Examples with TimeUnit uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.TimeUnit used on opensource projects

Example 1 with TimeUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.TimeUnit in project GDSC-SMLM by aherbert.

the class TimeUnitTest method check.

private static void check(double msPerFrame, ExpectedUnit<TimeUnit>... expectedUnits) {
    final int n = expectedUnits.length;
    TypeConverter<TimeUnit> conv;
    for (int i = 0; i < n; i++) {
        final TimeUnit u1 = expectedUnits[i].unit;
        final double v1 = expectedUnits[i].value;
        for (int j = 0; j < n; j++) {
            final TimeUnit u2 = expectedUnits[j].unit;
            conv = UnitConverterUtils.createConverter(u1, u2, msPerFrame);
            final double o = conv.convert(v1);
            Assertions.assertEquals(expectedUnits[j].value, o, 1e-5, () -> u1 + " to " + u2);
        }
    }
}

Example 2 with TimeUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.TimeUnit in project GDSC-SMLM by aherbert.

the class TraceExporter method exportSpotOn.

private void exportSpotOn(MemoryPeakResults results) {
    try (BufferedWriter out = Files.newBufferedWriter(Paths.get(settings.directory, results.getName() + ".csv"))) {
        out.write("frame,t,trajectory,x,y");
        out.newLine();
        final TypeConverter<TimeUnit> converter = UnitConverterUtils.createConverter(TimeUnit.FRAME, TimeUnit.SECOND, results.getCalibrationReader().getExposureTime());
        @SuppressWarnings("resource") final BufferedWriter writer = out;
        results.forEach(DistanceUnit.UM, (XyrResultProcedure) (x, y, result) -> {
            try {
                if (result.hasEndFrame()) {
                    final String sId = Integer.toString(result.getId());
                    final String sx = Float.toString(x);
                    final String sy = Float.toString(y);
                    for (int t = result.getFrame(); t <= result.getEndFrame(); t++) {
                        writer.write(Integer.toString(t));
                        writer.write(",");
                        writer.write(Float.toString(converter.convert(t)));
                        writer.write(",");
                        writer.write(sId);
                        writer.write(",");
                        writer.write(sx);
                        writer.write(",");
                        writer.write(sy);
                        writer.newLine();
                    }
                } else {
                    writer.write(Integer.toString(result.getFrame()));
                    writer.write(",");
                    writer.write(Float.toString(converter.convert(result.getFrame())));
                    writer.write(",");
                    writer.write(Integer.toString(result.getId()));
                    writer.write(",");
                    writer.write(Float.toString(x));
                    writer.write(",");
                    writer.write(Float.toString(y));
                    writer.newLine();
                }
            } catch (final IOException ex) {
                throw new RuntimeException(ex);
            }
        });
    } catch (final IOException | RuntimeException ex) {
        handleException(ex);
    }
}

Example 3 with TimeUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.TimeUnit in project GDSC-SMLM by aherbert.

the class LoadLocalisations method getFields.

