Search in sources :

Example 1 with StandardResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure 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 2 with StandardResultProcedure

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

the class PcPalmMolecules method extractLocalisations.

/**
 * Extract molecules for the PC-PALM analysis.
 *
 * <p>Estimate the localisation uncertainty (precision) of each molecule using the formula of
 * Mortensen, et al (2010), Nature Methods 7, 377-381. Store distance in nm and signal in photons
 * using the calibration
 *
 * @param results the results
 * @return the array list
 * @throws DataException If conversion to nm and photons with computed precision is not possible
 */
public List<Molecule> extractLocalisations(MemoryPeakResults results) {
    final ArrayList<Molecule> list = new ArrayList<>(results.size());
    // Access calibrated data
    final StandardResultProcedure sp = new StandardResultProcedure(results, DistanceUnit.NM, IntensityUnit.PHOTON);
    sp.getIxy();
    final PrecisionResultProcedure pp = new PrecisionResultProcedure(results);
    pp.getPrecision();
    for (int i = 0, size = pp.size(); i < size; i++) {
        list.add(new Molecule(sp.x[i], sp.y[i], pp.precisions[i], sp.intensity[i]));
    }
    return list;
}
Also used : TDoubleArrayList(gnu.trove.list.array.TDoubleArrayList) ArrayList(java.util.ArrayList) StandardResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure) PrecisionResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PrecisionResultProcedure) WeightedObservedPoint(org.apache.commons.math3.fitting.WeightedObservedPoint) ClusterPoint(uk.ac.sussex.gdsc.core.clustering.ClusterPoint)

Example 3 with StandardResultProcedure

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

the class ImageJ3DResultsViewer method getPoints.

