Examples with Trace uk.ac.sussex.gdsc.smlm.results.Trace used on opensource projects

Example 11 with Trace

use of uk.ac.sussex.gdsc.smlm.results.Trace in project GDSC-SMLM by aherbert.

the class TrackPopulationAnalysis method getTracks.

/**
 * Gets the tracks. Each track has contiguous frames and the length is enough to fit
 * {@code minTrackLength} overlapping windows of the specified size:
 *
 * <pre>
 * length >= window + minTrackLength - 1
 * </pre>
 *
 * @param combinedResults the combined results
 * @param window the window size
 * @param minTrackLength the minimum track length (assumed to be {@code >= 1})
 * @return the tracks
 */
private static List<Trace> getTracks(List<MemoryPeakResults> combinedResults, int window, int minTrackLength) {
    final LocalList<Trace> tracks = new LocalList<>();
    final Statistics stats = new Statistics();
    final int minSize = window + Math.max(minTrackLength, 1) - 1;
    combinedResults.forEach(results -> {
        final int start = tracks.size();
        // Sort by id then frame
        results = results.copy();
        results.sort(IdFramePeakResultComparator.INSTANCE);
        final int size = results.size();
        // Skip IDs not associated with clustering
        int index = 0;
        while (index < size && results.get(index).getId() < 1) {
            index++;
        }
        // Initialise current id and frame
        int id = results.get(index).getId() - 1;
        int frame = results.get(index).getFrame();
        Trace track = new Trace();
        for (; index < size; index++) {
            final PeakResult result = results.get(index);
            // Same ID and contiguous frames
            if (result.getId() != id || result.getFrame() != frame + 1) {
                addTrack(minSize, tracks, track);
                track = new Trace();
            }
            id = result.getId();
            frame = result.getFrame();
            track.add(result);
        }
        addTrack(minSize, tracks, track);
        stats.reset();
        for (int i = start; i < tracks.size(); i++) {
            stats.add(tracks.unsafeGet(i).size());
        }
        final StringBuilder sb = new StringBuilder(256);
        TextUtils.formatTo(sb, "%s tracks=%d, length=%s +/- %s", results.getName(), stats.getN(), MathUtils.rounded(stats.getMean(), 3), MathUtils.rounded(stats.getStandardDeviation(), 3));
        // Limit of diffusion coefficient from the localisation precision.
        // Just use the entire dataset for simplicity (i.e. not the tracks of min length).
        final PrecisionResultProcedure pp = new PrecisionResultProcedure(results);
        try {
            pp.getPrecision();
            final Mean mean = new Mean();
            for (final double p : pp.precisions) {
                mean.add(p);
            }
            // 2nDt = MSD (n = number of dimensions)
            // D = MSD / 2nt
            final CalibrationReader reader = results.getCalibrationReader();
            final double t = reader.getExposureTime() / 1000.0;
            // Assume computed in nm. Convert to um.
            final double x = mean.getMean() / 1000;
            final double d = x * x / (2 * t);
            TextUtils.formatTo(sb, ", precision=%s nm, D limit=%s um^2/s", MathUtils.rounded(x * 1000, 4), MathUtils.rounded(d, 4));
        } catch (final DataException ex) {
        // No precision
        }
        IJ.log(sb.toString());
    });
    return tracks;
}

Example 12 with Trace

use of uk.ac.sussex.gdsc.smlm.results.Trace in project GDSC-SMLM by aherbert.

the class SpotAnalysis method saveTraces.

