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

Example 1 with TraceManager

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

the class PcPalmMolecules method traceMolecules.

/**
 * Trace localisations.
 *
 * @param results The results
 * @param precisions the precisions
 * @param distance The distance threshold (nm)
 * @param time The time threshold (frames)
 * @param singles a list of the singles (not grouped into molecules)
 * @return a list of molecules
 */
private static ArrayList<Molecule> traceMolecules(MemoryPeakResults results, double[] precisions, double distance, int time, ArrayList<Molecule> singles) {
    // These plugins are not really supported so just leave them to throw an exception if
    // the data cannot be handled
    final TypeConverter<IntensityUnit> ic = results.getCalibrationReader().getIntensityConverter(IntensityUnit.PHOTON);
    final TypeConverter<DistanceUnit> dc = results.getCalibrationReader().getDistanceConverter(DistanceUnit.NM);
    // Create a new dataset with the precision
    final MemoryPeakResults results2 = new MemoryPeakResults(results.size());
    for (int i = 0, size = results.size(); i < size; i++) {
        final AttributePeakResult peak2 = new AttributePeakResult(results.get(i));
        peak2.setPrecision(precisions[i]);
        results2.add(peak2);
    }
    final TraceManager tm = new TraceManager(results2);
    final double distanceThreshold = dc.convertBack(distance);
    tm.traceMolecules(distanceThreshold, time);
    final Trace[] traces = tm.getTraces();
    final ArrayList<Molecule> molecules = new ArrayList<>(traces.length);
    for (final Trace t : traces) {
        final double p = t.getLocalisationPrecision(dc);
        final float[] centroid = t.getCentroid();
        final List<Molecule> list = t.size() == 1 ? singles : molecules;
        list.add(new Molecule(dc.convert(centroid[0]), dc.convert(centroid[1]), p, ic.convert(t.getSignal())));
    }
    log("  %d localisations traced to %d molecules (%d singles, %d traces) using d=%.2f nm," + " t=%d frames (%s s)", results.size(), molecules.size() + singles.size(), singles.size(), molecules.size(), distance, time, MathUtils.rounded(time * results.getCalibrationReader().getExposureTime() / 1000.0));
    return molecules;
}

Example 2 with TraceManager

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

the class NeighbourAnalysis 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;
    }
    final TraceManager manager = new TraceManager(results);
    // Run the tracing
    manager.setTracker(SimpleImageJTrackProgress.getInstance());
    final Trace[] traces = manager.findNeighbours(settings.distanceThreshold, settings.timeThreshold);
    saveTraces(traces);
}

Example 3 with TraceManager

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

the class TraceDiffusion method createTraceFunction.

/**
 * Creates the trace function for the configured trace diffusion mode.
 *
 * @return the function
 */
private Function<MemoryPeakResults, Trace[]> createTraceFunction() {
    if (clusteringSettings.getTraceDiffusionMode() == 1) {
        final DmttConfiguration config = createDmttConfiguration();
        return r -> new DynamicMultipleTargetTracing(r).traceMolecules(config).toArray(new Trace[0]);
    }
    // Nearest neighbour
    // Convert from NM to the native units of the results
    final Converter c = CalibrationHelper.getDistanceConverter(results.getCalibration(), DistanceUnit.NM);
    final double distanceThreshold = c.convertBack(clusteringSettings.getDistanceThreshold());
    final double distanceExclusion = c.convertBack(clusteringSettings.getDistanceExclusion());
    return r -> {
        final TraceManager manager = new TraceManager(r);
        // Run the tracing
        manager.setTracker(SimpleImageJTrackProgress.getInstance());
        manager.setDistanceExclusion(distanceExclusion);
        manager.traceMolecules(distanceThreshold, 1);
        return manager.getTraces();
    };
}

Example 4 with TraceManager

use of uk.ac.sussex.gdsc.smlm.results.TraceManager 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("");
}

Example 5 with TraceManager

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

the class HysteresisFilter method setup.

@Override
public void setup(MemoryPeakResults peakResults) {
    ok = new HashSet<>();
    // Create a set of candidates and valid peaks
    final MemoryPeakResults traceResults = new MemoryPeakResults();
    // Initialise peaks to check
    final LinkedList<PeakResult> candidates = new LinkedList<>();
    peakResults.forEach((PeakResultProcedure) result -> {
        switch(getStatus(result)) {
            case OK:
                ok.add(result);
                traceResults.add(result);
                break;
            case CANDIDATE:
                candidates.add(result);
                traceResults.add(result);
                break;
            default:
                break;
        }
    });
    if (candidates.isEmpty()) {
        // No candidates for tracing so just return
        return;
    }
    double distanceThreshold;
    switch(searchDistanceMode) {
        case 1:
            distanceThreshold = searchDistance / peakResults.getNmPerPixel();
            break;
        case 0:
        default:
            distanceThreshold = getSearchDistanceUsingCandidates(peakResults, candidates);
    }
    if (distanceThreshold <= 0) {
        return;
    }
    // This must be in frames
    int myTimeThreshold;
    if (timeThresholdMode == 1) {
        // time threshold is in Seconds.
        // Default to 1 frame if not calibrated.
        myTimeThreshold = 1;
        if (peakResults.hasCalibration()) {
            // Convert time threshold in seconds to frames
            final CalibrationReader cr = peakResults.getCalibrationReader();
            final double et = cr.getExposureTime();
            if (et > 0) {
                myTimeThreshold = (int) Math.round((this.timeThreshold / et));
            }
        }
    } else {
        // frames
        myTimeThreshold = (int) this.timeThreshold;
    }
    if (myTimeThreshold <= 0) {
        return;
    }
    // Trace through candidates
    final TraceManager tm = new TraceManager(traceResults);
    tm.setTraceMode(TraceMode.LATEST_FORERUNNER);
    tm.traceMolecules(distanceThreshold, myTimeThreshold);
    final Trace[] traces = tm.getTraces();
    for (final Trace trace : traces) {
        if (trace.size() > 1) {
            // Check if the trace touches a valid point
            boolean isOk = false;
            for (int i = 0; i < trace.size(); i++) {
                if (ok.contains(trace.get(i))) {
                    isOk = true;
                    break;
                }
            }
            // Add the entire trace to the OK points
            if (isOk) {
                for (int i = 0; i < trace.size(); i++) {
                    ok.add(trace.get(i));
                }
            }
        }
    }
}