Examples with LocalList uk.ac.sussex.gdsc.core.utils.LocalList used on opensource projects

Example 46 with LocalList

use of uk.ac.sussex.gdsc.core.utils.LocalList in project GDSC-SMLM by aherbert.

the class DynamicMultipleTargetTracingTest method testTrajectory.

@Test
void testTrajectory() {
    final PeakResult p1 = new PeakResult(0, 1, 2);
    final PeakResult p2 = new PeakResult(1, 2, 3);
    final PeakResult p3 = new PeakResult(2, 3, 4);
    final PeakResult p4 = new PeakResult(3, 4, 5);
    final Trajectory t = new Trajectory(42, p1, true);
    Assertions.assertEquals(42, t.getId());
    Assertions.assertSame(p1, t.getLast(-1));
    Assertions.assertEquals(1, t.size());
    Assertions.assertEquals(1, t.onSize());
    t.add(p2, false);
    t.add(p3, false);
    t.add(p4, true);
    Assertions.assertSame(p4, t.getLast(-1));
    Assertions.assertSame(p3, t.getLast(-2));
    Assertions.assertSame(p2, t.getLast(-3));
    Assertions.assertSame(p1, t.getLast(-4));
    Assertions.assertEquals(4, t.size());
    Assertions.assertEquals(2, t.onSize());
    final LocalList<PeakResult> list = new LocalList<>();
    t.forLast(2, list::add);
    Assertions.assertEquals(2, list.size());
    Assertions.assertSame(p3, list.pop());
    Assertions.assertSame(p4, list.pop());
    t.forLastOn(2, list::add);
    Assertions.assertEquals(2, list.size());
    Assertions.assertSame(p1, list.pop());
    Assertions.assertSame(p4, list.pop());
    final Trace trace = t.toTrace();
    Assertions.assertEquals(4, trace.size());
    Assertions.assertEquals(42, trace.getId());
    // Test setting the gap
    final int frame = t.getLast(-1).getFrame();
    for (int i = 1; i <= 3; i++) {
        t.reset(frame + i);
        Assertions.assertEquals(i - 1, t.gap);
    }
    // Test setting the local statistics
    t.setLocalIntensity(10, 0);
    Assertions.assertEquals(10, t.meanI);
    Assertions.assertEquals(0, t.sdI);
    Assertions.assertFalse(t.isLocalIntensity);
    t.setLocalIntensity(9, 1);
    Assertions.assertEquals(9, t.meanI);
    Assertions.assertEquals(1, t.sdI);
    Assertions.assertTrue(t.isLocalIntensity);
    t.setLocalDiffusion(10, 9);
    Assertions.assertEquals(10, t.r2);
    Assertions.assertFalse(t.isLocalDiffusion);
    t.setLocalDiffusion(9, 10);
    Assertions.assertEquals(9, t.r2);
    Assertions.assertTrue(t.isLocalDiffusion);
}

Example 47 with LocalList

use of uk.ac.sussex.gdsc.core.utils.LocalList in project GDSC-SMLM by aherbert.

the class ErfGaussian2DFunctionTest method functionIsFasterThanEquivalentGaussian2DFunction.

