Search in sources :

Example 1 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class CreateData method setNoise.

/**
 * Sets the noise in the results if missing.
 *
 * @param results the results
 * @param imp the imp
 */
private static void setNoise(MemoryPeakResults results, ImagePlus imp) {
    // Loaded results do not have noise
    if (results.hasNoise()) {
        return;
    }
    IJ.showStatus("Estimating noise ...");
    // Compute noise per frame
    final ImageStack stack = imp.getImageStack();
    final int width = stack.getWidth();
    final int height = stack.getHeight();
    final IJImageSource source = new IJImageSource(imp);
    final float[] noise = new float[source.getFrames() + 1];
    source.setReadHint(ReadHint.SEQUENTIAL);
    source.open();
    for (int slice = 1; slice < noise.length; slice++) {
        final float[] data = source.next();
        // Use the trimmed method as there may be a lot of spots in the frame
        noise[slice] = FitWorker.estimateNoise(data, width, height, NoiseEstimatorMethod.QUICK_RESIDUALS_LEAST_TRIMMED_OF_SQUARES);
    }
    // Statistics stats = Statistics.create(Arrays.copyOfRange(noise, 1, noise.length));
    // System.out.printf("Noise = %.3f +/- %.3f (%d)\n", stats.getMean(),
    // stats.getStandardDeviation(), stats.getN());
    // Convert noise units from counts to the result format
    final TypeConverter<IntensityUnit> c = results.getIntensityConverter(IntensityUnit.COUNT);
    for (int i = 0; i < noise.length; i++) {
        noise[i] = c.convertBack(noise[i]);
    }
    results.forEach((PeakResultProcedure) result -> {
        if (result.getFrame() < noise.length) {
            result.setNoise(noise[result.getFrame()]);
        }
    });
}
Also used : RandomUtils(uk.ac.sussex.gdsc.core.utils.rng.RandomUtils) LoadLocalisations(uk.ac.sussex.gdsc.smlm.ij.plugins.LoadLocalisations) Arrays(java.util.Arrays) PoissonSamplerUtils(uk.ac.sussex.gdsc.core.utils.rng.PoissonSamplerUtils) Molecule(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.Molecule) IdPeakResult(uk.ac.sussex.gdsc.smlm.results.IdPeakResult) ImageProcessor(ij.process.ImageProcessor) HistogramPlotBuilder(uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder) ConfigurationException(uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException) AiryPsfModel(uk.ac.sussex.gdsc.smlm.model.AiryPsfModel) GaussianPsfModel(uk.ac.sussex.gdsc.smlm.model.GaussianPsfModel) MemoryUtils(uk.ac.sussex.gdsc.core.utils.MemoryUtils) PSFType(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFType) HelpUrls(uk.ac.sussex.gdsc.smlm.ij.plugins.HelpUrls) ResultsManager(uk.ac.sussex.gdsc.smlm.ij.plugins.ResultsManager) GammaDistribution(org.apache.commons.math3.distribution.GammaDistribution) Future(java.util.concurrent.Future) Vector(java.util.Vector) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) Map(java.util.Map) DensityManager(uk.ac.sussex.gdsc.core.clustering.DensityManager) UnicodeReader(uk.ac.sussex.gdsc.core.utils.UnicodeReader) RadialFalloffIllumination(uk.ac.sussex.gdsc.smlm.model.RadialFalloffIllumination) DistanceUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit) RawResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.RawResultProcedure) ConcurrencyUtils(uk.ac.sussex.gdsc.core.utils.concurrent.ConcurrencyUtils) TextUtils(uk.ac.sussex.gdsc.core.utils.TextUtils) Gaussian2DFunction(uk.ac.sussex.gdsc.smlm.function.gaussian.Gaussian2DFunction) Executors(java.util.concurrent.Executors) PeakFit(uk.ac.sussex.gdsc.smlm.ij.plugins.PeakFit) TIntHashSet(gnu.trove.set.hash.TIntHashSet) ImagePlus(ij.ImagePlus) LocalisationList(uk.ac.sussex.gdsc.smlm.ij.plugins.LoadLocalisations.LocalisationList) UniformDistribution(uk.ac.sussex.gdsc.smlm.model.UniformDistribution) ShortProcessor(ij.process.ShortProcessor) FileUtils(uk.ac.sussex.gdsc.core.utils.FileUtils) CameraModelFisherInformationAnalysis(uk.ac.sussex.gdsc.smlm.ij.plugins.CameraModelFisherInformationAnalysis) CalibrationProtosHelper(uk.ac.sussex.gdsc.smlm.data.config.CalibrationProtosHelper) PlugIn(ij.plugin.PlugIn) LocalisationModelSet(uk.ac.sussex.gdsc.smlm.model.LocalisationModelSet) AiryPattern(uk.ac.sussex.gdsc.smlm.model.AiryPattern) Prefs(ij.Prefs) FrameCounter(uk.ac.sussex.gdsc.smlm.results.count.FrameCounter) WindowManager(ij.WindowManager) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) CreateDataSettings(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.CreateDataSettings) GridDistribution(uk.ac.sussex.gdsc.smlm.model.GridDistribution) ArrayList(java.util.ArrayList) Atom(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.Atom) AutoThreshold(uk.ac.sussex.gdsc.core.threshold.AutoThreshold) GenericDialog(ij.gui.GenericDialog) ImagePsfModel(uk.ac.sussex.gdsc.smlm.model.ImagePsfModel) PsfModel(uk.ac.sussex.gdsc.smlm.model.PsfModel) PeakResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure) PoissonGaussianFisherInformation(uk.ac.sussex.gdsc.smlm.function.PoissonGaussianFisherInformation) ImagePsfHelper(uk.ac.sussex.gdsc.smlm.ij.settings.ImagePsfHelper) UnivariateLikelihoodFisherInformationCalculator(uk.ac.sussex.gdsc.smlm.fitting.UnivariateLikelihoodFisherInformationCalculator) SpatialIllumination(uk.ac.sussex.gdsc.smlm.model.SpatialIllumination) PeakResultsReader(uk.ac.sussex.gdsc.smlm.results.PeakResultsReader) PsfCombiner(uk.ac.sussex.gdsc.smlm.ij.plugins.PsfCombiner) DiffusionType(uk.ac.sussex.gdsc.smlm.model.DiffusionType) Files(java.nio.file.Files) BufferedWriter(java.io.BufferedWriter) FitWorker(uk.ac.sussex.gdsc.smlm.engine.FitWorker) RandomGeneratorAdapter(uk.ac.sussex.gdsc.core.utils.rng.RandomGeneratorAdapter) AtomOrBuilder(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.AtomOrBuilder) IOException(java.io.IOException) SamplerUtils(uk.ac.sussex.gdsc.core.utils.rng.SamplerUtils) DiscreteUniformSampler(org.apache.commons.rng.sampling.distribution.DiscreteUniformSampler) File(java.io.File) SummaryStatistics(org.apache.commons.math3.stat.descriptive.SummaryStatistics) FloatProcessor(ij.process.FloatProcessor) BasePoissonFisherInformation(uk.ac.sussex.gdsc.smlm.function.BasePoissonFisherInformation) Paths(java.nio.file.Paths) AstigmatismZModel(uk.ac.sussex.gdsc.smlm.function.gaussian.AstigmatismZModel) TextFilePeakResults(uk.ac.sussex.gdsc.smlm.results.TextFilePeakResults) EmCcdCameraModel(uk.ac.sussex.gdsc.smlm.model.camera.EmCcdCameraModel) ImageStack(ij.ImageStack) PoissonSampler(org.apache.commons.rng.sampling.distribution.PoissonSampler) CameraModel(uk.ac.sussex.gdsc.smlm.model.camera.CameraModel) ExtendedPeakResult(uk.ac.sussex.gdsc.smlm.results.ExtendedPeakResult) PsfHelper(uk.ac.sussex.gdsc.smlm.data.config.PsfHelper) BufferedReader(java.io.BufferedReader) ImmutableMemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.ImmutableMemoryPeakResults) DoubleEquality(uk.ac.sussex.gdsc.core.utils.DoubleEquality) StandardResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure) SphericalDistribution(uk.ac.sussex.gdsc.smlm.model.SphericalDistribution) TIntArrayList(gnu.trove.list.array.TIntArrayList) GaussianFilter(uk.ac.sussex.gdsc.smlm.filters.GaussianFilter) TextWindow(ij.text.TextWindow) StandardValueProcedure(uk.ac.sussex.gdsc.smlm.function.StandardValueProcedure) ImagePSF(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.ImagePSF) Formatter(java.util.Formatter) FixedLifetimeImageModel(uk.ac.sussex.gdsc.smlm.model.FixedLifetimeImageModel) StoredDataStatistics(uk.ac.sussex.gdsc.core.utils.StoredDataStatistics) AtomicInteger(java.util.concurrent.atomic.AtomicInteger) PeakResults(uk.ac.sussex.gdsc.smlm.results.PeakResults) DataException(uk.ac.sussex.gdsc.core.data.DataException) PsfCalculator(uk.ac.sussex.gdsc.smlm.ij.plugins.PsfCalculator) EmpiricalDistribution(org.apache.commons.math3.random.EmpiricalDistribution) MathUtils(uk.ac.sussex