private static boolean getFields(LoadLocalisationsSettings.Builder settings) {
    settings.getLocalisationsFilename();
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Load delimited localisations");
    // Show a preview of the file in a text area
    final List<String> preview = loadLines(settings, 100);
    if (!preview.isEmpty()) {
        // Add a TextArea. This cannot add scroll bars after the constructor so we put up
        // with this. But we can use a monospaced font and size the text area nicely.
        gd.addTextAreas(preview.stream().collect(Collectors.joining("\n")), null, Math.min(10, preview.size()), Math.min(80, preview.stream().mapToInt(String::length).max().getAsInt()));
        final TextArea ta = gd.getTextArea1();
        final Font font = new Font(Font.MONOSPACED, Font.PLAIN, (int) (10 * Prefs.getGuiScale()));
        ta.setFont(font);
        ta.setEditable(false);
    }
    if (!settings.getHideFieldDatasetName()) {
        gd.addStringField("Dataset_name", settings.getName(), 30);
    }
    gd.addMessage("Calibration:");
    // Allow the full camera type top be captured
    final Calibration.Builder calibrationBuilder = settings.getCalibrationBuilder();
    final CalibrationWriter cw = new CalibrationWriter(calibrationBuilder);
    PeakFit.addCameraOptions(gd, 0, cw);
    // Only primitive support for other calibration
    gd.addNumericField("Pixel_size", cw.getNmPerPixel(), 3, 8, "nm");
    gd.addNumericField("Exposure_time", cw.getExposureTime(), 3, 8, "");
    // This is the unit for the exposure time (used to convert the exposure time to milliseconds).
    // Use the name as the list is a truncated list of the full enum.
    final TimeUnit t = calibrationBuilder.getTimeCalibration().getTimeUnit();
    gd.addChoice("Time_unit", TimeUnitLoader.getTimeUnits(), SettingsManager.getName(UnitHelper.getName(t), UnitHelper.getShortName(t)));
    gd.addMessage("Records:");
    gd.addNumericField("Header_lines", settings.getHeaderLines(), 0);
    gd.addStringField("Comment", settings.getComment());
    gd.addStringField("Delimiter", settings.getDelimiter());
    gd.addChoice("Distance_unit", SettingsManager.getDistanceUnitNames(), cw.getDistanceUnitValue());
    gd.addChoice("Intensity_unit", SettingsManager.getIntensityUnitNames(), cw.getIntensityUnitValue());
    gd.addMessage("Define the fields:");
    gd.addNumericField("Frame", settings.getFieldT(), 0);
    gd.addNumericField("ID", settings.getFieldId(), 0);
    gd.addNumericField("Category", settings.getFieldCategory(), 0);
    gd.addNumericField("X", settings.getFieldX(), 0);
    gd.addNumericField("Y", settings.getFieldY(), 0);
    gd.addNumericField("Z", settings.getFieldZ(), 0);
    gd.addNumericField("Intensity", settings.getFieldI(), 0);
    gd.addNumericField("Sx", settings.getFieldSx(), 0);
    gd.addNumericField("Sy", settings.getFieldSy(), 0);
    gd.addNumericField("Precision", settings.getFieldPrecision(), 0);
    gd.addChoice("Precision_method", SettingsManager.getPrecisionMethodNames(), cw.getPrecisionMethodValue());
    gd.addHelp(HelpUrls.getUrl("load-localisations"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    if (!settings.getHideFieldDatasetName()) {
        settings.setName(getNextString(gd, settings.getName()));
    }
    cw.setCameraType(SettingsManager.getCameraTypeValues()[gd.getNextChoiceIndex()]);
    cw.setNmPerPixel(gd.getNextNumber());
    cw.setExposureTime(gd.getNextNumber());
    // The time units used a truncated list so look-up the value from the index
    calibrationBuilder.getTimeCalibrationBuilder().setTimeUnit(TimeUnitLoader.getTimeUnitValues()[gd.getNextChoiceIndex()]);
    settings.setHeaderLines((int) gd.getNextNumber());
    settings.setComment(gd.getNextString());
    settings.setDelimiter(getNextString(gd, settings.getDelimiter()));
    cw.setDistanceUnit(DistanceUnit.forNumber(gd.getNextChoiceIndex()));
    cw.setIntensityUnit(IntensityUnit.forNumber(gd.getNextChoiceIndex()));
    final int[] columns = new int[10];
    for (int i = 0; i < columns.length; i++) {
        columns[i] = (int) gd.getNextNumber();
    }
    int index = 0;
    settings.setFieldT(columns[index++]);
    settings.setFieldId(columns[index++]);
    settings.setFieldCategory(columns[index++]);
    settings.setFieldX(columns[index++]);
    settings.setFieldY(columns[index++]);
    settings.setFieldZ(columns[index++]);
    settings.setFieldI(columns[index++]);
    settings.setFieldSx(columns[index++]);
    settings.setFieldSy(columns[index++]);
    settings.setFieldPrecision(columns[index]);
    cw.setPrecisionMethod(PrecisionMethod.forNumber(gd.getNextChoiceIndex()));
    // Collect the camera calibration
    gd.collectOptions();
    // Validate after reading the dialog (so we store the last entered values)
    if (gd.invalidNumber()) {
        IJ.error(TITLE, "Invalid number in input fields");
        return false;
    }
    for (int i = 0; i < columns.length; i++) {
        if (columns[i] < 0) {
            continue;
        }
        for (int j = i + 1; j < columns.length; j++) {
            if (columns[j] < 0) {
                continue;
            }
            if (columns[i] == columns[j]) {
                IJ.error(TITLE, "Duplicate indicies: " + columns[i]);
                return false;
            }
        }
    }
    if (cw.getNmPerPixel() <= 0) {
        IJ.error(TITLE, "Require positive pixel pitch");
        return false;
    }
    if (cw.isCcdCamera()) {
        if (!cw.hasCountPerPhoton()) {
            IJ.error(TITLE, "Require positive count/photon for CCD camera type");
            return false;
        }
    } else {
    // Q.Validate other camera types?
    }
    if (settings.getFieldX() < 0 || settings.getFieldY() < 0) {
        IJ.error(TITLE, "Require valid X and Y indices");
        return false;
    }
    return true;
}

