Examples with ConfigurationException uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException used on opensource projects

Example 1 with ConfigurationException

use of uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException in project GDSC-SMLM by aherbert.

the class CreateData method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    extraOptions = ImageJUtils.isExtraOptions();
    simpleMode = (arg != null && arg.contains("simple"));
    benchmarkMode = (arg != null && arg.contains("benchmark"));
    spotMode = (arg != null && arg.contains("spot"));
    trackMode = (arg != null && arg.contains("track"));
    if ("load".equals(arg)) {
        loadBenchmarkData();
        return;
    }
    // Each localisation set is a collection of localisations that represent all localisations
    // with the same ID that are on in the same image time frame (Note: the simulation
    // can create many localisations per fluorophore per time frame which is useful when
    // modelling moving particles)
    List<LocalisationModelSet> localisationSets = null;
    // Each fluorophore contains the on and off times when light was emitted
    List<? extends FluorophoreSequenceModel> fluorophores = null;
    if (simpleMode || benchmarkMode || spotMode) {
        if (!showSimpleDialog()) {
            return;
        }
        resetMemory();
        // 1 second frames
        settings.setExposureTime(1000);
        areaInUm = settings.getSize() * settings.getPixelPitch() * settings.getSize() * settings.getPixelPitch() / 1e6;
        // Number of spots per frame
        int count = 0;
        int[] nextN = null;
        SpatialDistribution dist;
        if (benchmarkMode) {
            // --------------------
            // BENCHMARK SIMULATION
            // --------------------
            // Draw the same point on the image repeatedly
            count = 1;
            dist = createFixedDistribution();
            try {
                reportAndSaveFittingLimits(dist);
            } catch (final Exception ex) {
                // This will be from the computation of the CRLB
                IJ.error(TITLE, ex.getMessage());
                return;
            }
        } else if (spotMode) {
            // ---------------
            // SPOT SIMULATION
            // ---------------
            // The spot simulation draws 0 or 1 random point per frame.
            // Ensure we have 50% of the frames with a spot.
            nextN = new int[settings.getParticles() * 2];
            Arrays.fill(nextN, 0, settings.getParticles(), 1);
            RandomUtils.shuffle(nextN, UniformRandomProviders.create());
            // Only put spots in the central part of the image
            final double border = settings.getSize() / 4.0;
            dist = createUniformDistribution(border);
        } else {
            // -----------------
            // SIMPLE SIMULATION
            // -----------------
            // The simple simulation draws n random points per frame to achieve a specified density.
            // No points will appear in multiple frames.
            // Each point has a random number of photons sampled from a range.
            // We can optionally use a mask. Create his first as it updates the areaInUm
            dist = createDistribution();
            // Randomly sample (i.e. not uniform density in all frames)
            if (settings.getSamplePerFrame()) {
                final double mean = areaInUm * settings.getDensity();
                ImageJUtils.log("Mean samples = %f", mean);
                if (mean < 0.5) {
                    final GenericDialog gd = new GenericDialog(TITLE);
                    gd.addMessage("The mean samples per frame is low: " + MathUtils.rounded(mean) + "\n \nContinue?");
                    gd.enableYesNoCancel();
                    gd.hideCancelButton();
                    gd.showDialog();
                    if (!gd.wasOKed()) {
                        return;
                    }
                }
                final PoissonSampler poisson = new PoissonSampler(createRandomGenerator(), mean);
                final StoredDataStatistics samples = new StoredDataStatistics(settings.getParticles());
                while (samples.getSum() < settings.getParticles()) {
                    samples.add(poisson.sample());
                }