.gdsc.core.utils.MathUtils) BinomialDiscreteInverseCumulativeProbabilityFunction(uk.ac.sussex.gdsc.core.utils.rng.BinomialDiscreteInverseCumulativeProbabilityFunction) CalibrationWriter(uk.ac.sussex.gdsc.smlm.data.config.CalibrationWriter) Offset(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.Offset) TextFormat(com.google.protobuf.TextFormat) PsfProtosHelper(uk.ac.sussex.gdsc.smlm.data.config.PsfProtosHelper) SettingsManager(uk.ac.sussex.gdsc.smlm.ij.settings.SettingsManager) ItemEvent(java.awt.event.ItemEvent) CameraType(uk.ac.sussex.gdsc.smlm.data.config.CalibrationProtos.CameraType) SpatialDistribution(uk.ac.sussex.gdsc.smlm.model.SpatialDistribution) ExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog) AstigmatismModelManager(uk.ac.sussex.gdsc.smlm.ij.plugins.AstigmatismModelManager) UniformRealDistribution(org.apache.commons.math3.distribution.UniformRealDistribution) MoleculeModel(uk.ac.sussex.gdsc.smlm.model.MoleculeModel) TIntIntHashMap(gnu.trove.map.hash.TIntIntHashMap) MarsagliaTsangGammaSampler(uk.ac.sussex.gdsc.core.utils.rng.MarsagliaTsangGammaSampler) WidthResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.WidthResultProcedure) Gaussian2DPeakResultHelper(uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultHelper) List(java.util.List) FluorophoreSequenceModel(uk.ac.sussex.gdsc.smlm.model.FluorophoreSequenceModel) BirResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.BirResultProcedure) Entry(java.util.Map.Entry) CompoundMoleculeModel(uk.ac.sussex.gdsc.smlm.model.CompoundMoleculeModel) RealDistribution(org.apache.commons.math3.distribution.RealDistribution) HoltzerAstigmatismZModel(uk.ac.sussex.gdsc.smlm.function.gaussian.HoltzerAstigmatismZModel) ImageModel(uk.ac.sussex.gdsc.smlm.model.ImageModel) MaskDistribution3D(uk.ac.sussex.gdsc.smlm.model.MaskDistribution3D) TypeConverter(uk.ac.sussex.gdsc.core.data.utils.TypeConverter) PrecisionResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PrecisionResultProcedure) Rectangle(java.awt.Rectangle) AtomicBoolean(java.util.concurrent.atomic.AtomicBoolean) PSF(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSF) WindowOrganiser(uk.ac.sussex.gdsc.core.ij.plugin.WindowOrganiser) IntensityUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.IntensityUnit) Mixture(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.Mixture) AtomicReference(java.util.concurrent.atomic.AtomicReference) SobolSequenceGenerator(org.apache.commons.math3.random.SobolSequenceGenerator) MaskDistribution(uk.ac.sussex.gdsc.smlm.model.MaskDistribution) OptionListener(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog.OptionListener) OpenDialog(ij.io.OpenDialog) ParameterUtils(uk.ac.sussex.gdsc.smlm.ij.plugins.ParameterUtils) IJImageSource(uk.ac.sussex.gdsc.smlm.ij.IJImageSource) NoiseEstimatorMethod(uk.ac.sussex.gdsc.smlm.data.config.FitProtos.NoiseEstimatorMethod) ReadHint(uk.ac.sussex.gdsc.smlm.results.ImageSource.ReadHint) ExponentialDistribution(org.apache.commons.math3.distribution.ExponentialDistribution) FisherInformationMatrix(uk.ac.sussex.gdsc.smlm.fitting.FisherInformationMatrix) UnitHelper(uk.ac.sussex.gdsc.smlm.data.config.UnitHelper) LinkedList(java.util.LinkedList) CcdCameraModel(uk.ac.sussex.gdsc.smlm.model.camera.CcdCameraModel) FileSaver(ij.io.FileSaver) Statistics(uk.ac.sussex.gdsc.core.utils.Statistics) ExecutorService(java.util.concurrent.ExecutorService) CreateDataSettingsHelper(uk.ac.sussex.gdsc.smlm.ij.settings.CreateDataSettingsHelper) TFloatArrayList(gnu.trove.list.array.TFloatArrayList) FunctionHelper(uk.ac.sussex.gdsc.smlm.function.FunctionHelper) UniformRandomProvider(org.apache.commons.rng.UniformRandomProvider) PoissonSamplerCache(org.apache.commons.rng.sampling.distribution.PoissonSamplerCache) AstigmatismModel(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.AstigmatismModel) ConversionException(uk.ac.sussex.gdsc.core.data.utils.ConversionException) SplitMix64(org.apache.commons.rng.core.source64.SplitMix64) Checkbox(java.awt.Checkbox) ActivationEnergyImageModel(uk.ac.sussex.gdsc.smlm.model.ActivationEnergyImageModel) LoadLocalisationsSettings(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.LoadLocalisationsSettings) FileInputStream(java.io.FileInputStream) Ticker(uk.ac.sussex.gdsc.core.logging.Ticker) PsfModelGradient1Function(uk.ac.sussex.gdsc.smlm.model.PsfModelGradient1Function) InterpolatedPoissonFisherInformation(uk.ac.sussex.gdsc.smlm.function.InterpolatedPoissonFisherInformation) Consumer(java.util.function.Consumer) CameraModelManager(uk.ac.sussex.gdsc.smlm.ij.plugins.CameraModelManager) LocalisationModel(uk.ac.sussex.gdsc.smlm.model.LocalisationModel) ImageJUtils(uk.ac.sussex.gdsc.core.ij.ImageJUtils) UniformIllumination(uk.ac.sussex.gdsc.smlm.model.UniformIllumination) SynchronizedPeakResults(uk.ac.sussex.gdsc.smlm.results.SynchronizedPeakResults) IJ(ij.IJ) NullArgumentException(org.apache.commons.math3.exception.NullArgumentException) SmlmUsageTracker(uk.ac.sussex.gdsc.smlm.ij.plugins.SmlmUsageTracker) InverseTransformDiscreteSampler(org.apache.commons.rng.sampling.distribution.InverseTransformDiscreteSampler) Comparator(java.util.Comparator) Collections(java.util.Collections) NormalizedGaussianSampler(org.apache.commons.rng.sampling.distribution.NormalizedGaussianSampler) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) UniformRandomProviders(uk.ac.sussex.gdsc.core.utils.rng.UniformRandomProviders) IJImageSource(uk.ac.sussex.gdsc.smlm.ij.IJImageSource) ImageStack(ij.ImageStack) IntensityUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.IntensityUnit) ReadHint(uk.ac.sussex.gdsc.smlm.results.ImageSource.ReadHint)

Example 2 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class CreateData method showSummary.

private double showSummary(List<? extends FluorophoreSequenceModel> fluorophores, List<LocalisationModel> localisations) {
    IJ.showStatus("Calculating statistics ...");
    final Statistics[] stats = new Statistics[NAMES.length];
    for (int i = 0; i < stats.length; i++) {
        stats[i] = (settings.getShowHistograms() || alwaysRemoveOutliers[i]) ? new StoredDataStatistics() : new Statistics();
    }
    // Find the largest timepoint
    final ImagePlus outputImp = WindowManager.getImage(benchmarkImageId);
    int frameCount;
    if (outputImp == null) {
        sortLocalisationsByTime(localisations);
        frameCount = localisations.get(localisations.size() - 1).getTime();
    } else {
        frameCount = outputImp.getStackSize();
    }
    final int[] countHistogram = new int[frameCount + 1];
    // Use the localisations that were drawn to create the sampled on/off times
    rebuildNeighbours(localisations);
    // Assume that there is at least one localisation
    final LocalisationModel first = localisations.get(0);
    // The current localisation
    int currentId = first.getId();
    // The last time this localisation was on
    int lastT = first.getTime();
    // Number of blinks
    int blinks = 0;
    // On-time of current pulse
    int currentT = 0;
    double signal = 0;
    final double centreOffset = settings.getSize() * 0.5;
    // Used to convert the sampled times in frames into seconds
    final double framesPerSecond = 1000.0 / settings.getExposureTime();
    // final double gain = new CreateDataSettingsHelper(settings).getTotalGainSafe();
    for (final LocalisationModel l : localisations) {
        final double[] data = l.getData();
        if (data == null) {
            throw new IllegalStateException("No localisation data. This should not happen!");
        }
        final double noise = data[1];
        final double sx = data[2];
        final double sy = data[3];
        final double intensityInPhotons = data[4];
        // Q. What if the noise is zero, i.e. no background photon / read noise?
