "\t");
        }
        out.writeBytes("\nparameter\tunits\tbits\t" + units.toString() + "\n");
        out.writeBytes("\nend\n");
        pixelOffset = out.getFilePointer();
    } else if (checkSuffix(currentId, "ics")) {
        RandomAccessInputStream in = new RandomAccessInputStream(currentId);
        in.findString("\nend\n");
        pixelOffset = in.getFilePointer();
        in.close();
    }
    if (checkSuffix(currentId, "ids")) {
        pixelOffset = 0;
    }
}