Examples with BufferedTextWindow uk.ac.sussex.gdsc.core.ij.BufferedTextWindow used on opensource projects

Example 1 with BufferedTextWindow

use of uk.ac.sussex.gdsc.core.ij.BufferedTextWindow in project GDSC-SMLM by aherbert.

the class TrackPopulationAnalysis method createModelTable.

/**
 * Creates a table to show the final model. This uses the assignments to create a mixture model
 * from the original data.
 *
 * @param data the data
 * @param weights the weights for each component
 * @param component the component
 */
private static void createModelTable(double[][] data, double[] weights, int[] component) {
    final MixtureMultivariateGaussianDistribution model = MultivariateGaussianMixtureExpectationMaximization.createMixed(data, component);
    final MultivariateGaussianDistribution[] distributions = model.getDistributions();
    // Get the fraction of each component
    final int[] count = new int[MathUtils.max(component) + 1];
    Arrays.stream(component).forEach(c -> count[c]++);
    try (BufferedTextWindow tw = new BufferedTextWindow(ImageJUtils.refresh(modelTableRef, () -> new TextWindow("Track Population Model", createHeader(), "", 800, 300)))) {
        final StringBuilder sb = new StringBuilder();
        for (int i = 0; i < weights.length; i++) {
            sb.setLength(0);
            sb.append(i).append('\t');
            sb.append(MathUtils.rounded((double) count[i] / component.length)).append('\t');
            sb.append(MathUtils.rounded(weights[i]));
            final double[] means = distributions[i].getMeans();
            final double[] sd = distributions[i].getStandardDeviations();
            for (int j = 0; j < means.length; j++) {
                sb.append('\t').append(MathUtils.rounded(means[j])).append('\t').append(MathUtils.rounded(sd[j]));
            }
            tw.append(sb.toString());
        }
    }
}

Example 2 with BufferedTextWindow

use of uk.ac.sussex.gdsc.core.ij.BufferedTextWindow in project GDSC-SMLM by aherbert.

the class ResultsMatchCalculator method showPairs.

/**
 * Show the match pairs in a results table.
 *
 * <p>Adds an ROI painter for the original image source of results set 1 (if it is visible) to the
 * table.
 *
 * @param results1 the first set of results
 * @param pairs the pairs
 * @param resultsWindow the results window
 */
private void showPairs(MemoryPeakResults results1, final List<PointPair> pairs, final TextWindow resultsWindow) {
    if (!settings.showPairs) {
        return;
    }
    final TextWindow pairsWindow = createPairsWindow(resultsWindow, results1.getSource());
    pairsWindow.getTextPanel().clear();
    final Ticker ticker = ImageJUtils.createTicker(pairs.size(), 0, "Writing pairs table");
    try (final BufferedTextWindow bw = new BufferedTextWindow(pairsWindow)) {
        final StringBuilder sb = new StringBuilder();
        for (final PointPair pair : pairs) {
            bw.append(addPairResult(sb, pair));
            ticker.tick();
        }
    }
    ImageJUtils.finished();
}

Example 3 with BufferedTextWindow

use of uk.ac.sussex.gdsc.core.ij.BufferedTextWindow in project GDSC-SMLM by aherbert.

the class FailCountManager method analyseData.