        // Just ignore it at current. This is only an approximation to the SNR estimate
        // if this is not a Gaussian spot.
        final double snr = Gaussian2DPeakResultHelper.getMeanSignalUsingP05(intensityInPhotons, sx, sy) / noise;
        stats[SIGNAL].add(intensityInPhotons);
        stats[NOISE].add(noise);
        if (noise != 0) {
            stats[SNR].add(snr);
        }
        // if (l.isContinuous())
        if (l.getNext() != null && l.getPrevious() != null) {
            stats[SIGNAL_CONTINUOUS].add(intensityInPhotons);
            if (noise != 0) {
                stats[SNR_CONTINUOUS].add(snr);
            }
        }
        final int id = l.getId();
        // Check if this a new fluorophore
        if (currentId != id) {
            // Add previous fluorophore
            stats[SAMPLED_BLINKS].add(blinks);
            stats[SAMPLED_T_ON].add(currentT / framesPerSecond);
            stats[TOTAL_SIGNAL].add(signal);
            // Reset
            blinks = 0;
            currentT = 1;
            currentId = id;
            signal = intensityInPhotons;
        } else {
            signal += intensityInPhotons;
            // Check if the current fluorophore pulse is broken (i.e. a blink)
            if (l.getTime() - 1 > lastT) {
                blinks++;
                stats[SAMPLED_T_ON].add(currentT / framesPerSecond);
                currentT = 1;
                stats[SAMPLED_T_OFF].add(((l.getTime() - 1) - lastT) / framesPerSecond);
            } else {
                // Continuous on-time
                currentT++;
            }
        }
        lastT = l.getTime();
        countHistogram[lastT]++;
        stats[X].add((l.getX() - centreOffset) * settings.getPixelPitch());
        stats[Y].add((l.getY() - centreOffset) * settings.getPixelPitch());
        stats[Z].add(l.getZ() * settings.getPixelPitch());
    }
    // Final fluorophore
    stats[SAMPLED_BLINKS].add(blinks);
    stats[SAMPLED_T_ON].add(currentT / framesPerSecond);
    stats[TOTAL_SIGNAL].add(signal);
    // Samples per frame
    for (int t = 1; t < countHistogram.length; t++) {
        stats[SAMPLES].add(countHistogram[t]);
    }
    if (fluorophores != null) {
        for (final FluorophoreSequenceModel f : fluorophores) {
            stats[BLINKS].add(f.getNumberOfBlinks());
            // On-time
            for (final double t : f.getOnTimes()) {
                stats[T_ON].add(t);
            }
            // Off-time
            for (final double t : f.getOffTimes()) {
                stats[T_OFF].add(t);
            }
        }
    } else {
        // show no blinks
        stats[BLINKS].add(0);
        stats[T_ON].add(1);
    }
    if (results != null) {
        // Convert depth-of-field to pixels
        final double depth = settings.getDepthOfField() / settings.getPixelPitch();
        try {
            // Get widths
            final WidthResultProcedure wp = new WidthResultProcedure(results, DistanceUnit.PIXEL);
            wp.getW();
            stats[WIDTH].add(wp.wx);
        } catch (final DataException ex) {
            ImageJUtils.log("Unable to compute width: " + ex.getMessage());
        }
        try {
            // Get z depth
            final StandardResultProcedure sp = new StandardResultProcedure(results, DistanceUnit.PIXEL);
            sp.getXyz();
            // Get precision
            final PrecisionResultProcedure pp = new PrecisionResultProcedure(results);
            pp.getPrecision();
            stats[PRECISION].add(pp.precisions);
            for (int i = 0; i < pp.size(); i++) {
                if (Math.abs(sp.z[i]) < depth) {
                    stats[PRECISION_IN_FOCUS].add(pp.precisions[i]);
                }
            }
        } catch (final DataException ex) {
            ImageJUtils.log("Unable to compute LSE precision: " + ex.getMessage());
        }
        // Compute density per frame. Multi-thread for speed
        if (settings.getDensityRadius() > 0) {
            final int threadCount = Prefs.getThreads();
            final Ticker ticker = ImageJUtils.createTicker(results.getLastFrame(), threadCount, "Calculating density ...");
            final ExecutorService threadPool = Executors.newFixedThreadPool(threadCount);
            final List<Future<?>> futures = new LinkedList<>();
            final TFloatArrayList coordsX = new TFloatArrayList();
            final TFloatArrayList coordsY = new TFloatArrayList();
            final Statistics densityStats = stats[DENSITY];
            final float radius = (float) (settings.getDensityRadius() * getHwhm());
            final Rectangle bounds = results.getBounds();
            final double area = (double) bounds.width * bounds.height;
            // Store the density for each result.
            final int[] allDensity = new int[results.size()];
            final FrameCounter counter = results.newFrameCounter();
            results.forEach((PeakResultProcedure) result -> {
                if (counter.advance(result.getFrame())) {
                    counter.increment(runDensityCalculation(threadPool, futures, coordsX, coordsY, densityStats, radius, area, allDensity, counter.getCount(), ticker));
                }
                coordsX.add(result.getXPosition());
                coordsY.add(result.getYPosition());
            });
            runDensityCalculation(threadPool, futures, coordsX, coordsY, densityStats, radius, area, allDensity, counter.getCount(), ticker);
            ConcurrencyUtils.waitForCompletionUnchecked(futures);
            threadPool.shutdown();
            ImageJUtils.finished();
            // Split results into singles (density = 0) and clustered (density > 0)
            final MemoryPeakResults singles = copyMemoryPeakResults("No Density");
            final MemoryPeakResults clustered = copyMemoryPeakResults("Density");
            counter.reset();
            results.forEach((PeakResultProcedure) result -> {
                final int density = allDensity[counter.getAndIncrement()];
                result.setOrigValue(density);
                if (density == 0) {
                    singles.add(result);
                } else {
                    clustered.add(result);
                }
            });
        }
    }
    final StringBuilder sb = new StringBuilder();
    sb.append(datasetNumber).append('\t');
    if (settings.getCameraType() == CameraType.SCMOS) {
        sb.append("sCMOS (").append(settings.getCameraModelName()).append(") ");
        final Rectangle bounds = cameraModel.getBounds();
        sb.append(" ").append(bounds.x).append(",").append(bounds.y);
        final int size = settings.getSize();
        sb.append(" ").append(size).append("x").append(size);
    } else if (CalibrationProtosHelper.isCcdCameraType(settings.getCameraType())) {
        sb.append(CalibrationProtosHelper.getName(settings.getCameraType()));
        final int size = settings.getSize();
        sb.append(" ").append(size).append("x").append(size);
        if (settings.getCameraType() == CameraType.EMCCD) {
            sb.append(" EM=").append(settings.getEmGain());
        }
        sb.append(" CG=").append(settings.getCameraGain());
        sb.append(" RN=").append(settings.getReadNoise());
        sb.append(" B=").append(settings.getBias());
    } else {
        throw new IllegalStateException();
    }
    sb.append(" QE=").append(settings.getQuantumEfficiency()).append('\t');
    sb.append(settings.getPsfModel());
    if (psfModelType == PSF_MODEL_IMAGE) {
        sb.append(" Image").append(settings.getPsfImageName());
    } else if (psfModelType == PSF_MODEL_ASTIGMATISM) {
        sb.append(" model=").append(settings.getAstigmatismModel());
    } else {
        sb.append(" DoF=").append(MathUtils.rounded(settings.getDepthOfFocus()));
        if (settings.getEnterWidth()) {
            sb.append(" SD=").append(MathUtils.rounded(settings.getPsfSd()));
        } else {
            sb.append(" λ=").append(MathUtils.rounded(settings.getWavelength()));
            sb.append(" NA=").append(MathUtils.rounded(settings.getNumericalAperture()));
        }
    }
    sb.append('\t');
    sb.append((fluorophores == null) ? localisations.size() : fluorophores.size()).append('\t');
    sb.append(stats[SAMPLED_BLINKS].getN() + (int) stats[SAMPLED_BLINKS].getSum()).append('\t');
    sb.append(localisations.size()).append('\t');
    sb.append(frameCount).append('\t');
    sb.append(MathUtils.rounded(areaInUm)).append('\t');
    sb.append(MathUtils.rounded(localisations.size() / (areaInUm * frameCount), 4)).append('\t');
    sb.append(MathUtils.rounded(getHwhm(), 4)).append('\t');
    double sd = getPsfSd();
    sb.append(MathUtils.rounded(sd, 4)).append('\t');
    sd *= settings.getPixelPitch();
    final double sa = PsfCalculator.squarePixelAdjustment(sd, settings.getPixelPitch()) / settings.getPixelPitch();
    sb.append(MathUtils.rounded(sa, 4)).append('\t');
    // Width not valid for the Image PSF.
