Examples with GenericDialog ij.gui.GenericDialog used on opensource projects

Example 31 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class YeastMask method showDialog.

private boolean showDialog() {
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Create a mask of a yeast cell as a tube plus end-caps");
    gd.addSlider("Tube_length (um)", 10, 20, length);
    gd.addSlider("Radius (um)", 0.5, 5, radius);
    gd.addCheckbox("Exclude_nucleus", excludeNucleus);
    gd.addSlider("Nucleus (fraction)", 0.5, 1, nucleus);
    gd.addNumericField("Pixel_pitch", nmPerPixel, 1, 6, "nm");
    gd.addNumericField("Pixel_depth", nmPerSlice, 1, 6, "nm");
    gd.addCheckbox("Square_output", squareOutput);
    gd.addSlider("Border", 0, 10, border);
    gd.addCheckbox("2D", is2D);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    length = gd.getNextNumber();
    radius = gd.getNextNumber();
    excludeNucleus = gd.getNextBoolean();
    nucleus = gd.getNextNumber();
    nmPerPixel = gd.getNextNumber();
    nmPerSlice = gd.getNextNumber();
    squareOutput = gd.getNextBoolean();
    border = (int) gd.getNextNumber();
    is2D = gd.getNextBoolean();
    if (radius < 0.5)
        radius = 0.5;
    if (length < 0)
        length = 0;
    if (nmPerPixel < 1)
        nmPerPixel = 1;
    if (nmPerSlice < 1)
        nmPerSlice = 1;
    return true;
}

Example 32 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class PCPALMAnalysis method showDialog.

private boolean showDialog() {
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    if (blinkingRate < 1 || copiedBlinkingRate != PCPALMMolecules.blinkingRate) {
        copiedBlinkingRate = blinkingRate = PCPALMMolecules.blinkingRate;
    }
    if (nmPerPixel < 1 || copiedNmPerPixel != PCPALMMolecules.nmPerPixel) {
        copiedNmPerPixel = nmPerPixel = PCPALMMolecules.nmPerPixel;
    }
    gd.addMessage("Analyse clusters using Pair Correlation.");
    gd.addNumericField("Correlation_distance (nm)", correlationDistance, 0);
    if (!spatialDomain) {
        gd.addMessage("-=- Frequency domain analysis -=-");
        gd.addCheckbox("Binary_image", binaryImage);
        gd.addNumericField("Blinking_rate", blinkingRate, 2);
        gd.addNumericField("nm_per_pixel", nmPerPixel, 2);
        gd.addCheckbox("Show_error_bars", showErrorBars);
        gd.addCheckbox("Apply_window", applyWindow);
        gd.addCheckbox("Show_high_res_image", showHighResolutionImage);
        gd.addCheckbox("Show_correlation_images", showCorrelationImages);
    } else {
        gd.addMessage("-=- Spatial domain analysis -=-");
        gd.addCheckbox("Use_border", useBorder);
        gd.addNumericField("Correlation_interval (nm)", correlationInterval, 0);
    }
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    correlationDistance = gd.getNextNumber();
    if (!spatialDomain) {
        binaryImage = gd.getNextBoolean();
        blinkingRate = gd.getNextNumber();
        nmPerPixel = gd.getNextNumber();
        showErrorBars = gd.getNextBoolean();
        applyWindow = gd.getNextBoolean();
        showHighResolutionImage = gd.getNextBoolean();
        showCorrelationImages = gd.getNextBoolean();
    } else {
        useBorder = gd.getNextBoolean();
        correlationInterval = gd.getNextNumber();
    }
    // Check arguments
    try {
        if (!spatialDomain) {
            Parameters.isAbove("Correlation distance", correlationDistance, 1);
            Parameters.isEqualOrAbove("Blinking_rate", blinkingRate, 1);
            Parameters.isAboveZero("nm per pixel", nmPerPixel);
        } else {
            Parameters.isAboveZero("Correlation interval", correlationInterval);
        }
    } catch (IllegalArgumentException ex) {
        error(ex.getMessage());
        return false;
    }
    return true;
}

Example 33 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class CreateData method run.