/**
 * Gets the points.
 *
 * @param results the results
 * @param settings the settings
 * @return the points
 */
static LocalList<Point3f> getPoints(MemoryPeakResults results, ImageJ3DResultsViewerSettingsOrBuilder settings) {
    final LocalList<Point3f> points = new LocalList<>(results.size());
    if (results.is3D()) {
        results.forEach(DistanceUnit.NM, (XyzResultProcedure) (x, y, z) -> {
            points.push(new Point3f(x, y, z));
        });
    } else {
        results.forEach(DistanceUnit.NM, (XyResultProcedure) (x, y) -> {
            points.push(new Point3f(x, y, 0));
        });
        final double range = settings.getDepthRange();
        if (range > 0 && results.size() > 1) {
            final DepthMode mode = DepthMode.forNumber(settings.getDepthMode());
            final double min = -settings.getDepthRange() / 2;
            switch(mode) {
                case DITHER:
                    final SplitMix r = SplitMix.new64(settings.getDitherSeed());
                    for (int i = points.size(); i-- > 0; ) {
                        points.unsafeGet(i).z += (min + r.nextDouble() * range);
                    }
                    break;
                case INTENSITY:
                    // Rank by intensity, highest first
                    final StandardResultProcedure p = new StandardResultProcedure(results);
                    p.getI();
                    final int[] indices = SimpleArrayUtils.natural(results.size());
                    SortUtils.sortIndices(indices, p.intensity, true);
                    final double inc = range / indices.length;
                    for (int i = 0; i < indices.length; i++) {
                        // The standard rendering has +z going away so put the highest rank at min
                        points.unsafeGet(indices[i]).z += (min + i * inc);
                    }
                    break;
                case NONE:
                    break;
                default:
                    throw new IllegalStateException("Unknown depth mode: " + mode);
            }
        }
    }
    return points;
}
Also used : Color(java.awt.Color) Arrays(java.util.Arrays) PickInfo(org.scijava.java3d.PickInfo) IndexedGeometryArray(org.scijava.java3d.IndexedGeometryArray) ItemGroup(uk.ac.sussex.gdsc.smlm.ij.ij3d.ItemGroup) GUI(ij.gui.GUI) DefaultListSelectionModel(javax.swing.DefaultListSelectionModel) JCheckBoxMenuItem(javax.swing.JCheckBoxMenuItem) ResultsSettings(uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsSettings) TransparentItemShape(uk.ac.sussex.gdsc.smlm.ij.ij3d.TransparentItemShape) Future(java.util.concurrent.Future) Pair(org.apache.commons.lang3.tuple.Pair) MemoryPeakResults(uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults) Map(java.util.Map) FitProtosHelper(uk.ac.sussex.gdsc.smlm.data.config.FitProtosHelper) ImageWindow3D(ij3d.ImageWindow3D) Triple(org.apache.commons.lang3.tuple.Triple) LutHelper(uk.ac.sussex.gdsc.core.ij.process.LutHelper) KeyStroke(javax.swing.KeyStroke) Appearance(org.scijava.java3d.Appearance) CustomMesh(customnode.CustomMesh) ImageCanvas3D(ij3d.ImageCanvas3D) Rendering(uk.ac.sussex.gdsc.smlm.ij.ij3d.Shape3DHelper.Rendering) InputSource(uk.ac.sussex.gdsc.smlm.ij.plugins.ResultsManager.InputSource) TObjectIntHashMap(gnu.trove.map.hash.TObjectIntHashMap) ImageJ3DResultsViewerSettings(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.ImageJ3DResultsViewerSettings) UniverseSettings(ij3d.UniverseSettings) NamedObject(uk.ac.sussex.gdsc.smlm.data.NamedObject) DistanceUnit(uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit) ItemGeometryGroup(uk.ac.sussex.gdsc.smlm.ij.ij3d.ItemGeometryGroup) StopWatch(org.apache.commons.lang3.time.StopWatch) RawResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.RawResultProcedure) KeyEvent(java.awt.event.KeyEvent) WindowAdapter(java.awt.event.WindowAdapter) TextUtils(uk.ac.sussex.gdsc.core.utils.TextUtils) Executors(java.util.concurrent.Executors) ImagePlus(ij.ImagePlus) PlugIn(ij.plugin.PlugIn) WindowConstants(javax.swing.WindowConstants) Color3f(org.scijava.vecmath.Color3f) ListSelectionModel(javax.swing.ListSelectionModel) TransformGroup(org.scijava.java3d.TransformGroup) PeakResultProcedureX(uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedureX) XyzResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.XyzResultProcedure) WindowManager(ij.WindowManager) PeakResult(uk.ac.sussex.gdsc.smlm.results.PeakResult) Point3f(org.scijava.vecmath.Point3f) Point3d(org.scijava.vecmath.Point3d) ContentNode(ij3d.ContentNode) SortUtils(uk.ac.sussex.gdsc.core.utils.SortUtils) CustomPointMesh(customnode.CustomPointMesh) RounderUtils(uk.ac.sussex.gdsc.core.data.utils.RounderUtils) PeakResultTableModel(uk.ac.sussex.gdsc.smlm.ij.gui.PeakResultTableModel) PeakResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PeakResultProcedure) CustomLineMesh(customnode.CustomLineMesh) ItemPointMesh(uk.ac.sussex.gdsc.smlm.ij.ij3d.ItemPointMesh) GeometryArray(org.scijava.java3d.GeometryArray) Field(java.lang.reflect.Field) IntersectionInfo(org.scijava.java3d.PickInfo.IntersectionInfo) Point2d(org