                nextN = new int[samples.getN()];
                for (int i = 0; i < nextN.length; i++) {
                    nextN[i] = (int) samples.getValue(i);
                }
            } else {
                // Use the density to get the number per frame
                count = (int) Math.max(1, Math.round(areaInUm * settings.getDensity()));
            }
        }
        UniformRandomProvider rng = null;
        localisationSets = new ArrayList<>(settings.getParticles());
        final int minPhotons = (int) settings.getPhotonsPerSecond();
        final int range = (int) settings.getPhotonsPerSecondMaximum() - minPhotons + 1;
        if (range > 1) {
            rng = createRandomGenerator();
        }
        // Add frames at the specified density until the number of particles has been reached
        int id = 0;
        int time = 0;
        while (id < settings.getParticles()) {
            // Allow the number per frame to be specified
            if (nextN != null) {
                if (time >= nextN.length) {
                    break;
                }
                count = nextN[time];
            }
            // Simulate random positions in the frame for the specified density
            time++;
            for (int j = 0; j < count; j++) {
                final double[] xyz = dist.next();
                // Ignore within border. We do not want to draw things we cannot fit.
                // if (!distBorder.isWithinXy(xyz))
                // continue;
                // Simulate random photons
                final int intensity = minPhotons + ((rng != null) ? rng.nextInt(range) : 0);
                final LocalisationModel m = new LocalisationModel(id, time, xyz, intensity, LocalisationModel.CONTINUOUS);
                // Each localisation can be a separate localisation set
                final LocalisationModelSet set = new LocalisationModelSet(id, time);
                set.add(m);
                localisationSets.add(set);
                id++;
            }
        }
    } else {
        if (!showDialog()) {
            return;
        }
        resetMemory();
        areaInUm = settings.getSize() * settings.getPixelPitch() * settings.getSize() * settings.getPixelPitch() / 1e6;
        int totalSteps;
        double correlation = 0;
        ImageModel imageModel;
        if (trackMode) {
            // ----------------
            // TRACK SIMULATION
            // ----------------
            // In track mode we create fixed lifetime fluorophores that do not overlap in time.
            // This is the simplest simulation to test moving molecules.
            settings.setSeconds((int) Math.ceil(settings.getParticles() * (settings.getExposureTime() + settings.getTOn()) / 1000));
            totalSteps = 0;
            final double simulationStepsPerFrame = (settings.getStepsPerSecond() * settings.getExposureTime()) / 1000.0;
            imageModel = new FixedLifetimeImageModel(settings.getStepsPerSecond() * settings.getTOn() / 1000.0, simulationStepsPerFrame, createRandomGenerator());
        } else {
            // ---------------
            // FULL SIMULATION
            // ---------------
            // The full simulation draws n random points in space.
            // The same molecule may appear in multiple frames, move and blink.
            // 
            // Points are modelled as fluorophores that must be activated and then will
            // blink and photo-bleach. The molecules may diffuse and this can be simulated
            // with many steps per image frame. All steps from a frame are collected
            // into a localisation set which can be drawn on the output image.
            final SpatialIllumination activationIllumination = createIllumination(settings.getPulseRatio(), settings.getPulseInterval());
            // Generate additional frames so that each frame has the set number of simulation steps
            totalSteps = (int) Math.ceil(settings.getSeconds() * settings.getStepsPerSecond());
            // Since we have an exponential decay of activations
            // ensure half of the particles have activated by 30% of the frames.
            final double eAct = totalSteps * 0.3 * activationIllumination.getAveragePhotons();
            // Q. Does tOn/tOff change depending on the illumination strength?
