Examples with LocalisationModelSet uk.ac.sussex.gdsc.smlm.model.LocalisationModelSet used on opensource projects

Example 1 with LocalisationModelSet

use of uk.ac.sussex.gdsc.smlm.model.LocalisationModelSet in project GDSC-SMLM by aherbert.

the class CreateData method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    extraOptions = ImageJUtils.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 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.setExposureTime(1000);
        areaInUm = settings.getSize() * settings.getPixelPitch() * settings.getSize() * settings.getPixelPitch() / 1e6;
        // Number of spots per frame
        int count = 0;
        int[] nextN = null;
        SpatialDistribution dist;
        if (benchmarkMode) {
            // --------------------
            // BENCHMARK SIMULATION
            // --------------------
            // Draw the same point on the image repeatedly
            count = 1;
            dist = createFixedDistribution();
            try {
                reportAndSaveFittingLimits(dist);
            } catch (final Exception ex) {
                // This will be from the computation of the CRLB
                IJ.error(TITLE, ex.getMessage());
                return;
            }
        } 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.getParticles() * 2];
            Arrays.fill(nextN, 0, settings.getParticles(), 1);
            RandomUtils.shuffle(nextN, UniformRandomProviders.create());
            // Only put spots in the central part of the image
            final double border = settings.getSize() / 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.getSamplePerFrame()) {
                final double mean = areaInUm * settings.getDensity();
                ImageJUtils.log("Mean samples = %f", mean);
                if (mean < 0.5) {
                    final GenericDialog gd = new GenericDialog(TITLE);
                    gd.addMessage("The mean samples per frame is low: " + MathUtils.rounded(mean) + "\n \nContinue?");
                    gd.enableYesNoCancel();
                    gd.hideCancelButton();
                    gd.showDialog();
                    if (!gd.wasOKed()) {
                        return;
                    }
                }
                final PoissonSampler poisson = new PoissonSampler(createRandomGenerator(), mean);
                final StoredDataStatistics samples = new StoredDataStatistics(settings.getParticles());
                while (samples.getSum() < settings.getParticles()) {
                    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
                count = (int) Math.max(1, Math.round(areaInUm * settings.getDensity()));
            }
        }
        UniformRandomProvider rng = null;
        localisationSets = new ArrayList<>(settings.getParticles());
        final int minPhotons = (int) settings.getPhotonsPerSecond();
        final int range = (int) settings.getPhotonsPerSecondMaximum() - minPhotons + 1;
        if (range > 1) {
            rng = createRandomGenerator();
        }
        // Add frames at the specified density until the number of particles has been reached
        int id = 0;
        int time = 0;
        while (id < settings.getParticles()) {
            // Allow the number per frame to be specified
            if (nextN != null) {
                if (time >= nextN.length) {
                    break;
                }
                count = nextN[time];
            }
            // Simulate random positions in the frame for the specified density
            time++;
            for (int j = 0; j < count; 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 + ((rng != null) ? rng.nextInt(range) : 0);
                final LocalisationModel m = new LocalisationModel(id, time, xyz, intensity, LocalisationModel.CONTINUOUS);
                // Each localisation can be a separate localisation set
                final LocalisationModelSet set = new LocalisationModelSet(id, time);
                set.add(m);
                localisationSets.add(set);
                id++;
            }
        }
    } else {
        if (!showDialog()) {
            return;
        }
        resetMemory();
        areaInUm = settings.getSize() * settings.getPixelPitch() * settings.getSize() * settings.getPixelPitch() / 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.setSeconds((int) Math.ceil(settings.getParticles() * (settings.getExposureTime() + settings.getTOn()) / 1000));
            totalSteps = 0;
            final double simulationStepsPerFrame = (settings.getStepsPerSecond() * settings.getExposureTime()) / 1000.0;