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

Example 34 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class Configuration method showDialog.

/**
	 * Show the current properties
	 */
@SuppressWarnings("unchecked")
public void showDialog() {
    configurationChanged = false;
    String filename = SettingsManager.getSettingsFilename();
    GlobalSettings settings = SettingsManager.loadSettings(filename);
    FitEngineConfiguration config = settings.getFitEngineConfiguration();
    FitConfiguration fitConfig = config.getFitConfiguration();
    Calibration calibration = settings.getCalibration();
    GenericDialog gd = new GenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Configuration settings for the single-molecule localisation microscopy plugins");
    gd.addStringField("Config_file", filename, 40);
    gd.addNumericField("Calibration (nm/px)", calibration.getNmPerPixel(), 2);
    gd.addNumericField("Gain", calibration.getGain(), 2);
    gd.addCheckbox("EM-CCD", calibration.isEmCCD());
    gd.addNumericField("Exposure_time (ms)", calibration.getExposureTime(), 2);
    gd.addMessage("--- Gaussian parameters ---");
    gd.addNumericField("Initial_StdDev0", fitConfig.getInitialPeakStdDev0(), 3);
    gd.addNumericField("Initial_StdDev1", fitConfig.getInitialPeakStdDev1(), 3);
    gd.addNumericField("Initial_Angle", fitConfig.getInitialAngle(), 3);
    gd.addMessage("--- Maxima identification ---");
    String[] filterTypes = SettingsManager.getNames((Object[]) DataFilterType.values());
    gd.addChoice("Spot_filter_type", filterTypes, filterTypes[config.getDataFilterType().ordinal()]);
    String[] filterNames = SettingsManager.getNames((Object[]) DataFilter.values());
    gd.addChoice("Spot_filter", filterNames, filterNames[config.getDataFilter(0).ordinal()]);
    gd.addSlider("Smoothing", 0, 2.5, config.getSmooth(0));
    gd.addSlider("Search_width", 0.5, 2.5, config.getSearch());
    gd.addSlider("Border", 0.5, 2.5, config.getBorder());
    gd.addSlider("Fitting_width", 2, 4.5, config.getFitting());
    gd.addMessage("--- Gaussian fitting ---");
    Component splitLabel = gd.getMessage();
    String[] solverNames = SettingsManager.getNames((Object[]) FitSolver.values());
    gd.addChoice("Fit_solver", solverNames, solverNames[fitConfig.getFitSolver().ordinal()]);
    String[] functionNames = SettingsManager.getNames((Object[]) FitFunction.values());
    gd.addChoice("Fit_function", functionNames, functionNames[fitConfig.getFitFunction().ordinal()]);
    // Parameters specific to each Fit solver are collected in a second dialog 
    gd.addNumericField("Fail_limit", config.getFailuresLimit(), 0);
    gd.addCheckbox("Include_neighbours", config.isIncludeNeighbours());
    gd.addSlider("Neighbour_height", 0.01, 1, config.getNeighbourHeightThreshold());
    gd.addSlider("Residuals_threshold", 0.01, 1, config.getResidualsThreshold());
    gd.addSlider("Duplicate_distance", 0, 1.5, fitConfig.getDuplicateDistance());
    gd.addMessage("--- Peak filtering ---\nDiscard fits that shift; are too low; or expand/contract");
    gd.addCheckbox("Smart_filter", fitConfig.isSmartFilter());
    gd.addCheckbox("Disable_simple_filter", fitConfig.isDisableSimpleFilter());
    gd.addSlider("Shift_factor", 0.01, 2, fitConfig.getCoordinateShiftFactor());
    gd.addNumericField("Signal_strength", fitConfig.getSignalStrength(), 2);
    gd.addNumericField("Min_photons", fitConfig.getMinPhotons(), 0);
    gd.addSlider("Min_width_factor", 0, 0.99, fitConfig.getMinWidthFactor());
    gd.addSlider("Width_factor", 1.01, 5, fitConfig.getWidthFactor());
    gd.addNumericField("Precision_threshold", fitConfig.getPrecisionThreshold(), 2);
    // Add a mouse listener to the config file field
    if (Utils.isShowGenericDialog()) {
