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

Example 96 with ExtendedGenericDialog

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

the class ResultsMatchCalculator method showDialog.

private boolean showDialog() {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    settings = Settings.load();
    gd.addMessage("Compare the points in two results sets\nand compute the match statistics");
    ResultsManager.addInput(gd, "Results1", settings.inputOption1, InputSource.MEMORY);
    ResultsManager.addInput(gd, "Results2", settings.inputOption2, InputSource.MEMORY);
    gd.addChoice("Coordinate_method1", CoordinateMethodDescriptions.descriptions, settings.coordinateMethod1.getDescription());
    gd.addChoice("Coordinate_method2", CoordinateMethodDescriptions.descriptions, settings.coordinateMethod2.getDescription());
    gd.addNumericField("Distance", settings.distanceThreshold, 2);
    gd.addSlider("Increments", 0, 10, settings.increments);
    gd.addNumericField("Delta", settings.delta, 2);
    gd.addNumericField("Beta", settings.beta, 2);
    gd.addCheckbox("Show_table", settings.showTable);
    gd.addCheckbox("Show_pairs", settings.showPairs);
    gd.addChoice("Save_classifications", Settings.saveClassificationsOptions, settings.saveClassificationsOption);
    gd.addCheckbox("Id_analysis", settings.idAnalysis);
    gd.addCheckbox("Save_pairs", settings.savePairs);
    gd.addCheckbox("Output_end_frame", settings.outputEndFrame);
    gd.addHelp(HelpUrls.getUrl("results-match-calculator"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.inputOption1 = gd.getNextChoice();
    settings.inputOption2 = gd.getNextChoice();
    settings.coordinateMethod1 = CoordinateMethod.fromDescription(gd.getNextChoice(), CoordinateMethod.ALL);
    settings.coordinateMethod2 = CoordinateMethod.fromDescription(gd.getNextChoice(), CoordinateMethod.ALL);
    settings.distanceThreshold = gd.getNextNumber();
    settings.increments = (int) gd.getNextNumber();
    settings.delta = gd.getNextNumber();
    settings.beta = gd.getNextNumber();
    settings.showTable = gd.getNextBoolean();
    settings.showPairs = gd.getNextBoolean();
    settings.saveClassificationsOption = gd.getNextChoiceIndex();
    settings.idAnalysis = gd.getNextBoolean();
    settings.savePairs = gd.getNextBoolean();
    settings.outputEndFrame = gd.getNextBoolean();
    settings.save();
    if (!(settings.showTable || settings.showPairs || !settings.isSaveClassifications())) {
        IJ.error(TITLE, "No outputs specified");
        return false;
    }
    // Check arguments
    try {
        ParameterUtils.isPositive("Distance threshold", settings.distanceThreshold);
        ParameterUtils.isPositive("Increments", settings.increments);
        ParameterUtils.isAboveZero("Delta", settings.delta);
        ParameterUtils.isPositive("Beta", settings.beta);
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    return true;
}

Example 97 with ExtendedGenericDialog

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

the class UpdateResultsBounds 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("update-results-bounds"));
    gd.addMessage("Select results to update");
    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 98 with ExtendedGenericDialog

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

the class UpdateResultsBounds method showDialog.

private static boolean showDialog(MemoryPeakResults results) {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("update-results-bounds"));
    // Force computation of bounds
    Rectangle currentBounds = results.getBounds();
    results.setBounds(null);
    Rectangle autoBounds;
    try {
        autoBounds = results.getBounds(true);
    } catch (final DataException ex) {
        IJ.error(TITLE, "No calibration found to convert to pixel units");
        return false;
    } finally {
        // Reset after forcing computation
        if (currentBounds != null) {
            results.setBounds(currentBounds);
        }
    }
    // Re-acquire the bounds (either the existing bounds or the auto-bounds)
    currentBounds = results.getBounds();
    gd.addMessage(TextUtils.wrap("Set the bounds of the original source image.\n \nAuto-bounds = " + format(autoBounds) + "\n \nThe new bounds will be the union of the auto-bounds and specified bounds " + "to ensure all data is within the bounds.", 80));
    gd.addNumericField("Min_x", currentBounds.x, 0, 6, "px");
    gd.addNumericField("Min_y", currentBounds.y, 0, 6, "px");
    gd.addNumericField("Width", currentBounds.width, 0, 6, "px");
    gd.addNumericField("Height", currentBounds.height, 0, 6, "px");
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    final int x = (int) gd.getNextNumber();
    final int y = (int) gd.getNextNumber();
    final int width = (int) gd.getNextNumber();
    final int height = (int) gd.getNextNumber();
    // Check the bounds are not smaller than the auto-bounds
    final Rectangle newBounds = new Rectangle(x, y, width, height).union(autoBounds);
    if (newBounds.isEmpty()) {
        IJ.error(TITLE, "New bounds are not valid: " + format(newBounds));
        return false;
    }
    results.setBounds(newBounds);
    return true;
}

Example 99 with ExtendedGenericDialog

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

the class CameraModelFisherInformationAnalysis method createExponents.

@Nullable
private double[] createExponents() {
    final int n = 1 + Math.max(0, settings.getSubDivisions());
    final double h = 1.0 / n;
    final double minExp = settings.getMinExponent();
    final double maxExp = settings.getMaxExponent();
    final double size = (maxExp - minExp) * n + 1;
    if (size > 100) {
        final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Number of exponents is " + Math.ceil(size) + ". OK to continue?");
        gd.showDialog();
        if (gd.wasCanceled()) {
            return null;
        }
    }
    final TDoubleArrayList list = new TDoubleArrayList();
    for (int i = 0; ; i++) {
        final double e = minExp + i * h;
        list.add(e);
        if (e >= settings.getMaxExponent()) {
            break;
        }
    }
    return list.toArray();
}

Example 100 with ExtendedGenericDialog

use of uk.ac.sussex.gdsc.core.ij.gui.ExtendedGenericDialog 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;
}