            imageModel = new FixedLifetimeImageModel(settings.getStepsPerSecond() * settings.getTOn() / 1000.0, simulationStepsPerFrame, createRandomGenerator());
        } 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.
            final SpatialIllumination activationIllumination = createIllumination(settings.getPulseRatio(), settings.getPulseInterval());
            // Generate additional frames so that each frame has the set number of simulation steps
            totalSteps = (int) Math.ceil(settings.getSeconds() * settings.getStepsPerSecond());
            // Since we have an exponential decay of activations
            // ensure half of the particles have activated by 30% of the frames.
            final double eAct = totalSteps * 0.3 * activationIllumination.getAveragePhotons();
            // Q. Does tOn/tOff change depending on the illumination strength?
            imageModel = new ActivationEnergyImageModel(eAct, activationIllumination, settings.getStepsPerSecond() * settings.getTOn() / 1000.0, settings.getStepsPerSecond() * settings.getTOffShort() / 1000.0, settings.getStepsPerSecond() * settings.getTOffLong() / 1000.0, settings.getNBlinksShort(), settings.getNBlinksLong(), createRandomGenerator());
            imageModel.setUseGeometricDistribution(settings.getNBlinksGeometricDistribution());
            // Only use the correlation if selected for the distribution
            if (PHOTON_DISTRIBUTION[PHOTON_CORRELATED].equals(settings.getPhotonDistribution())) {
                correlation = settings.getCorrelation();
            }
        }
        imageModel.setPhotonBudgetPerFrame(true);
        imageModel.setDiffusion2D(settings.getDiffuse2D());
        imageModel.setRotation2D(settings.getRotate2D());
        IJ.showStatus("Creating molecules ...");
        final SpatialDistribution distribution = createDistribution();
        final List<CompoundMoleculeModel> compounds = createCompoundMolecules();
        if (compounds == null) {
            return;
        }
        final List<CompoundMoleculeModel> molecules = imageModel.createMolecules(compounds, settings.getParticles(), distribution, settings.getRotateInitialOrientation());
        // 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;
        }
        // Map the fluorophore ID to the compound for mixtures
        if (compounds.size() > 1) {
            idToCompound = new TIntIntHashMap(fluorophores.size());
            for (final FluorophoreSequenceModel l : fluorophores) {
                idToCompound.put(l.getId(), l.getLabel());
            }
        }
        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());
        try {
            imageModel.setConfinementDistribution(createConfinementDistribution());
        } catch (final ConfigurationException ex) {
            // We asked the user if it was OK to continue and they said no
            return;
        }
        // This should be optimised
        imageModel.setConfinementAttempts(10);
        final List<LocalisationModel> localisations = imageModel.createImage(molecules, settings.getFixedFraction(), totalSteps, settings.getPhotonsPerSecond() / settings.getStepsPerSecond(), correlation, settings.getRotateDuringSimulation());
        // Re-adjust the fluorophores to the correct time
        if (settings.getStepsPerSecond() != 1) {
            final double scale = 1.0 / settings.getStepsPerSecond();
            for (final FluorophoreSequenceModel f : fluorophores) {
                f.adjustTime(scale);
            }
        }
        // Integrate the frames
        localisationSets = combineSimulationSteps(localisations);
        localisationSets = filterToImageBounds(localisationSets);
    }
    datasetNumber.getAndIncrement();
    final List<LocalisationModel> localisations = drawImage(localisationSets);
    if (localisations == null || localisations.isEmpty()) {
        IJ.error(TITLE, "No localisations created");
        return;
    }
    fluorophores = removeFilteredFluorophores(fluorophores, localisations);
    final double signalPerFrame = showSummary(fluorophores, localisations);
    if (!benchmarkMode) {
        final boolean fullSimulation = (!(simpleMode || spotMode));
        saveSimulationParameters(localisations.size(), fullSimulation, signalPerFrame);
    }
    IJ.showStatus("Saving data ...");
    saveFluorophores(fluorophores);
    saveImageResults(results);
    saveLocalisations(localisations);
    // The settings for the filenames may have changed
    SettingsManager.writeSettings(settings.build());
    IJ.showStatus("Done");
}

Example 2 with LocalisationModelSet

use of uk.ac.sussex.gdsc.smlm.model.LocalisationModelSet in project GDSC-SMLM by aherbert.

the class CreateData method drawImage.

