Examples with FitConfiguration uk.ac.sussex.gdsc.smlm.engine.FitConfiguration used on opensource projects

Example 6 with FitConfiguration

use of uk.ac.sussex.gdsc.smlm.engine.FitConfiguration in project GDSC-SMLM by aherbert.

the class DoubletAnalysis method showDialog.

/**
 * Show dialog.
 *
 * @return true, if successful
 */
private boolean showDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    final String helpKey = "doublet-analysis";
    settings = Settings.load();
    config = configRef.get().createCopy();
    final FitConfiguration fitConfig = config.getFitConfiguration();
    final double sa = getSa();
    ImageJUtils.addMessage(gd, "Fits the benchmark image created by CreateData plugin.\nPSF width = %s, adjusted = %s", MathUtils.rounded(simulationParameters.sd / simulationParameters.pixelPitch), MathUtils.rounded(sa));
    // For each new benchmark width, reset the PSF width to the square pixel adjustment
    if (lastId.get() != simulationParameters.id) {
        final double w = sa;
        settings.matchDistance = w * Gaussian2DFunction.SD_TO_HWHM_FACTOR;
        settings.lowerDistance = 0.5 * settings.matchDistance;
        fitConfig.setInitialPeakStdDev(w);
        final CalibrationWriter cal = new CalibrationWriter(fitConfig.getCalibration());
        cal.setNmPerPixel(simulationParameters.pixelPitch);
        cal.setCountPerPhoton(simulationParameters.gain);
        cal.setQuantumEfficiency(simulationParameters.qe);
        cal.setExposureTime(100);
        cal.setReadNoise(simulationParameters.readNoise);
        cal.setBias(simulationParameters.bias);
        cal.setCameraType(simulationParameters.cameraType);
        fitConfig.setCameraModel(CreateData.getCameraModel(simulationParameters));
        fitConfig.setCalibration(cal.getCalibration());
    }
    // Support for using templates
    final String[] templates = ConfigurationTemplate.getTemplateNames(true);
    gd.addChoice("Template", templates, templates[0]);
    // Allow the settings from the benchmark analysis to be used
    gd.addCheckbox("Benchmark_settings", settings.useBenchmarkSettings);
    // Collect options for fitting
    PeakFit.addPsfOptions(gd, fitConfig);
    final PeakFit.SimpleFitEngineConfigurationProvider provider = new PeakFit.SimpleFitEngineConfigurationProvider(config);
    PeakFit.addDataFilterOptions(gd, provider);
    PeakFit.addSearchOptions(gd, provider);
    PeakFit.addBorderOptions(gd, provider);
    PeakFit.addFittingOptions(gd, provider);
    gd.addChoice("Fit_solver", SettingsManager.getFitSolverNames(), fitConfig.getFitSolver().ordinal());
    gd.addSlider("Iteration_increase", 1, 4.5, settings.iterationIncrease);
    gd.addCheckbox("Ignore_with_neighbours", settings.ignoreWithNeighbours);
    gd.addCheckbox("Show_overlay", settings.showOverlay);
    gd.addCheckbox("Show_histograms", settings.showHistograms);
    gd.addCheckbox("Show_results", settings.showResults);
    gd.addCheckbox("Show_Jaccard_Plot", settings.showJaccardPlot);
    gd.addCheckbox("Use_max_residuals", settings.useMaxResiduals);
    gd.addNumericField("Match_distance", settings.matchDistance, 2);
    gd.addNumericField("Lower_distance", settings.lowerDistance, 2);
    gd.addNumericField("Signal_factor", settings.signalFactor, 2);
    gd.addNumericField("Lower_factor", settings.lowerSignalFactor, 2);
    gd.addChoice("Matching", Settings.MATCHING_METHODS, settings.matchingMethod);
    // Add a mouse listener to the config file field
    if (ImageJUtils.isShowGenericDialog()) {
        final Vector<TextField> numerics = gd.getNumericFields();
        final Vector<Choice> choices = gd.getChoices();
        final Iterator<TextField> nu = numerics.iterator();
