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

Example 61 with MemoryPeakResults

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

the class ClassificationMatchCalculator 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
    final MemoryPeakResults results1 = ResultsManager.loadInputResults(settings.inputOption1, false, null, null);
    final MemoryPeakResults results2 = ResultsManager.loadInputResults(settings.inputOption2, false, null, null);
    IJ.showStatus("");
    if (results1 == null || results1.size() == 0) {
        IJ.error(TITLE, "No results 1 could be loaded");
        return;
    }
    if (results2 == null || results2.size() == 0) {
        IJ.error(TITLE, "No results 2 could be loaded");
        return;
    }
    // Check the results can be loaded in the pixels
    try {
        results1.getDistanceConverter(DistanceUnit.PIXEL);
        results2.getDistanceConverter(DistanceUnit.PIXEL);
    } catch (ConversionException | ConfigurationException ex) {
        IJ.error(TITLE, "Distances cannot be loaded in pixels");
        return;
    }
    final long start = System.nanoTime();
    runCompareClassifications(results1, results2);
    final long nanoseconds = System.nanoTime() - start;
    IJ.showStatus(String.format("%s = %s", TITLE, TextUtils.nanosToString(nanoseconds)));
}

Example 62 with MemoryPeakResults

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

the class ClassificationMatchCalculator method getCoordinates.

/**
 * Build a map between the peak id (time point) and a list of coordinates that pass the filter.
 *
 * @param results the results
 * @param test the test
 * @return the coordinates
 */
public static TIntObjectHashMap<List<PeakResultPoint>> getCoordinates(MemoryPeakResults results, Predicate<PeakResult> test) {
    final TIntObjectHashMap<List<PeakResultPoint>> coords = new TIntObjectHashMap<>();
    if (results.size() > 0) {
        // Do not use HashMap directly to build the coords object since there
        // will be many calls to getEntry(). Instead sort the results and use
        // a new list for each time point
        results.sort();
        // Create list
        final LocalList<PeakResultPoint> tmpCoords = new LocalList<>();
        // Add the results for each frame
        final FrameCounter counter = results.newFrameCounter();
        results.forEach(DistanceUnit.PIXEL, (XyzrResultProcedure) (x, y, z, r) -> {
            if (counter.advance(r.getFrame()) && !tmpCoords.isEmpty()) {
                coords.put(counter.previousFrame(), tmpCoords.copy());
                tmpCoords.clear();
            }
            if (test.test(r)) {
                tmpCoords.add(new PeakResultPoint(r.getFrame(), x, y, z, r));
            }
        });
        if (!tmpCoords.isEmpty()) {
            coords.put(counter.currentFrame(), tmpCoords.copy());
        }
    }
    return coords;
}

Example 63 with MemoryPeakResults

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

the class ConvertResults method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (!showInputDialog()) {
        return;
    }
    final MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    if (!showDialog(results)) {
        return;
    }
    IJ.showStatus("Converted " + results.getName());
}

Example 64 with MemoryPeakResults

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

the class Filter method filter.

/**
 * Filter the results.
 *
 * <p>The number of consecutive rejections are counted per frame. When the configured number of
 * failures is reached all remaining results for the frame are rejected. This assumes the results
 * are ordered by the frame.
 *
 * @param results the results
 * @param failures the number of failures to allow per frame before all peaks are rejected
 * @return the filtered results
 */
public MemoryPeakResults filter(MemoryPeakResults results, final int failures) {
    final MemoryPeakResults newResults = new MemoryPeakResults();
    final FrameCounter counter = new FrameCounter();
    newResults.copySettings(results);
    setup(results);
    results.forEach((PeakResultProcedure) peak -> {
        counter.advanceAndReset(peak.getFrame());
        final boolean isPositive;
        if (counter.getCount() > failures) {
            isPositive = false;
        } else {
            isPositive = accept(peak);
        }
        if (isPositive) {
            counter.reset();
            newResults.add(peak);
        } else {
            counter.increment();
        }
    });
    end();
    return newResults;
}

Example 65 with MemoryPeakResults

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

the class Filter method fractionScoreSubset.

/**
 * Filter the results and return the performance score. Allows benchmarking the filter by marking
 * the results as true or false.
 *
 * <p>Input PeakResults must be allocated a score for true positive, false positive, true negative
 * and false negative (accessed via the object property get methods). The filter is run and
 * results that pass accumulate scores for true positive and false positive, otherwise the scores
 * are accumulated for true negative and false negative. The simplest scoring scheme is to mark
 * valid results as tp=fn=1 and fp=tn=0 and invalid results the opposite.
 *
 * <p>The number of consecutive rejections are counted per frame. When the configured number of
 * failures is reached all remaining results for the frame are rejected. This assumes the results
 * are ordered by the frame.
 *
 * <p>Note that this method is to be used to score a subset that was generated using
 * {@link #filterSubset(MemoryPeakResults, int, double[])} since the number of consecutive
 * failures before each peak are expected to be stored in the origX property.
 *
 * @param resultsList a list of results to analyse
 * @param failures the number of failures to allow per frame before all peaks are rejected
 * @param tn The initial true negatives (used when the results have been pre-filtered)
 * @param fn The initial false negatives (used when the results have been pre-filtered)
 * @param initialNegatives The initial negatives (used when the results have been pre-filtered)
 * @return the score
 */
public FractionClassificationResult fractionScoreSubset(List<MemoryPeakResults> resultsList, final int failures, double tn, double fn, int initialNegatives) {
    final double[] s = new double[4];
    s[TN] = tn;
    s[FN] = fn;
    final Counter p = new Counter();
    int negatives = initialNegatives;
    for (final MemoryPeakResults peakResults : resultsList) {
        setup(peakResults);
        final FrameCounter counter = new FrameCounter();
        peakResults.forEach((PeakResultProcedure) peak -> {
            counter.advanceAndReset(peak.getFrame());
            counter.increment(peak.getOrigX());
            final boolean isPositive;
            if (counter.getCount() > failures) {
                isPositive = false;
            } else {
                isPositive = accept(peak);
            }
            if (isPositive) {
                counter.reset();
            } else {
                counter.increment();
            }
            if (isPositive) {
                p.increment();
                s[TP] += peak.getTruePositiveScore();
                s[FP] += peak.getFalsePositiveScore();
            } else {
                s[FN] += peak.getFalseNegativeScore();
                s[TN] += peak.getTrueNegativeScore();
            }
        });
        negatives += peakResults.size();
        end();
    }
    negatives -= p.getCount();
    return new FractionClassificationResult(s[TP], s[FP], s[TN], s[FN], p.getCount(), negatives);
}