            imageModel = new ActivationEnergyImageModel(eAct, activationIllumination, settings.getStepsPerSecond() * settings.getTOn() / 1000.0, settings.getStepsPerSecond() * settings.getTOffShort() / 1000.0, settings.getStepsPerSecond() * settings.getTOffLong() / 1000.0, settings.getNBlinksShort(), settings.getNBlinksLong(), createRandomGenerator());
            imageModel.setUseGeometricDistribution(settings.getNBlinksGeometricDistribution());
            // Only use the correlation if selected for the distribution
            if (PHOTON_DISTRIBUTION[PHOTON_CORRELATED].equals(settings.getPhotonDistribution())) {
                correlation = settings.getCorrelation();
            }
        }
        imageModel.setPhotonBudgetPerFrame(true);
        imageModel.setDiffusion2D(settings.getDiffuse2D());
        imageModel.setRotation2D(settings.getRotate2D());
        IJ.showStatus("Creating molecules ...");
        final SpatialDistribution distribution = createDistribution();
        final List<CompoundMoleculeModel> compounds = createCompoundMolecules();
        if (compounds == null) {
            return;
        }
        final List<CompoundMoleculeModel> molecules = imageModel.createMolecules(compounds, settings.getParticles(), distribution, settings.getRotateInitialOrientation());
        // Activate fluorophores
        IJ.showStatus("Creating fluorophores ...");
        // Note: molecules list will be converted to compounds containing fluorophores
        fluorophores = imageModel.createFluorophores(molecules, totalSteps);
        if (fluorophores.isEmpty()) {
            IJ.error(TITLE, "No fluorophores created");
            return;
        }
        // Map the fluorophore ID to the compound for mixtures
        if (compounds.size() > 1) {
            idToCompound = new TIntIntHashMap(fluorophores.size());
            for (final FluorophoreSequenceModel l : fluorophores) {
                idToCompound.put(l.getId(), l.getLabel());
            }
        }
        IJ.showStatus("Creating localisations ...");
        // TODO - Output a molecule Id for each fluorophore if using compound molecules. This allows
        // analysis
        // of the ratio of trimers, dimers, monomers, etc that could be detected.
        totalSteps = checkTotalSteps(totalSteps, fluorophores);
        if (totalSteps == 0) {
            return;
        }
        imageModel.setPhotonDistribution(createPhotonDistribution());
        try {
            imageModel.setConfinementDistribution(createConfinementDistribution());
        } catch (final ConfigurationException ex) {
            // We asked the user if it was OK to continue and they said no
            return;
        }
        // This should be optimised
        imageModel.setConfinementAttempts(10);
        final List<LocalisationModel> localisations = imageModel.createImage(molecules, settings.getFixedFraction(), totalSteps, settings.getPhotonsPerSecond() / settings.getStepsPerSecond(), correlation, settings.getRotateDuringSimulation());
        // Re-adjust the fluorophores to the correct time
        if (settings.getStepsPerSecond() != 1) {
            final double scale = 1.0 / settings.getStepsPerSecond();
            for (final FluorophoreSequenceModel f : fluorophores) {
                f.adjustTime(scale);
            }
        }
        // Integrate the frames
        localisationSets = combineSimulationSteps(localisations);
        localisationSets = filterToImageBounds(localisationSets);
    }
    datasetNumber.getAndIncrement();
    final List<LocalisationModel> localisations = drawImage(localisationSets);
    if (localisations == null || localisations.isEmpty()) {
        IJ.error(TITLE, "No localisations created");
        return;
    }
    fluorophores = removeFilteredFluorophores(fluorophores, localisations);
    final double signalPerFrame = showSummary(fluorophores, localisations);
    if (!benchmarkMode) {
        final boolean fullSimulation = (!(simpleMode || spotMode));
        saveSimulationParameters(localisations.size(), fullSimulation, signalPerFrame);
    }
    IJ.showStatus("Saving data ...");
    saveFluorophores(fluorophores);
    saveImageResults(results);
    saveLocalisations(localisations);
    // The settings for the filenames may have changed
    SettingsManager.writeSettings(settings.build());
    IJ.showStatus("Done");
}

