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Example 6 with FluorophoreSequenceModel

use of gdsc.smlm.model.FluorophoreSequenceModel in project GDSC-SMLM by aherbert.

the class BlinkEstimatorTest method estimateBlinking.

private TIntHashSet estimateBlinking(double nBlinks, double tOn, double tOff, int particles, double fixedFraction, boolean timeAtLowerBound, boolean doAssert) {
    SpatialIllumination activationIllumination = new UniformIllumination(100);
    int totalSteps = 100;
    double eAct = totalSteps * 0.3 * activationIllumination.getAveragePhotons();
    ImageModel imageModel = new ActivationEnergyImageModel(eAct, activationIllumination, tOn, 0, tOff, 0, nBlinks);
    imageModel.setRandomGenerator(rand);
    double[] max = new double[] { 256, 256, 32 };
    double[] min = new double[3];
    SpatialDistribution distribution = new UniformDistribution(min, max, rand.nextInt());
    List<CompoundMoleculeModel> compounds = new ArrayList<CompoundMoleculeModel>(1);
    CompoundMoleculeModel c = new CompoundMoleculeModel(1, 0, 0, 0, Arrays.asList(new MoleculeModel(0, 0, 0, 0)));
    c.setDiffusionRate(diffusionRate);
    c.setDiffusionType(DiffusionType.RANDOM_WALK);
    compounds.add(c);
    List<CompoundMoleculeModel> molecules = imageModel.createMolecules(compounds, particles, distribution, false);
    // Activate fluorophores
    List<? extends FluorophoreSequenceModel> fluorophores = imageModel.createFluorophores(molecules, totalSteps);
    totalSteps = checkTotalSteps(totalSteps, fluorophores);
    List<LocalisationModel> localisations = imageModel.createImage(molecules, fixedFraction, totalSteps, photons, 0.5, false);
    //		// Remove localisations to simulate missed counts. 
    //		List<LocalisationModel> newLocalisations = new ArrayList<LocalisationModel>(localisations.size());
    //		boolean[] id = new boolean[fluorophores.size() + 1];
    //		Statistics photonStats = new Statistics();
    //		for (LocalisationModel l : localisations)
    //		{
    //			photonStats.add(l.getIntensity());
    //			// Remove by intensity threshold and optionally at random.
    //			if (l.getIntensity() < minPhotons || rand.nextDouble() < pDelete)
    //				continue;
    //			newLocalisations.add(l);
    //			id[l.getId()] = true;
    //		}
    //		localisations = newLocalisations;
    //		System.out.printf("Photons = %f\n", photonStats.getMean());
    //
    //		List<FluorophoreSequenceModel> newFluorophores = new ArrayList<FluorophoreSequenceModel>(fluorophores.size());
    //		for (FluorophoreSequenceModel f : fluorophores)
    //		{
    //			if (id[f.getId()])
    //				newFluorophores.add(f);
    //		}
    //		fluorophores = newFluorophores;
    MemoryPeakResults results = new MemoryPeakResults();
    results.setCalibration(new Calibration(pixelPitch, 1, msPerFrame));
    for (LocalisationModel l : localisations) {
        // Remove by intensity threshold and optionally at random.
        if (l.getIntensity() < minPhotons || rand.nextDouble() < pDelete)
            continue;
        float[] params = new float[7];
        params[Gaussian2DFunction.X_POSITION] = (float) l.getX();
        params[Gaussian2DFunction.Y_POSITION] = (float) l.getY();
        params[Gaussian2DFunction.X_SD] = params[Gaussian2DFunction.Y_SD] = psfWidth;
        params[Gaussian2DFunction.SIGNAL] = (float) (l.getIntensity());
        results.addf(l.getTime(), 0, 0, 0, 0, 0, params, null);
    }
    // Add random localisations
    for (int i = (int) (localisations.size() * pAdd); i-- > 0; ) {
        float[] params = new float[7];
        params[Gaussian2DFunction.X_POSITION] = (float) (rand.nextDouble() * max[0]);
        params[Gaussian2DFunction.Y_POSITION] = (float) (rand.nextDouble() * max[1]);
        params[Gaussian2DFunction.X_SD] = params[Gaussian2DFunction.Y_SD] = psfWidth;
        // Intensity doesn't matter at the moment for tracing
        params[Gaussian2DFunction.SIGNAL] = (float) (photons);
        results.addf(1 + rand.nextInt(totalSteps), 0, 0, 0, 0, 0, params, null);
    }
    // Get actual simulated stats ...
    Statistics statsNBlinks = new Statistics();
    Statistics statsTOn = new Statistics();
    Statistics statsTOff = new Statistics();
    Statistics statsSampledNBlinks = new Statistics();
    Statistics statsSampledTOn = new Statistics();
    StoredDataStatistics statsSampledTOff = new StoredDataStatistics();
    for (FluorophoreSequenceModel f : fluorophores) {
        statsNBlinks.add(f.getNumberOfBlinks());
        statsTOn.add(f.getOnTimes());
        statsTOff.add(f.getOffTimes());
        int[] on = f.getSampledOnTimes();
        statsSampledNBlinks.add(on.length);
        statsSampledTOn.add(on);
        statsSampledTOff.add(f.getSampledOffTimes());
    }
    System.out.printf("N = %d (%d), N-blinks = %f, tOn = %f, tOff = %f, Fixed = %f\n", fluorophores.size(), localisations.size(), nBlinks, tOn, tOff, fixedFraction);
    System.out.printf("Actual N-blinks = %f (%f), tOn = %f (%f), tOff = %f (%f), 95%% = %f, max = %f\n", statsNBlinks.getMean(), statsSampledNBlinks.getMean(), statsTOn.getMean(), statsSampledTOn.getMean(), statsTOff.getMean(), statsSampledTOff.getMean(), statsSampledTOff.getStatistics().getPercentile(95), statsSampledTOff.getStatistics().getMax());
    System.out.printf("-=-=--=-\n");
    BlinkEstimator be = new BlinkEstimator();
    be.maxDarkTime = (int) (tOff * 10);
    be.msPerFrame = msPerFrame;
    be.relativeDistance = false;
    double d = ImageModel.getRandomMoveDistance(diffusionRate);
    be.searchDistance = (fixedFraction < 1) ? Math.sqrt(2 * d * d) * 3 : 0;
    be.timeAtLowerBound = timeAtLowerBound;
    be.showPlots = false;
    //Assert.assertTrue("Max dark time must exceed the dark time of the data (otherwise no plateau)",
    //		be.maxDarkTime > statsSampledTOff.getStatistics().getMax());
    int nMolecules = fluorophores.size();
    if (usePopulationStatistics) {
        nBlinks = statsNBlinks.getMean();
        tOff = statsTOff.getMean();
    } else {
        nBlinks = statsSampledNBlinks.getMean();
        tOff = statsSampledTOff.getMean();
    }
    // See if any fitting regime gets a correct answer
    TIntHashSet ok = new TIntHashSet();
    for (int nFittedPoints = MIN_FITTED_POINTS; nFittedPoints <= MAX_FITTED_POINTS; nFittedPoints++) {
        be.nFittedPoints = nFittedPoints;
        be.computeBlinkingRate(results, true);
        double moleculesError = DoubleEquality.relativeError(nMolecules, be.getNMolecules());
        double blinksError = DoubleEquality.relativeError(nBlinks, be.getNBlinks());
        double offError = DoubleEquality.relativeError(tOff * msPerFrame, be.getTOff());
        System.out.printf("Error %d: N = %f, blinks = %f, tOff = %f : %f\n", nFittedPoints, moleculesError, blinksError, offError, (moleculesError + blinksError + offError) / 3);
        if (moleculesError < relativeError && blinksError < relativeError && offError < relativeError) {
            ok.add(nFittedPoints);
            System.out.printf("-=-=--=-\n");
            System.out.printf("*** Correct at %d fitted points ***\n", nFittedPoints);
            if (doAssert)
                break;
        }
    //if (!be.isIncreaseNFittedPoints())
    //	break;
    }
    System.out.printf("-=-=--=-\n");
    if (doAssert)
        Assert.assertFalse(ok.isEmpty());
    //Assert.assertEquals("Invalid t-off", tOff * msPerFrame, be.getTOff(), tOff * msPerFrame * relativeError);
    return ok;
}
Also used : ActivationEnergyImageModel(gdsc.smlm.model.ActivationEnergyImageModel) CompoundMoleculeModel(gdsc.smlm.model.CompoundMoleculeModel) ArrayList(java.util.ArrayList) TIntHashSet(gnu.trove.set.hash.TIntHashSet) CompoundMoleculeModel(gdsc.smlm.model.CompoundMoleculeModel) MoleculeModel(gdsc.smlm.model.MoleculeModel) SpatialIllumination(gdsc.smlm.model.SpatialIllumination) MemoryPeakResults(gdsc.smlm.results.MemoryPeakResults) SpatialDistribution(gdsc.smlm.model.SpatialDistribution) UniformDistribution(gdsc.smlm.model.UniformDistribution) StoredDataStatistics(gdsc.core.utils.StoredDataStatistics) Calibration(gdsc.smlm.results.Calibration) StoredDataStatistics(gdsc.core.utils.StoredDataStatistics) Statistics(gdsc.core.utils.Statistics) UniformIllumination(gdsc.smlm.model.UniformIllumination) LocalisationModel(gdsc.smlm.model.LocalisationModel) FluorophoreSequenceModel(gdsc.smlm.model.FluorophoreSequenceModel) ImageModel(gdsc.smlm.model.ImageModel) ActivationEnergyImageModel(gdsc.smlm.model.ActivationEnergyImageModel)