// Speed test verses equivalent Gaussian2DFunction
@SpeedTag
@Test
void functionIsFasterThanEquivalentGaussian2DFunction() {
    Assumptions.assumeTrue(TestSettings.allow(TestComplexity.MEDIUM));
    final int flags = this.flags & ~GaussianFunctionFactory.FIT_ERF;
    final Gaussian2DFunction gf = GaussianFunctionFactory.create2D(1, maxx, maxy, flags, zModel);
    final boolean zDepth = (flags & GaussianFunctionFactory.FIT_Z) != 0;
    final LocalList<double[]> params1 = new LocalList<>();
    final LocalList<double[]> params2 = new LocalList<>();
    for (final double background : testbackground) {
        // Peak 1
        for (final double signal1 : testsignal1) {
            for (final double cx1 : testcx1) {
                for (final double cy1 : testcy1) {
                    for (final double cz1 : testcz1) {
                        for (final double[] w1 : testw1) {
                            for (final double angle1 : testangle1) {
                                double[] params = createParameters(background, signal1, cx1, cy1, cz1, w1[0], w1[1], angle1);
                                params1.add(params);
                                if (zDepth) {
                                    // Change to a standard free circular function
                                    params = params.clone();
                                    params[Gaussian2DFunction.X_SD] *= zModel.getSx(params[Gaussian2DFunction.Z_POSITION]);
                                    params[Gaussian2DFunction.Y_SD] *= zModel.getSy(params[Gaussian2DFunction.Z_POSITION]);
                                    params[Gaussian2DFunction.Z_POSITION] = 0;
                                    params2.add(params);
                                }
                            }
                        }
                    }
                }
            }
        }
    }
    final double[][] x = params1.toArray(new double[0][]);
    final double[][] x2 = (zDepth) ? params2.toArray(new double[0][]) : x;
    final int runs = 10000 / x.length;
    final TimingService ts = new TimingService(runs);
    ts.execute(new FunctionTimingTask(gf, x2, 1));
    ts.execute(new FunctionTimingTask(gf, x2, 0));
    ts.execute(new FunctionTimingTask(f1, x, 2));
    ts.execute(new FunctionTimingTask(f1, x, 1));
    ts.execute(new FunctionTimingTask(f1, x, 0));
    final int size = ts.getSize();
    ts.repeat(size);
    if (logger.isLoggable(Level.INFO)) {
        logger.info(ts.getReport());
    }
    for (int i = 1; i <= 2; i++) {
        final TimingResult slow = ts.get(-i - 3);
        final TimingResult fast = ts.get(-i);
        logger.log(TestLogUtils.getTimingRecord(slow, fast));
    }
}

Example 48 with LocalList

use of uk.ac.sussex.gdsc.core.utils.LocalList in project GDSC-SMLM by aherbert.

the class CameraModelFisherInformationAnalysis method getAlpha.

private double[] getAlpha(final double[] photons, double[] exp, final BasePoissonFisherInformation fi, FiKey key) {
    final CameraType type = key.getType();
    final double[] alpha = new double[photons.length];
    if (!type.isFast()) {
        final int[] index;
        // Try and load from the cache
        final PoissonFisherInformationData data = load(key);
        if (data != null) {
            // Dump the samples
            final TDoubleArrayList meanList = new TDoubleArrayList(data.getAlphaSampleCount());
            final TDoubleArrayList alphalist = new TDoubleArrayList(data.getAlphaSampleCount());
            for (final AlphaSample sample : data.getAlphaSampleList()) {
                meanList.add(sample.getLog10Mean());
                alphalist.add(sample.getAlpha());
            }
            final double[] exp2 = meanList.toArray();
            final double[] alphas = alphalist.toArray();
            SortUtils.sortData(alphas, exp2, true, false);
            // Find any exponent not in the array
            final TIntArrayList list = new TIntArrayList(exp.length);
            for (int i = 0; i < exp.length; i++) {
                // Assume exp2 is sorted
                final int j = Arrays.binarySearch(exp2, exp[i]);
                if (j < 0) {
                    // Add to indices to compute
                    list.add(i);
                } else {
                    // Get alpha
                    alpha[i] = alphas[j];
                }
            }
            index = list.toArray();
        } else {
            // Compute all
            index = SimpleArrayUtils.natural(alpha.length);
        }
        if (index.length > 0) {
            IJ.showStatus("Computing " + getName(key));
            final int nThreads = Prefs.getThreads();
            if (es == null) {
                es = Executors.newFixedThreadPool(nThreads);
            }
            final Ticker ticker = ImageJUtils.createTicker(index.length, nThreads);
            final int nPerThread = (int) Math.ceil((double) index.length / nThreads);
            final LocalList<Future<?>> futures = new LocalList<>(nThreads);
            for (int i = 0; i < index.length; i += nPerThread) {
                final int start = i;
                final int end = Math.min(index.length, i + nPerThread);
                futures.add(es.submit(() -> {
                    final BasePoissonFisherInformation fi2 = fi.copy();
                    for (int ii = start; ii < end; ii++) {
                        final int j = index[ii];
                        alpha[j] = fi2.getAlpha(photons[j]);
                        ticker.tick();
                    }
                }));
            }
            ConcurrencyUtils.waitForCompletionUnchecked(futures);
            ImageJUtils.finished();
            save(key, exp, alpha);
        }
    } else {
        // Simple single threaded method.
        for (int i = 0; i < alpha.length; i++) {
            alpha[i] = fi.getAlpha(photons[i]);
        }
    }
    return alpha;
}