    // Q. Is this true? We can approximate the FHWM for a spot-like image PSF.
    final int nStats = (psfModelType == PSF_MODEL_IMAGE) ? stats.length - 1 : stats.length;
    for (int i = 0; i < nStats; i++) {
        final double centre = (alwaysRemoveOutliers[i]) ? ((StoredDataStatistics) stats[i]).getStatistics().getPercentile(50) : stats[i].getMean();
        sb.append(MathUtils.rounded(centre, 4)).append('\t');
    }
    createSummaryTable().accept(sb.toString());
    // Show histograms
    if (settings.getShowHistograms() && !java.awt.GraphicsEnvironment.isHeadless()) {
        IJ.showStatus("Calculating histograms ...");
        final boolean[] chosenHistograms = getChoosenHistograms();
        final WindowOrganiser wo = new WindowOrganiser();
        final HistogramPlotBuilder builder = new HistogramPlotBuilder(TITLE);
        for (int i = 0; i < NAMES.length; i++) {
            if (chosenHistograms[i]) {
                builder.setData((StoredDataStatistics) stats[i]).setName(NAMES[i]).setIntegerBins(integerDisplay[i]).setRemoveOutliersOption((settings.getRemoveOutliers() || alwaysRemoveOutliers[i]) ? 2 : 0).setNumberOfBins(settings.getHistogramBins()).show(wo);
            }
        }
        wo.tile();
    }
    IJ.showStatus("");
    return stats[SIGNAL].getMean();
}
Also used : RandomUtils(uk.ac.sussex.gdsc.core.utils.rng.RandomUtils) LoadLocalisations(uk.ac.sussex.gdsc.smlm.ij.plugins.LoadLocalisations) Arrays(java.util.Arrays) PoissonSamplerUtils(uk.ac.sussex.gdsc.core.utils.rng.PoissonSamplerUtils) Molecule(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.Molecule) IdPeakResult(uk.ac.sussex.gdsc.smlm.results.IdPeakResult) ImageProcessor(ij.process.ImageProcessor) HistogramPlotBuilder(uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder) ConfigurationException(uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException) AiryPsfModel(uk.ac.sussex.gdsc.smlm.model.AiryPsfModel) GaussianPsfModel(uk.ac.sussex.gdsc.smlm.model.GaussianPsfModel) MemoryUtils(uk.ac.sussex.gdsc.core.utils.MemoryUtils) PSFType(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFType) HelpUrls(uk.ac.sussex.gdsc.smlm.ij.plugins.HelpUrls) ResultsManager(uk.ac.sussex.gdsc.smlm.ij.plugins.ResultsManager) GammaDistribution(org.apache.commons.math3.distribution.GammaDistribution) Future(java.util.concurrent.Future) Vector(java.util.Vector) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) Map(java.util.Map) DensityManager(uk.ac.sussex.gdsc.core.clustering.DensityManager) UnicodeReader(uk.ac.sussex.gdsc.core.utils.UnicodeReader) RadialFalloffIllumination(uk.ac.sussex.gdsc.smlm.model.RadialFalloffIllumination) DistanceUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit) RawResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.RawResultProcedure) ConcurrencyUtils(uk.ac.sussex.gdsc.core.utils.concurrent.ConcurrencyUtils) TextUtils(uk.ac.sussex.gdsc.core.utils.TextUtils) Gaussian2DFunction(uk.ac.sussex.gdsc.smlm.function.gaussian.Gaussian2DFunction) Executors(java.util.concurrent.Executors) PeakFit(uk.ac.sussex.gdsc.smlm.ij.plugins.PeakFit) TIntHashSet(gnu.trove.set.hash.TIntHashSet) ImagePlus(ij.ImagePlus) LocalisationList(uk.ac.sussex.gdsc.smlm.ij.plugins.LoadLocalisations.LocalisationList) UniformDistribution(uk.ac.sussex.gdsc.smlm.model.UniformDistribution) ShortProcessor(ij.process.ShortProcessor) FileUtils(uk.ac.sussex.gdsc.core.utils.FileUtils) CameraModelFisherInformationAnalysis(uk.ac.sussex.gdsc.smlm.ij.plugins.CameraModelFisherInformationAnalysis) CalibrationProtosHelper(uk.ac.sussex.gdsc.smlm.data.config.CalibrationProtosHelper) PlugIn(ij.plugin.PlugIn) LocalisationModelSet(uk.ac.sussex.gdsc.smlm.model.LocalisationModelSet) AiryPattern(uk.ac.sussex.gdsc.smlm.model.AiryPattern) Prefs(ij.Prefs) FrameCounter(uk.ac.sussex.gdsc.smlm.results.count.FrameCounter) WindowManager(ij.WindowManager) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) CreateDataSettings(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.CreateDataSettings) GridDistribution(uk.ac.sussex.gdsc.smlm.model.GridDistribution) ArrayList(java.util.ArrayList) Atom(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.Atom) AutoThreshold(uk.ac.sussex.gdsc.core.threshold.AutoThreshold) GenericDialog(ij.gui.GenericDialog) ImagePsfModel(uk.ac.sussex.gdsc.smlm.model.ImagePsfModel) PsfModel(uk.ac.sussex.gdsc.smlm.model.PsfModel) PeakResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure) PoissonGaussianFisherInformation(uk.ac.sussex.gdsc.smlm.function.PoissonGaussianFisherInformation) ImagePsfHelper(uk.ac.sussex.gdsc.smlm.ij.settings.ImagePsfHelper) UnivariateLikelihoodFisherInformationCalculator(uk.ac.sussex.gdsc.smlm.fitting.UnivariateLikelihoodFisherInformationCalculator) SpatialIllumination(uk.ac.sussex.gdsc.smlm.model.SpatialIllumination) PeakResultsReader(uk.ac.sussex.gdsc.smlm.results.PeakResultsReader) PsfCombiner(uk.ac.sussex.gdsc.smlm.ij.plugins.PsfCombiner) DiffusionType(uk.ac.sussex.gdsc.smlm.model.DiffusionType) Files(java.nio.file.Files) BufferedWriter(java.io.BufferedWriter) FitWorker(uk.ac.sussex.gdsc.smlm.engine.FitWorker) RandomGeneratorAdapter(uk.ac.sussex.gdsc.core.utils.rng.RandomGeneratorAdapter) AtomOrBuilder(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.AtomOrBuilder) IOException(java.io.IOException) SamplerUtils(uk.ac.sussex.gdsc.core.utils.rng.SamplerUtils) DiscreteUniformSampler(org.apache.commons.rng.sampling.distribution.DiscreteUniformSampler) File(java.io.File) SummaryStatistics(org.apache.commons.math3.stat.descriptive.SummaryStatistics) FloatProcessor(ij.process.FloatProcessor) BasePoissonFisherInformation(uk.ac.sussex.gdsc.smlm.function.BasePoissonFisherInformation) Paths(java.nio.file.Paths) AstigmatismZModel(uk.ac.sussex.gdsc.smlm.function.gaussian.AstigmatismZModel) TextFilePeakResults(uk.ac.sussex.gdsc.smlm.results.TextFilePeakResults) EmCcdCameraModel(uk.ac.sussex.gdsc.smlm.model.camera.EmCcdCameraModel) ImageStack(ij.ImageStack) PoissonSampler(org.apache.commons.rng.sampling.distribution.PoissonSampler) CameraModel(uk.ac.sussex.gdsc.smlm.model.camera.CameraModel) ExtendedPeakResult(uk.ac.sussex.gdsc.smlm.results.ExtendedPeakResult) PsfHelper(uk.ac.sussex.gdsc.smlm.data.config.PsfHelper) BufferedReader(java.io.BufferedReader) ImmutableMemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.ImmutableMemoryPeakResults) DoubleEquality(uk.ac.sussex.gdsc.core.utils.DoubleEquality) StandardResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure) SphericalDistribution(uk.ac.sussex.gdsc.smlm.model.SphericalDistribution) TIntArrayList(gnu.trove.list.array.TIntArrayList) GaussianFilter(uk.ac.sussex.gdsc.smlm.filters.GaussianFilter) TextWindow(ij.text.TextWindow) StandardValueProcedure(uk.ac.sussex.gdsc.smlm.function.StandardValueProcedure) ImagePSF(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.ImagePSF) Formatter(java.util.Formatter) FixedLifetimeImageModel(uk.ac.sussex.gdsc.smlm.model.FixedLifetimeImageModel) StoredDataStatistics(uk.ac.sussex.gdsc.core.utils.StoredDataStatistics) AtomicInteger(java.util.concurrent.atomic.AtomicInteger) PeakResults(uk.ac.sussex.gdsc.smlm.results.PeakResults) DataException