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

Example 16 with Trace

use of uk.ac.sussex.gdsc.smlm.results.Trace 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));
                }
            }
        }
    }
}

Example 17 with Trace

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

the class TraceDiffusion method filterTraces.

/**
 * Split traces to contiguous traces and filter traces that are not the minimum length. Re-assigns
 * the ID for the output traces.
 *
 * @param name the name
 * @param traces the traces
 * @param minimumTraceLength the minimum trace length
 * @param ignoreEnds the ignore ends
 * @return The new traces
 */
private static Trace[] filterTraces(String name, Trace[] traces, int minimumTraceLength, boolean ignoreEnds) {
    final LocalList<Trace> list = new LocalList<>(traces.length);
    final int minLength = (ignoreEnds) ? minimumTraceLength + 2 : minimumTraceLength;
    final Consumer<Trace> action = (ignoreEnds) ? t -> {
        if (t.size() >= minLength) {
            t.removeEnds();
            list.add(t);
            t.setId(list.size());
        }
    } : t -> {
        if (t.size() >= minLength) {
            list.add(t);
            t.setId(list.size());
        }
    };
    final Consumer<ArrayPeakResultStore> action2 = (ignoreEnds) ? r -> {
        if (r.size() >= minLength) {
            r.remove(0);
            r.remove(r.size() - 1);
            final Trace t = new Trace(r);
            list.add(t);
            t.setId(list.size());
        }
    } : r -> {
        if (r.size() >= minLength) {
            final Trace t = new Trace(r);
            list.add(t);
            t.setId(list.size());
        }
    };
    final ArrayPeakResultStore results = new ArrayPeakResultStore(11);
    for (final Trace trace : traces) {
        if (trace.size() < minLength) {
            // Too short
            continue;
        }
        if (trace.size() == trace.getTail().getFrame() - trace.getHead().getFrame() + 1) {
            // Contiguous
            action.accept(trace);
        } else {
            // Split the trace
            int t1 = trace.getHead().getFrame();
            for (int i = 0; i < trace.size(); i++) {
                final PeakResult peak = trace.get(i);
                final int t2 = peak.getFrame();
                if (t2 - t1 > 1) {
                    // Non-contiguous
                    action2.accept(results);
                    results.clear();
                }
                t1 = t2;
                results.add(peak);
            }
            // Final trace
            action2.accept(results);
            results.clear();
        }
    }
    ImageJUtils.log("Filtered results '%s' : %s split and filtered to %d using " + "minimum length %d (Ignore ends = %b)", name, TextUtils.pleural(traces.length, "trace"), list.size(), minimumTraceLength, ignoreEnds);
    return list.toArray(new Trace[0]);
}

Example 18 with Trace

use of uk.ac.sussex.gdsc.smlm.results.Trace 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 19 with Trace

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

the class TraceMolecules method saveTraces.

/**
 * Save the traces to the file. A File open dialog is presented and the selected filename
 * returned.
 *
 * <p>If the id is above zero then the file open dialog title will have the id appended and the
 * filename is searched for .[0-9]+. and it is replaced with .id.
 *
 * @param sourceResults the source results
 * @param traces the traces
 * @param comment the comment
 * @param filename The initial filename
 * @param id The traces id (used if above 0)
 * @return The select filename (or null)
 */
static String saveTraces(MemoryPeakResults sourceResults, Trace[] traces, String comment, String filename, int id) {
    IJ.showStatus("Saving traces");
    String title = "Traces_File";
    if (id > 0) {
        title += id;
        final String regex = "\\.[0-9]+\\.";
        if (filename.matches(regex)) {
            filename = filename.replaceAll(regex, "." + (id) + ".");
        } else {
            filename = FileUtils.replaceExtension(filename, id + ".xls");
        }
    }
    filename = ImageJUtils.getFilename(title, filename);
    if (filename != null) {
        filename = FileUtils.replaceExtension(filename, "xls");
        final boolean showDeviations = sourceResults.hasDeviations();
        // Assume that are results are from a single frame but store the trace ID
        final TextFilePeakResults traceResults = new TextFilePeakResults(filename, showDeviations, false, true);
        traceResults.copySettings(sourceResults);
        traceResults.begin();
        if (!traceResults.isActive()) {
            IJ.error("Failed to write to file: " + filename);
        } else {
            traceResults.addComment(comment);
            for (final Trace trace : traces) {
                traceResults.addTrace(trace);
            }
            traceResults.end();
        }
    }
    IJ.showStatus("");
    return filename;
}

Example 20 with Trace

use of uk.ac.sussex.gdsc.smlm.results.Trace 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));
}