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

Example 31 with ExtendedGenericDialog

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

the class BlinkEstimator method showDialog.

private boolean showDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Compute the blinking rate by fitting counts to dark-time.\nSee Annibale et al (2011) PLos ONE 6, e22678.");
    ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
    gd.addNumericField("Max_dark_time (frames)", s_maxDarkTime, 0);
    gd.addNumericField("Histogram_bins", histogramBins, 0);
    gd.addCheckbox("Show_histogram", showHistogram);
    gd.addSlider("Search_distance", 0.5, 5, s_searchDistance);
    gd.addCheckbox("Relative_distance", s_relativeDistance);
    gd.addSlider("Fitted_points", 4, 15, s_nFittedPoints);
    gd.addSlider("Range_of_fitted_points", 0, 15, rangeFittedPoints);
    gd.addCheckbox("Time_at_lower_bound", s_timeAtLowerBound);
    //gd.addCheckbox("Fit_intercept", fitIntercept);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    inputOption = gd.getNextChoice();
    maxDarkTime = s_maxDarkTime = (int) gd.getNextNumber();
    histogramBins = (int) gd.getNextNumber();
    showHistogram = gd.getNextBoolean();
    searchDistance = s_searchDistance = gd.getNextNumber();
    relativeDistance = s_relativeDistance = gd.getNextBoolean();
    nFittedPoints = s_nFittedPoints = (int) gd.getNextNumber();
    rangeFittedPoints = (int) gd.getNextNumber();
    timeAtLowerBound = s_timeAtLowerBound = gd.getNextBoolean();
    // Check arguments
    try {
        Parameters.isAbove("Max dark time", maxDarkTime, 3);
        Parameters.isAbove("Histogram bins", histogramBins, 1);
        Parameters.isAboveZero("Search distance", searchDistance);
        Parameters.isAbove("n-Fitted points", nFittedPoints, 3);
        Parameters.isPositive("Range of fitted points", rangeFittedPoints);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    return true;
}

Example 32 with ExtendedGenericDialog

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

the class TraceMolecules method fitTraces.