// StoredDataStatistics rawPhotons = new StoredDataStatistics();
// StoredDataStatistics drawPhotons = new StoredDataStatistics();
// private synchronized void addRaw(double d)
// {
// //rawPhotons.add(d);
// }
// 
// private synchronized void addDraw(double d)
// {
// //drawPhotons.add(d);
// }
/**
 * Create an image from the localisations using the configured PSF width. Draws a new stack image.
 *
 * <p>Note that the localisations are filtered using the signal. The input list of localisations
 * will be updated.
 *
 * @param localisationSets the localisation sets
 * @return The localisations
 */
private List<LocalisationModel> drawImage(final List<LocalisationModelSet> localisationSets) {
    if (localisationSets.isEmpty()) {
        return null;
    }
    // Create a new list for all localisation that are drawn (i.e. pass the signal filters)
    List<LocalisationModelSet> newLocalisations = Collections.synchronizedList(new ArrayList<LocalisationModelSet>(localisationSets.size()));
    photonsRemoved = new AtomicInteger();
    removedT1 = new AtomicInteger();
    removedTn = new AtomicInteger();
    photonStats = new SummaryStatistics();
    // Add drawn spots to memory
    results = new MemoryPeakResults();
    final CalibrationWriter c = new CalibrationWriter();
    c.setDistanceUnit(DistanceUnit.PIXEL);
    c.setIntensityUnit(IntensityUnit.PHOTON);
    c.setNmPerPixel(settings.getPixelPitch());
    c.setExposureTime(settings.getExposureTime());
    c.setCameraType(settings.getCameraType());
    if (settings.getCameraType() == CameraType.SCMOS) {
        c.setCameraModelName(settings.getCameraModelName());
    } else {
        final CreateDataSettingsHelper helper = new CreateDataSettingsHelper(settings);
        c.setCountPerPhoton(helper.getTotalGainSafe());
        c.setBias(settings.getBias());
        c.setReadNoise(helper.getReadNoiseInCounts());
        c.setQuantumEfficiency(helper.getQuantumEfficiency());
    }
    results.setCalibration(c.getCalibration());
    results.setSortAfterEnd(true);
    results.begin();
    maxT = localisationSets.get(localisationSets.size() - 1).getTime();
    // Display image
    final ImageStack stack = new ImageStack(settings.getSize(), settings.getSize(), maxT);
    final double psfSd = getPsfSd();
    if (psfSd <= 0) {
        return null;
    }
    final PsfModel psfModel = createPsfModel(localisationSets);
    if (psfModel == null) {
        return null;
    }
    // Create the camera noise model
    createPerPixelCameraModelData(cameraModel);
    createBackgroundPixels();
    final int threadCount = Prefs.getThreads();
    IJ.showStatus("Drawing image ...");
    // Multi-thread for speed
    final PeakResults syncResults = SynchronizedPeakResults.create(results, threadCount);
    final ExecutorService threadPool = Executors.newFixedThreadPool(threadCount);
    final List<Future<?>> futures = new LinkedList<>();
    // Count all the frames to process
    final Ticker ticker = ImageJUtils.createTicker(maxT, threadCount);
    // Collect statistics on the number of photons actually simulated
    // Process all frames
    int index = 0;
    int lastT = -1;
    for (final LocalisationModelSet l : localisationSets) {
        if (ImageJUtils.isInterrupted()) {
            break;
        }
        if (l.getTime() != lastT) {
            lastT = l.getTime();
            futures.add(threadPool.submit(new ImageGenerator(localisationSets, newLocalisations, index, lastT, psfModel.copy(), syncResults, stack, poissonNoise, createRandomGenerator(), ticker)));
        }
        index++;
    }
    // Finish processing data
    ConcurrencyUtils.waitForCompletionUnchecked(futures);
    futures.clear();
    if (ImageJUtils.isInterrupted()) {
        IJ.showProgress(1);
        return null;
    }
    // Do all the frames that had no localisations
    float[] limits = null;
    for (int t = 1; t <= maxT; t++) {
        if (ImageJUtils.isInterrupted()) {
            break;
        }
        final Object pixels = stack.getPixels(t);
        if (pixels == null) {
            futures.add(threadPool.submit(new ImageGenerator(localisationSets, newLocalisations, maxT, t, null, syncResults, stack, poissonNoise, createRandomGenerator(), ticker)));
        } else if (limits == null) {
            limits = MathUtils.limits((float[]) pixels);
        }
    }
    // Finish
    ConcurrencyUtils.waitForCompletionUnchecked(futures);
    futures.clear();
    threadPool.shutdown();
    IJ.showProgress(1);
    if (ImageJUtils.isInterrupted() || limits == null) {
        return null;
    }
    results.end();
    if (photonsRemoved.get() > 0) {
        ImageJUtils.log("Removed %d localisations with less than %.1f rendered photons", photonsRemoved.get(), settings.getMinPhotons());