        Vector<TextField> texts = (Vector<TextField>) gd.getStringFields();
        Vector<TextField> numerics = (Vector<TextField>) gd.getNumericFields();
        Vector<Checkbox> checkboxes = (Vector<Checkbox>) gd.getCheckboxes();
        Vector<Choice> choices = (Vector<Choice>) gd.getChoices();
        int n = 0;
        int t = 0;
        int b = 0;
        int ch = 0;
        textConfigFile = texts.get(t++);
        textConfigFile.addMouseListener(this);
        textConfigFile.addTextListener(this);
        // TODO: add a value changed listener to detect when typing a new file
        textNmPerPixel = numerics.get(n++);
        textGain = numerics.get(n++);
        textEMCCD = checkboxes.get(b++);
        textExposure = numerics.get(n++);
        textInitialPeakStdDev0 = numerics.get(n++);
        textInitialPeakStdDev1 = numerics.get(n++);
        textInitialAngleD = numerics.get(n++);
        textDataFilterType = choices.get(ch++);
        textDataFilter = choices.get(ch++);
        textSmooth = numerics.get(n++);
        textSearch = numerics.get(n++);
        textBorder = numerics.get(n++);
        textFitting = numerics.get(n++);
        textFitSolver = choices.get(ch++);
        textFitFunction = choices.get(ch++);
        textFailuresLimit = numerics.get(n++);
        textIncludeNeighbours = checkboxes.get(b++);
        textNeighbourHeightThreshold = numerics.get(n++);
        textResidualsThreshold = numerics.get(n++);
        textDuplicateDistance = numerics.get(n++);
        textSmartFilter = checkboxes.get(b++);
        textDisableSimpleFilter = checkboxes.get(b++);
        textCoordinateShiftFactor = numerics.get(n++);
        textSignalStrength = numerics.get(n++);
        textMinPhotons = numerics.get(n++);
        textMinWidthFactor = numerics.get(n++);
        textWidthFactor = numerics.get(n++);
        textPrecisionThreshold = numerics.get(n++);
        updateFilterInput();
        textSmartFilter.addItemListener(this);
        textDisableSimpleFilter.addItemListener(this);
    }
    if (gd.getLayout() != null) {
        GridBagLayout grid = (GridBagLayout) gd.getLayout();
        int xOffset = 0, yOffset = 0;
        int lastY = -1, rowCount = 0;
        for (Component comp : gd.getComponents()) {
            // Check if this should be the second major column
            if (comp == splitLabel) {
                xOffset += 2;
                yOffset -= rowCount;
            }
            // Reposition the field
            GridBagConstraints c = grid.getConstraints(comp);
            if (lastY != c.gridy)
                rowCount++;
            lastY = c.gridy;
            c.gridx = c.gridx + xOffset;
            c.gridy = c.gridy + yOffset;
            c.insets.left = c.insets.left + 10 * xOffset;
            c.insets.top = 0;
            c.insets.bottom = 0;
            grid.setConstraints(comp, c);
        }
        if (IJ.isLinux())
            gd.setBackground(new Color(238, 238, 238));
    }
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    filename = gd.getNextString();
    calibration.setNmPerPixel(gd.getNextNumber());
    calibration.setGain(gd.getNextNumber());
    calibration.setEmCCD(gd.getNextBoolean());
    calibration.setExposureTime(gd.getNextNumber());
    fitConfig.setInitialPeakStdDev0(gd.getNextNumber());
    fitConfig.setInitialPeakStdDev1(gd.getNextNumber());
    fitConfig.setInitialAngleD(gd.getNextNumber());
    config.setDataFilterType(gd.getNextChoiceIndex());
    config.setDataFilter(gd.getNextChoiceIndex(), Math.abs(gd.getNextNumber()), 0);
    config.setSearch(gd.getNextNumber());
    config.setBorder(gd.getNextNumber());
    config.setFitting(gd.getNextNumber());
    fitConfig.setFitSolver(gd.getNextChoiceIndex());
