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

Example 1 with DynamicMultipleTargetTracing

use of uk.ac.sussex.gdsc.smlm.results.DynamicMultipleTargetTracing 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 2 with DynamicMultipleTargetTracing

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

the class TraceMolecules method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(pluginTitle, "No localisations in memory");
        return;
    }
    altKeyDown = ImageJUtils.isExtraOptions();
    Trace[] traces = null;
    int totalFiltered = 0;
    if ("dynamic".equals(arg)) {
        // -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
        // Dynamic Mutliple Target Tracing
        // -=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-
        outputName = "Dynamic Trace";
        if (!showDynamicTraceDialog()) {
            return;
        }
        final DmttConfiguration config = createDmttConfiguration();
        traces = new DynamicMultipleTargetTracing(results).traceMolecules(config).toArray(new Trace[0]);
    } else if ("cluster".equals(arg)) {
        // -=-=-=-=-=
        // Clustering
        // -=-=-=-=-=
        outputName = "Cluster";
        if (!showClusterDialog()) {
            return;
        }
        final ClusteringEngine engine = new ClusteringEngine(Prefs.getThreads(), getClusteringAlgorithm(settings.getClusteringAlgorithm()), SimpleImageJTrackProgress.getInstance());
        if (settings.getSplitPulses()) {
            engine.setPulseInterval(settings.getPulseInterval());
            limitTimeThreshold(settings.getPulseInterval());
        }
        final List<Cluster> clusters = engine.findClusters(convertToClusterPoints(), getDistance(settings.getDistanceThreshold(), results.getCalibration()), timeThresholdInFrames());
        if (clusters == null) {
            ImageJUtils.log("Aborted");
            return;
        }
        traces = convertToTraces(clusters);
    } else {
        // -=-=-=-
        // Tracing
        // -=-=-=-
        outputName = "Trace";
        if (!showDialog()) {
            return;
        }
        final TraceManager manager = new TraceManager(results);
        manager.setTraceMode(getTraceMode(settings.getTraceMode()));
        manager.setActivationFrameInterval(settings.getPulseInterval());
        manager.setActivationFrameWindow(settings.getPulseWindow());
        manager.setDistanceExclusion(getDistance(settings.getDistanceExclusion(), results.getCalibration()));
        if (settings.getOptimise()) {
            // Optimise before configuring for a pulse interval
            runOptimiser(manager);
        }
        if (settings.getSplitPulses()) {
            manager.setPulseInterval(settings.getPulseInterval());
            limitTimeThreshold(settings.getPulseInterval());
        }
        manager.setTracker(SimpleImageJTrackProgress.getInstance());
        manager.traceMolecules(getDistance(settings.getDistanceThreshold(), results.getCalibration()), timeThresholdInFrames());
        traces = manager.getTraces();
        totalFiltered = manager.getTotalFiltered();
    }
    // --=-=-=-=-=-
    // Results processing
    // --=-=-=-=-=-
    outputName += (outputName.endsWith("e") ? "" : "e") + "d";
    saveResults(results, traces, outputName);
    // Save singles + single localisations in a trace
    saveCentroidResults(results, getSingles(traces), outputName + " Singles");
    final Trace[] multiTraces = getTraces(traces);
    saveResults(results, multiTraces, outputName + " Multi");
    // Save centroids
    outputName += " Centroids";
    final MemoryPeakResults tracedResults = saveCentroidResults(results, traces, outputName);
    // Save traces separately
    saveCentroidResults(results, multiTraces, outputName + " Multi");
    // 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.
    sortByTime(traces);
    if (settings.getSaveTraces()) {
        saveTraces(traces);
    }
    summarise(createSummaryTable(), traces, totalFiltered, settings.getDistanceThreshold(), timeThresholdInSeconds());
    IJ.showStatus(String.format("%d localisations => %d traces (%d filtered)", results.size(), tracedResults.size(), totalFiltered));
}