Examples with ExtendedGenericDialog uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog used on opensource projects

Example 76 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class AstigmatismModelManager method viewModel.

private void viewModel() {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    final String[] models = listAstigmatismModels(false);
    gd.addChoice("Model", models, pluginSettings.getSelected());
    gd.addChoice("z_distance_unit", SettingsManager.getDistanceUnitNames(), pluginSettings.getZDistanceUnitValue());
    gd.addChoice("s_distance_unit", SettingsManager.getDistanceUnitNames(), pluginSettings.getSDistanceUnitValue());
    gd.addCheckbox("Show_depth_of_focus", pluginSettings.getShowDepthOfFocus());
    gd.addCheckbox("Show_combined_width", pluginSettings.getShowCombinedWidth());
    gd.addCheckbox("Show_PSF", pluginSettings.getShowPsf());
    gd.addHelp(HelpUrls.getUrl("astigmatism-model-manager-view"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    final String name = gd.getNextChoice();
    pluginSettings.setSelected(name);
    pluginSettings.setZDistanceUnitValue(gd.getNextChoiceIndex());
    pluginSettings.setSDistanceUnitValue(gd.getNextChoiceIndex());
    pluginSettings.setShowDepthOfFocus(gd.getNextBoolean());
    pluginSettings.setShowCombinedWidth(gd.getNextBoolean());
    pluginSettings.setShowPsf(gd.getNextBoolean());
    // Try and get the named resource
    AstigmatismModel model = AstigmatismModelSettingsHolder.getSettings().getAstigmatismModelResourcesMap().get(name);
    if (model == null) {
        IJ.error(TITLE, "Failed to find astigmatism model: " + name);
        return;
    }
    try {
        model = convert(model, pluginSettings.getZDistanceUnit(), pluginSettings.getSDistanceUnit());
    } catch (final ConversionException ex) {
        ImageJUtils.log("Bad conversion (%s), defaulting to native model units", ex.getMessage());
    }
    ImageJUtils.log("Astigmatism model: %s\n%s", name, model);
    // Plot the curve. Do this so we encompass twice the depth-of-field.
    final double gamma = model.getGamma();
    final double d = model.getD();
    final double s0x = model.getS0X();
    final double Ax = model.getAx();
    final double Bx = model.getBx();
    final double s0y = model.getS0Y();
    final double Ay = model.getAy();
    final double By = model.getBy();
    final double range = Math.abs(gamma) + 1.5 * d;
    final int n = 200;
    final double step = range / n;
    final double[] z = new double[2 * n + 1];
    final double[] sx = new double[z.length];
    final double[] sy = new double[z.length];
    // Use the same class that is used during fitting
    final HoltzerAstigmatismZModel m = HoltzerAstigmatismZModel.create(s0x, s0y, gamma, d, Ax, Bx, Ay, By);
    for (int i = 0; i < z.length; i++) {
        final double zz = -range + i * step;
        z[i] = zz;
        sx[i] = m.getSx(zz);
        sy[i] = m.getSy(zz);
    }
    final String title = TITLE + " Width Curve";
    final Plot plot = new Plot(title, "Z (" + UnitHelper.getShortName(model.getZDistanceUnit()) + ")", "Width (" + UnitHelper.getShortName(model.getSDistanceUnit()) + ")");
    double[] limits = MathUtils.limits(sx);
    limits = MathUtils.limits(limits, sy);
    final double rangex = (z[z.length - 1] - z[0]) * 0.05;
    final double rangey = (limits[1] - limits[0]) * 0.05;
    final double miny = limits[0] - rangey;
    final double maxy = limits[1] + rangey;
    plot.setLimits(z[0] - rangex, z[z.length - 1] + rangex, miny, maxy);
    plot.setColor(Color.RED);
    plot.addPoints(z, sx, Plot.LINE);
    plot.setColor(Color.BLUE);
    plot.addPoints(z, sy, Plot.LINE);
    plot.setColor(Color.YELLOW);
    if (pluginSettings.getShowDepthOfFocus()) {
        final double z0x = gamma;
        final double z0y = -gamma;
        plot.setColor(Color.RED.darker());
        plot.drawDottedLine(z0x - d, miny, z0x - d, maxy, 4);
        plot.drawDottedLine(z0x + d, miny, z0x + d, maxy, 4);
        plot.setColor(Color.BLUE.darker());
        plot.drawDottedLine(z0y - d, miny, z0y - d, maxy, 4);
        plot.drawDottedLine(z0y + d, miny, z0y + d, maxy, 4);
    }
    String legend = "Sx\nSy";
    if (pluginSettings.getShowCombinedWidth()) {
        final double[] s = new double[z.length];
        for (int i = 0; i < z.length; i++) {
            s[i] = Gaussian2DPeakResultHelper.getStandardDeviation(sx[i], sy[i]);
        }
        plot.setColor(Color.GREEN);
        plot.addPoints(z, s, Plot.LINE);
        legend += "\tS";
    }
    plot.setColor(Color.BLACK);
    plot.addLegend(legend);
    plot.addLabel(0, 0, String.format("Model = %s (%s nm/pixel)", name, MathUtils.rounded(model.getNmPerPixel())));
    ImageJUtils.display(title, plot);
    if (!pluginSettings.getShowPsf()) {
        return;
    }
    // Get pixel range using 3x[max SD]
    final int width = 1 + 2 * ((int) Math.ceil(limits[1] * 3));
    new ModelRenderer(name, model, m, range, width, plot).run();
}