    }
    if (removedT1.get() > 0) {
        ImageJUtils.log("Removed %d localisations with no neighbours @ SNR %.2f", removedT1.get(), settings.getMinSnrT1());
    }
    if (removedTn.get() > 0) {
        ImageJUtils.log("Removed %d localisations with valid neighbours @ SNR %.2f", removedTn.get(), settings.getMinSnrTN());
    }
    if (photonStats.getN() > 0) {
        ImageJUtils.log("Average photons rendered = %s +/- %s", MathUtils.rounded(photonStats.getMean()), MathUtils.rounded(photonStats.getStandardDeviation()));
    }
    // System.out.printf("rawPhotons = %f\n", rawPhotons.getMean());
    // System.out.printf("drawPhotons = %f\n", drawPhotons.getMean());
    // new HistogramPlotBuilder("draw photons", drawPhotons, "photons", true, 0, 1000);
    // Update with all those localisation that have been drawn
    localisationSets.clear();
    localisationSets.addAll(newLocalisations);
    newLocalisations = null;
    IJ.showStatus("Displaying image ...");
    ImageStack newStack = stack;
    if (!settings.getRawImage()) {
        // Get the global limits and ensure all values can be represented
        final Object[] imageArray = stack.getImageArray();
        limits = MathUtils.limits((float[]) imageArray[0]);
        for (int j = 1; j < imageArray.length; j++) {
            limits = MathUtils.limits(limits, (float[]) imageArray[j]);
        }
        // float limits0 = limits[0];
        // Leave bias in place
        final float limits0 = 0;
        // Check if the image will fit in a 16-bit range
        if ((limits[1] - limits0) < 65535) {
            // Convert to 16-bit
            newStack = new ImageStack(stack.getWidth(), stack.getHeight(), stack.getSize());
            // Account for rounding
            final float min = (float) (limits0 - 0.5);
            for (int j = 0; j < imageArray.length; j++) {
                final float[] image = (float[]) imageArray[j];
                final short[] pixels = new short[image.length];
                for (int k = 0; k < pixels.length; k++) {
                    pixels[k] = (short) (image[k] - min);
                }
                newStack.setPixels(pixels, j + 1);
                // Free memory
                imageArray[j] = null;
                // Attempt to stay within memory (check vs 32MB)
                if (MemoryUtils.getFreeMemory() < 33554432L) {
                    MemoryUtils.runGarbageCollectorOnce();
                }
            }
            for (int k = 2; k-- > 0; ) {
                limits[k] = (float) Math.floor(limits[k] - min);
            }
        } else {
            // Keep as 32-bit but round to whole numbers
            for (int j = 0; j < imageArray.length; j++) {
                final float[] pixels = (float[]) imageArray[j];
                for (int k = 0; k < pixels.length; k++) {
                    pixels[k] = Math.round(pixels[k]);
                }
            }
            for (int k = 2; k-- > 0; ) {
                limits[k] = Math.round(limits[k]);
            }
        }
    }
    // Show image
    final ImagePlus imp = ImageJUtils.display(CREATE_DATA_IMAGE_TITLE, newStack);
    final ij.measure.Calibration cal = new ij.measure.Calibration();
    String unit = "nm";
    double unitPerPixel = settings.getPixelPitch();
    if (unitPerPixel > 100) {
        unit = "um";
        unitPerPixel /= 1000.0;
    }
    cal.setUnit(unit);
    cal.pixelHeight = cal.pixelWidth = unitPerPixel;
    final Rectangle bounds = cameraModel.getBounds();
    if (bounds != null) {
        cal.xOrigin = -bounds.x;
        cal.yOrigin = -bounds.y;
    }
    imp.setCalibration(cal);
    imp.setDimensions(1, 1, newStack.getSize());
    imp.setDisplayRange(limits[0], limits[1]);
    imp.updateAndDraw();
    saveImage(imp);
    final IJImageSource imageSource = new IJImageSource(imp);
    // Shift simulation image source to correct location
    results.setSource(imageSource);
    results.setName(CREATE_DATA_IMAGE_TITLE + " (" + TITLE + ")");
    // Bounds are relative to the image source
    results.setBounds(new Rectangle(settings.getSize(), settings.getSize()));
    results.setPsf(createPsf(psfSd));
    MemoryPeakResults.addResults(results);
    setBenchmarkResults(imp, results);
    if (benchmarkMode && benchmarkParameters != null) {
        benchmarkParameters.setPhotons(results);
    }
    final List<LocalisationModel> localisations = toLocalisations(localisationSets);
    savePulses(localisations, results);
    // Saved the fixed and moving localisations into different datasets
    saveFixedAndMoving(results);
    saveCompoundMolecules(results);
    return localisations;
}

