Examples with FitEngineConfigurationProvider uk.ac.sussex.gdsc.smlm.ij.plugins.PeakFit.FitEngineConfigurationProvider used on opensource projects

Example 1 with FitEngineConfigurationProvider

use of uk.ac.sussex.gdsc.smlm.ij.plugins.PeakFit.FitEngineConfigurationProvider in project GDSC-SMLM by aherbert.

the class BenchmarkSpotFit method showDialog.

private boolean showDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("fit-spot-data"));
    ImageJUtils.addMessage(gd, "Fit candidate spots in the benchmark image created by " + CreateData.TITLE + " plugin\nand identified by the " + BenchmarkSpotFilter.TITLE + " plugin.\nPSF width = %s nm (Square pixel adjustment = %s nm)\n \n" + "Configure the fitting:", MathUtils.rounded(simulationParameters.sd), MathUtils.rounded(getSa()));
    gd.addSlider("Fraction_positives", 50, 100, settings.fractionPositives);
    gd.addSlider("Fraction_negatives_after_positives", 0, 100, settings.fractionNegativesAfterAllPositives);
    gd.addSlider("Min_negatives_after_positives", 0, 30, settings.negativesAfterAllPositives);
    gd.addSlider("Match_distance", 0.5, 3.5, settings.distance);
    gd.addSlider("Lower_distance", 0, 3.5, settings.lowerDistance);
    gd.addSlider("Match_signal", 0, 3.5, settings.signalFactor);
    gd.addSlider("Lower_signal", 0, 3.5, settings.lowerSignalFactor);
    final FitEngineConfigurationProvider fitEngineConfigurationProvider = new PeakFit.SimpleFitEngineConfigurationProvider(config);
    // Collect options for fitting
    final double sa = getSa();
    final FitConfiguration fitConfig = config.getFitConfiguration();
    fitConfig.setInitialPeakStdDev(MathUtils.round(sa / simulationParameters.pixelPitch));
    PeakFit.addPsfOptions(gd, fitConfig);
    PeakFit.addFittingOptions(gd, fitEngineConfigurationProvider);
    gd.addChoice("Fit_solver", SettingsManager.getFitSolverNames(), FitProtosHelper.getName(fitConfig.getFitSolver()));
    gd.addMessage("Multi-path filter (used to pick optimum results during fitting)");
    // Allow loading the best filter for these results
    final boolean benchmarkSettingsCheckbox = BenchmarkSpotFitResult.fitResultsId.get() == BenchmarkFilterAnalysis.getLastFittingId();
    Checkbox cbBenchmark = null;
    if (benchmarkSettingsCheckbox) {
        // This should always be an opt-in decision. Otherwise the user cannot use the previous
        // settings.
        cbBenchmark = gd.addAndGetCheckbox("Benchmark_settings", false);
    }
    gd.addTextAreas(XmlUtils.convertQuotes(multiFilter.toXml()), null, 6, 60);
    textFailLimit = gd.addAndGetNumericField("Fail_limit", config.getFailuresLimit(), 0);
    cbIncludeNeighbours = gd.addAndGetCheckbox("Include_neighbours", config.isIncludeNeighbours());
    gd.addAndGetSlider("Neighbour_height", 0.01, 1, config.getNeighbourHeightThreshold());
    textNeighbourHeight = gd.getLastTextField();
    cbComputeDoublets = gd.addAndGetCheckbox("Compute_doublets", settings.computeDoublets);
    PeakFit.addDuplicateDistanceOptions(gd, fitEngineConfigurationProvider);
    gd.addCheckbox("Show_score_histograms", settings.showFilterScoreHistograms);
    gd.addCheckbox("Show_correlation", settings.showCorrelation);
    gd.addCheckbox("Plot_rank_by_intensity", settings.rankByIntensity);
    gd.addCheckbox("Save_filter_range", settings.saveFilterRange);
    if (extraOptions) {
    // No extra options
    }
    // Add a mouse listener to the config file field
    if (cbBenchmark != null && ImageJUtils.isShowGenericDialog()) {
        taFilterXml = gd.getTextArea1();
        cbBenchmark.addItemListener(this);
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.fractionPositives = Math.abs(gd.getNextNumber());
    settings.fractionNegativesAfterAllPositives = Math.abs(gd.getNextNumber());
    settings.negativesAfterAllPositives = (int) Math.abs(gd.getNextNumber());
    settings.distance = Math.abs(gd.getNextNumber());
    settings.lowerDistance = Math.abs(gd.getNextNumber());
    settings.signalFactor = Math.abs(gd.getNextNumber());
    settings.lowerSignalFactor = Math.abs(gd.getNextNumber());
    fitConfig.setPsfType(PeakFit.getPsfTypeValues()[gd.getNextChoiceIndex()]);
    config.setFitting(gd.getNextNumber());
    // Some enum values are not supported
    fitConfig.setFitSolver(SettingsManager.getFitSolverValues()[gd.getNextChoiceIndex()]);
    boolean myUseBenchmarkSettings = false;
    if (benchmarkSettingsCheckbox) {
        // useBenchmarkSettings =
        myUseBenchmarkSettings = gd.getNextBoolean();
    }
    // Read dialog settings
    final String xml = gd.getNextText();
    final int failLimit = (int) gd.getNextNumber();