Example 2 with ConfigurationException

use of uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException in project GDSC-SMLM by aherbert.

the class BenchmarkSpotFilter method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    extraOptions = ImageJUtils.isExtraOptions();
    batchMode = "batch".equals(arg);
    simulationParameters = CreateData.getSimulationParameters();
    if (simulationParameters == null) {
        IJ.error(TITLE, "No benchmark spot parameters in memory");
        return;
    }
    imp = CreateData.getImage();
    if (imp == null) {
        IJ.error(TITLE, "No benchmark image");
        return;
    }
    results = CreateData.getResults();
    if (results == null) {
        IJ.error(TITLE, "No benchmark results in memory");
        return;
    }
    // Set-up for the simulation
    try {
        if (results.getCalibration() == null) {
            throw new ConfigurationException("Require calibrated results");
        }
        if (results.getCalibrationReader().getDistanceUnit() != DistanceUnit.PIXEL) {
            throw new ConfigurationException("Require results in pixel distance units");
        }
        if (results.getCalibrationReader().getIntensityUnit() != IntensityUnit.PHOTON) {
            throw new ConfigurationException("Require results in photon units");
        }
        // This plugin is heavily reliant on the results being represented as a
        // Gaussian2D function.
        final int flags = Gaussian2DPeakResultHelper.AMPLITUDE | Gaussian2DPeakResultHelper.PIXEL_AMPLITUDE;
        calculator = Gaussian2DPeakResultHelper.create(results.getPsf(), results.getCalibration(), flags);
        cameraModel = CreateData.getCameraModel(simulationParameters);
    } catch (final ConfigurationException ex) {
        IJ.error(TITLE, "Bad configuration: " + ex.getMessage());
        return;
    }
    if (!showDialog()) {
        return;
    }
    // Get the simulation results into a list per frame
    simulationCoords = getSimulationCoordinates();
    // Clear old results to free memory
    BenchmarkSpotFilterResult localFilterResult;
    filterResult.set(null);
    // For graphs
    windowOrganiser = new WindowOrganiser();
    if (batchMode) {
        // Clear the cached results if the setting changed
        final SettingsList settingList = new SettingsList(simulationParameters.id, settings.filterRelativeDistances, // search, maxSearch, // Ignore search distance for smart caching
        settings.border, settings.scoreRelativeDistances, settings.analysisBorder, settings.hardBorder, settings.matchingMethod, settings.upperDistance, settings.lowerDistance, settings.upperSignalFactor, settings.lowerSignalFactor, settings.recallFraction);
        final ArrayList<BatchResult[]> cachedResults = getCachedBatchResults(settingList);
        // Batch mode to test enumeration of filters
        final double sd = simulationParameters.sd / simulationParameters.pixelPitch;
        final int limit = (int) Math.floor(3 * sd);
        // This should be in integers otherwise we may repeat search box sizes
        final int[] searchParam = SimpleArrayUtils.newArray(settings.maxSearch - settings.minSearch + 1, settings.minSearch, 1);
        // Continuous parameters
        final double[] pEmpty = new double[0];
        final double[] mParam = (settings.batchMean) ? getRange(limit, 0.05) : pEmpty;
        final double[] gParam = (settings.batchGaussian) ? getRange(limit, 0.05) : pEmpty;
        // Less continuous parameters
        final double[] cParam = (settings.batchCircular) ? getRange(limit, 0.5) : pEmpty;
        // Discrete parameters
        final double[] medParam = (settings.batchMedian) ? getRange(limit, 1) : pEmpty;
        setupProgress((long) imp.getImageStackSize() * searchParam.length * (mParam.length + gParam.length + cParam.length + medParam.length), "Frame");
        ArrayList<BatchResult[]> batchResults = new ArrayList<>(cachedResults.size());
        double param2 = 0;
        if (settings.differenceFilter && settings.differenceSmooth > 0) {
            if (settings.filterRelativeDistances) {
                // Convert to absolute for batch run