Example 3 with LocalisationModelSet

use of uk.ac.sussex.gdsc.smlm.model.LocalisationModelSet in project GDSC-SMLM by aherbert.

the class CreateData method filterToImageBounds.

/**
 * Filter those not in the bounds of the distribution.
 *
 * @param localisationSets the localisation sets
 * @return the list
 */
private List<LocalisationModelSet> filterToImageBounds(List<LocalisationModelSet> localisationSets) {
    final List<LocalisationModelSet> newLocalisations = new ArrayList<>(localisationSets.size());
    final SpatialDistribution bounds = createUniformDistribution(0);
    for (final LocalisationModelSet s : localisationSets) {
        if (bounds.isWithinXy(s.toLocalisation().getCoordinates())) {
            newLocalisations.add(s);
        }
    }
    return newLocalisations;
}

Example 4 with LocalisationModelSet

use of uk.ac.sussex.gdsc.smlm.model.LocalisationModelSet in project GDSC-SMLM by aherbert.

the class CreateData method combineSimulationSteps.

private List<LocalisationModelSet> combineSimulationSteps(List<LocalisationModel> localisations) {
    // Allow fractional integration steps
    final double simulationStepsPerFrame = (settings.getStepsPerSecond() * settings.getExposureTime()) / 1000.0;
    final List<LocalisationModelSet> newLocalisations = new ArrayList<>((int) (localisations.size() / simulationStepsPerFrame));
    // System.out.printf("combineSimulationSteps @ %f\n", simulationStepsPerFrame);
    // final double gain = new CreateDataSettingsHelper(settings).getTotalGainSafe();
    sortLocalisationsByIdThenTime(localisations);
    final int[] idList = getIds(localisations);
    movingMolecules = new TIntHashSet(idList.length);
    int index = 0;
    for (final int id : idList) {
        final int fromIndex = findIndexById(localisations, index, id);
        if (fromIndex > -1) {
            final int toIndex = findLastIndexById(localisations, fromIndex, id);
            final List<LocalisationModel> subset = localisations.subList(fromIndex, toIndex + 1);
            index = toIndex;
            // Store the IDs of any moving molecules
            if (isMoving(subset)) {
                movingMolecules.add(id);
            }
            // The frames may be longer or shorter than the simulation steps. Allocate the step
            // proportionately to each frame it overlaps:
            // 
            // Steps: |-- 0 --|-- 1 --|-- 2 --|--
            // Frames: |--- 0 ---|--- 1 ---|--- 2 ---|
            // 
            // ^ ^
            // | |
            // | End frame
            // |
            // Start frame
            final double firstFrame = getStartFrame(subset.get(0), simulationStepsPerFrame);
            final double lastFrame = getEndFrame(subset.get(subset.size() - 1), simulationStepsPerFrame);
            // Get the first frame offset and allocate space to store all potential frames
            final int intFirstFrame = (int) firstFrame;
            final int intLastFrame = (int) Math.ceil(lastFrame);
            final LocalisationModelSet[] sets = new LocalisationModelSet[intLastFrame - intFirstFrame + 1];
            // Process each step
            for (final LocalisationModel l : subset) {
                // Get the fractional start and end frames
                final double startFrame = getStartFrame(l, simulationStepsPerFrame);
                final double endFrame = getEndFrame(l, simulationStepsPerFrame);
                // Round down to get the actual frames that are overlapped
                final int start = (int) startFrame;
                int end = (int) endFrame;
                // that frame
                if (end > start && endFrame == end) {
                    // E.g. convert
                    // Steps: |-- 0 --|