    final boolean includeNeighbours = gd.getNextBoolean();
    final double neighbourHeightThreshold = gd.getNextNumber();
    final boolean myComputeDoublets = gd.getNextBoolean();
    final double myDuplicateDistance = gd.getNextNumber();
    gd.collectOptions();
    MultiPathFilter myMultiFilter = null;
    if (myUseBenchmarkSettings && !ImageJUtils.isShowGenericDialog()) {
        // Only copy the benchmark settings if not interactive
        final FitEngineConfiguration tmp = new FitEngineConfiguration();
        final FitConfiguration tmpFitConfig = tmp.getFitConfiguration();
        // Collect the residuals threshold
        tmpFitConfig.setComputeResiduals(true);
        if (BenchmarkFilterAnalysis.updateConfiguration(tmp, false)) {
            config.setFailuresLimit(tmp.getFailuresLimit());
            config.setIncludeNeighbours(tmp.isIncludeNeighbours());
            config.setNeighbourHeightThreshold(tmp.getNeighbourHeightThreshold());
            settings.computeDoublets = (tmp.getResidualsThreshold() < 1);
            config.setDuplicateDistance(tmp.getDuplicateDistance());
            config.setDuplicateDistanceAbsolute(tmp.getDuplicateDistanceAbsolute());
            final DirectFilter primaryFilter = tmpFitConfig.getSmartFilter();
            final double residualsThreshold = tmp.getResidualsThreshold();
            myMultiFilter = new MultiPathFilter(primaryFilter, FitWorker.createMinimalFilter(tmpFitConfig.getFilterPrecisionMethod()), residualsThreshold);
        }
    } else {
        myMultiFilter = MultiPathFilter.fromXml(xml);
        config.setFailuresLimit(failLimit);
        config.setIncludeNeighbours(includeNeighbours);
        config.setNeighbourHeightThreshold(neighbourHeightThreshold);
        settings.computeDoublets = myComputeDoublets;
        config.setDuplicateDistance(myDuplicateDistance);
    }
    if (myMultiFilter == null) {
        gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("The multi-path filter was invalid.\n \nContinue with a default filter?");
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.showDialog();
        if (!gd.wasOKed()) {
            return false;
        }
    } else {
        multiFilter = myMultiFilter;
    }
    if (settings.computeDoublets) {
        config.setResidualsThreshold(0);
        fitConfig.setComputeResiduals(true);
    } else {
        config.setResidualsThreshold(1);
        fitConfig.setComputeResiduals(false);
    }
    settings.showFilterScoreHistograms = gd.getNextBoolean();
    settings.showCorrelation = gd.getNextBoolean();
    settings.rankByIntensity = gd.getNextBoolean();
    settings.saveFilterRange = gd.getNextBoolean();
    // Avoid stupidness, i.e. things that move outside the fit window and are bad widths
    // TODO - Fix this for simple or smart filter...
    fitConfig.setDisableSimpleFilter(false);
    // Realistically we cannot fit lower than this
    fitConfig.setMinPhotons(15);
    // Disable shift as candidates may be re-mapped to alternative candidates so the initial
    // position is wrong.
    fitConfig.setCoordinateShiftFactor(0);
    fitConfig.setMinWidthFactor(1.0 / 5);
    fitConfig.setMaxWidthFactor(5);
    // Disable the direct filter
    fitConfig.setDirectFilter(null);
    if (extraOptions) {
    // No extra options
    }
    if (gd.invalidNumber()) {
        return false;
    }
    if (settings.lowerDistance > settings.distance) {
        settings.lowerDistance = settings.distance;
    }
    if (settings.lowerSignalFactor > settings.signalFactor) {
        settings.lowerSignalFactor = settings.signalFactor;
    }
    // Distances relative to sa (not s) as this is the same as the BenchmarkSpotFilter plugin
    distanceInPixels = settings.distance * sa / simulationParameters.pixelPitch;
    lowerDistanceInPixels = settings.lowerDistance * sa / simulationParameters.pixelPitch;
    // Copy simulation defaults if a new simulation.
    // if (lastSimulationId.get() != simulationParameters.id) {
    // This is needed to configure the fit solver.
    fitConfig.setNmPerPixel(simulationParameters.pixelPitch);
    fitConfig.setGain(simulationParameters.gain);
    fitConfig.setQuantumEfficiency(simulationParameters.qe);
    fitConfig.setReadNoise(simulationParameters.readNoise);
    fitConfig.setBias(simulationParameters.bias);
    fitConfig.setCameraType(simulationParameters.cameraType);
    fitConfig.setCameraModel(CreateData.getCameraModel(simulationParameters));
    // }
    if (!PeakFit.configurePsfModel(config)) {
        return false;
    }
    return PeakFit.configureFitSolver(config, IJImageSource.getBounds(imp), null, (extraOptions) ? PeakFit.FLAG_EXTRA_OPTIONS : 0);
}