private void saveTraces() {
    if (!onFrames.isEmpty() && updated) {
        final GenericDialog gd = new GenericDialog(PLUGIN_TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("The list contains unsaved selected frames.\n \nDo you want to continue?");
        gd.showDialog();
        if (!gd.wasOKed()) {
            return;
        }
    }
    // For all spots in the results window, get the ID and then save the traces to memory
    if (!ImageJUtils.isShowing(resultsWindow)) {
        return;
    }
    // Create a results set in memory
    final MemoryPeakResults results = new MemoryPeakResults();
    results.setName(PLUGIN_TITLE);
    results.begin();
    MemoryPeakResults.addResults(results);
    final ArrayList<TraceResult> traceResults = new ArrayList<>(resultsWindow.getTextPanel().getLineCount());
    for (int i = 0; i < resultsWindow.getTextPanel().getLineCount(); i++) {
        final String line = resultsWindow.getTextPanel().getLine(i);
        try (Scanner s = new Scanner(line)) {
            s.useDelimiter("\t");
            int id = -1;
            double signal = -1;
            // Be careful as the text panel may not contain what we expect, i.e. empty lines, etc
            if (s.hasNextInt()) {
                id = s.nextInt();
                try {
                    // cx
                    s.nextDouble();
                    // cy
                    s.nextDouble();
                    signal = s.nextDouble();
                } catch (final NoSuchElementException ex) {
                // Ignore
                }
            }
            if (id != -1 && signal != -1) {
                final Trace trace = traces.get(id);
                if (trace != null) {
                    results.addAll(trace.getPoints());
                    traceResults.add(new TraceResult(new Spot(id, signal), trace));
                }
            }
        }
    }
    results.end();
    saveTracesToFile(traceResults);
    IJ.showStatus("Saved traces");
}

Example 13 with Trace

use of uk.ac.sussex.gdsc.smlm.results.Trace in project GDSC-SMLM by aherbert.

the class SpotAnalysis method saveSpot.

private void saveSpot() {
    if (onFrames.isEmpty() || !updated) {
        return;
    }
    createResultsWindow();
    id++;
    double signal = 0;
    Trace trace = null;
    final float psfWidth = Float.parseFloat(widthTextField.getText());
    final float cx = areaBounds.x + areaBounds.width / 2.0f;
    final float cy = areaBounds.y + areaBounds.height / 2.0f;
    for (final Spot s : onFrames) {
        // Get the signal again since the background may have changed.
        final double spotSignal = getSignal(s.frame);
        signal += spotSignal;
        final float[] params = Gaussian2DPeakResultHelper.createOneAxisParams(0, (float) (spotSignal), cx, cy, 0, psfWidth);
        final PeakResult result = new PeakResult(s.frame, (int) cx, (int) cy, 0, 0, 0, 0, params, null);
        if (trace == null) {
            trace = new Trace(result);
        } else {
            trace.add(result);
        }
    }
    if (trace == null) {
        return;
    }
    final Statistics tOn = Statistics.create(trace.getOnTimes());
    final Statistics tOff = Statistics.create(trace.getOffTimes());
    resultsWindow.append(String.format("%d\t%.1f\t%.1f\t%s\t%s\t%s\t%d\t%s\t%s\t%s", id, cx, cy, MathUtils.rounded(signal, 4), MathUtils.rounded(tOn.getSum() * msPerFrame, 3), MathUtils.rounded(tOff.getSum() * msPerFrame, 3), trace.getBlinks() - 1, MathUtils.rounded(tOn.getMean() * msPerFrame, 3), MathUtils.rounded(tOff.getMean() * msPerFrame, 3), imp.getTitle()));
    // Save the individual on/off times for use in creating a histogram
    traces.put(id, trace);
    updated = false;
}

Example 14 with Trace

use of uk.ac.sussex.gdsc.smlm.results.Trace in project GDSC-SMLM by aherbert.

the class TraceDiffusion method getTraces.

private Trace[] getTraces(ArrayList<MemoryPeakResults> allResults) {
    this.results = allResults.get(0);
    // Results should be checked for calibration by this point
    exposureTime = results.getCalibrationReader().getExposureTime() / 1000;
    final Function<MemoryPeakResults, Trace[]> traceFunction = createTraceFunction();
    final ArrayList<Trace> allTraces = new ArrayList<>();
    additionalDatasets = -1;
    for (final MemoryPeakResults r : allResults) {
        additionalDatasets++;
        Trace[] traces = traceFunction.apply(r);
        traces = filterTraces(r.getName(), traces, clusteringSettings.getMinimumTraceLength(), clusteringSettings.getIgnoreEnds());
        allTraces.addAll(Arrays.asList(traces));
        // --- Save results ---
        if (traces.length != 0) {
            // Save the traces to memory
            TraceMolecules.saveResults(r, traces, "Tracks");
            if (clusteringSettings.getSaveTraces()) {
                // Sort traces by time to assist the results source in extracting frames sequentially.
                // Do this before saving to assist in debugging using the saved traces file.
                TraceMolecules.sortByTime(traces);
                final String newFilename = TraceMolecules.saveTraces(r, traces, createSettingsComment(), settings.tracesFilename, additionalDatasets);
                // Only keep the main filename in memory
                if (additionalDatasets == 0) {
                    settings.tracesFilename = newFilename;
                }
            }
        }
    }
    final Trace[] all = allTraces.toArray(new Trace[0]);
    if (additionalDatasets != 0) {
        ImageJUtils.log("Multiple inputs provide %d traces", allTraces.size());
        final MemoryPeakResults tracedResults = TraceManager.toPeakResults(all, results.getCalibration(), true);
        tracedResults.copySettings(results);
        tracedResults.setName(createCombinedName() + " Tracks");
        MemoryPeakResults.addResults(tracedResults);
    }
    return all;
}