(uk.ac.sussex.gdsc.core.data.DataException) PsfCalculator(uk.ac.sussex.gdsc.smlm.ij.plugins.PsfCalculator) EmpiricalDistribution(org.apache.commons.math3.random.EmpiricalDistribution) MathUtils(uk.ac.sussex.gdsc.core.utils.MathUtils) BinomialDiscreteInverseCumulativeProbabilityFunction(uk.ac.sussex.gdsc.core.utils.rng.BinomialDiscreteInverseCumulativeProbabilityFunction) CalibrationWriter(uk.ac.sussex.gdsc.smlm.data.config.CalibrationWriter) Offset(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.Offset) TextFormat(com.google.protobuf.TextFormat) PsfProtosHelper(uk.ac.sussex.gdsc.smlm.data.config.PsfProtosHelper) SettingsManager(uk.ac.sussex.gdsc.smlm.ij.settings.SettingsManager) ItemEvent(java.awt.event.ItemEvent) CameraType(uk.ac.sussex.gdsc.smlm.data.config.CalibrationProtos.CameraType) SpatialDistribution(uk.ac.sussex.gdsc.smlm.model.SpatialDistribution) ExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog) AstigmatismModelManager(uk.ac.sussex.gdsc.smlm.ij.plugins.AstigmatismModelManager) UniformRealDistribution(org.apache.commons.math3.distribution.UniformRealDistribution) MoleculeModel(uk.ac.sussex.gdsc.smlm.model.MoleculeModel) TIntIntHashMap(gnu.trove.map.hash.TIntIntHashMap) MarsagliaTsangGammaSampler(uk.ac.sussex.gdsc.core.utils.rng.MarsagliaTsangGammaSampler) WidthResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.WidthResultProcedure) Gaussian2DPeakResultHelper(uk.ac.sussex.gdsc.smlm.results.Gaussian2DPeakResultHelper) List(java.util.List) FluorophoreSequenceModel(uk.ac.sussex.gdsc.smlm.model.FluorophoreSequenceModel) BirResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.BirResultProcedure) Entry(java.util.Map.Entry) CompoundMoleculeModel(uk.ac.sussex.gdsc.smlm.model.CompoundMoleculeModel) RealDistribution(org.apache.commons.math3.distribution.RealDistribution) HoltzerAstigmatismZModel(uk.ac.sussex.gdsc.smlm.function.gaussian.HoltzerAstigmatismZModel) ImageModel(uk.ac.sussex.gdsc.smlm.model.ImageModel) MaskDistribution3D(uk.ac.sussex.gdsc.smlm.model.MaskDistribution3D) TypeConverter(uk.ac.sussex.gdsc.core.data.utils.TypeConverter) PrecisionResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PrecisionResultProcedure) Rectangle(java.awt.Rectangle) AtomicBoolean(java.util.concurrent.atomic.AtomicBoolean) PSF(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSF) WindowOrganiser(uk.ac.sussex.gdsc.core.ij.plugin.WindowOrganiser) IntensityUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.IntensityUnit) Mixture(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.Mixture) AtomicReference(java.util.concurrent.atomic.AtomicReference) SobolSequenceGenerator(org.apache.commons.math3.random.SobolSequenceGenerator) MaskDistribution(uk.ac.sussex.gdsc.smlm.model.MaskDistribution) OptionListener(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog.OptionListener) OpenDialog(ij.io.OpenDialog) ParameterUtils(uk.ac.sussex.gdsc.smlm.ij.plugins.ParameterUtils) IJImageSource(uk.ac.sussex.gdsc.smlm.ij.IJImageSource) NoiseEstimatorMethod(uk.ac.sussex.gdsc.smlm.data.config.FitProtos.NoiseEstimatorMethod) ReadHint(uk.ac.sussex.gdsc.smlm.results.ImageSource.ReadHint) ExponentialDistribution(org.apache.commons.math3.distribution.ExponentialDistribution) FisherInformationMatrix(uk.ac.sussex.gdsc.smlm.fitting.FisherInformationMatrix) UnitHelper(uk.ac.sussex.gdsc.smlm.data.config.UnitHelper) LinkedList(java.util.LinkedList) CcdCameraModel(uk.ac.sussex.gdsc.smlm.model.camera.CcdCameraModel) FileSaver(ij.io.FileSaver) Statistics(uk.ac.sussex.gdsc.core.utils.Statistics) ExecutorService(java.util.concurrent.ExecutorService) CreateDataSettingsHelper(uk.ac.sussex.gdsc.smlm.ij.settings.CreateDataSettingsHelper) TFloatArrayList(gnu.trove.list.array.TFloatArrayList) FunctionHelper(uk.ac.sussex.gdsc.smlm.function.FunctionHelper) UniformRandomProvider(org.apache.commons.rng.UniformRandomProvider) PoissonSamplerCache(org.apache.commons.rng.sampling.distribution.PoissonSamplerCache) AstigmatismModel(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.AstigmatismModel) ConversionException(uk.ac.sussex.gdsc.core.data.utils.ConversionException) SplitMix64(org.apache.commons.rng.core.source64.SplitMix64) Checkbox(java.awt.Checkbox) ActivationEnergyImageModel(uk.ac.sussex.gdsc.smlm.model.ActivationEnergyImageModel) LoadLocalisationsSettings(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.LoadLocalisationsSettings) FileInputStream(java.io.FileInputStream) Ticker(uk.ac.sussex.gdsc.core.logging.Ticker) PsfModelGradient1Function(uk.ac.sussex.gdsc.smlm.model.PsfModelGradient1Function) InterpolatedPoissonFisherInformation(uk.ac.sussex.gdsc.smlm.function.InterpolatedPoissonFisherInformation) Consumer(java.util.function.Consumer) CameraModelManager(uk.ac.sussex.gdsc.smlm.ij.plugins.CameraModelManager) LocalisationModel(uk.ac.sussex.gdsc.smlm.model.LocalisationModel) ImageJUtils(uk.ac.sussex.gdsc.core.ij.ImageJUtils) UniformIllumination(uk.ac.sussex.gdsc.smlm.model.UniformIllumination) SynchronizedPeakResults(uk.ac.sussex.gdsc.smlm.results.SynchronizedPeakResults) IJ(ij.IJ) NullArgumentException(org.apache.commons.math3.exception.NullArgumentException) SmlmUsageTracker(uk.ac.sussex.gdsc.smlm.ij.plugins.SmlmUsageTracker) InverseTransformDiscreteSampler(org.apache.commons.rng.sampling.distribution.InverseTransformDiscreteSampler) Comparator(java.util.Comparator) Collections(java.util.Collections) NormalizedGaussianSampler(org.apache.commons.rng.sampling.distribution.NormalizedGaussianSampler) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) UniformRandomProviders(uk.ac.sussex.gdsc.core.utils.rng.UniformRandomProviders) Rectangle(java.awt.Rectangle) HistogramPlotBuilder(uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) ImmutableMemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.ImmutableMemoryPeakResults) Ticker(uk.ac.sussex.gdsc.core.logging.Ticker) FrameCounter(uk.ac.sussex.gdsc.smlm.results.count.FrameCounter) StoredDataStatistics(uk.ac.sussex.gdsc.core.utils.StoredDataStatistics) WidthResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.WidthResultProcedure) WindowOrganiser(uk.ac.sussex.gdsc.core.ij.plugin.WindowOrganiser) PrecisionResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PrecisionResultProcedure) SummaryStatistics(org.apache.commons.math3.stat.descriptive.SummaryStatistics) StoredDataStatistics(uk.ac.sussex.gdsc.core.utils.StoredDataStatistics) Statistics(uk.ac.sussex.gdsc.core.utils.Statistics) ImagePlus(ij.ImagePlus) ReadHint(uk.ac.sussex.gdsc.smlm.results.ImageSource.ReadHint) LinkedList(java.util.LinkedList) TFloatArrayList(gnu.trove.list.array.TFloatArrayList) DataException(uk.ac.sussex.gdsc.core.data.DataException) LocalisationModel(uk.ac.sussex.gdsc.smlm.model.LocalisationModel) FluorophoreSequenceModel(uk.ac.sussex.gdsc.smlm.model.FluorophoreSequenceModel) ExecutorService(java.util.concurrent.ExecutorService) Future(java.util.concurrent.Future) StandardResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure)

Example 3 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class CreateData method loadBenchmarkData.

/**
 * Load benchmark data using an open image and a XYZ text file.