                param2 = MathUtils.roundUsingDecimalPlaces(settings.differenceSmooth * config.getHwhmMin(), 3);
            } else {
                // Already an absolute value
                param2 = settings.differenceSmooth;
            }
            config.setDataFilterType(DataFilterType.DIFFERENCE);
        } else {
            config.setDataFilterType(DataFilterType.SINGLE);
        }
        for (final int search : searchParam) {
            // Batch runs use absolute distance
            config.setSearch(search, true);
            // Allow re-use of these if they are cached to allow quick reanalysis of results.
            if (settings.batchMean) {
                batchResults.add(getOrCompute(cachedResults, DataFilterMethod.MEAN, mParam, search, param2));
            }
            if (settings.batchGaussian) {
                batchResults.add(getOrCompute(cachedResults, DataFilterMethod.GAUSSIAN, gParam, search, param2));
            }
            if (settings.batchCircular) {
                batchResults.add(getOrCompute(cachedResults, DataFilterMethod.CIRCULAR_MEAN, cParam, search, param2));
            }
            if (settings.batchMean) {
                batchResults.add(getOrCompute(cachedResults, DataFilterMethod.MEDIAN, medParam, search, param2));
            }
        }
        IJ.showProgress(-1);
        IJ.showStatus("");
        if (ImageJUtils.isInterrupted()) {
            return;
        }
        // Save the results in a cache
        setCachedBatchResults(settingList, cachedResults);
        // Analysis options
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        final boolean haveCached = cachedResults.size() > batchResults.size();
        if (haveCached) {
            gd.addCheckbox("Use_cached_results", settings.useCached);
        }
        gd.addMessage("Choose performance plots:");
        for (int i = 0; i < settings.batchPlot.length; i++) {
            gd.addCheckbox(Settings.batchPlotNames[i], settings.batchPlot[i]);
        }
        gd.addChoice("Selection", Settings.SELECTION_METHOD, settings.selectionMethod);
        gd.addCheckbox("Show_plots", settings.showPlot);
        gd.addCheckbox("Plot_rank_by_intensity", settings.rankByIntensity);
        gd.addCheckbox("Show_failures_plots", settings.showFailuresPlot);
        gd.addCheckbox("Show_TP", settings.showTP);
        gd.addCheckbox("Show_FP", settings.showFP);
        gd.addCheckbox("Show_FN", settings.showFN);
        gd.addHelp(HelpUrls.getUrl("filter-spot-data-batch"));
        gd.showDialog();
        if (gd.wasCanceled()) {
            return;
        }
        if (haveCached) {
            settings.useCached = gd.getNextBoolean();
            if (settings.useCached) {
                batchResults = cachedResults;
            }
        }
        for (int i = 0; i < settings.batchPlot.length; i++) {
            settings.batchPlot[i] = gd.getNextBoolean();
        }
        settings.selectionMethod = gd.getNextChoiceIndex();
        settings.showPlot = gd.getNextBoolean();
        settings.rankByIntensity = gd.getNextBoolean();
        settings.showFailuresPlot = gd.getNextBoolean();
        settings.showTP = gd.getNextBoolean();
        settings.showFP = gd.getNextBoolean();
        settings.showFN = gd.getNextBoolean();
        // Plot charts
        for (int i = 0; i < settings.batchPlot.length; i++) {
            plot(i, batchResults);
        }
        // Store in global singleton
        localFilterResult = analyse(batchResults);
    } else {
        // Single filter mode
        setupProgress(imp.getImageStackSize(), "Frame");
        localFilterResult = runAnalysis(config);
    }
    ImageJUtils.clearSlowProgress();
    IJ.showStatus("");
    if (localFilterResult == null) {
        return;
    }
    // Store the latest result
    filterResult.set(localFilterResult);
    // Debugging the matches
    if (settings.debug) {
        addSpotsToMemory(localFilterResult.filterResults);
    }
    if (settings.showFailuresPlot) {
        showFailuresPlot(localFilterResult);
    }
    if (settings.showPlot) {
        showPlot(localFilterResult);
    }
    if (isShowOverlay()) {
        showOverlay(imp, localFilterResult);
    }
    windowOrganiser.tile();
}