private void analyseData() {
    final LocalList<FailCountData> failCountData = failCountDataRef.get();
    if (failCountData.isEmpty()) {
        IJ.error(TITLE, "No fail count data in memory");
        return;
    }
    if (!showAnalysisDialog()) {
        return;
    }
    final int maxCons = getMaxConsecutiveFailCount(failCountData);
    final int maxFail = getMaxFailCount(failCountData);
    // Create a set of fail counters
    final LocalList<FailCounter> counters = new LocalList<>();
    final TByteArrayList type = new TByteArrayList();
    for (int i = 0; i <= maxCons; i++) {
        counters.add(ConsecutiveFailCounter.create(i));
    }
    fill(type, counters, 0);
    // The other counters are user configured.
    // Ideally this would be a search to optimise the best parameters
    // for each counter as any enumeration may be way off the mark.
    // Note that 0 failures in a window can be scored using the consecutive fail counter.
    int max = Math.min(maxFail, settings.getRollingCounterMaxAllowedFailures());
    for (int fail = MathUtils.clip(1, maxFail, settings.getRollingCounterMinAllowedFailures()); fail <= max; fail++) {
        // Note that n-1 failures in window n can be scored using the consecutive fail counter.
        for (int window = Math.max(fail + 2, settings.getRollingCounterMinWindow()); window <= settings.getRollingCounterMaxWindow(); window++) {
            counters.add(RollingWindowFailCounter.create(fail, window));
        }
        switch(checkCounters(counters)) {
            case ANALYSE:
                break;
            case CONTINUE:
                break;
            case RETURN:
                return;
            default:
                throw new IllegalStateException();
        }
    }
    fill(type, counters, 1);
    max = Math.min(maxFail, settings.getWeightedCounterMaxAllowedFailures());
    for (int fail = MathUtils.min(maxFail, settings.getWeightedCounterMinAllowedFailures()); fail <= max; fail++) {
        for (int w = settings.getWeightedCounterMinPassDecrement(); w <= settings.getWeightedCounterMaxPassDecrement(); w++) {
            counters.add(WeightedFailCounter.create(fail, 1, w));
        }
        switch(checkCounters(counters)) {
            case ANALYSE:
                break;
            case CONTINUE:
                break;
            case RETURN:
                return;
            default:
                throw new IllegalStateException();
        }
    }
    fill(type, counters, 2);
    max = Math.min(maxFail, settings.getResettingCounterMaxAllowedFailures());
    for (int fail = MathUtils.min(maxFail, settings.getResettingCounterMinAllowedFailures()); fail <= max; fail++) {
        for (double f = settings.getResettingCounterMinResetFraction(); f <= settings.getResettingCounterMaxResetFraction(); f += settings.getResettingCounterIncResetFraction()) {
            counters.add(ResettingFailCounter.create(fail, f));
        }
        switch(checkCounters(counters)) {
            case ANALYSE:
                break;
            case CONTINUE:
                break;
            case RETURN:
                return;
            default:
                throw new IllegalStateException();
        }
    }
    fill(type, counters, 3);
    for (int count = settings.getPassRateCounterMinAllowedCounts(); count <= settings.getPassRateCounterMaxAllowedCounts(); count++) {
        for (double f = settings.getPassRateCounterMinPassRate(); f <= settings.getPassRateCounterMaxPassRate(); f += settings.getPassRateCounterIncPassRate()) {
            counters.add(PassRateFailCounter.create(count, f));
        }
        switch(checkCounters(counters)) {
            case ANALYSE:
                break;
            case CONTINUE:
                break;
            case RETURN:
                return;
            default:
                throw new IllegalStateException();
        }
    }
    fill(type, counters, 4);
    counters.trimToSize();
    // Score each of a set of standard fail counters against each frame using how
    // close they are to the target.
    final double[] score = new double[counters.size()];