        final Iterator<Choice> ch = choices.iterator();
        ch.next().addItemListener(this);
        final Checkbox b = (Checkbox) gd.getCheckboxes().get(0);
        b.addItemListener(this);
        textPsf = ch.next();
        textDataFilterType = ch.next();
        textDataFilter = ch.next();
        textSmooth = nu.next();
        textSearch = nu.next();
        textBorder = nu.next();
        textFitting = nu.next();
        textFitSolver = ch.next();
        // Iteration increase
        nu.next();
        textMatchDistance = nu.next();
        textLowerDistance = nu.next();
        textSignalFactor = nu.next();
        textLowerFactor = nu.next();
    }
    gd.addHelp(HelpUrls.getUrl(helpKey));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    // Ignore the template
    gd.getNextChoice();
    settings.useBenchmarkSettings = gd.getNextBoolean();
    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()]);
    // Avoid stupidness. Note: We are mostly ignoring the validation result and
    // checking the results for the doublets manually.
    // Realistically we cannot fit lower than this
    fitConfig.setMinPhotons(15);
    // Set the width factors to help establish bounds for bounded fitters
    fitConfig.setMinWidthFactor(1.0 / 10);
    fitConfig.setMaxWidthFactor(10);
    settings.iterationIncrease = gd.getNextNumber();
    settings.ignoreWithNeighbours = gd.getNextBoolean();
    settings.showOverlay = gd.getNextBoolean();
    settings.showHistograms = gd.getNextBoolean();
    settings.showResults = gd.getNextBoolean();
    settings.showJaccardPlot = gd.getNextBoolean();
    settings.useMaxResiduals = gd.getNextBoolean();
    settings.matchDistance = Math.abs(gd.getNextNumber());
    settings.lowerDistance = Math.abs(gd.getNextNumber());
    settings.signalFactor = Math.abs(gd.getNextNumber());
    settings.lowerSignalFactor = Math.abs(gd.getNextNumber());
    settings.matchingMethod = gd.getNextChoiceIndex();
    gd.collectOptions();
    settings.save();
    configRef.set(config);
    if (gd.invalidNumber()) {
        return false;
    }
    if (settings.lowerDistance > settings.matchDistance) {
        settings.lowerDistance = settings.matchDistance;
    }
    if (settings.lowerSignalFactor > settings.signalFactor) {
        settings.lowerSignalFactor = settings.signalFactor;
    }
    if (settings.useBenchmarkSettings && !updateFitConfiguration(config)) {
        return false;
    }
    boolean configure = true;
    if (settings.useBenchmarkSettings) {
        // Only configure the fit solver if not in a macro
        configure = Macro.getOptions() == null;
    }
    if (configure && !PeakFit.configurePsfModel(config)) {
        return false;
    }
    if (configure && !PeakFit.configureFitSolver(config, IJImageSource.getBounds(imp), null, PeakFit.FLAG_NO_SAVE)) {
        return false;
    }
    lastId.set(simulationParameters.id);
    if (settings.showHistograms) {
        gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Select the histograms to display");
        for (int i = 0; i < Settings.NAMES.length; i++) {
            gd.addCheckbox(Settings.NAMES[i].replace(' ', '_'), settings.displayHistograms[i]);
        }
        for (int i = 0; i < Settings.NAMES2.length; i++) {
            gd.addCheckbox(Settings.NAMES2[i].replace(' ', '_'), settings.displayHistograms[i + Settings.NAMES.length]);
        }
        gd.addHelp(HelpUrls.getUrl(helpKey));
        gd.showDialog();
        if (gd.wasCanceled()) {
            return false;
        }
        for (int i = 0; i < settings.displayHistograms.length; i++) {
            settings.displayHistograms[i] = gd.getNextBoolean();
        }
    }
    return true;
}

