Examples with HistogramPlotBuilder uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder used on opensource projects

Example 6 with HistogramPlotBuilder

use of uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder in project GDSC-SMLM by aherbert.

the class TcPalmAnalysis method reportAnalysis.

/**
 * Report statistics on the analysis results.
 *
 * @param settings the settings
 * @param clusters the clusters
 * @param calibration the data calibration
 */
private static void reportAnalysis(TcPalmAnalysisSettings settings, LocalList<ClusterData> clusters, DataCalibration calibration) {
    final WindowOrganiser wo = new WindowOrganiser();
    final Consumer<HistogramPlotBuilder> action = builder -> {
    /* noop. */
    };
    plotHistogram(settings.getShowSizeHistogram(), wo, clusters, "Size", c -> c.results.size(), null, action);
    plotHistogram(settings.getShowDurationHistogram(), wo, clusters, "Duration (" + calibration.getTimeUnitName() + ")", c -> calibration.timeConverter.convert(c.getDuration()), null, action);
    plotHistogram(settings.getShowAreaHistogram(), wo, clusters, "Area (" + calibration.getDistanceUnitName() + "^2)", c -> calibration.convertArea(c.getArea()), null, action);
    plotHistogram(settings.getShowDensityHistogram(), wo, clusters, "Density (" + calibration.getDistanceUnitName() + "^-2)", c -> c.results.size() / calibration.convertArea(c.getArea()), Double::isFinite, action);
    wo.tile();
}

Example 7 with HistogramPlotBuilder

use of uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder in project GDSC-SMLM by aherbert.

the class SpotInspector method plotHistogram.

private void plotHistogram(float[] data) {
    if (settings.plotHistogram) {
        final String title = TITLE + " Histogram";
        new HistogramPlotBuilder(title, StoredDataStatistics.create(data), Settings.SORT_ORDER[settings.sortOrderIndex]).setRemoveOutliersOption((settings.removeOutliers) ? 1 : 0).setNumberOfBins(settings.histogramBins).show();
    }
}

Example 8 with HistogramPlotBuilder

use of uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder in project GDSC-SMLM by aherbert.