Example 77 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class AstigmatismModelManager method showConfigurationDialog.

private boolean showConfigurationDialog() {
    fitConfig = config.getFitConfiguration();
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("astigmatism-model-manager"));
    gd.addMessage("Configuration settings for the single-molecule localisation microscopy plugins");
    PeakFit.addCameraOptions(gd, fitConfig);
    CalibrationWriter calibration = fitConfig.getCalibrationWriter();
    gd.addNumericField("Calibration (nm/px)", calibration.getNmPerPixel(), 2);
    // gd.addNumericField("Exposure_time (ms)", calibration.getExposureTime(), 2);
    PeakFit.addPsfOptions(gd, fitConfig);
    final FitEngineConfigurationProvider provider = new PeakFit.SimpleFitEngineConfigurationProvider(config);
    PeakFit.addFittingOptions(gd, provider);
    gd.addChoice("Fit_solver", SettingsManager.getFitSolverNames(), FitProtosHelper.getName(fitConfig.getFitSolver()));
    gd.addCheckbox("Log_fit_progress", pluginSettings.getLogFitProgress());
    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());
    // Fitting may need to be extra wide
    final double w = fitConfig.getMaxWidthFactor();
    gd.addSlider("Width_factor", 1.01, Math.max(10, w), w);
    PeakFit.addPrecisionOptions(gd, new PeakFit.SimpleFitConfigurationProvider(fitConfig));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    // In case a template update the calibration
    calibration = fitConfig.getCalibrationWriter();
    calibration.setCameraType(SettingsManager.getCameraTypeValues()[gd.getNextChoiceIndex()]);
    calibration.setNmPerPixel(gd.getNextNumber());
    // Arbitrary
    calibration.setExposureTime(100);
    fitConfig.setCalibration(calibration.getCalibration());
    fitConfig.setPsfType(PeakFit.getPsfTypeValues()[gd.getNextChoiceIndex()]);
    config.setFitting(gd.getNextNumber());
    // Some enum values are not supported
    fitConfig.setFitSolver(SettingsManager.getFitSolverValues()[gd.getNextChoiceIndex()]);
    pluginSettings.setLogFitProgress(gd.getNextBoolean());
    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.setMaxWidthFactor(gd.getNextNumber());
    fitConfig.setPrecisionThreshold(gd.getNextNumber());
    gd.collectOptions();
    // Check arguments
    try {
        ParameterUtils.isAboveZero("nm per pixel", calibration.getNmPerPixel());
        ParameterUtils.isAboveZero("Initial SD0", fitConfig.getInitialXSd());
        if (fitConfig.getPsf().getParametersCount() > 1) {
            ParameterUtils.isAboveZero("Initial SD1", fitConfig.getInitialYSd());
        }
        ParameterUtils.isAboveZero("Fitting_width", config.getFitting());
        if (!fitConfig.isSmartFilter()) {
            ParameterUtils.isPositive("Coordinate Shift factor", fitConfig.getCoordinateShiftFactor());
            ParameterUtils.isPositive("Signal strength", fitConfig.getSignalStrength());
            ParameterUtils.isPositive("Min photons", fitConfig.getMinPhotons());
            ParameterUtils.isPositive("Min width factor", fitConfig.getMinWidthFactor());
            ParameterUtils.isPositive("Width factor", fitConfig.getMaxWidthFactor());
            ParameterUtils.isPositive("Precision threshold", fitConfig.getPrecisionThreshold());
        }
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    if (gd.invalidNumber()) {
        return false;
    }
    final int flags = PeakFit.FLAG_NO_SAVE;
    if (!PeakFit.configureSmartFilter(config, flags)) {
        return false;
    }
    PeakFit.configureFitSolver(config, null, null, flags);
    return true;
}

Example 78 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class AstigmatismModelManager method save.