Example 7 with FitConfiguration

use of uk.ac.sussex.gdsc.smlm.engine.FitConfiguration in project GDSC-SMLM by aherbert.

the class SettingsManager method writeSettings.

/**
 * Write to a settings file in the settings directory.
 *
 * @param fitEngineConfiguration the fit engine configuration
 * @param flags the flags
 * @return true, if successful
 */
public static boolean writeSettings(FitEngineConfiguration fitEngineConfiguration, int flags) {
    final FitConfiguration fitConfig = fitEngineConfiguration.getFitConfiguration();
    // This is fail fast
    boolean result = writeSettings(fitEngineConfiguration.getFitEngineSettings(), flags);
    result &= writeSettings(fitConfig.getCalibration(), flags);
    result &= writeSettings(fitConfig.getPsf(), flags);
    return result;
}

Example 8 with FitConfiguration

use of uk.ac.sussex.gdsc.smlm.engine.FitConfiguration in project GDSC-SMLM by aherbert.

the class ConfigurationTemplateTest method canCreateResourceTemplate.

@Test
void canCreateResourceTemplate() throws IOException {
    // This is not really a test.
    // It creates some templates so that they can be put in the resources folder.
    final File tmpFile = File.createTempFile("template", ".json.txt");
    tmpFile.deleteOnExit();
    final FitEngineConfiguration config = new FitEngineConfiguration();
    final FitConfiguration fitConfig = config.getFitConfiguration();
    fitConfig.setMaxIterations(150);
    fitConfig.setMinWidthFactor(0.2);
    fitConfig.setMinWidthFactor(5);
    fitConfig.setSmartFilter(true);
    fitConfig.setDirectFilter(new MultiFilter2(0, 22, 0.56, 2.55, 3.3, 0, 31, 0, 0));
    config.setSearch(0.607);
    config.setBorder(1);
    config.setFitting(3);
    config.setFailuresLimit(3);
    config.setIncludeNeighbours(true);
    config.setNeighbourHeightThreshold(0.3);
    config.setResidualsThreshold(0.4);
    config.setDataFilterType(DataFilterType.SINGLE);
    config.setDataFilter(DataFilterMethod.GAUSSIAN, 0.425, false, 0);
    // System.out.println(tmpFile.getPath());
    final TemplateSettings.Builder builder = TemplateSettings.newBuilder();
    builder.setFitEngineSettings(config.getFitEngineSettings());
    Assertions.assertTrue(SettingsManager.toJson(builder.build(), tmpFile, SettingsManager.FLAG_JSON_WHITESPACE));
}

Example 9 with FitConfiguration

use of uk.ac.sussex.gdsc.smlm.engine.FitConfiguration in project GDSC-SMLM by aherbert.

the class PeakFit method configurePsfModel.

/**
 * Show a dialog to configure the PSF model. The updated settings are saved to the settings file.
 *
 * <p>If the configuration is for a 3D PSF then a dialog to configure the z model is shown.
 *
 * @param config the config
 * @param flags the flags
 * @return true, if successful
 */
public static boolean configurePsfModel(FitEngineConfiguration config, int flags) {
    final FitConfiguration fitConfig = config.getFitConfiguration();
    if (fitConfig.getPsfTypeValue() != PSFType.ASTIGMATIC_GAUSSIAN_2D_VALUE) {
        return true;
    }
    // Get the astigmatism z-model
    final AstigmatismModel model = AstigmatismModelManager.getModel(fitConfig.getPsfModelName());
    if (model == null) {
        IJ.error(TITLE, "Failed to load the model: " + fitConfig.getPsfModelName());
        return false;
    }
    // Conversion to the correct units in pixels is done within the FitConfiguration object.
    fitConfig.setAstigmatismModel(model);
    if (BitFlagUtils.anyNotSet(flags, FLAG_NO_SAVE)) {
        SettingsManager.writeSettings(config, 0);
    }
    return true;
}

Example 10 with FitConfiguration

use of uk.ac.sussex.gdsc.smlm.engine.FitConfiguration in project GDSC-SMLM by aherbert.

the class PeakFit method updateFitConfiguration.

/**
 * Updates the configuration for peak fitting. Configures the calculation of residuals, logging
 * and peak validation.
 *
 * @param config the config
 * @return true, if successful
 */
private boolean updateFitConfiguration(FitEngineConfiguration config) {
    final FitConfiguration localFitConfig = config.getFitConfiguration();
    // Adjust the settings that are relevant within the fitting configuration.
    localFitConfig.setComputeResiduals(config.getResidualsThreshold() < 1);
    logger = (resultsSettings.getLogProgress()) ? ImageJPluginLoggerHelper.getLogger(getClass()) : null;
    localFitConfig.setLog(logger);
    if (resultsSettings.getShowDeviations()) {
        // Note: This may already by true if the deviations are needed for the smart filter
        localFitConfig.setComputeDeviations(resultsSettings.getShowDeviations());
    }
    config.configureOutputUnits();
    return checkCameraModel(localFitConfig, source.getBounds(), bounds, true);
}