Examples with CompoundMoleculeModel gdsc.smlm.model.CompoundMoleculeModel used on opensource projects

Example 1 with CompoundMoleculeModel

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

the class CreateData method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    extraOptions = Utils.isExtraOptions();
    simpleMode = (arg != null && arg.contains("simple"));
    benchmarkMode = (arg != null && arg.contains("benchmark"));
    spotMode = (arg != null && arg.contains("spot"));
    trackMode = (arg != null && arg.contains("track"));
    if ("load".equals(arg)) {
        loadBenchmarkData();
        return;
    }
    // Each localisation is a simulated emission of light from a point in space and time
    List<LocalisationModel> localisations = null;
    // Each localisation set is a collection of localisations that represent all localisations
    // with the same ID that are on in the same image time frame (Note: the simulation
    // can create many localisations per fluorophore per time frame which is useful when 
    // modelling moving particles)
    List<LocalisationModelSet> localisationSets = null;
    // Each fluorophore contains the on and off times when light was emitted 
    List<? extends FluorophoreSequenceModel> fluorophores = null;
    if (simpleMode || benchmarkMode || spotMode) {
        if (!showSimpleDialog())
            return;
        resetMemory();
        // 1 second frames
        settings.exposureTime = 1000;
        areaInUm = settings.size * settings.pixelPitch * settings.size * settings.pixelPitch / 1e6;
        // Number of spots per frame
        int n = 0;
        int[] nextN = null;
        SpatialDistribution dist;
        if (benchmarkMode) {
            // --------------------
            // BENCHMARK SIMULATION
            // --------------------
            // Draw the same point on the image repeatedly
            n = 1;
            dist = createFixedDistribution();
            reportAndSaveFittingLimits(dist);
        } else if (spotMode) {
            // ---------------
            // SPOT SIMULATION
            // ---------------
            // The spot simulation draws 0 or 1 random point per frame. 
            // Ensure we have 50% of the frames with a spot.
            nextN = new int[settings.particles * 2];
            Arrays.fill(nextN, 0, settings.particles, 1);
            Random rand = new Random();
            rand.shuffle(nextN);
            // Only put spots in the central part of the image
            double border = settings.size / 4.0;
            dist = createUniformDistribution(border);
        } else {
            // -----------------
            // SIMPLE SIMULATION
            // -----------------
            // The simple simulation draws n random points per frame to achieve a specified density.
            // No points will appear in multiple frames.
            // Each point has a random number of photons sampled from a range.
            // We can optionally use a mask. Create his first as it updates the areaInUm
            dist = createDistribution();
            // Randomly sample (i.e. not uniform density in all frames)
            if (settings.samplePerFrame) {
                final double mean = areaInUm * settings.density;
                System.out.printf("Mean samples = %f\n", mean);
                if (mean < 0.5) {
                    GenericDialog gd = new GenericDialog(TITLE);
                    gd.addMessage("The mean samples per frame is low: " + Utils.rounded(mean) + "\n \nContinue?");
                    gd.enableYesNoCancel();
                    gd.hideCancelButton();
                    gd.showDialog();
                    if (!gd.wasOKed())
                        return;
                }
                PoissonDistribution poisson = new PoissonDistribution(createRandomGenerator(), mean, PoissonDistribution.DEFAULT_EPSILON, PoissonDistribution.DEFAULT_MAX_ITERATIONS);
                StoredDataStatistics samples = new StoredDataStatistics(settings.particles);
                while (samples.getSum() < settings.particles) {
                    samples.add(poisson.sample());
                }
                nextN = new int[samples.getN()];
                for (int i = 0; i < nextN.length; i++) nextN[i] = (int) samples.getValue(i);
            } else {
                // Use the density to get the number per frame
                n = (int) FastMath.max(1, Math.round(areaInUm * settings.density));
            }
        }
        RandomGenerator random = null;
        localisations = new ArrayList<LocalisationModel>(settings.particles);
        localisationSets = new ArrayList<LocalisationModelSet>(settings.particles);
        final int minPhotons = (int) settings.photonsPerSecond;
        final int range = (int) settings.photonsPerSecondMaximum - minPhotons + 1;
        if (range > 1)
            random = createRandomGenerator();
        // Add frames at the specified density until the number of particles has been reached
        int id = 0;
        int t = 0;
        while (id < settings.particles) {
            // Allow the number per frame to be specified
            if (nextN != null) {
                if (t >= nextN.length)
                    break;
                n = nextN[t];
            }
            // Simulate random positions in the frame for the specified density
            t++;
            for (int j = 0; j < n; j++) {
                final double[] xyz = dist.next();
                // Ignore within border. We do not want to draw things we cannot fit.
                //if (!distBorder.isWithinXY(xyz))
                //	continue;
                // Simulate random photons
                final int intensity = minPhotons + ((random != null) ? random.nextInt(range) : 0);
                LocalisationModel m = new LocalisationModel(id, t, xyz, intensity, LocalisationModel.CONTINUOUS);
                localisations.add(m);
                // Each localisation can be a separate localisation set