private boolean save(String name, AstigmatismModel.Builder model) {
    pluginSettings.setModelName(name);
    // Check existing names
    final AstigmatismModelSettings settings = AstigmatismModelSettingsHolder.getSettings();
    final Map<String, AstigmatismModel> map = settings.getAstigmatismModelResourcesMap();
    if (map.containsKey(name)) {
        name = suggest(map, name);
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Model name " + pluginSettings.getModelName() + " already exists.\n \nSuggest renaming to:");
        gd.addStringField("Model_name", name);
        gd.enableYesNoCancel("Rename", "Overwrite");
        gd.showDialog(true);
        if (gd.wasCanceled()) {
            return false;
        }
        if (gd.wasOKed()) {
            // Rename
            pluginSettings.setModelName(name);
        }
    }
    // Save the model
    if (!AstigmatismModelSettingsHolder.setSettings(settings.toBuilder().putAstigmatismModelResources(pluginSettings.getModelName(), model.build()).build())) {
        IJ.error(TITLE, "Failed to save the model");
        return false;
    }
    return true;
}

Example 79 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class CalibrateResults method showInputDialog.

private boolean showInputDialog() {
    final int size = MemoryPeakResults.countMemorySize();
    if (size == 0) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return false;
    }
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("calibrate-results"));
    gd.addMessage("Select results to calibrate");
    settings = Settings.load();
    ResultsManager.addInput(gd, settings.inputOption, InputSource.MEMORY);
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.inputOption = ResultsManager.getInputSource(gd);
    settings.save();
    return true;
}

Example 80 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog in project GDSC-SMLM by aherbert.

the class CameraModelFisherInformationAnalysis method plotFromCache.

private static void plotFromCache() {
    // Build a list of curve stored in the cache
    final String[] names = new String[cache.size()];
    final PoissonFisherInformationData[] datas = new PoissonFisherInformationData[cache.size()];
    int count = 0;
    for (final Entry<FiKey, PoissonFisherInformationData> e : cache.entrySet()) {
        names[count] = e.getKey().toString();
        datas[count] = e.getValue();
        count++;
    }
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addChoice("Fisher_information", names, cachePlot);
    gd.addChoice("Plot_point", POINT_OPTION, pointOption);
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    final int index = gd.getNextChoiceIndex();
    pointOption = gd.getNextChoiceIndex();
    cachePlot = names[index];
    final PoissonFisherInformationData data = datas[index];
    final FiKey key = new FiKey(data);
    count = 0;
    final double[] exp = new double[data.getAlphaSampleCount()];
    final double[] alpha = new double[data.getAlphaSampleCount()];
    for (final AlphaSample s : data.getAlphaSampleList()) {
        exp[count] = s.getLog10Mean();
        alpha[count] = s.getAlpha();
        count++;
    }
    // Just in case
    // Sort.sortArrays(alpha, exp, true);
    // Test if we can use ImageJ support for a X log scale
    final boolean logScaleX = ((float) Math.pow(10, exp[0]) != 0);
    double[] x = exp;
    String xTitle = "log10(photons)";
    if (logScaleX) {
        final double[] photons = new double[exp.length];
        for (int i = 0; i < photons.length; i++) {
            photons[i] = Math.pow(10, exp[i]);
        }
        x = photons;
        xTitle = "photons";
    }
    // Get interpolation for alpha. Convert to base e.
    final double[] logU = exp.clone();
    final double scale = Math.log(10);
    for (int i = 0; i < logU.length; i++) {
        logU[i] *= scale;
    }
    final BasePoissonFisherInformation if1 = getInterpolatedPoissonFisherInformation(key.getType(), logU, alpha, null);
    // Interpolate with 5 points per sample for smooth curve
    final int n = 5;
    final TDoubleArrayList iexp = new TDoubleArrayList();
    final TDoubleArrayList iphotons = new TDoubleArrayList();
    for (int i = 1; i < exp.length; i++) {
        final int i_1 = i - 1;
        final double h = (exp[i] - exp[i_1]) / n;
        for (int j = 0; j < n; j++) {
            final double e = exp[i_1] + j * h;
            iexp.add(e);
            iphotons.add(Math.pow(10, e));
        }
    }
    iexp.add(exp[exp.length - 1]);
    iphotons.add(Math.pow(10, exp[exp.length - 1]));
    final double[] photons = iphotons.toArray();
    final double[] ix = (logScaleX) ? photons : iexp.toArray();
    final double[] ialpha1 = getAlpha(if1, photons);
    final int pointShape = getPointShape(pointOption);
    final String title = "Cached Relative Fisher Information";
    final Plot plot = new Plot(title, xTitle, "Noise coefficient (alpha)");
    plot.setLimits(x[0], x[x.length - 1], -0.05, 1.05);
    if (logScaleX) {
        plot.setLogScaleX();
    }
    plot.setColor(Color.blue);
    plot.addPoints(ix, ialpha1, Plot.LINE);
    // Option to show nodes
    if (pointShape != -1) {
        plot.addPoints(x, alpha, pointShape);
    }
    plot.setColor(Color.BLACK);
    plot.addLabel(0, 0, cachePlot);
    ImageJUtils.display(title, plot);
}