.scijava.vecmath.Point2d) MouseEvent(java.awt.event.MouseEvent) ExecutionException(java.util.concurrent.ExecutionException) ReferenceItemMesh(uk.ac.sussex.gdsc.smlm.ij.ij3d.ReferenceItemMesh) Canvas3D(org.scijava.java3d.Canvas3D) MouseMotionListener(java.awt.event.MouseMotionListener) LineAttributes(org.scijava.java3d.LineAttributes) ItemTriangleMesh(uk.ac.sussex.gdsc.smlm.ij.ij3d.ItemTriangleMesh) ResultsTableSettings(uk.ac.sussex.gdsc.smlm.data.config.ResultsProtos.ResultsTableSettings) ListSelectionListener(javax.swing.event.ListSelectionListener) UniverseListener(ij3d.UniverseListener) TransparentItemTriangleMesh(uk.ac.sussex.gdsc.smlm.ij.ij3d.TransparentItemTriangleMesh) Builder(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.ImageJ3DResultsViewerSettings.Builder) StandardResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure) TriangleArray(org.scijava.java3d.TriangleArray) Transform3D(org.scijava.java3d.Transform3D) CustomContentHelper(uk.ac.sussex.gdsc.smlm.ij.ij3d.CustomContentHelper) PointAttributes(org.scijava.java3d.PointAttributes) SplitMix(uk.ac.sussex.gdsc.core.utils.rng.SplitMix) ItemGroupNode(uk.ac.sussex.gdsc.smlm.ij.ij3d.ItemGroupNode) Content(ij3d.Content) PickCanvas(org.scijava.java3d.utils.pickfast.PickCanvas) ItemShape(uk.ac.sussex.gdsc.smlm.ij.ij3d.ItemShape) TransparentItemPointMesh(uk.ac.sussex.gdsc.smlm.ij.ij3d.TransparentItemPointMesh) CoordinatePredicateUtils(uk.ac.sussex.gdsc.core.ij.roi.CoordinatePredicateUtils) XyResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.XyResultProcedure) CustomContent(uk.ac.sussex.gdsc.smlm.ij.ij3d.CustomContent) Image3DUniverse(ij3d.Image3DUniverse) Locale(java.util.Locale) ListSelectionModelHelper(uk.ac.sussex.gdsc.smlm.ij.gui.ListSelectionModelHelper) MouseAdapter(java.awt.event.MouseAdapter) DataException(uk.ac.sussex.gdsc.core.data.DataException) ColoringAttributes(org.scijava.java3d.ColoringAttributes) MacroRunner(ij.macro.MacroRunner) MathUtils(uk.ac.sussex.gdsc.core.utils.MathUtils) ListSelectionEvent(javax.swing.event.ListSelectionEvent) UpdateableItemShape(uk.ac.sussex.gdsc.smlm.ij.ij3d.UpdateableItemShape) MouseListener(java.awt.event.MouseListener) SettingsManager(uk.ac.sussex.gdsc.smlm.ij.settings.SettingsManager) JMenuBar(javax.swing.JMenuBar) CoordinatePredicate(uk.ac.sussex.gdsc.core.ij.roi.CoordinatePredicate) ExtendedGenericDialog(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog) ConcurrentHashMap(java.util.concurrent.ConcurrentHashMap) JMenu(javax.swing.JMenu) WindowEvent(java.awt.event.WindowEvent) List(java.util.List) PeakResultTableModelFrame(uk.ac.sussex.gdsc.smlm.ij.gui.PeakResultTableModelFrame) OrderedItemGeometryGroup(uk.ac.sussex.gdsc.smlm.ij.ij3d.OrderedItemGeometryGroup) Modifier(java.lang.reflect.Modifier) SimpleArrayUtils(uk.ac.sussex.gdsc.core.utils.SimpleArrayUtils) Shape3DHelper(uk.ac.sussex.gdsc.smlm.ij.ij3d.Shape3DHelper) TransparencyAttributes(org.scijava.java3d.TransparencyAttributes) LUT(ij.process.LUT) SceneGraphPath(org.scijava.java3d.SceneGraphPath) TypeConverter(uk.ac.sussex.gdsc.core.data.utils.TypeConverter) Roi(ij.gui.Roi) PolygonAttributes(org.scijava.java3d.PolygonAttributes) PrecisionResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.PrecisionResultProcedure) PrecisionMethod(uk.ac.sussex.gdsc.smlm.data.config.FitProtos.PrecisionMethod) AtomicBoolean(java.util.concurrent.atomic.AtomicBoolean) HashMap(java.util.HashMap) AtomicReference(java.util.concurrent.atomic.AtomicReference) TextField(java.awt.TextField) OptionListener(uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog.OptionListener) ItemMesh(uk.ac.sussex.gdsc.smlm.ij.ij3d.ItemMesh) JMenuItem(javax.swing.JMenuItem) ImageJTrackProgress(uk.ac.sussex.gdsc.core.ij.ImageJTrackProgress) CustomMeshNode(customnode.CustomMeshNode) View(org.scijava.java3d.View) ExecutorService(java.util.concurrent.ExecutorService) Shape3D(org.scijava.java3d.Shape3D) DefaultUniverse(ij3d.DefaultUniverse) TFloatArrayList(gnu.trove.list.array.TFloatArrayList) Vector3d(org.scijava.vecmath.Vector3d) PeakResultsDigest(uk.ac.sussex.gdsc.smlm.results.PeakResultsDigest) Iterator(java.util.Iterator) BranchGroup(org.scijava.java3d.BranchGroup) AxisAngle4d(org.scijava.vecmath.AxisAngle4d) Image3DMenubar(ij3d.Image3DMenubar) LutColour(uk.ac.sussex.gdsc.core.ij.process.LutHelper.LutColour) Ticker(uk.ac.sussex.gdsc.core.logging.Ticker) ActionEvent(java.awt.event.ActionEvent) ContentInstant(ij3d.ContentInstant) Rounder(uk.ac.sussex.gdsc.core.data.utils.Rounder) TimeUnit(java.util.concurrent.TimeUnit) CustomContentInstant(uk.ac.sussex.gdsc.smlm.ij.ij3d.CustomContentInstant) ImageJUtils(uk.ac.sussex.gdsc.core.ij.ImageJUtils) IJ(ij.IJ) Nullable(uk.ac.sussex.gdsc.core.annotation.Nullable) ImageJ3DResultsViewerSettingsOrBuilder(uk.ac.sussex.gdsc.smlm.ij.settings.GUIProtos.ImageJ3DResultsViewerSettingsOrBuilder) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) LocalList(uk.ac.sussex.gdsc.core.utils.LocalList) Point3f(org.scijava.vecmath.Point3f) SplitMix(uk.ac.sussex.gdsc.core.utils.rng.SplitMix) StandardResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure)

