Examples with IJTrackProgress gdsc.core.ij.IJTrackProgress used on opensource projects

Example 1 with IJTrackProgress

use of gdsc.core.ij.IJTrackProgress in project GDSC-SMLM by aherbert.

the class ResequenceResults method run.

/*
	 * (non-)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    if (!showDialog())
        return;
    MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, true);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    if (resequenceResults(results, start, block, skip, (logMapping) ? new IJTrackProgress() : null))
        IJ.showStatus("Resequenced " + results.getName());
}

Example 2 with IJTrackProgress

use of gdsc.core.ij.IJTrackProgress in project GDSC-SMLM by aherbert.

the class ResultsManager method loadInputResults.

/**
	 * Load the results from the named input option
	 * 
	 * @param inputOption
	 * @param checkCalibration
	 *            Set to true to ensure the results have a valid calibration
	 * @return
	 */
public static MemoryPeakResults loadInputResults(String inputOption, boolean checkCalibration) {
    MemoryPeakResults results = null;
    PeakResultsReader reader = null;
    if (inputOption.equals(INPUT_NONE)) {
    } else if (inputOption.equals(INPUT_FILE)) {
        IJ.showStatus("Reading results file ...");
        reader = new PeakResultsReader(inputFilename);
        IJ.showStatus("Reading " + reader.getFormat() + " results file ...");
        ResultOption[] options = reader.getOptions();
        if (options != null)
            collectOptions(reader, options);
        reader.setTracker(new IJTrackProgress());
        results = reader.getResults();
        reader.getTracker().progress(1.0);
        if (results != null && results.size() > 0) {
            // If the name contains a .tif suffix then create an image source
            if (results.getName() != null && results.getName().contains(".tif") && results.getSource() == null) {
                int index = results.getName().indexOf(".tif");
                results.setSource(new IJImageSource(results.getName().substring(0, index)));
            }
        }
    } else {
        results = loadMemoryResults(inputOption);
    }
    if (results != null && results.size() > 0 && checkCalibration) {
        if (!checkCalibration(results, reader))
            results = null;
    }
    IJ.showStatus("");
    return results;
}

Example 3 with IJTrackProgress

use of gdsc.core.ij.IJTrackProgress in project GDSC-SMLM by aherbert.

the class DarkTimeAnalysis method analyse.

private void analyse(MemoryPeakResults results) {
    // Find min and max time frames
    results.sort();
    int min = results.getHead().getFrame();
    int max = results.getTail().getEndFrame();
    // Trace results
    double d = searchDistance / results.getCalibration().getNmPerPixel();
    int range = max - min + 1;
    if (maxDarkTime > 0)
        range = FastMath.max(1, (int) Math.round(maxDarkTime * 1000 / msPerFrame));
    IJTrackProgress tracker = new IJTrackProgress();
    tracker.status("Analysing ...");
    tracker.log("Analysing (d=%s nm (%s px) t=%s s (%d frames)) ...", Utils.rounded(searchDistance), Utils.rounded(d), Utils.rounded(range * msPerFrame / 1000.0), range);
    Trace[] traces;
    if (method == 0) {
        TraceManager tm = new TraceManager(results);
        tm.setTracker(tracker);
        tm.traceMolecules(d, range);
        traces = tm.getTraces();
    } else {
        ClusteringEngine engine = new ClusteringEngine(Prefs.getThreads(), algorithms[method - 1], tracker);
        List<PeakResult> peakResults = results.getResults();
        ArrayList<Cluster> clusters = engine.findClusters(TraceMolecules.convertToClusterPoints(peakResults), d, range);
        traces = TraceMolecules.convertToTraces(peakResults, clusters);
    }
    tracker.status("Computing histogram ...");
    // Build dark-time histogram
    int[] times = new int[range];
    StoredData stats = new StoredData();
    for (Trace trace : traces) {
        if (trace.getNBlinks() > 1) {
            for (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];
    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;
        y[i] = (100.0 * times[i]) / total;
        if (// 100%
        times[i] == total) {
            truncate = i + 1;
            break;
        }
    }
    if (truncate > 0) {
        x = Arrays.copyOf(x, truncate);
        y = Arrays.copyOf(y, truncate);
    }
    String title = "Cumulative Dark-time";
    Plot2 plot = new Plot2(title, "Time (ms)", "Percentile", x, y);
    Utils.display(title, plot);
    // Report percentile
    for (int i = 0; i < y.length; i++) {
        if (y[i] >= percentile) {
            Utils.log("Dark-time Percentile %.1f @ %s ms = %s s", percentile, Utils.rounded(x[i]), Utils.rounded(x[i] / 1000));
            break;
        }
    }
    tracker.status("");
}

Example 4 with IJTrackProgress

use of gdsc.core.ij.IJTrackProgress 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.getCalibration().getExposureTime() / 1000;
    final double nmPerPixel = results.getCalibration().getNmPerPixel();
    ArrayList<Trace> allTraces = new ArrayList<Trace>();
    additionalDatasets = -1;
    for (MemoryPeakResults r : allResults) {
        additionalDatasets++;
        TraceManager manager = new TraceManager(r);
        // Run the tracing
        manager.setTracker(new IJTrackProgress());
        manager.setDistanceExclusion(settings.distanceExclusion / nmPerPixel);
        manager.traceMolecules(settings.distanceThreshold / nmPerPixel, 1);
        Trace[] traces = manager.getTraces();
        traces = filterTraces(r.getName(), traces, settings.minimumTraceLength, settings.ignoreEnds);
        allTraces.addAll(Arrays.asList(traces));
        //--- Save results ---
        if (traces.length > 0) {
            // Save the traces to memory
            TraceMolecules.saveResults(r, traces, "Tracks");
            if (settings.saveTraces) {
                // 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);
                String newFilename = TraceMolecules.saveTraces(r, traces, createSettingsComment(), tracesFilename, additionalDatasets);
                // Only keep the main filename in memory
                if (additionalDatasets == 0)
                    tracesFilename = newFilename;
            }
        }
    }
    Trace[] all = allTraces.toArray(new Trace[allTraces.size()]);
    if (additionalDatasets > 0) {
        Utils.log("Multiple inputs provide %d traces", allTraces.size());
        MemoryPeakResults tracedResults = TraceManager.toPeakResults(all, results.getCalibration(), true);
        tracedResults.copySettings(results);
        tracedResults.setName(createCombinedName() + " Tracks");
        MemoryPeakResults.addResults(tracedResults);
    }
    return all;
}

Example 5 with IJTrackProgress

use of gdsc.core.ij.IJTrackProgress in project GDSC-SMLM by aherbert.

the class NeighbourAnalysis method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "No localisations in memory");
        return;
    }
    if (!showDialog())
        return;
    TraceManager manager = new TraceManager(results);
    // Run the tracing
    manager.setTracker(new IJTrackProgress());
    Trace[] traces = manager.findNeighbours(distanceThreshold, timeThreshold);
    saveTraces(traces);
}