Example 4 with TimeUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.TimeUnit in project GDSC-SMLM by aherbert.

the class TraceMolecules method runOptimiser.

private void runOptimiser(TraceManager manager) {
    // Get an estimate of the number of molecules without blinking
    final Statistics stats = new Statistics();
    final double nmPerPixel = this.results.getNmPerPixel();
    final PrecisionResultProcedure pp = new PrecisionResultProcedure(results);
    pp.getPrecision();
    stats.add(pp.precisions);
    // Use twice the precision to get the initial distance threshold
    // Use 2.5x sigma as per the PC-PALM protocol in Sengupta, et al (2013) Nature Protocols 8, 345
    final double dEstimate = stats.getMean() * 2.5 / nmPerPixel;
    final int traceCount = manager.traceMolecules(dEstimate, 1);
    if (!getParameters(traceCount, dEstimate)) {
        return;
    }
    // TODO - Convert the distance threshold to use nm instead of pixels?
    final List<double[]> results = runTracing(manager, settings.getMinDistanceThreshold(), settings.getMaxDistanceThreshold(), settings.getMinTimeThreshold(), settings.getMaxTimeThreshold(), settings.getOptimiserSteps());
    // Compute fractional difference from the true value:
    // Use blinking rate directly or the estimated number of molecules
    double reference;
    int statistic;
    if (optimiseBlinkingRate) {
        reference = settings.getBlinkingRate();
        statistic = 3;
        IJ.log(String.format("Estimating blinking rate: %.2f", reference));
    } else {
        reference = traceCount / settings.getBlinkingRate();
        statistic = 2;
        IJ.log(String.format("Estimating number of molecules: %d / %.2f = %.2f", traceCount, settings.getBlinkingRate(), reference));
    }
    for (final double[] result : results) {
        if (optimiseBlinkingRate) {
            result[2] = (reference - result[statistic]) / reference;
        } else {
            result[2] = (result[statistic] - reference) / reference;
        }
    }
    // Locate the optimal parameters with a fit of the zero contour
    final boolean found = findOptimalParameters(results);
    createPlotResults(results);
    if (!found) {
        return;
    }
    // Make fractional difference absolute so that lowest is best
    for (final double[] result : results) {
        result[2] = Math.abs(result[2]);
    }
    // Set the optimal thresholds using the lowest value
    double[] best = new double[] { 0, 0, Double.MAX_VALUE };
    for (final double[] result : results) {
        if (best[2] > result[2]) {
            best = result;
        }
    }
    settings.setDistanceThreshold(best[0]);
    // The optimiser works using frames so convert back to the correct units
    final TypeConverter<TimeUnit> convert = UnitConverterUtils.createConverter(TimeUnit.FRAME, settings.getTimeUnit(), getExposureTimeInMilliSeconds());
    settings.setTimeThreshold(convert.convert(best[1]));
    IJ.log(String.format("Optimal fractional difference @ D-threshold=%g nm, T-threshold=%f s (%d frames)", settings.getDistanceThreshold(), timeThresholdInSeconds(), timeThresholdInFrames()));
    writeSettings();
}

Example 5 with TimeUnit

use of uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.TimeUnit in project GDSC-SMLM by aherbert.

the class TraceMolecules method findOptimalParameters.