    final double targetPassFraction = settings.getTargetPassFraction();
    final int nThreads = Prefs.getThreads();
    final ExecutorService executor = Executors.newFixedThreadPool(nThreads);
    final LocalList<Future<?>> futures = new LocalList<>(nThreads);
    final Ticker ticker = ImageJUtils.createTicker(failCountData.size(), nThreads);
    IJ.showStatus("Analysing " + TextUtils.pleural(counters.size(), "counter"));
    for (int i = 0; i < failCountData.size(); i++) {
        final FailCountData data = failCountData.unsafeGet(i);
        futures.add(executor.submit(() -> {
            if (IJ.escapePressed()) {
                return;
            }
            // TODO - Ideally this plugin should be run on benchmark data with ground truth.
            // The target could be to ensure all the correct results are fit
            // and false positives are excluded from incrementing the pass counter.
            // This could be done by saving the results from a benchmarking scoring
            // plugin to memory as the current dataset.
            data.initialiseAnalysis(targetPassFraction);
            // Score in blocks and then do a synchronized write to the combined score
            final Thread t = Thread.currentThread();
            final double[] s = new double[8192];
            int index = 0;
            while (index < counters.size()) {
                if (t.isInterrupted()) {
                    break;
                }
                final int block = Math.min(8192, counters.size() - index);
                for (int j = 0; j < block; j++) {
                    final FailCounter counter = counters.unsafeGet(index + j).newCounter();
                    s[j] = data.score(counter);
                }
                // Write to the combined score
                synchronized (score) {
                    for (int j = 0; j < block; j++) {
                        score[index + j] += s[j];
                    }
                }
                index += block;
            }
            ticker.tick();
        }));
    }
    executor.shutdown();
    ConcurrencyUtils.waitForCompletionUnchecked(futures);
    IJ.showProgress(1);
    if (IJ.escapePressed()) {
        IJ.showStatus("");
        IJ.error(TITLE, "Cancelled analysis");
        return;
    }
    IJ.showStatus("Summarising results ...");
    // TODO - check if the top filter is at the bounds of the range
    final int minIndex = SimpleArrayUtils.findMinIndex(score);
    ImageJUtils.log(TITLE + " Analysis : Best counter = %s (Score = %f)", counters.unsafeGet(minIndex).getDescription(), score[minIndex]);
    // Show a table of results for the top N for each type
    final int topN = Math.min(settings.getTableTopN(), score.length);
    if (topN > 0) {
        final byte[] types = type.toArray();
        final byte maxType = types[types.length - 1];
        final TextWindow resultsWindow = createTable();
        for (byte b = 0; b <= maxType; b++) {
            int[] indices;
            // Use a heap to avoid a full sort
            final IntDoubleMinHeap heap = new IntDoubleMinHeap(topN);
            for (int i = 0; i < score.length; i++) {
                if (types[i] == b) {
                    heap.offer(score[i], i);
                }
            }
            if (heap.getSize() == 0) {
                continue;
            }
            indices = heap.getItems();
            // Ensure sorted
            SortUtils.sortIndices(indices, score, false);
            final StringBuilder sb = new StringBuilder();
            try (final BufferedTextWindow tw = new BufferedTextWindow(resultsWindow)) {
                for (int i = 0; i < topN; i++) {
                    sb.setLength(0);
                    final int j = indices[i];
                    sb.append(i + 1).append('\t');
                    sb.append(counters.unsafeGet(j).getDescription()).append('\t');
                    sb.append(score[j]);
                    tw.append(sb.toString());
                }
            }
        }
    }
    // TODO - Save the best fail counter to the current fit configuration.
    IJ.showStatus("");
}