                LocalisationModelSet set = new LocalisationModelSet(id, t);
                set.add(m);
                localisationSets.add(set);
                id++;
            }
        }
    } else {
        if (!showDialog())
            return;
        resetMemory();
        areaInUm = settings.size * settings.pixelPitch * settings.size * settings.pixelPitch / 1e6;
        int totalSteps;
        double correlation = 0;
        ImageModel imageModel;
        if (trackMode) {
            // ----------------
            // TRACK SIMULATION
            // ----------------
            // In track mode we create fixed lifetime fluorophores that do not overlap in time.
            // This is the simplest simulation to test moving molecules.
            settings.seconds = (int) Math.ceil(settings.particles * (settings.exposureTime + settings.tOn) / 1000);
            totalSteps = 0;
            final double simulationStepsPerFrame = (settings.stepsPerSecond * settings.exposureTime) / 1000.0;
            imageModel = new FixedLifetimeImageModel(settings.stepsPerSecond * settings.tOn / 1000.0, simulationStepsPerFrame);
        } else {
            // ---------------
            // FULL SIMULATION
            // ---------------
            // The full simulation draws n random points in space.
            // The same molecule may appear in multiple frames, move and blink.
            //
            // Points are modelled as fluorophores that must be activated and then will 
            // blink and photo-bleach. The molecules may diffuse and this can be simulated 
            // with many steps per image frame. All steps from a frame are collected
            // into a localisation set which can be drawn on the output image.
            SpatialIllumination activationIllumination = createIllumination(settings.pulseRatio, settings.pulseInterval);
            // Generate additional frames so that each frame has the set number of simulation steps
            totalSteps = (int) Math.ceil(settings.seconds * settings.stepsPerSecond);
            // Since we have an exponential decay of activations
            // ensure half of the particles have activated by 30% of the frames.
            double eAct = totalSteps * 0.3 * activationIllumination.getAveragePhotons();
            // Q. Does tOn/tOff change depending on the illumination strength?
            imageModel = new ActivationEnergyImageModel(eAct, activationIllumination, settings.stepsPerSecond * settings.tOn / 1000.0, settings.stepsPerSecond * settings.tOffShort / 1000.0, settings.stepsPerSecond * settings.tOffLong / 1000.0, settings.nBlinksShort, settings.nBlinksLong);
            imageModel.setUseGeometricDistribution(settings.nBlinksGeometricDistribution);
            // Only use the correlation if selected for the distribution
            if (PHOTON_DISTRIBUTION[PHOTON_CORRELATED].equals(settings.photonDistribution))
                correlation = settings.correlation;
        }
        imageModel.setRandomGenerator(createRandomGenerator());
        imageModel.setPhotonBudgetPerFrame(true);
        imageModel.setDiffusion2D(settings.diffuse2D);
        imageModel.setRotation2D(settings.rotate2D);
        IJ.showStatus("Creating molecules ...");
        SpatialDistribution distribution = createDistribution();
        List<CompoundMoleculeModel> compounds = createCompoundMolecules();
        if (compounds == null)
            return;
        List<CompoundMoleculeModel> molecules = imageModel.createMolecules(compounds, settings.particles, distribution, settings.rotateInitialOrientation);
        // Activate fluorophores
        IJ.showStatus("Creating fluorophores ...");
        // Note: molecules list will be converted to compounds containing fluorophores
        fluorophores = imageModel.createFluorophores(molecules, totalSteps);
        if (fluorophores.isEmpty()) {
            IJ.error(TITLE, "No fluorophores created");
            return;
        }
        IJ.showStatus("Creating localisations ...");
        // TODO - Output a molecule Id for each fluorophore if using compound molecules. This allows analysis
        // of the ratio of trimers, dimers, monomers, etc that could be detected.
        totalSteps = checkTotalSteps(totalSteps, fluorophores);
        if (totalSteps == 0)
            return;
        imageModel.setPhotonDistribution(createPhotonDistribution());
        imageModel.setConfinementDistribution(createConfinementDistribution());
        // This should be optimised
        imageModel.setConfinementAttempts(10);
        localisations = imageModel.createImage(molecules, settings.fixedFraction, totalSteps, (double) settings.photonsPerSecond / settings.stepsPerSecond, correlation, settings.rotateDuringSimulation);
        // Re-adjust the fluorophores to the correct time
        if (settings.stepsPerSecond != 1) {
            final double scale = 1.0 / settings.stepsPerSecond;
            for (FluorophoreSequenceModel f : fluorophores) f.adjustTime(scale);
        }
        // Integrate the frames
        localisationSets = combineSimulationSteps(localisations);
        localisationSets = filterToImageBounds(localisationSets);
    }
    datasetNumber++;
    localisations = drawImage(localisationSets);
    if (localisations == null || localisations.isEmpty()) {
        IJ.error(TITLE, "No localisations created");
        return;
    }
    fluorophores = removeFilteredFluorophores(fluorophores, localisations);
    double signalPerFrame = showSummary(fluorophores, localisations);
    if (!benchmarkMode) {
        boolean fullSimulation = (!(simpleMode || spotMode));
        saveSimulationParameters(localisations.size(), fullSimulation, signalPerFrame);
    }
    IJ.showStatus("Saving data ...");
    //convertRelativeToAbsolute(molecules);
    saveFluorophores(fluorophores);
    saveImageResults(results);
    saveLocalisations(localisations);
    // The settings for the filenames may have changed
    SettingsManager.saveSettings(globalSettings);
    IJ.showStatus("Done");
}

