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

Example 41 with PeakResult

use of uk.ac.sussex.gdsc.smlm.results.PeakResult 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 42 with PeakResult

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

the class TraceLengthAnalysis 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;
    }
    // Load the results
    MemoryPeakResults results = ResultsManager.loadInputResults(settings.inputOption, false, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    try {
        distanceConverter = results.getDistanceConverter(DistanceUnit.UM);
        timeConverter = results.getTimeConverter(TimeUnit.SECOND);
    } catch (final Exception ex) {
        IJ.error(TITLE, "Cannot convert units to um or seconds: " + ex.getMessage());
        return;
    }
    // Get the localisation error (4s^2) in raw units^2
    double precision = 0;
    try {
        final PrecisionResultProcedure p = new PrecisionResultProcedure(results);
        p.getPrecision();
        // Precision in nm using the median
        precision = new Percentile().evaluate(p.precisions, 50);
        // Convert from nm to um to raw units
        final double rawPrecision = distanceConverter.convertBack(precision / 1e3);
        // Get the localisation error (4s^2) in units^2
        error = 4 * rawPrecision * rawPrecision;
    } catch (final Exception ex) {
        ImageJUtils.log(TITLE + " - Unable to compute precision: " + ex.getMessage());
    }
    // Analyse the track lengths
    results = results.copy();
    results.sort(IdFramePeakResultComparator.INSTANCE);
    // Ensure the first result triggers an id change
    lastid = results.getFirst().getId() - 1;
    results.forEach(this::processTrackLength);
    // For the final track
    store();
    msds = msdList.toArray();
    lengths = lengthList.toArray();
    ids = idList.toArray();
    final int[] limits = MathUtils.limits(lengths);
    h1 = new int[limits[1] + 1];
    h2 = new int[h1.length];
    x1 = SimpleArrayUtils.newArray(h1.length, 0, 1f);
    y1 = new float[x1.length];
    y2 = new float[x1.length];
    // Sort by MSD
    final int[] indices = SimpleArrayUtils.natural(msds.length);
    SortUtils.sortIndices(indices, msds, false);
    final double[] msds2 = msds.clone();
    final int[] lengths2 = lengths.clone();
    final int[] ids2 = ids.clone();
    for (int i = 0; i < indices.length; i++) {
        msds[i] = msds2[indices[i]];
        lengths[i] = lengths2[indices[i]];
        ids[i] = ids2[indices[i]];
    }
    // Interactive analysis
    final NonBlockingExtendedGenericDialog gd = new NonBlockingExtendedGenericDialog(TITLE);
    ImageJUtils.addMessage(gd, "Split traces into fixed or moving using the track diffusion coefficient (D).\n" + "Localisation error has been subtracted from jumps (%s nm).", MathUtils.rounded(precision));
    final Statistics s = Statistics.create(msds);
    final double av = s.getMean();
    final String msg = String.format("Average D per track = %s um^2/s", MathUtils.rounded(av));
    gd.addMessage(msg);
    // Histogram the diffusion coefficients
    final WindowOrganiser wo = new WindowOrganiser();
    final HistogramPlot histogramPlot = new HistogramPlotBuilder("Trace diffusion coefficient", StoredData.create(msds), "D (um^2/s)").setRemoveOutliersOption(1).setPlotLabel(msg).build();
    histogramPlot.show(wo);
    final double[] xvalues = histogramPlot.getPlotXValues();
    final double min = xvalues[0];
    final double max = xvalues[xvalues.length - 1];
    // see if we can build a nice slider range from the histogram limits
    if (max - min < 5) {
        // Because sliders are used when the range is <5 and floating point
        gd.addSlider("D_threshold", min, max, settings.msdThreshold);
    } else {
        gd.addNumericField("D_threshold", settings.msdThreshold, 2, 6, "um^2/s");
    }
    gd.addCheckbox("Normalise", settings.normalise);
    gd.addDialogListener((gd1, event) -> {
        settings.msdThreshold = gd1.getNextNumber();
        settings.normalise = gd1.getNextBoolean();
        update();
        return true;
    });
    if (ImageJUtils.isShowGenericDialog()) {
        draw(wo);
        wo.tile();
    }
    gd.setOKLabel("Save datasets");
    gd.setCancelLabel("Close");
    gd.addHelp(HelpUrls.getUrl("trace-length-analysis"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    // Sort by ID
    final PeakResult[] list = results.toArray();
    Arrays.sort(list, IdFramePeakResultComparator.INSTANCE);
    createResults(results, "Fixed", 0, lastIndex, list);
    createResults(results, "Moving", lastIndex, msds.length, list);
}