Aggregations

FluorophoreSequenceModel (gdsc.smlm.model.FluorophoreSequenceModel)6 LocalisationModel (gdsc.smlm.model.LocalisationModel)4 StoredDataStatistics (gdsc.core.utils.StoredDataStatistics)3 ArrayList (java.util.ArrayList)3 Statistics (gdsc.core.utils.Statistics)2 ActivationEnergyImageModel (gdsc.smlm.model.ActivationEnergyImageModel)2 CompoundMoleculeModel (gdsc.smlm.model.CompoundMoleculeModel)2 ImageModel (gdsc.smlm.model.ImageModel)2 SpatialDistribution (gdsc.smlm.model.SpatialDistribution)2 SpatialIllumination (gdsc.smlm.model.SpatialIllumination)2 MemoryPeakResults (gdsc.smlm.results.MemoryPeakResults)2 TIntHashSet (gnu.trove.set.hash.TIntHashSet)2 GenericDialog (ij.gui.GenericDialog)2 Random (gdsc.core.utils.Random)1 FixedLifetimeImageModel (gdsc.smlm.model.FixedLifetimeImageModel)1 LocalisationModelSet (gdsc.smlm.model.LocalisationModelSet)1 MoleculeModel (gdsc.smlm.model.MoleculeModel)1 UniformDistribution (gdsc.smlm.model.UniformDistribution)1 UniformIllumination (gdsc.smlm.model.UniformIllumination)1 Calibration (gdsc.smlm.results.Calibration)1