                    // Frames: |- 0 -|- 1 -|- 2 -|
                    // to
                    // Steps: |-- 0 --|
                    // Frames: |- 0 -|- 1 -|
                    end--;
                }
                if (start == end) {
                    // If the step falls within one frame then add it to the set
                    final int tIndex = start - intFirstFrame;
                    if (sets[tIndex] == null) {
                        sets[tIndex] = new LocalisationModelSet(id, start);
                    }
                    sets[tIndex].add(l);
                } else {
                    // Add the localisation to all the frames that the step spans
                    final double total = endFrame - startFrame;
                    // double t = 0;
                    for (int frame = start; frame <= end; frame++) {
                        // Get the fraction to allocate to this frame
                        double fraction;
                        int state = (l.isContinuous() ? LocalisationModel.CONTINUOUS : 0);
                        if (frame == start) {
                            state |= LocalisationModel.NEXT | (l.hasPrevious() ? LocalisationModel.PREVIOUS : 0);
                            // start
                            if (startFrame == start) {
                                fraction = 1;
                            } else {
                                fraction = (Math.ceil(startFrame) - startFrame);
                            }
                        } else if (frame == end) {
                            state |= LocalisationModel.PREVIOUS | (l.hasNext() ? LocalisationModel.NEXT : 0);
                            // |=====|----|
                            // | |
                            // | endFrame
                            // end
                            fraction = (endFrame - end);
                        } else {
                            state |= LocalisationModel.CONTINUOUS;
                            fraction = 1;
                        }
                        // t += fraction;
                        // Add to the set
                        final int tIndex = frame - intFirstFrame;
                        if (sets[tIndex] == null) {
                            sets[tIndex] = new LocalisationModelSet(id, frame);
                        }
                        sets[tIndex].add(getFraction(l, fraction / total, state));
                    }
                // if (t < total * 0.98)
                // {
                // System.out.printf("Total error %g < %g : %f (%d) -> %f (%d)\n", t, total, startFrame,
                // start, endFrame, end);
                // }
                }
            }
            LocalisationModelSet previous = null;
            for (int i = 0; i < sets.length; i++) {
                if (sets[i] != null) {
                    sets[i].setPrevious(previous);
                    // Create a data array and store the current intensity.
                    // This is used later to filter based on SNR
                    sets[i].setData(new double[] { // * gain
                    0, // * gain
                    0, // * gain
                    0, // * gain
                    0, // * gain
                    sets[i].getIntensity() });
                    newLocalisations.add(sets[i]);
                }
                previous = sets[i];
            }
        }
    }
    // Sort by time
    Collections.sort(newLocalisations, (r1, r2) -> Integer.compare(r1.getTime(), r2.getTime()));
    return newLocalisations;
}

Example 5 with LocalisationModelSet

use of uk.ac.sussex.gdsc.smlm.model.LocalisationModelSet in project GDSC-SMLM by aherbert.

the class CreateData method createImagePsf.