the class TraceLengthAnalysis method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "No localisations in memory");
        return;
    }
    if (!showDialog()) {
        return;
    }
    // Load the results
    MemoryPeakResults results = ResultsManager.loadInputResults(settings.inputOption, false, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    try {
        distanceConverter = results.getDistanceConverter(DistanceUnit.UM);
        timeConverter = results.getTimeConverter(TimeUnit.SECOND);
    } catch (final Exception ex) {
        IJ.error(TITLE, "Cannot convert units to um or seconds: " + ex.getMessage());
        return;
    }
    // Get the localisation error (4s^2) in raw units^2
    double precision = 0;
    try {
        final PrecisionResultProcedure p = new PrecisionResultProcedure(results);
        p.getPrecision();
        // Precision in nm using the median
        precision = new Percentile().evaluate(p.precisions, 50);
        // Convert from nm to um to raw units
        final double rawPrecision = distanceConverter.convertBack(precision / 1e3);
        // Get the localisation error (4s^2) in units^2
        error = 4 * rawPrecision * rawPrecision;
    } catch (final Exception ex) {
        ImageJUtils.log(TITLE + " - Unable to compute precision: " + ex.getMessage());
    }
    // Analyse the track lengths
    results = results.copy();
    results.sort(IdFramePeakResultComparator.INSTANCE);
    // Ensure the first result triggers an id change
    lastid = results.getFirst().getId() - 1;
    results.forEach(this::processTrackLength);
    // For the final track
    store();
    msds = msdList.toArray();
    lengths = lengthList.toArray();
    ids = idList.toArray();
    final int[] limits = MathUtils.limits(lengths);
    h1 = new int[limits[1] + 1];
    h2 = new int[h1.length];
    x1 = SimpleArrayUtils.newArray(h1.length, 0, 1f);
    y1 = new float[x1.length];
    y2 = new float[x1.length];
    // Sort by MSD
    final int[] indices = SimpleArrayUtils.natural(msds.length);
    SortUtils.sortIndices(indices, msds, false);
    final double[] msds2 = msds.clone();
    final int[] lengths2 = lengths.clone();
    final int[] ids2 = ids.clone();
    for (int i = 0; i < indices.length; i++) {
        msds[i] = msds2[indices[i]];
        lengths[i] = lengths2[indices[i]];
        ids[i] = ids2[indices[i]];
    }
    // Interactive analysis
    final NonBlockingExtendedGenericDialog gd = new NonBlockingExtendedGenericDialog(TITLE);
    ImageJUtils.addMessage(gd, "Split traces into fixed or moving using the track diffusion coefficient (D).\n" + "Localisation error has been subtracted from jumps (%s nm).", MathUtils.rounded(precision));
    final Statistics s = Statistics.create(msds);
    final double av = s.getMean();
    final String msg = String.format("Average D per track = %s um^2/s", MathUtils.rounded(av));
    gd.addMessage(msg);
    // Histogram the diffusion coefficients
    final WindowOrganiser wo = new WindowOrganiser();
    final HistogramPlot histogramPlot = new HistogramPlotBuilder("Trace diffusion coefficient", StoredData.create(msds), "D (um^2/s)").setRemoveOutliersOption(1).setPlotLabel(msg).build();
    histogramPlot.show(wo);
    final double[] xvalues = histogramPlot.getPlotXValues();
    final double min = xvalues[0];
    final double max = xvalues[xvalues.length - 1];
    // see if we can build a nice slider range from the histogram limits
    if (max - min < 5) {
        // Because sliders are used when the range is <5 and floating point
        gd.addSlider("D_threshold", min, max, settings.msdThreshold);
    } else {
        gd.addNumericField("D_threshold", settings.msdThreshold, 2, 6, "um^2/s");
    }
    gd.addCheckbox("Normalise", settings.normalise);
    gd.addDialogListener((gd1, event) -> {
        settings.msdThreshold = gd1.getNextNumber();
        settings.normalise = gd1.getNextBoolean();
        update();
        return true;
    });
    if (ImageJUtils.isShowGenericDialog()) {
        draw(wo);
        wo.tile();
    }
    gd.setOKLabel("Save datasets");
    gd.setCancelLabel("Close");
    gd.addHelp(HelpUrls.getUrl("trace-length-analysis"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    // Sort by ID
    final PeakResult[] list = results.toArray();
    Arrays.sort(list, IdFramePeakResultComparator.INSTANCE);
    createResults(results, "Fixed", 0, lastIndex, list);
    createResults(results, "Moving", lastIndex, msds.length, list);
}

Example 9 with HistogramPlotBuilder

use of uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder in project GDSC-SMLM by aherbert.

the class TraceMolecules method summarise.