Example 49 with LocalList

use of uk.ac.sussex.gdsc.core.utils.LocalList in project GDSC-SMLM by aherbert.

the class CameraModelFisherInformationAnalysis method save.

/**
 * Save the data to the cache.
 *
 * @param key the key
 * @param log10photons the log 10 photons
 * @param alpha the alpha
 */
private static void save(FiKey key, double[] log10photons, double[] alpha) {
    final CameraType type = key.getType();
    if (type.isFast()) {
        return;
    }
    PoissonFisherInformationData data = cache.get(key);
    if (data != null) {
        // This should only be called if new values have been computed.
        // so assume we must merge the lists.
        // Note: The lists must be sorted.
        final AlphaSample[] list1 = data.getAlphaSampleList().toArray(new AlphaSample[0]);
        final LocalList<AlphaSample> list = new LocalList<>(list1.length + log10photons.length);
        int i1 = 0;
        int i2 = 0;
        final AlphaSample.Builder a2 = AlphaSample.newBuilder();
        while (i1 < list1.length && i2 < log10photons.length) {
            final AlphaSample a1 = list1[i1];
            final double mean = log10photons[i2];
            if (a1.getLog10Mean() == mean) {
                list.add(a1);
                i1++;
                i2++;
            } else if (a1.getLog10Mean() < mean) {
                list.add(a1);
                i1++;
            } else {
                // (a1.getLog10Mean() > mean)
                a2.setLog10Mean(mean);
                a2.setAlpha(alpha[i2++]);
                list.add(a2.build());
            }
        }
        while (i1 < list1.length) {
            list.add(list1[i1++]);
        }
        while (i2 < log10photons.length) {
            a2.setLog10Mean(log10photons[i2]);
            a2.setAlpha(alpha[i2++]);
            list.add(a2.build());
        }
        final PoissonFisherInformationData.Builder b = data.toBuilder();
        b.clearAlphaSample();
        b.addAllAlphaSample(list);
        data = b.build();
    } else {
        final PoissonFisherInformationData.Builder b = PoissonFisherInformationData.newBuilder();
        final AlphaSample.Builder sample = AlphaSample.newBuilder();
        b.setType(key.type);
        b.setGain(key.gain);
        b.setNoise(key.noise);
        for (int i = 0; i < log10photons.length; i++) {
            sample.setLog10Mean(log10photons[i]);
            sample.setAlpha(alpha[i]);
            b.addAlphaSample(sample);
        }
        data = b.build();
    }
    cache.put(key, data);
    // Also save EM-CCD data to file
    if (type == CameraType.EM_CCD) {
        final int t = type.ordinal();
        // Get the EM-CCD keys
        final LocalList<FiKey> list = new LocalList<>(cache.size());
        for (final FiKey k : cache.keySet()) {
            if (k.type == t) {
                list.add(k);
            }
        }
        if (list.size() > MAX_DATA_TO_FILE) {
            // Sort by age - Youngest first
            list.sort((o1, o2) -> Long.compare(o2.timeStamp, o1.timeStamp));
        }
        final PoissonFisherInformationCache.Builder cacheData = PoissonFisherInformationCache.newBuilder();
        for (int i = Math.min(list.size(), MAX_DATA_TO_FILE); i-- > 0; ) {
            cacheData.addData(cache.get(list.unsafeGet(i)));
        }
        SettingsManager.writeSettings(cacheData);
    }
}

Example 50 with LocalList

use of uk.ac.sussex.gdsc.core.utils.LocalList in project GDSC-SMLM by aherbert.