    fitConfig.setFitFunction(gd.getNextChoiceIndex());
    config.setFailuresLimit((int) gd.getNextNumber());
    config.setIncludeNeighbours(gd.getNextBoolean());
    config.setNeighbourHeightThreshold(gd.getNextNumber());
    config.setResidualsThreshold(gd.getNextNumber());
    fitConfig.setDuplicateDistance(gd.getNextNumber());
    fitConfig.setSmartFilter(gd.getNextBoolean());
    fitConfig.setDisableSimpleFilter(gd.getNextBoolean());
    fitConfig.setCoordinateShiftFactor(gd.getNextNumber());
    fitConfig.setSignalStrength(gd.getNextNumber());
    fitConfig.setMinPhotons(gd.getNextNumber());
    fitConfig.setMinWidthFactor(gd.getNextNumber());
    fitConfig.setWidthFactor(gd.getNextNumber());
    fitConfig.setPrecisionThreshold(gd.getNextNumber());
    // Check arguments
    try {
        Parameters.isAboveZero("nm per pixel", calibration.getNmPerPixel());
        Parameters.isAboveZero("Gain", calibration.getGain());
        Parameters.isAboveZero("Exposure time", calibration.getExposureTime());
        Parameters.isAboveZero("Initial SD0", fitConfig.getInitialPeakStdDev0());
        Parameters.isAboveZero("Initial SD1", fitConfig.getInitialPeakStdDev1());
        Parameters.isPositive("Initial angle", fitConfig.getInitialAngleD());
        Parameters.isAboveZero("Search_width", config.getSearch());
        Parameters.isAboveZero("Fitting_width", config.getFitting());
        Parameters.isPositive("Failures limit", config.getFailuresLimit());
        Parameters.isPositive("Neighbour height threshold", config.getNeighbourHeightThreshold());
        Parameters.isPositive("Residuals threshold", config.getResidualsThreshold());
        Parameters.isPositive("Duplicate distance", fitConfig.getDuplicateDistance());
        Parameters.isPositive("Coordinate Shift factor", fitConfig.getCoordinateShiftFactor());
        Parameters.isPositive("Signal strength", fitConfig.getSignalStrength());
        Parameters.isPositive("Min photons", fitConfig.getMinPhotons());
        Parameters.isPositive("Min width factor", fitConfig.getMinWidthFactor());
        Parameters.isPositive("Width factor", fitConfig.getWidthFactor());
        Parameters.isPositive("Precision threshold", fitConfig.getPrecisionThreshold());
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return;
    }
    if (gd.invalidNumber())
        return;
    configurationChanged = SettingsManager.saveSettings(settings, filename);
    if (configurationChanged)
        SettingsManager.saveSettingsFilename(filename);
    if (!PeakFit.configureSmartFilter(settings, filename))
        return;
    if (!PeakFit.configureDataFilter(settings, filename, false))
        return;
    PeakFit.configureFitSolver(settings, filename, false);
}

Example 35 with GenericDialog

use of ij.gui.GenericDialog in project GDSC-SMLM by aherbert.

the class BlinkEstimator method calculateAveragePrecision.

private double calculateAveragePrecision(MemoryPeakResults results, boolean verbose) {
    PCPALMMolecules fitter = new PCPALMMolecules();
    ArrayList<Molecule> molecules = fitter.extractLocalisations(results);
    String title = (verbose) ? TITLE + " Localisation Precision" : null;
    double fittedAverage = fitter.calculateAveragePrecision(molecules, title, histogramBins, true, true);
    // Sense check the precision
    if (fittedAverage < 5 || fittedAverage > 60) {
        GenericDialog gd = new GenericDialog(TITLE);
        gd.addMessage("Estimated precision is not within expected bounds.\nPlease enter an estimate:");
        gd.addSlider("Precision", 5, 60, fittedAverage);
        gd.showDialog();
        if (!gd.wasCanceled())
            fittedAverage = gd.getNextNumber();
    }
    // The fitter does checks for a good fit to the histogram so just return the value
    return fittedAverage;
}