Example 4 with StandardResultProcedure

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

the class ImageJ3DResultsViewer method createRankByDepth.

private static float[] createRankByDepth(MemoryPeakResults results) {
    if (results.is3D()) {
        final StandardResultProcedure procedure = new StandardResultProcedure(results);
        procedure.getZ();
        return procedure.z;
    }
    return null;
}
Also used : StandardResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure)

Example 5 with StandardResultProcedure

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

the class DensityImage method createDensityManager.

private static DensityManager createDensityManager(MemoryPeakResults results) {
    if (MemoryPeakResults.isEmpty(results)) {
        throw new IllegalArgumentException("Results are null or empty");
    }
    final StandardResultProcedure sp = new StandardResultProcedure(results, DistanceUnit.PIXEL);
    sp.getXy();
    final Rectangle bounds = results.getBounds();
    final double area = (double) bounds.width * bounds.height;
    return new DensityManager(sp.x, sp.y, area);
}
Also used : Rectangle(java.awt.Rectangle) StandardResultProcedure(uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure) DensityManager(uk.ac.sussex.gdsc.core.clustering.DensityManager)

Aggregations

StandardResultProcedure (uk.ac.sussex.gdsc.smlm.results.procedures.StandardResultProcedure)11 PrecisionResultProcedure (uk.ac.sussex.gdsc.smlm.results.procedures.PrecisionResultProcedure)5 ArrayList (java.util.ArrayList)4 PeakResult (uk.ac.sussex.gdsc.smlm.results.PeakResult)4 IJ (ij.IJ)3 ImagePlus (ij.ImagePlus)3 WindowManager (ij.WindowManager)3 PlugIn (ij.plugin.PlugIn)3 Rectangle (java.awt.Rectangle)3 List (java.util.List)3 AtomicReference (java.util.concurrent.atomic.AtomicReference)3 DataException (uk.ac.sussex.gdsc.core.data.DataException)3 TypeConverter (uk.ac.sussex.gdsc.core.data.utils.TypeConverter)3 ImageJUtils (uk.ac.sussex.gdsc.core.ij.ImageJUtils)3 ExtendedGenericDialog (uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog)3 LocalList (uk.ac.sussex.gdsc.core.utils.LocalList)3 MathUtils (uk.ac.sussex.gdsc.core.utils.MathUtils)3 DistanceUnit (uk.ac.sussex.gdsc.smlm.data.config.UnitProtos.DistanceUnit)3 MemoryPeakResults (uk.ac.sussex.gdsc.smlm.results.MemoryPeakResults)3 TFloatArrayList (gnu.trove.list.array.TFloatArrayList)2