Example 2 with FitEngineConfigurationProvider

use of uk.ac.sussex.gdsc.smlm.ij.plugins.PeakFit.FitEngineConfigurationProvider 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 3 with FitEngineConfigurationProvider

use of uk.ac.sussex.gdsc.smlm.ij.plugins.PeakFit.FitEngineConfigurationProvider in project GDSC-SMLM by aherbert.

the class Configuration method showDialog.

/**
 * Show the current properties.
 *
 * @param fitEngineConfiguration the fit engine configuration
 * @param save the save
 * @return true, if successful
 */
public boolean showDialog(FitEngineConfiguration fitEngineConfiguration, boolean save) {
    this.config = fitEngineConfiguration;
    fitConfig = config.getFitConfiguration();
    pluginSettings = Settings.load();
    pluginSettings.save();
    final CalibrationReader calibrationReader = fitConfig.getCalibrationReader();
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("fit-configuration"));
    gd.addMessage("Configuration settings for the single-molecule localisation microscopy plugins");
    final String[] templates = ConfigurationTemplate.getTemplateNames(true);
    gd.addChoice("Template", templates, templates[0]);
    PeakFit.addCameraOptions(gd, fitConfig);
    gd.addNumericField("Calibration (nm/px)", calibrationReader.getNmPerPixel(), 2);
    gd.addNumericField("Exposure_time (ms)", calibrationReader.getExposureTime(), 2);
    gd.addMessage("--- Gaussian parameters ---");
    PeakFit.addPsfOptions(gd, fitConfig);
    gd.addMessage("--- Maxima identification ---");
    final FitEngineConfigurationProvider provider = this::getFitEngineConfiguration;
    PeakFit.addDataFilterOptions(gd, provider);
    PeakFit.addSearchOptions(gd, provider);
    PeakFit.addBorderOptions(gd, provider);
    PeakFit.addFittingOptions(gd, provider);
    gd.addMessage("--- Gaussian fitting ---");
    gd.addChoice("Fit_solver", SettingsManager.getFitSolverNames(), FitProtosHelper.getName(fitConfig.getFitSolver()));
    // Parameters specific to each Fit solver are collected in a second dialog
    gd.addNumericField("Fail_limit", config.getFailuresLimit(), 0);
    gd.addNumericField("Pass_rate", config.getPassRate(), 2);
    gd.addCheckbox("Include_neighbours", config.isIncludeNeighbours());
    gd.addSlider("Neighbour_height", 0.01, 1, config.getNeighbourHeightThreshold());
    gd.addSlider("Residuals_threshold", 0.01, 1, config.getResidualsThreshold());
    PeakFit.addDuplicateDistanceOptions(gd, provider);
    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, 4.5, fitConfig.getMaxWidthFactor());
    PeakFit.addPrecisionOptions(gd, this::getFitConfiguration);
    // Add a mouse listener to the config file field
    if (ImageJUtils.isShowGenericDialog()) {
        final Vector<TextField> numerics = gd.getNumericFields();
        final Vector<Checkbox> checkboxes = gd.getCheckboxes();
        final Vector<Choice> choices = gd.getChoices();
        final Iterator<TextField> nu = numerics.iterator();
        final Iterator<Checkbox> cb = checkboxes.iterator();
        final Iterator<Choice> ch = choices.iterator();
        final Choice textTemplate = ch.next();
        textTemplate.addItemListener(this::itemStateChanged);
        textCameraType = ch.next();
        textNmPerPixel = nu.next();
        textExposure = nu.next();
        textPsf = ch.next();
        textDataFilterType = ch.next();
        textDataFilterMethod = ch.next();
        textSmooth = nu.next();
        textSearch = nu.next();
        textBorder = nu.next();
        textFitting = nu.next();
        textFitSolver = ch.next();
        textFailuresLimit = nu.next();
        textPassRate = nu.next();
        textIncludeNeighbours = cb.next();
        textNeighbourHeightThreshold = nu.next();
        textResidualsThreshold = nu.next();
        textDuplicateDistance = nu.next();
        textSmartFilter = cb.next();
        textDisableSimpleFilter = cb.next();
        textCoordinateShiftFactor = nu.next();
        textSignalStrength = nu.next();
        textMinPhotons = nu.next();
        textMinWidthFactor = nu.next();
        textWidthFactor = nu.next();
        textPrecisionThreshold = nu.next();
        updateFilterInput();
        textSmartFilter.addItemListener(this::itemStateChanged);
        textDisableSimpleFilter.addItemListener(this::itemStateChanged);
    }
    if (save) {
        gd.enableYesNoCancel("Save", "Save template");