Example 4 with BufferedTextWindow

use of uk.ac.sussex.gdsc.core.ij.BufferedTextWindow in project GDSC-SMLM by aherbert.

the class SummariseResults method showSummary.

private static void showSummary(Collection<MemoryPeakResults> results, int[] removeNullResults) {
    final TextWindow summary = createSummaryTable();
    final StringBuilder sb = new StringBuilder();
    try (BufferedTextWindow tw = new BufferedTextWindow(summary)) {
        for (final MemoryPeakResults result : results) {
            tw.append(createSummary(sb, result, removeNullResults));
        }
        tw.append("");
    }
    summary.toFront();
}

Example 5 with BufferedTextWindow

use of uk.ac.sussex.gdsc.core.ij.BufferedTextWindow in project GDSC-SMLM by aherbert.

the class ClassificationMatchCalculator method runCompareClassifications.

private void runCompareClassifications(MemoryPeakResults results1, MemoryPeakResults results2) {
    final List<PointPair> allMatches = new LinkedList<>();
    // Optionally exclude results which do not have an id and/or category
    Predicate<PeakResult> test = settings.useId == ClassAnalysis.IGNORE_ZERO ? r -> r.getId() != 0 : null;
    if (settings.useCategory == ClassAnalysis.IGNORE_ZERO) {
        final Predicate<PeakResult> test2 = r -> r.getCategory() != 0;
        test = test == null ? test2 : test.and(test2);
    } else if (test == null) {
        test = r -> true;
    }
    // Divide the results into time points
    final TIntObjectHashMap<List<PeakResultPoint>> coordinates1 = getCoordinates(results1, test);
    final TIntObjectHashMap<List<PeakResultPoint>> coordinates2 = getCoordinates(results2, test);
    // Process each time point
    int n1 = 0;
    int n2 = 0;
    for (final int t : getTimepoints(coordinates1, coordinates2)) {
        final Coordinate[] c1 = getCoordinates(coordinates1, t);
        final Coordinate[] c2 = getCoordinates(coordinates2, t);
        n1 += c1.length;
        n2 += c2.length;
        final List<PointPair> matches = new LinkedList<>();
        MatchCalculator.analyseResults3D(c1, c2, settings.matchDistance, null, null, null, matches);
        allMatches.addAll(matches);
    }
    if (allMatches.isEmpty()) {
        IJ.error(TITLE, "No localisation matches between the two results sets");
        return;
    }
    // Get the unique Ids and Categories in the matches.
    final Mapper ids = getMapper(allMatches, PeakResult::getId, settings.useId);
    final Mapper cats = getMapper(allMatches, PeakResult::getCategory, settings.useCategory);
    // Map id/category to an index = stride * cat + id
    final int stride = ids.size();
    // Any integer is allowed as an index
    if ((long) stride * cats.size() > 1L << 32) {
        IJ.error(TITLE, "Too many combinations of id and category to assigne unique labels");
        return;
    }
    // Extract indices
    final int[] set1 = new int[allMatches.size()];
    final int[] set2 = new int[allMatches.size()];
    int i = 0;
    for (final PointPair r : allMatches) {
        set1[i] = toIndex(stride, ids, cats, ((PeakResultPoint) r.getPoint1()).getPeakResult());
        set2[i] = toIndex(stride, ids, cats, ((PeakResultPoint) r.getPoint2()).getPeakResult());
        i++;
    }
    final Resequencer re = new Resequencer();
    re.setCacheMap(true);
    re.renumber(set1);
    re.renumber(set2);
    // Compare
    final RandIndex r = new RandIndex().compute(set1, set2);
    final TextWindow resultsWindow = ImageJUtils.refresh(resultsWindowRef, () -> new TextWindow(TITLE + " Results", "Results1\tResults2\tID\tCategory\tn1\tc1\tn2\tc2\tMatched\tRand Index\tAdjusted RI", "", 900, 300));
    try (BufferedTextWindow bw = new BufferedTextWindow(resultsWindow)) {
        final StringBuilder sb = new StringBuilder(2048);
        sb.append(results1.getName()).append('\t');
        sb.append(results2.getName()).append('\t');
        sb.append(ANALYSIS_OPTION[settings.useId.ordinal()]).append('\t');
        sb.append(ANALYSIS_OPTION[settings.useCategory.ordinal()]).append('\t');
        sb.append(n1).append('\t');
        sb.append(MathUtils.max(set1) + 1).append('\t');
        sb.append(n2).append('\t');
        sb.append(MathUtils.max(set2) + 1).append('\t');
        sb.append(set1.length).append('\t');
        sb.append(MathUtils.rounded(r.getRandIndex())).append('\t');
        sb.append(MathUtils.rounded(r.getAdjustedRandIndex())).append('\t');
        bw.append(sb.toString());
    }
}