/**
 * Find the contour that intersects zero on the fractional difference plot. Find the point on the
 * contour nearest the origin.
 *
 * @param results the results
 * @return true, if successful
 */
private boolean findOptimalParameters(List<double[]> results) {
    // This method only works if there are many results and if the results
    // cover enough of the search space to go from above zero (i.e. not enough traces)
    // to below zero (i.e. too many traces)
    final int maxx = timeThresholds.length;
    final int maxy = ddistanceThresholds.length;
    // --------
    // Find zero crossings using linear interpolation
    zeroCrossingPoints = new ArrayList<>();
    // --------
    // Pass across all time points
    boolean noZeroCrossingAtT0 = false;
    boolean noZeroCrossingAtTn = false;
    for (int x = 0; x < maxx; x++) {
        // Find zero crossings on distance points
        final double[] data = new double[maxy];
        for (int y = 0; y < maxy; y++) {
            final int i = y * maxx + x;
            final double[] result = results.get(i);
            data[y] = result[2];
        }
        final double zeroCrossing = findZeroCrossing(data, ddistanceThresholds);
        if (zeroCrossing > 0) {
            zeroCrossingPoints.add(new double[] { timeThresholds[x], zeroCrossing });
        } else if (x == 0) {
            noZeroCrossingAtT0 = true;
        } else if (x == maxx - 1) {
            noZeroCrossingAtTn = true;
        }
    }
    // If there were not enough zero crossings then the ranges are wrong
    if (zeroCrossingPoints.size() < 3) {
        IJ.log(String.format("Very few zero crossings (%d). Increase the optimisation space", zeroCrossingPoints.size()));
        return false;
    }
    // --------
    // Use relative distances to find the zero crossing with the smallest distance from origin
    // and set this as the optimal parameters
    // --------
    double minD = Double.MAX_VALUE;
    final double maxTimeThresholdInFrames = settings.getMaxTimeThreshold();
    // The optimiser works using frames so convert back to the correct units
    final TypeConverter<TimeUnit> convert = UnitConverterUtils.createConverter(TimeUnit.FRAME, settings.getTimeUnit(), getExposureTimeInMilliSeconds());
    for (final double[] point : zeroCrossingPoints) {
        final double dx = point[0] / maxTimeThresholdInFrames;
        final double dy = point[1] / settings.getMaxDistanceThreshold();
        final double d = dx * dx + dy * dy;
        if (d < minD) {
            minD = d;
            settings.setDistanceThreshold(point[1]);
            settings.setTimeThreshold(convert.convert(point[0]));
        }
    }
    // --------
    // Add more points to make the plotted line look better when showing the plot.
    // --------
    // Pass across all distance points
    boolean noZeroCrossingAtD0 = false;
    boolean noZeroCrossingAtDn = false;
    final double[] tThresholdsD = SimpleArrayUtils.toDouble(timeThresholds);
    for (int y = 0; y < maxy; y++) {
        // Find zero crossings on time points
        final double[] data = new double[maxx];
        for (int x = 0; x < maxx; x++) {
            final int i = y * maxx + x;
            final double[] result = results.get(i);
            data[x] = result[2];
        }
        final double zeroCrossing = findZeroCrossing(data, tThresholdsD);
        if (zeroCrossing > 0) {
            zeroCrossingPoints.add(new double[] { zeroCrossing, ddistanceThresholds[y] });
        } else if (y == 0) {
            noZeroCrossingAtD0 = true;
        } else if (y == maxy - 1) {
            noZeroCrossingAtDn = true;
        }
    }
    sortPoints();
    // --------
    // Output a message suggesting if the limits should be updated.
    // --------
    final StringBuilder sb = new StringBuilder();
    boolean reduceTime = false;
    boolean reduceDistance = false;
    if (noZeroCrossingAtDn && settings.getMinTimeThreshold() > 1) {
        sb.append(" * No zero crossing at max distance\n");
        reduceTime = true;
    }
    if (noZeroCrossingAtTn && settings.getMinDistanceThreshold() > 0) {
        sb.append(" * No zero crossing at max time\n");
        reduceDistance = true;
    }
    if (!noZeroCrossingAtD0 && settings.getMinDistanceThreshold() > 0) {
        sb.append(" * Zero crossing at min distance\n");
        reduceDistance = true;
    }
    if (!noZeroCrossingAtT0 && settings.getMinTimeThreshold() > 1) {
        sb.append(" * Zero crossing at min time\n");
        reduceTime = true;
    }
    if (reduceTime) {
        sb.append(" => Reduce the min time threshold\n");
    }
    if (reduceDistance) {
        sb.append(" => Reduce the min distance threshold\n");
    }
    if (sb.length() > 0) {
        sb.insert(0, "\nWarning:\n");
        sb.append("\n");
        IJ.log(sb.toString());
    }
    return true;
}