Example 43 with PeakResult

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

the class SpotAnalysis method saveTracesToFile.

private void saveTracesToFile(ArrayList<TraceResult> traceResults) {
    final String resultsDirectory = IJ.getDirectory(PLUGIN_TITLE);
    if (resultsDirectory == null) {
        return;
    }
    // Save the traces to a single file.
    // Also save the blinks and on/off times into data files for histogram analysis
    final BufferedWriter[] files = new BufferedWriter[5];
    try {
        files[0] = openBufferedWriter(resultsDirectory + "traces.txt", String.format("#ms/frame = %s%n#Id\tcx\tcy\tsignal\tn-Blinks\tStart\tStop\t...", MathUtils.rounded(msPerFrame, 3)));
        files[1] = openBufferedWriter(resultsDirectory + "tOn.txt", "");
        files[2] = openBufferedWriter(resultsDirectory + "tOff.txt", "");
        files[3] = openBufferedWriter(resultsDirectory + "blinks.txt", "");
        files[4] = openBufferedWriter(resultsDirectory + "signal.txt", "");
        for (final TraceResult traceResult : traceResults) {
            final StringBuilder sb = new StringBuilder();
            sb.append(traceResult.spot.frame).append('\t');
            sb.append(traceResult.trace.getHead().getXPosition()).append('\t');
            sb.append(traceResult.trace.getHead().getYPosition()).append('\t');
            sb.append(traceResult.spot.signal).append('\t');
            final int nBlinks = traceResult.trace.getBlinks() - 1;
            sb.append(nBlinks);
            final int[] on = traceResult.trace.getOnTimes();
            final int[] off = traceResult.trace.getOffTimes();
            int time = traceResult.trace.getHead().getFrame();
            for (int i = 0; i < on.length; i++) {
                writeLine(files[1], Double.toString(msPerFrame * on[i]));
                sb.append('\t').append(time).append('\t').append(time + on[i] - 1);
                if (off != null && i < off.length) {
                    writeLine(files[2], Double.toString(msPerFrame * off[i]));
                    time += on[i] + off[i];
                }
            }
            writeLine(files[0], sb.toString());
            writeLine(files[3], Integer.toString(nBlinks));
            writeLine(files[4], String.format("# Id=%d, Blinks=%d, Signal=%f", traceResult.spot.frame, nBlinks, traceResult.spot.signal));
            for (int k = 0; k < traceResult.trace.size(); k++) {
                final PeakResult r = traceResult.trace.get(k);
                writeLine(files[4], String.format("%d %f", r.getFrame(), r.getIntensity()));
            }
        }
    } catch (final Exception ex) {
        // Q. Add better handling of errors?
        Logger.getLogger(getClass().getName()).log(Level.WARNING, ex, () -> "Failed to save traces to results directory: " + resultsDirectory);
    } finally {
        for (final BufferedWriter tracesFile : files) {
            if (tracesFile != null) {
                try {
                    tracesFile.close();
                } catch (final IOException ex) {
                    Logger.getLogger(getClass().getName()).log(Level.WARNING, "Failed to close traces file", ex);
                }
            }
        }
    }
}

Example 44 with PeakResult

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

the class TraceExporter method splitTraces.

private MemoryPeakResults splitTraces(MemoryPeakResults results) {
    if (settings.maxJump < 1) {
        // Disabled
        return results;
    }
    int id = 0;
    final int lastT = 0;
    for (int i = 0, size = results.size(); i < size; i++) {
        final PeakResult r = results.get(i);
        if (r.getId() != id) {
            id = r.getId();
        } else if (r.getFrame() - lastT > settings.maxJump) {
            return doSplit(results);
        }
    }
    return results;
}

Example 45 with PeakResult

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

the class TraceExporter method doSplit.

private MemoryPeakResults doSplit(MemoryPeakResults results) {
    final MemoryPeakResults results2 = new MemoryPeakResults(results.size());
    results2.copySettings(results);
    int nextId = results.getLast().getId();
    int id = 0;
    int idOut = 0;
    int lastT = 0;
    for (int i = 0, size = results.size(); i < size; i++) {
        final PeakResult r = results.get(i);
        if (r.getId() != id) {
            id = r.getId();
            idOut = id;
        } else if (r.getFrame() - lastT > settings.maxJump) {
            idOut = ++nextId;
        }
        final AttributePeakResult r2 = new AttributePeakResult(r);
        r2.setId(idOut);
        results2.add(r2);
        lastT = r.getEndFrame();
    }
    return results2;
}