 */
private void loadBenchmarkData() {
    if (!showLoadDialog()) {
        // resetMemory();
        return;
    }
    // Load the image
    final ImagePlus imp = WindowManager.getImage(benchmarkImage);
    if (imp == null) {
        IJ.error(TITLE, "No benchmark image: " + benchmarkImage);
        // resetMemory();
        return;
    }
    // Load the results
    final MemoryPeakResults results = getSimulationResults();
    if (results == null) {
        IJ.error(TITLE, "No benchmark results: " + benchmarkResultsName);
        // resetMemory();
        return;
    }
    results.setName(imp.getTitle() + " (Results)");
    results.setBounds(new Rectangle(0, 0, imp.getWidth(), imp.getHeight()));
    final IJImageSource imageSource = new IJImageSource(imp);
    results.setSource(imageSource);
    // Load the settings as these are used in the dialog
    settings = SettingsManager.readCreateDataSettings(0).toBuilder();
    simulationParameters = showSimulationParametersDialog(imp, results);
    if (simulationParameters != null) {
        // Convert data to allow analysis as if a Gaussian2D PSF
        final boolean isGaussian2D = PsfHelper.isGaussian2D(results.getPsf());
        if (isGaussian2D) {
            Gaussian2DPeakResultHelper.addMeanIntensity(results.getPsf(), results);
        } else if (simulationParameters.sd > 0) {
            final TypeConverter<DistanceUnit> dc = results.getDistanceConverter(DistanceUnit.NM);
            final PSF.Builder psf = PsfProtosHelper.getDefaultPsf(PSFType.ONE_AXIS_GAUSSIAN_2D).toBuilder();
            psf.getParametersBuilder(0).setValue(dc.convertBack(simulationParameters.sd));
            results.setPsf(psf.build());
            // Update all the results. This assumes the results do not have data for a custom PSF,
            // i.e. the parameters only have [t,i,x,y,z]
            final LocalList<PeakResult> newResults = new LocalList<>(results.size());
            final float sd = (float) dc.convertBack(simulationParameters.sd);
            final double meanFactor = Gaussian2DPeakResultHelper.getMeanSignalUsingP05(1, sd, sd);
            results.forEach((PeakResultProcedure) r -> {
                final PeakResult peak = r.resize(PeakResult.STANDARD_PARAMETERS + 1);
                peak.setMeanIntensity((float) (peak.getIntensity() * meanFactor));
                peak.setParameter(PeakResult.STANDARD_PARAMETERS, sd);
                newResults.add(peak);
            });
            results.begin();
            results.addAll(newResults);
            results.end();
        }
        setBackground(results);
        setNoise(results, imp);
        setBenchmarkResults(imp, results);
        IJ.showStatus("Loaded " + TextUtils.pleural(results.size(), "result"));
    } else {
        resetMemory();
    }
}
Also used : TypeConverter(uk.ac.sussex.gdsc.core.data.utils.TypeConverter) IJImageSource(uk.ac.sussex.gdsc.smlm.ij.IJImageSource) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) PeakResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure) HistogramPlotBuilder(uk.ac.sussex.gdsc.core.ij.HistogramPlot.HistogramPlotBuilder) AtomOrBuilder(uk.ac.sussex.gdsc.smlm.data.config.MoleculeProtos.AtomOrBuilder) Rectangle(java.awt.Rectangle) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) ImmutableMemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.ImmutableMemoryPeakResults) ImagePlus(ij.ImagePlus) IdPeakResult(uk.ac.sussex.gdsc.smlm.results.IdPeakResult) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) ExtendedPeakResult(uk.ac.sussex.gdsc.smlm.results.ExtendedPeakResult)

Example 4 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class PsfCreator method fitPsf.

/**
 * Fit the new PSF image and show a graph of the amplitude/width.
 *
 * @param psfStack the psf stack
 * @param loess the loess
 * @param cz the cz
 * @param averageRange the average range
 * @param fitCom the fit com
 * @return The width of the PSF in the z-centre
 */
private double fitPsf(ImageStack psfStack, LoessInterpolator loess, int cz, double averageRange, final double[][] fitCom) {
    IJ.showStatus("Fitting final PSF");
    // is not appropriate for a normalised PSF.
    if (fitConfig.getFitSolver() != FitSolver.LVM_LSE) {
        ImageJUtils.log("  " + FitProtosHelper.getName(fitConfig.getFitSolver()) + " is not appropriate for final PSF fitting.");
        ImageJUtils.log("  Switching to Least Square Estimation");
        fitConfig.setFitSolver(FitSolver.LVM_LSE);
        if (settings.getInteractiveMode()) {
            // This assumes the LVM does not need the calibration
            PeakFit.configureFitSolver(config, null, null, 0);
        }
    }
    // Update the box radius since this is used in the fitSpot method.
    boxRadius = psfStack.getWidth() / 2;
    final int x = boxRadius;
    final int y = boxRadius;
    final double shift = fitConfig.getCoordinateShiftFactor();
    // Scale the PSF
    final PSF.Builder localPsf = fitConfig.getPsf().toBuilder();
    for (int i = 0; i < localPsf.getParametersCount(); i++) {
        final PSFParameter param = localPsf.getParameters(i);
        if (param.getUnit() == PSFParameterUnit.DISTANCE) {
            final PSFParameter.Builder b = param.toBuilder();
            b.setValue(b.getValue() * settings.getMagnification());
            localPsf.setParameters(i, b);
        }
    }
    fitConfig.setPsf(localPsf.build());
    // Need to be updated after the widths have been set
    fitConfig.setCoordinateShiftFactor(shift);
    fitConfig.setBackgroundFitting(false);
    // Since the PSF will be normalised remove the camera calibration
    fitConfig.setCameraType(CameraType.CAMERA_TYPE_NA);
    fitConfig.setMinPhotons(0);
    fitConfig.setBias(0);
    fitConfig.setGain(1);
    // No complex filtering so we get a fit. It should be easy to fit anyway.
    fitConfig.setPrecisionThreshold(0);
    fitConfig.setDirectFilter(null);
    // fitConfig.setDisableSimpleFilter(true);
    // Use this for debugging the fit
    // fitConfig.setLog(uk.ac.sussex.gdsc.core.ij.ImageJPluginLoggerHelper.getDefaultLogger());
    final MemoryPeakResults results = fitSpot(psfStack, psfStack.getWidth(), psfStack.getHeight(), x, y);
    if (results.size() < 5) {
        ImageJUtils.log("  Final PSF: Not enough fit results %d", results.size());
        return 0;
    }
    // Get the results for the spot centre and width
    final double[] z = new double[results.size()];
    final double[] xCoord = new double[z.length];
    final double[] yCoord = new double[z.length];
    final double[] sd = new double[z.length];
    final double[] a = new double[z.length];
    // Set limits for the fit
    final float maxWidth = (float) (Math.max(fitConfig.getInitialXSd(), fitConfig.getInitialYSd()) * settings.getMagnification() * 4);
    // PSF is normalised to 1
    final float maxSignal = 2;
    final WidthResultProcedure wp = new WidthResultProcedure(results, DistanceUnit.PIXEL);
    wp.getWxWy();
    final HeightResultProcedure hp = new HeightResultProcedure(results, IntensityUnit.COUNT);
    hp.getH();
    final Counter counter = new Counter();
    final Counter counterOk = new Counter();
    // We have fit the results so they will be in the preferred units
    results.forEach((PeakResultProcedure) peak -> {
        int index = counter.getAndIncrement();
        final float w = Math.max(wp.wx[index], wp.wy[index]);
        if (peak.getIntensity() > maxSignal || w > maxWidth) {
            return;
        }
        index = counterOk.getAndIncrement();
        z[index] = peak.getFrame();
        fitCom[0][peak.getFrame() - 1] = xCoord[index] = peak.getXPosition() - x;
        fitCom[1][peak.getFrame() - 1] = yCoord[index] = peak.getYPosition() - y;
        sd[index] = w;
        a[index] = hp.heights[index];
    });
    // Truncate
    final double[] z2 = Arrays.copyOf(z, counter.getCount());
    final double[] xCoord2 = Arrays.copyOf(xCoord, z2.length);
    final double[] yCoord2 = Arrays.copyOf(yCoord, z2.length);
    final double[] sd2 = Arrays.copyOf(sd, z2.length);
    final double[] a2 = Arrays.copyOf(a, z2.length);
    // Extract the average smoothed range from the individual fits
    final int r = (int) Math.ceil(averageRange / 2);
    int start = 0;
    int stop = z2.length - 1;
    for (int j = 0; j < z2.length; j++) {
        if (z2[j] > cz - r) {
            start = j;
            break;
        }
    }
    for (int j = z2.length; j-- > 0; ) {
        if (z2[j] < cz + r) {
            stop = j;
            break;
        }
    }
    // Extract xy centre coords and smooth
    double[] smoothX = new double[stop - start + 1];
    double[] smoothY = new double[smoothX.length];
    double[] smoothSd = new double[smoothX.length];
    double[] smoothA = new double[smoothX.length];
    final double[] newZ = new double[smoothX.length];
    int smoothCzIndex = 0;
    for (int j = start, k = 0; j <= stop; j++, k++) {
        smoothX[k] = xCoord2[j];
        smoothY[k] = yCoord2[j];
        smoothSd[k] = sd2[j];