/**
 * Create a PSF model from the image that contains all the z-slices needed to draw the given
 * localisations.
 *
 * @param localisationSets the localisation sets
 * @return the image PSF model
 */
private ImagePsfModel createImagePsf(List<LocalisationModelSet> localisationSets) {
    final ImagePlus imp = WindowManager.getImage(settings.getPsfImageName());
    if (imp == null) {
        IJ.error(TITLE, "Unable to create the PSF model from image: " + settings.getPsfImageName());
        return null;
    }
    try {
        final ImagePSF psfSettings = ImagePsfHelper.fromString(imp.getProperty("Info").toString());
        if (psfSettings == null) {
            throw new IllegalStateException("Unknown PSF settings for image: " + imp.getTitle());
        }
        // Check all the settings have values
        if (psfSettings.getPixelSize() <= 0) {
            throw new IllegalStateException("Missing nmPerPixel calibration settings for image: " + imp.getTitle());
        }
        if (psfSettings.getPixelDepth() <= 0) {
            throw new IllegalStateException("Missing nmPerSlice calibration settings for image: " + imp.getTitle());
        }
        if (psfSettings.getCentreImage() <= 0) {
            throw new IllegalStateException("Missing zCentre calibration settings for image: " + imp.getTitle());
        }
        if (psfSettings.getFwhm() <= 0) {
            throw new IllegalStateException("Missing FWHM calibration settings for image: " + imp.getTitle());
        }
        // To save memory construct the Image PSF using only the slices that are within
        // the depth of field of the simulation
        double minZ = Double.POSITIVE_INFINITY;
        double maxZ = Double.NEGATIVE_INFINITY;
        for (final LocalisationModelSet l : localisationSets) {
            for (final LocalisationModel m : l.getLocalisations()) {
                final double z = m.getZ();
                if (minZ > z) {
                    minZ = z;
                }
                if (maxZ < z) {
                    maxZ = z;
                }
            }
        }
        final int nSlices = imp.getStackSize();
        // z-centre should be an index and not the ImageJ slice number so subtract 1
        final int zCentre = psfSettings.getCentreImage() - 1;
        // Calculate the start/end slices to cover the depth of field
        // This logic must match the ImagePSFModel.
        final double unitsPerSlice = psfSettings.getPixelDepth() / settings.getPixelPitch();
        // We assume the PSF was imaged axially with increasing z-stage position (moving the stage
        // closer to the objective). Thus higher z-coordinate are for higher slice numbers.
        int lower = (int) Math.round(minZ / unitsPerSlice) + zCentre;
        int upper = (int) Math.round(maxZ / unitsPerSlice) + zCentre;
        // Add extra to the range so that gradients can be computed.
        lower--;
        upper++;
        upper = (upper < 0) ? 0 : (upper >= nSlices) ? nSlices - 1 : upper;
        lower = (lower < 0) ? 0 : (lower >= nSlices) ? nSlices - 1 : lower;
        // Image PSF requires the z-centre for normalisation
        if (!(lower <= zCentre && upper >= zCentre)) {
            // Ensure we include the zCentre
            lower = Math.min(lower, zCentre);
            upper = Math.max(upper, zCentre);
        }
        final double noiseFraction = 1e-3;
        final float[][] image = extractImageStack(imp, lower, upper);
        final ImagePsfModel model = new ImagePsfModel(image, zCentre - lower, psfSettings.getPixelSize() / settings.getPixelPitch(), unitsPerSlice, noiseFraction);
        // Add the calibrated centres. The map will not be null
        final Map<Integer, Offset> map = psfSettings.getOffsetsMap();
        if (!map.isEmpty()) {
            final int sliceOffset = lower + 1;
            for (final Entry<Integer, Offset> entry : map.entrySet()) {
                model.setRelativeCentre(entry.getKey() - sliceOffset, entry.getValue().getCx(), entry.getValue().getCy());
            }
        } else {
            // Use the CoM if present
            final double cx = psfSettings.getXCentre();
            final double cy = psfSettings.getYCentre();
            if (cx != 0 || cy != 0) {
                for (int slice = 0; slice < image.length; slice++) {
                    model.setCentre(slice, cx, cy);
                }
            }
        }
        // Initialise the HWHM table so that it can be cloned
        model.initialiseHwhm();
        return model;
    } catch (final Exception ex) {
        IJ.error(TITLE, "Unable to create the image PSF model:\n" + ex.getMessage());
        return null;
    }
}