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    // In case a template updated the calibration
    final CalibrationWriter calibrationWriter = fitConfig.getCalibrationWriter();
    // Ignore the template
    gd.getNextChoice();
    calibrationWriter.setCameraType(SettingsManager.getCameraTypeValues()[gd.getNextChoiceIndex()]);
    calibrationWriter.setNmPerPixel(gd.getNextNumber());
    calibrationWriter.setExposureTime(gd.getNextNumber());
    fitConfig.setCalibration(calibrationWriter.getCalibration());
    fitConfig.setPsfType(PeakFit.getPsfTypeValues()[gd.getNextChoiceIndex()]);
    config.setDataFilterType(gd.getNextChoiceIndex());
    config.setDataFilter(gd.getNextChoiceIndex(), Math.abs(gd.getNextNumber()), false, 0);
    config.setSearch(gd.getNextNumber());
    config.setBorder(gd.getNextNumber());
    config.setFitting(gd.getNextNumber());
    // Some enum values are not supported
    fitConfig.setFitSolver(SettingsManager.getFitSolverValues()[gd.getNextChoiceIndex()]);
    config.setFailuresLimit((int) gd.getNextNumber());
    config.setPassRate(gd.getNextNumber());
    config.setIncludeNeighbours(gd.getNextBoolean());
    config.setNeighbourHeightThreshold(gd.getNextNumber());
    config.setResidualsThreshold(gd.getNextNumber());
    config.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.setMaxWidthFactor(gd.getNextNumber());
    fitConfig.setPrecisionThreshold(gd.getNextNumber());
    gd.collectOptions();
    // Check arguments
    try {
        ParameterUtils.isAboveZero("nm per pixel", calibrationWriter.getNmPerPixel());
        ParameterUtils.isAboveZero("Exposure time", calibrationWriter.getExposureTime());
        if (fitConfig.getPsfTypeValue() != PSFType.ASTIGMATIC_GAUSSIAN_2D_VALUE) {
            ParameterUtils.isAboveZero("Initial SD0", fitConfig.getInitialXSd());
            if (fitConfig.getPsf().getParametersCount() > 1) {
                ParameterUtils.isAboveZero("Initial SD1", fitConfig.getInitialYSd());
            }
        }
        ParameterUtils.isAboveZero("Search_width", config.getSearch());
        ParameterUtils.isAboveZero("Fitting_width", config.getFitting());
        ParameterUtils.isPositive("Neighbour height threshold", config.getNeighbourHeightThreshold());
        ParameterUtils.isPositive("Residuals threshold", config.getResidualsThreshold());
        ParameterUtils.isPositive("Duplicate distance", config.getDuplicateDistance());
        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.configurePsfModel(config, flags)) {
        return false;
    }
    if (!PeakFit.configureResultsFilter(config, flags)) {
        return false;
    }
    if (!PeakFit.configureDataFilter(config, flags)) {
        return false;
    }
    PeakFit.configureFitSolver(config, null, null, flags);
    if (save) {
        final boolean saveToFile = !gd.wasOKed();
        if (saveToFile) {
            gd = new ExtendedGenericDialog(TITLE);
            gd.addFilenameField("Template_filename", pluginSettings.templateFilename);
            gd.addMessage("Add notes to the template ...");
            gd.addTextAreas(pluginSettings.notes, null, 10, 60);
            gd.showDialog();
            if (gd.wasCanceled()) {
                return false;
            }
            pluginSettings.save();
            final String filename = gd.getNextString();
            pluginSettings.notes = gd.getNextText();
            if (filename != null) {
                pluginSettings.templateFilename = FileUtils.replaceExtension(filename, ".txt");
                final File file = new File(pluginSettings.templateFilename);
                final String name = FileUtils.removeExtension(file.getName());
                final TemplateSettings.Builder settings = TemplateSettings.newBuilder();
                settings.addNotes(pluginSettings.notes);
                settings.setCalibration(fitConfig.getCalibration());
                settings.setFitEngineSettings(config.getFitEngineSettings());
                // Note: No results settings are currently supported
                settings.setPsf(fitConfig.getPsf());
                if (!ConfigurationTemplate.saveTemplate(name, settings.build(), file)) {
                    IJ.error(TITLE, "Failed to save to file: " + pluginSettings.templateFilename);
                }
            }
        } else {
            SettingsManager.writeSettings(config, 0);
        }
    }
    return true;
}