Example 3 with ConfigurationException

use of uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException in project GDSC-SMLM by aherbert.

the class CreateData method checkConfiguration.

private static void checkConfiguration(String message) {
    final GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage(TextUtils.wrap("Warning: " + message, 80));
    gd.setOKLabel("Continue");
    gd.showDialog();
    if (gd.wasCanceled()) {
        throw new ConfigurationException(message);
    }
}

Example 4 with ConfigurationException

use of uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException in project GDSC-SMLM by aherbert.

the class ImageJTablePeakResults method begin.

@Override
public void begin() {
    tableActive = false;
    // Set-up unit processing that requires the calibration
    toPixelConverter = new IdentityTypeConverter<>(null);
    calculator = null;
    canComputePrecision = false;
    rounder = RounderUtils.create(roundingPrecision);
    // We must correctly convert all the PSF parameter types
    helper = new PeakResultConversionHelper(getCalibration(), getPsf());
    helper.setIntensityUnit(intensityUnit);
    helper.setDistanceUnit(distanceUnit);
    helper.setAngleUnit(angleUnit);
    converters = helper.getConverters();
    if (hasCalibration()) {
        if (showPrecision) {
            if (computePrecision) {
                try {
                    calculator = Gaussian2DPeakResultHelper.create(getPsf(), getCalibrationReader(), Gaussian2DPeakResultHelper.LSE_PRECISION);
                    canComputePrecision = true;
                } catch (final ConfigurationException ex) {
                // Cannot compute precision
                } catch (final ConversionException ex) {
                // Cannot compute precision
                }
            }
        }
        try {
            if (helper.hasDistanceConverter()) {
                toPixelConverter = UnitConverterUtils.createConverter(distanceUnit, DistanceUnit.PIXEL, getCalibrationReader().getNmPerPixel());
            }
        } catch (final ConversionException ex) {
        // Gracefully fail so ignore this
        }
    }
    ic = converters[PeakResult.INTENSITY];
    outIndices = SimpleArrayUtils.natural(converters.length);
    if (!showZ) {
        final TIntArrayList list = new TIntArrayList(outIndices);
        list.remove(PeakResult.Z);
        outIndices = list.toArray();
    }
    // Update the calibration if converters were created
    if (helper.isCalibrationChanged()) {
        setCalibration(helper.getCalibration());
    }
    createSourceText();
    createResultsWindow();
    if (clearAtStart) {
        tp.clear();
    }
    size = 0;
    // Let some results appear before drawing.
    // ImageJ will auto-layout columns if it has less than 10 rows
    nextRepaintSize = 9;
    tableActive = true;
}

Example 5 with ConfigurationException

use of uk.ac.sussex.gdsc.smlm.data.config.ConfigurationException in project GDSC-SMLM by aherbert.

the class PsfImagePeakResults method preBegin.

@Override
protected void preBegin() {
    // this.displayFlags should be OK so don't call super.preBegin()
    requirePsfParameters = true;
    int flags = 0;
    if ((displayFlags & DISPLAY_SIGNAL) != 0) {
        flags |= Gaussian2DPeakResultHelper.AMPLITUDE;
    }
    if (fixedWidth) {
        // Check if we need the amplitude for the fixed width PSF
        requirePsfParameters = flags != 0;
    } else if (calculatedPrecision) {
        flags |= Gaussian2DPeakResultHelper.LSE_PRECISION;
        // To convert the precision to pixels
        if (!hasCalibration()) {
            throw new ConfigurationException("nm/pixel is required when drawing using the precision");
        }
        dc = UnitConverterUtils.createConverter(DistanceUnit.NM, DistanceUnit.PIXEL, getCalibrationReader().getNmPerPixel());
    } else {
        // We need to know the parameters for the Gaussian 2D PSF
        final int[] indices = PsfHelper.getGaussian2DWxWyIndices(getPsf());
        isx = indices[0];
        isy = indices[1];
        try {
            ia = PsfHelper.getGaussian2DAngleIndex(getPsf());
        } catch (final ConfigurationException ex) {
            // No rotation angle
            ia = 0;
        }
    }
    if (flags != 0) {
        calculator = Gaussian2DPeakResultHelper.create(getPsf(), getCalibrationReader(), flags);
    }
}