Example 2 with CompoundMoleculeModel

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

the class CreateData method convertRelativeToAbsolute.

/**
	 * Update the fluorophores relative coordinates to absolute
	 * 
	 * @param molecules
	 */
@SuppressWarnings("unused")
private void convertRelativeToAbsolute(List<CompoundMoleculeModel> molecules) {
    for (CompoundMoleculeModel c : molecules) {
        final double[] xyz = c.getCoordinates();
        for (int n = c.getSize(); n-- > 0; ) {
            MoleculeModel m = c.getMolecule(n);
            double[] xyz2 = m.getCoordinates();
            for (int i = 0; i < 3; i++) xyz2[i] += xyz[i];
        }
    }
}

Example 3 with CompoundMoleculeModel

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

the class CreateData method createCompoundMolecules.

@SuppressWarnings("unchecked")
private List<CompoundMoleculeModel> createCompoundMolecules() {
    // Diffusion rate is um^2/sec. Convert to pixels per simulation frame.
    final double diffusionFactor = (1000000.0 / (settings.pixelPitch * settings.pixelPitch)) / settings.stepsPerSecond;
    List<CompoundMoleculeModel> compounds;
    if (settings.compoundMolecules) {
        // Try and load the compounds from the XML specification
        try {
            Object fromXML = createXStream().fromXML(settings.compoundText);
            List<Compound> rawCompounds = (List<Compound>) fromXML;
            // Convert from the XML serialised objects to the compound model
            compounds = new ArrayList<CompoundMoleculeModel>(rawCompounds.size());
            int id = 1;
            for (Compound c : rawCompounds) {
                MoleculeModel[] molecules = new MoleculeModel[c.atoms.length];
                for (int i = 0; i < c.atoms.length; i++) {
                    Atom a = c.atoms[i];
                    molecules[i] = new MoleculeModel(a.mass, a.x, a.y, a.z);
                }
                CompoundMoleculeModel m = new CompoundMoleculeModel(id++, 0, 0, 0, Arrays.asList(molecules));
                m.setFraction(c.fraction);
                m.setDiffusionRate(c.D * diffusionFactor);
                m.setDiffusionType(DiffusionType.fromString(c.diffusionType));
                compounds.add(m);
            }
            // Convert coordinates from nm to pixels
            final double scaleFactor = 1.0 / settings.pixelPitch;
            for (CompoundMoleculeModel c : compounds) {
                c.scale(scaleFactor);
            }
        } catch (Exception e) {
            IJ.error(TITLE, "Unable to create compound molecules");
            return null;
        }
    } else {
        // Create a simple compound with one molecule at the origin
        compounds = new ArrayList<CompoundMoleculeModel>(1);
        CompoundMoleculeModel m = new CompoundMoleculeModel(1, 0, 0, 0, Arrays.asList(new MoleculeModel(0, 0, 0, 0)));
        m.setDiffusionRate(settings.diffusionRate * diffusionFactor);
        m.setDiffusionType(settings.getDiffusionType());
        compounds.add(m);
    }
    return compounds;
}

Example 4 with CompoundMoleculeModel

use of gdsc.smlm.model.CompoundMoleculeModel 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;
}