Example 15 with Trace

use of uk.ac.sussex.gdsc.smlm.results.Trace in project GDSC-SMLM by aherbert.

the class DarkTimeAnalysis method analyse.

private void analyse(MemoryPeakResults results) {
    // Find min and max time frames
    results.sort();
    final int min = results.getFirstFrame();
    final int max = results.getLastFrame();
    // Trace results:
    // TODO - The search distance could have units to avoid assuming the results are in pixels
    final double d = settings.searchDistance / results.getCalibrationReader().getNmPerPixel();
    int range = max - min + 1;
    if (settings.maxDarkTime > 0) {
        range = Math.max(1, (int) Math.round(settings.maxDarkTime * 1000 / msPerFrame));
    }
    final TrackProgress tracker = SimpleImageJTrackProgress.getInstance();
    tracker.status("Analysing ...");
    tracker.log("Analysing (d=%s nm (%s px) t=%s s (%d frames)) ...", MathUtils.rounded(settings.searchDistance), MathUtils.rounded(d), MathUtils.rounded(range * msPerFrame / 1000.0), range);
    Trace[] traces;
    if (settings.method == 0) {
        final TraceManager tm = new TraceManager(results);
        tm.setTracker(tracker);
        tm.traceMolecules(d, range);
        traces = tm.getTraces();
    } else {
        final ClusteringEngine engine = new ClusteringEngine(Prefs.getThreads(), algorithms[settings.method - 1], tracker);
        final List<Cluster> clusters = engine.findClusters(TraceMolecules.convertToClusterPoints(results), d, range);
        traces = TraceMolecules.convertToTraces(results, clusters);
    }
    tracker.status("Computing histogram ...");
    // Build dark-time histogram
    final int[] times = new int[range];
    final StoredData stats = new StoredData();
    for (final Trace trace : traces) {
        if (trace.getBlinks() > 1) {
            for (final int t : trace.getOffTimes()) {
                times[t]++;
            }
            stats.add(trace.getOffTimes());
        }
    }
    plotDarkTimeHistogram(stats);
    // Cumulative histogram
    for (int i = 1; i < times.length; i++) {
        times[i] += times[i - 1];
    }
    final int total = times[times.length - 1];
    // Plot dark-time up to 100%
    double[] x = new double[range];
    double[] y = new double[range];
    int truncate = 0;
    for (int i = 0; i < x.length; i++) {
        x[i] = i * msPerFrame;
        if (times[i] == total) {
            // Final value at 100%
            y[i] = 100.0;
            truncate = i + 1;
            break;
        }
        y[i] = (100.0 * times[i]) / total;
    }
    if (truncate > 0) {
        x = Arrays.copyOf(x, truncate);
        y = Arrays.copyOf(y, truncate);
    }
    final String title = "Cumulative Dark-time";
    final Plot plot = new Plot(title, "Time (ms)", "Percentile");
    plot.addPoints(x, y, Plot.LINE);
    ImageJUtils.display(title, plot);
    // Report percentile
    for (int i = 0; i < y.length; i++) {
        if (y[i] >= settings.percentile) {
            ImageJUtils.log("Dark-time Percentile %.1f @ %s ms = %s s", settings.percentile, MathUtils.rounded(x[i]), MathUtils.rounded(x[i] / 1000));
            break;
        }
    }
    tracker.status("");
}