the class DensityEstimator method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    // Require some fit results and selected regions
    if (MemoryPeakResults.countMemorySize() == 0) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    if (!showDialog()) {
        return;
    }
    // Currently this only supports pixel distance units
    final MemoryPeakResults results = ResultsManager.loadInputResults(settings.inputOption, false, DistanceUnit.PIXEL, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        IJ.showStatus("");
        return;
    }
    final long start = System.currentTimeMillis();
    IJ.showStatus("Calculating density ...");
    // Scale to um^2 from px^2
    final double scale = Math.pow(results.getDistanceConverter(DistanceUnit.UM).convertBack(1), 2);
    results.sort();
    final FrameCounter counter = results.newFrameCounter();
    final double localisationsPerFrame = (double) results.size() / (results.getLastFrame() - counter.currentFrame() + 1);
    final Rectangle bounds = results.getBounds(true);
    final double globalDensity = localisationsPerFrame / bounds.width / bounds.height;
    final int border = settings.border;
    final boolean includeSingles = settings.includeSingles;
    final int size = 2 * border + 1;
    final double minDensity = Math.pow(size, -2);
    ImageJUtils.log("%s : %s : Global density %s. Minimum density in %dx%d px = %s um^-2", TITLE, results.getName(), MathUtils.rounded(globalDensity * scale), size, size, MathUtils.rounded(minDensity * scale));
    final TIntArrayList x = new TIntArrayList();
    final TIntArrayList y = new TIntArrayList();
    final ExecutorService es = Executors.newFixedThreadPool(Prefs.getThreads());
    final LocalList<FrameDensity> densities = new LocalList<>();
    final LocalList<Future<?>> futures = new LocalList<>();
    results.forEach((PeakResultProcedure) (peak) -> {
        if (counter.advance(peak.getFrame())) {
            final FrameDensity fd = new FrameDensity(peak.getFrame(), x.toArray(), y.toArray(), border, includeSingles);
            densities.add(fd);
            futures.add(es.submit(fd));
            x.resetQuick();
            y.resetQuick();
        }
        x.add((int) peak.getXPosition());
        y.add((int) peak.getYPosition());
    });
    densities.add(new FrameDensity(counter.currentFrame(), x.toArray(), y.toArray(), border, includeSingles));
    futures.add(es.submit(densities.get(densities.size() - 1)));
    es.shutdown();
    // Wait
    ConcurrencyUtils.waitForCompletionUnchecked(futures);
    densities.sort((o1, o2) -> Integer.compare(o1.frame, o2.frame));
    final int total = densities.stream().mapToInt(fd -> fd.counts.length).sum();
    // Plot density
    final Statistics stats = new Statistics();
    final float[] frame = new float[total];
    final float[] density = new float[total];
    densities.stream().forEach(fd -> {
        for (int i = 0; i < fd.counts.length; i++) {
            final double d = (fd.counts[i] / fd.values[i]) * scale;
            frame[stats.getN()] = fd.frame;
            density[stats.getN()] = (float) d;
            stats.add(d);
        }
    });
    final double mean = stats.getMean();
    final double sd = stats.getStandardDeviation();
    final String label = String.format("Density = %s +/- %s um^-2", MathUtils.rounded(mean), MathUtils.rounded(sd));
    final Plot plot = new Plot("Frame vs Density", "Frame", "Density (um^-2)");
    plot.addPoints(frame, density, Plot.CIRCLE);
    plot.addLabel(0, 0, label);
    final WindowOrganiser wo = new WindowOrganiser();
    ImageJUtils.display(plot.getTitle(), plot, wo);
    // Histogram density
    new HistogramPlotBuilder("Local", StoredData.create(density), "Density (um^-2)").setPlotLabel(label).show(wo);
    wo.tile();
    // Log the number of singles
    final int singles = densities.stream().mapToInt(fd -> fd.singles).sum();
    ImageJUtils.log("Singles %d / %d (%s%%)", singles, results.size(), MathUtils.rounded(100.0 * singles / results.size()));
    IJ.showStatus(TITLE + " complete : " + TextUtils.millisToString(System.currentTimeMillis() - start));
}