private void summarise(Consumer<String> output, Trace[] traces, int filtered, double distanceThreshold, double timeThreshold) {
    IJ.showStatus("Calculating summary ...");
    final Statistics[] stats = new Statistics[NAMES.length];
    for (int i = 0; i < stats.length; i++) {
        stats[i] = (settings.getShowHistograms() || settings.getSaveTraceData()) ? new StoredDataStatistics() : new Statistics();
    }
    int singles = 0;
    for (final Trace trace : traces) {
        final int nBlinks = trace.getBlinks() - 1;
        stats[BLINKS].add(nBlinks);
        final int[] onTimes = trace.getOnTimes();
        final int[] offTimes = trace.getOffTimes();
        double timeOn = 0;
        for (final int t : onTimes) {
            stats[T_ON].add(t * exposureTime);
            timeOn += t * exposureTime;
        }
        stats[TOTAL_T_ON].add(timeOn);
        if (offTimes != null) {
            double timeOff = 0;
            for (final int t : offTimes) {
                stats[T_OFF].add(t * exposureTime);
                timeOff += t * exposureTime;
            }
            stats[TOTAL_T_OFF].add(timeOff);
        }
        final double signal = trace.getSignal() / results.getGain();
        stats[TOTAL_SIGNAL].add(signal);
        stats[SIGNAL_PER_FRAME].add(signal / trace.size());
        stats[DWELL_TIME].add((trace.getTail().getEndFrame() - trace.getHead().getFrame() + 1) * exposureTime);
        if (trace.size() == 1) {
            singles++;
        }
    }
    // Add to the summary table
    final StringBuilder sb = new StringBuilder();
    sb.append(results.getName()).append('\t');
    sb.append(outputName.equals("Cluster") ? getClusteringAlgorithm(settings.getClusteringAlgorithm()) : getTraceMode(settings.getTraceMode())).append('\t');
    sb.append(MathUtils.rounded(getExposureTimeInMilliSeconds(), 3)).append('\t');
    sb.append(MathUtils.rounded(distanceThreshold, 3)).append('\t');
    sb.append(MathUtils.rounded(timeThreshold, 3));
    if (settings.getSplitPulses()) {
        sb.append(" *");
    }
    sb.append('\t');
    sb.append(convertSecondsToFrames(timeThreshold)).append('\t');
    sb.append(traces.length).append('\t');
    sb.append(filtered).append('\t');
    sb.append(singles).append('\t');
    sb.append(traces.length - singles).append('\t');
    for (int i = 0; i < stats.length; i++) {
        sb.append(MathUtils.rounded(stats[i].getMean(), 3)).append('\t');
    }
    if (java.awt.GraphicsEnvironment.isHeadless()) {
        IJ.log(sb.toString());
        return;
    }
    output.accept(sb.toString());
    if (settings.getShowHistograms()) {
        IJ.showStatus("Calculating histograms ...");
        final WindowOrganiser windowOrganiser = new WindowOrganiser();
        final HistogramPlotBuilder builder = new HistogramPlotBuilder(pluginTitle).setNumberOfBins(settings.getHistogramBins());
        for (int i = 0; i < NAMES.length; i++) {
            if (pluginSettings.displayHistograms[i]) {
                builder.setData((StoredDataStatistics) stats[i]).setName(NAMES[i]).setIntegerBins(integerDisplay[i]).setRemoveOutliersOption((settings.getRemoveOutliers() || alwaysRemoveOutliers[i]) ? 2 : 0).show(windowOrganiser);
            }
        }
        windowOrganiser.tile();
    }
    if (settings.getSaveTraceData()) {
        saveTraceData(stats);
    }
    IJ.showStatus("");
}

Example 10 with HistogramPlotBuilder

use of uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder in project GDSC-SMLM by aherbert.

the class CmosAnalysis method showHistogram.

private static void showHistogram(String name, double[] values, int bins, Statistics stats, WindowOrganiser wo) {
    final DoubleData data = DoubleData.wrap(values);
    final double minWidth = 0;
    final int removeOutliers = 0;
    final int shape = Plot.CIRCLE;
    final String label = String.format("Mean = %s +/- %s", MathUtils.rounded(stats.getMean()), MathUtils.rounded(stats.getStandardDeviation()));
    final HistogramPlot histogramPlot = new HistogramPlotBuilder(TITLE, data, name).setMinBinWidth(minWidth).setRemoveOutliersOption(removeOutliers).setNumberOfBins(bins).setPlotShape(shape).setPlotLabel(label).build();
    histogramPlot.show(wo);
    // Redraw using a log scale. This requires a non-zero y-min
    final Plot plot = histogramPlot.getPlot();
    final double[] limits = plot.getLimits();
    plot.setLimits(limits[0], limits[1], 1, limits[3]);
    plot.setAxisYLog(true);
    plot.updateImage();
}