        smoothA[k] = a2[j];
        newZ[k] = z2[j];
        if (newZ[k] == cz) {
            smoothCzIndex = k;
        }
    }
    smoothX = loess.smooth(newZ, smoothX);
    smoothY = loess.smooth(newZ, smoothY);
    smoothSd = loess.smooth(newZ, smoothSd);
    smoothA = loess.smooth(newZ, smoothA);
    // Update the widths and positions using the magnification
    final double scale = 1.0 / settings.getMagnification();
    for (int j = 0; j < xCoord2.length; j++) {
        xCoord2[j] *= scale;
        yCoord2[j] *= scale;
        sd2[j] *= scale;
    }
    for (int j = 0; j < smoothX.length; j++) {
        smoothX[j] *= scale;
        smoothY[j] *= scale;
        smoothSd[j] *= scale;
    }
    showPlots(z2, a2, newZ, smoothA, xCoord2, yCoord2, sd2, newZ, smoothX, smoothY, smoothSd, cz);
    // Store the data for replotting
    this.z = z2;
    this.amplitude = a2;
    this.smoothAz = newZ;
    this.smoothA = smoothA;
    this.xCoord = xCoord2;
    this.yCoord = yCoord2;
    this.sd = sd2;
    this.newZ = newZ;
    this.smoothX = smoothX;
    this.smoothY = smoothY;
    this.smoothSd = smoothSd;
    // maximumIndex = findMinimumIndex(smoothSd, maximumIndex - start);
    return smoothSd[smoothCzIndex];
}
Also used : HeightResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.HeightResultProcedure) Color(java.awt.Color) Tensor2D(uk.ac.sussex.gdsc.smlm.utils.Tensor2D) Arrays(java.util.Arrays) ByteProcessor(ij.process.ByteProcessor) UnitConverterUtils(uk.ac.sussex.gdsc.smlm.data.config.UnitConverterUtils) ImageProcessor(ij.process.ImageProcessor) WindowMethod(uk.ac.sussex.gdsc.core.utils.ImageWindow.WindowMethod) MemoryUtils(uk.ac.sussex.gdsc.core.utils.MemoryUtils) PSFType(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFType) CustomTricubicFunction(uk.ac.sussex.gdsc.core.math.interpolation.CustomTricubicFunction) Future(java.util.concurrent.Future) PSFCreatorSettings(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.PSFCreatorSettings) ImageWindow(uk.ac.sussex.gdsc.core.utils.ImageWindow) ImageCanvas(ij.gui.ImageCanvas) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) Blitter(ij.process.Blitter) FitProtosHelper(uk.ac.sussex.gdsc.smlm.data.config.FitProtosHelper) ImageJImageConverter(uk.ac.sussex.gdsc.smlm.ij.utils.ImageJImageConverter) SoftLock(uk.ac.sussex.gdsc.core.utils.SoftLock) Frame(java.awt.Frame) LoessInterpolator(org.apache.commons.math3.analysis.interpolation.LoessInterpolator) DistanceUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit) ConcurrencyUtils(uk.ac.sussex.gdsc.core.utils.concurrent.ConcurrencyUtils) GuiProtosHelper(uk.ac.sussex.gdsc.smlm.ij.settings.GuiProtosHelper) TextUtils(uk.ac.sussex.gdsc.core.utils.TextUtils) Gaussian2DFunction(uk.ac.sussex.gdsc.smlm.function.gaussian.Gaussian2DFunction) Plot(ij.gui.Plot) Executors(java.util.concurrent.Executors) ImagePlus(ij.ImagePlus) Line(ij.gui.Line) ExceptionUtils(org.apache.commons.lang3.exception.ExceptionUtils) Prefs(ij.Prefs) StoredData(uk.ac.sussex.gdsc.core.utils.StoredData) SimpleDateFormat(java.text.SimpleDateFormat) WindowManager(ij.WindowManager) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) ArrayList(java.util.ArrayList) GenericDialog(ij.gui.GenericDialog) SortUtils(uk.ac.sussex.gdsc.core.utils.SortUtils) RounderUtils(uk.ac.sussex.gdsc.core.data.utils.RounderUtils) SubPixelMethod(uk.ac.sussex.gdsc.core.ij.AlignImagesFft.SubPixelMethod) PeakResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure) ImagePsfHelper(uk.ac.sussex.gdsc.smlm.ij.settings.ImagePsfHelper) FitConfiguration(uk.ac.sussex.gdsc.smlm.engine.FitConfiguration) Overlay(ij.gui.Overlay) ImageExtractor(uk.ac.sussex.gdsc.core.utils.ImageExtractor) SimpleImageJTrackProgress(uk.ac.sussex.gdsc.core.ij.SimpleImageJTrackProgress) Size(uk.ac.sussex.gdsc.core.math.interpolation.CustomTricubicInterpolatingFunction.Size) FitEngine(uk.ac.sussex.gdsc.smlm.engine.FitEngine) FloatProcessor(ij.process.FloatProcessor) FloatStackTrivalueProvider(uk.ac.sussex.gdsc.core.data.FloatStackTrivalueProvider) CubicSplinePsf(uk.ac.sussex.gdsc.smlm.ij.plugins.CubicSplineManager.CubicSplinePsf) DescriptiveStatistics(org.apache.commons.math3.stat.descriptive.DescriptiveStatistics) ImageStack(ij.ImageStack) CameraModel(uk.ac.sussex.gdsc.smlm.model.camera.CameraModel) PsfHelper(uk.ac.sussex.gdsc.smlm.data.config.PsfHelper) Erf(uk.ac.sussex.gdsc.smlm.function.Erf) FloatStackTrivalueProcedure(uk.ac.sussex.gdsc.core.data.procedures.FloatStackTrivalueProcedure) AngleUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.AngleUnit) Date(java.util.Date) Point(java.awt.Point) ImagePSF(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.ImagePSF) PSFParameter(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFParameter) FitSolver(uk.ac.sussex.gdsc.smlm.data.config.FitProtos.FitSolver) StoredDataStatistics(uk.ac.sussex.gdsc.core.utils.StoredDataStatistics) OptionCollectedListener(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog.OptionCollectedListener) Locale(java.util.Locale) DataException(uk.ac.sussex.gdsc.core.data.DataException) NonBlockingExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.NonBlockingExtendedGenericDialog) PlotWindow(ij.gui.PlotWindow) MathUtils(uk.ac.sussex.gdsc.core.utils.MathUtils) CalibrationWriter(uk.ac.sussex.gdsc.smlm.data.config.CalibrationWriter) CustomTricubicInterpolatingFunction(uk.ac.sussex.gdsc.core.math.interpolation.CustomTricubicInterpolatingFunction) PlugInFilter(ij.plugin.filter.PlugInFilter) PsfProtosHelper(uk.ac.sussex.gdsc.smlm.data.config.PsfProtosHelper) FitParameters(uk.ac.sussex.gdsc.smlm.engine.FitParameters) SettingsManager(uk.ac.sussex.gdsc.smlm.ij.settings.SettingsManager) BasePoint(uk.ac.sussex.gdsc.core.match.BasePoint) CameraType(uk.ac.sussex.gdsc.smlm.data.config.CalibrationProtos.CameraType) BlockMeanFilter(uk.ac.sussex.gdsc.smlm.filters.BlockMeanFilter) CustomTricubicInterpolator(uk.ac.sussex.gdsc.core.math.interpolation.CustomTricubicInterpolator) HeightResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.HeightResultProcedure) ExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog) AlignImagesFft(uk.ac.sussex.gdsc.core.ij.AlignImagesFft) FitEngineConfiguration(uk.ac.sussex.gdsc.smlm.engine.FitEngineConfiguration) FloatPolygon(ij.process.FloatPolygon) OffsetPointRoi(uk.ac.sussex.gdsc.core.ij.gui.OffsetPointRoi) WidthResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.WidthResultProcedure) PSFParameterUnit(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFParameterUnit) List(java.util.List) SimpleArrayUtils(uk.ac.sussex.gdsc.core.utils.SimpleArrayUtils) OptionCollectedEvent(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog.OptionCollectedEvent) FitQueue(uk.ac.sussex.gdsc.smlm.engine.FitQueue) TypeConverter(uk.ac.sussex.gdsc.core.data.utils.TypeConverter) Roi(ij.gui.Roi) ParameterisedFitJob(uk.ac.sussex.gdsc.smlm.engine.ParameterisedFitJob) Image3DAligner(uk.ac.sussex.gdsc.smlm.ij.utils.Image3DAligner) Rectangle(java.awt.Rectangle) PSF(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSF) HashMap(java.util.HashMap) WindowOrganiser(uk.ac.sussex.gdsc.core.ij.plugin.WindowOrganiser) IntensityUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.IntensityUnit) AtomicReference(java.util.concurrent.atomic.AtomicReference) TextField(java.awt.TextField) OptionListener(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog.OptionListener) AWTEvent(java.awt.AWTEvent) IJImageSource(uk.ac.sussex.gdsc.smlm.ij.IJImageSource) LinkedList(java.util.LinkedList) CcdCameraModel(uk.ac.sussex.gdsc.smlm.model.camera.CcdCameraModel) Statistics(uk.ac.sussex.gdsc.core.utils.Statistics) ExecutorService(java.util.concurrent.ExecutorService) DialogListener(ij.gui.DialogListener) Calibration(ij.measure.Calibration) Checkbox(java.awt.Checkbox) CubicSplinePosition(uk.ac.sussex.gdsc.core.math.interpolation.CubicSplinePosition) Label(java.awt.Label) CreateData(uk.ac.sussex.gdsc.smlm.ij.plugins.benchmark.CreateData) Rounder(uk.ac.sussex.gdsc.core.data.utils.Rounder) CalibrationReader(uk.ac.sussex.gdsc.smlm.data.config.CalibrationReader) Counter(uk.ac.sussex.gdsc.smlm.results.count.Counter) ImageJUtils(uk.ac.sussex.gdsc.core.ij.ImageJUtils) SynchronizedPeakResults(uk.ac.sussex.gdsc.smlm.results.SynchronizedPeakResults) IJ(ij.IJ) FileInfo(ij.io.FileInfo) Image2DAligner(uk.ac.sussex.gdsc.smlm.ij.utils.Image2DAligner) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) ImagePSF(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.ImagePSF) PSF(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSF) PSFParameter(uk.ac.sussex.gdsc.smlm.data.config.PSFProtos.PSFParameter) WidthResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.WidthResultProcedure) Point(java.awt.Point) BasePoint(uk.ac.sussex.gdsc.core.match.BasePoint) Counter(uk.ac.sussex.gdsc.smlm.results.count.Counter) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults)

Example 5 with PeakResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure in project GDSC-SMLM by aherbert.

the class TraceExporter method exportVbSpt.

@SuppressWarnings("resource")
private void exportVbSpt(MemoryPeakResults results) {
    // vbSPT file format:
    // https://sourceforge.net/projects/vbspt/
    // Matlab matrix file (.mat) containing at least one variable that is a cell
    // array where each element, representing a trajectory, is a matrix
    // where the rows define the coordinates in one, two or three dimensions
    // in subsequent timesteps. The number of dimensions to be used for the
    // analysis will be set by the runinputfile.
    // The units are arbitrary but vbSPT starting estimates must be in the same
    // units. Either nm or μm are recommended.
    // 3 columns for n rows of localisations
    // 1. x coordinate (μm)
    // 2. y coordinate (μm)
    // 3. z coordinate (μm)
    // 
    // Note: An extra column is added containing the frame. This allows results to
    // be uniquely identified using frame,x,y,z
    // Count the IDs. Each new result ID will increment the count.
    final FrameCounter idCounter = new FrameCounter(results.getFirst().getId() - 1);
    results.forEach((PeakResultProcedure) result -> {
        if (idCounter.advance(result.getId())) {
            idCounter.increment();
        }
    });
    // Create the cell array as 1xN
    final Cell out = Mat5.newCell(1, idCounter.getCount());
    // This will reset the counter to zero and ensure the current frame does not match
    // in the event of a single track
    idCounter.advanceAndReset(idCounter.currentFrame() + 1);
    final boolean is3d = results.is3D();
    // Write the tracks
    final LocalList<double[]> list = new LocalList<>();
    results.forEach(DistanceUnit.UM, (XyzrResultProcedure) (x, y, z, result) -> {
        if (idCounter.advance(result.getId())) {
            addTrack(out, idCounter.getCount() - 1, list, is3d);
            idCounter.increment();
            list.clear();
        }
        list.add(new double[] { x, y, z, result.getFrame() });
    });
    addTrack(out, idCounter.getCount() - 1, list, is3d);
    try (MatFile matFile = Mat5.newMatFile()) {
        matFile.addArray("tracks", out);
        Mat5.writeToFile(matFile, Paths.get(settings.directory, results.getName() + ".mat").toFile());
    } catch (final IOException ex) {
        handleException(ex);
    }
}
Also used : MemoryResultsList(uk.ac.sussex.gdsc.smlm.ij.plugins.ResultsManager.MemoryResultsList) Cell(us.hebi.matlab.mat.types.Cell) UnitConverterUtils(uk.ac.sussex.gdsc.smlm.data.config.UnitConverterUtils) IdFramePeakResultComparator(uk.ac.sussex.gdsc.smlm.results.sort.IdFramePeakResultComparator) FrameCounter(uk.ac.sussex.gdsc.smlm.results.count.FrameCounter) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) MatFile(us.hebi.matlab.mat.types.MatFile) AtomicReference(java.util.concurrent.atomic.AtomicReference) Matrix(us.hebi.matlab.mat.types.Matrix) ArrayList(java.util.ArrayList) Level(java.util.logging.Level) MultiDialog(uk.ac.sussex.gdsc.core.ij.gui.MultiDialog) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) PeakResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure) SettingsManager(uk.ac.sussex.gdsc.smlm.ij.settings.SettingsManager) XyrResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.XyrResultProcedure) UniformRandomProvider(org.apache.commons.rng.UniformRandomProvider) Files(java.nio.file.Files) BufferedWriter(java.io.BufferedWriter) ExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog) IOException(java.io.IOException) NamedObject(uk.ac.sussex.gdsc.smlm.data.NamedObject) DistanceUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit) Logger(java.util.logging.Logger) SamplerUtils(uk.ac.sussex.gdsc.core.utils.rng.SamplerUtils) AttributePeakResult(uk.ac.sussex.gdsc.smlm.results.AttributePeakResult) TextUtils(uk.ac.sussex.gdsc.core.utils.TextUtils) Plot(ij.gui.Plot) TIntHashSet(gnu.trove.set.hash.TIntHashSet) TimeUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.TimeUnit) XyzrResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.XyzrResultProcedure) List(java.util.List) Counter(uk.ac.sussex.gdsc.smlm.results.count.Counter) Paths(java.nio.file.Paths) ImageJUtils(uk.ac.sussex.gdsc.core.ij.ImageJUtils) IJ(ij.IJ) SimpleArrayUtils(uk.ac.sussex.gdsc.core.utils.SimpleArrayUtils) Mat5(us.hebi.matlab.mat.format.Mat5) PlugIn(ij.plugin.PlugIn) NormalizedGaussianSampler(org.apache.commons.rng.sampling.distribution.NormalizedGaussianSampler) TypeConverter(uk.ac.sussex.gdsc.core.data.utils.TypeConverter) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) UniformRandomProviders(uk.ac.sussex.gdsc.core.utils.rng.UniformRandomProviders) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) MatFile(us.hebi.matlab.mat.types.MatFile) FrameCounter(uk.ac.sussex.gdsc.smlm.results.count.FrameCounter) IOException(java.io.IOException) Cell(us.hebi.matlab.mat.types.Cell)

Aggregations

PeakResultProcedure (uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure)40 MemoryPeakResults (uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults)35 PeakResult (uk.ac.sussex.gdsc.smlm.results.PeakResult)33 List (java.util.List)29 Counter (uk.ac.sussex.gdsc.smlm.results.count.Counter)26 SimpleArrayUtils (uk.ac.sussex.gdsc.core.utils.SimpleArrayUtils)24 FrameCounter (uk.ac.sussex.gdsc.smlm.results.count.FrameCounter)20 IJ (ij.IJ)19 Nullable (uk.ac.sussex.gdsc.core.annotation.Nullable)19 PlugIn (ij.plugin.PlugIn)18 AtomicReference (java.util.concurrent.atomic.AtomicReference)18 ImageJUtils (uk.ac.sussex.gdsc.core.ij.ImageJUtils)18 ExtendedGenericDialog (uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog)18 DistanceUnit (uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit)16 ClassificationResult (uk.ac.sussex.gdsc.core.match.ClassificationResult)15 MathUtils (uk.ac.sussex.gdsc.core.utils.MathUtils)15 TextUtils (uk.ac.sussex.gdsc.core.utils.TextUtils)15 Chromosome (uk.ac.sussex.gdsc.smlm.ga.Chromosome)15 XStreamOmitField (com.thoughtworks.xstream.annotations.XStreamOmitField)14 ArrayList (java.util.ArrayList)14