private void fitTraces(MemoryPeakResults results, Trace[] traces) {
    // Check if the original image is open and the fit configuration can be extracted
    ImageSource source = results.getSource();
    if (source == null)
        return;
    if (!source.open())
        return;
    FitEngineConfiguration config = (FitEngineConfiguration) XmlUtils.fromXML(results.getConfiguration());
    if (config == null)
        return;
    // Show a dialog asking if the traces should be refit
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Do you want to fit the traces as a single peak using a combined image?");
    gd.addCheckbox("Fit_closest_to_centroid", !fitOnlyCentroid);
    gd.addSlider("Distance_threshold", 0.01, 3, distanceThreshold);
    gd.addSlider("Expansion_factor", 1, 4.5, expansionFactor);
    // Allow fitting settings to be adjusted
    FitConfiguration fitConfig = config.getFitConfiguration();
    gd.addMessage("--- Gaussian fitting ---");
    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());
    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()]);
    String[] criteriaNames = SettingsManager.getNames((Object[]) FitCriteria.values());
    gd.addChoice("Fit_criteria", criteriaNames, criteriaNames[fitConfig.getFitCriteria().ordinal()]);
    gd.addNumericField("Significant_digits", fitConfig.getSignificantDigits(), 0);
    gd.addNumericField("Coord_delta", fitConfig.getDelta(), 4);
    gd.addNumericField("Lambda", fitConfig.getLambda(), 4);
    gd.addNumericField("Max_iterations", fitConfig.getMaxIterations(), 0);
    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", fitConfig.getPrecisionThreshold(), 2);
    gd.addCheckbox("Debug_failures", debugFailures);
    gd.showDialog();
    if (!gd.wasOKed()) {
        source.close();
        return;
    }
    // Get parameters for the fit
    fitOnlyCentroid = !gd.getNextBoolean();
    distanceThreshold = (float) gd.getNextNumber();
    expansionFactor = (float) 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());
    fitConfig.setFitCriteria(gd.getNextChoiceIndex());
    fitConfig.setSignificantDigits((int) gd.getNextNumber());
    fitConfig.setDelta(gd.getNextNumber());
    fitConfig.setLambda(gd.getNextNumber());
    fitConfig.setMaxIterations((int) gd.getNextNumber());
    config.setFailuresLimit((int) gd.getNextNumber());
    config.setIncludeNeighbours(gd.getNextBoolean());
    config.setNeighbourHeightThreshold(gd.getNextNumber());
    config.setResidualsThreshold(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("Distance threshold", distanceThreshold);
        Parameters.isAbove("Expansion factor", expansionFactor, 1);
        Parameters.isAboveZero("Search_width", config.getSearch());
        Parameters.isAboveZero("Fitting_width", config.getFitting());
        Parameters.isAboveZero("Significant digits", fitConfig.getSignificantDigits());
        Parameters.isAboveZero("Delta", fitConfig.getDelta());
        Parameters.isAboveZero("Lambda", fitConfig.getLambda());
        Parameters.isAboveZero("Max iterations", fitConfig.getMaxIterations());
        Parameters.isPositive("Failures limit", config.getFailuresLimit());
        Parameters.isPositive("Neighbour height threshold", config.getNeighbourHeightThreshold());
        Parameters.isPositive("Residuals threshold", config.getResidualsThreshold());
        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());
        source.close();
        return;
    }
    debugFailures = gd.getNextBoolean();
    if (!PeakFit.configureSmartFilter(globalSettings, filename))
        return;
    if (!PeakFit.configureDataFilter(globalSettings, filename, false))
        return;
    if (!PeakFit.configureFitSolver(globalSettings, filename, false))
        return;
    // Adjust settings for a single maxima
    config.setIncludeNeighbours(false);
    fitConfig.setDuplicateDistance(0);
    // Create a fit engine
    MemoryPeakResults refitResults = new MemoryPeakResults();
    refitResults.copySettings(results);
    refitResults.setName(results.getName() + " Trace Fit");
    refitResults.setSortAfterEnd(true);
    refitResults.begin();
    // No border since we know where the peaks are and we must not miss them due to truncated searching 
    FitEngine engine = new FitEngine(config, refitResults, Prefs.getThreads(), FitQueue.BLOCKING);
    // Either : Only fit the centroid
    // or     : Extract a bigger region, allowing all fits to run as normal and then 
    //          find the correct spot using Euclidian distance.
    // Set up the limits
    final double stdDev = FastMath.max(fitConfig.getInitialPeakStdDev0(), fitConfig.getInitialPeakStdDev1());
    float fitWidth = (float) (stdDev * config.getFitting() * ((fitOnlyCentroid) ? 1 : expansionFactor));
    IJ.showStatus("Refitting traces ...");
    List<JobItem> jobItems = new ArrayList<JobItem>(traces.length);
    int singles = 0;
    int fitted = 0;
    for (int n = 0; n < traces.length; n++) {
        Trace trace = traces[n];
        if (n % 32 == 0)
            IJ.showProgress(n, traces.length);
        // Skip traces with one peak
        if (trace.size() == 1) {
            singles++;
            // Use the synchronized method to avoid thread clashes with the FitEngine
            refitResults.addSync(trace.getHead());
            continue;
        }
        Rectangle bounds = new Rectangle();
        double[] combinedNoise = new double[1];
        float[] data = buildCombinedImage(source, trace, fitWidth, bounds, combinedNoise, false);
        if (data == null)
            continue;
        // Fit the combined image
        FitParameters params = new FitParameters();
        params.noise = (float) combinedNoise[0];
        float[] centre = trace.getCentroid();
        if (fitOnlyCentroid) {
            int newX = (int) Math.round(centre[0]) - bounds.x;
            int newY = (int) Math.round(centre[1]) - bounds.y;
            params.maxIndices = new int[] { newY * bounds.width + newX };
        } else {
            params.filter = new ArrayList<float[]>();
            params.filter.add(new float[] { centre[0] - bounds.x, centre[1] - bounds.y });
            params.distanceThreshold = distanceThreshold;
        }
        // This is not needed since the bounds are passed using the FitJob
        //params.setOffset(new float[] { bounds.x, bounds.y });
        int startT = trace.getHead().getFrame();
        params.endT = trace.getTail().getFrame();
        ParameterisedFitJob job = new ParameterisedFitJob(n, params, startT, data, bounds);
        jobItems.add(new JobItem(job, trace, centre));
        engine.run(job);
        fitted++;
    }
    engine.end(false);
    IJ.showStatus("");
    IJ.showProgress(1);
    // Check the success ...
    FitStatus[] values = FitStatus.values();
    int[] statusCount = new int[values.length + 1];
    ArrayList<String> names = new ArrayList<String>(Arrays.asList(SettingsManager.getNames((Object[]) values)));
    names.add(String.format("No maxima within %.2f of centroid", distanceThreshold));
    int separated = 0;
    int success = 0;
    final int debugLimit = 3;
    for (JobItem jobItem : jobItems) {
        int id = jobItem.getId();
        ParameterisedFitJob job = jobItem.job;
        Trace trace = jobItem.trace;
        int[] indices = job.getIndices();
        FitResult fitResult = null;
        int status;
        if (indices.length < 1) {
            status = values.length;
        } else if (indices.length > 1) {
            // Choose the first OK result. This is all that matters for the success reporting
            for (int n = 0; n < indices.length; n++) {
                if (job.getFitResult(n).getStatus() == FitStatus.OK) {
                    fitResult = job.getFitResult(n);
                    break;
                }
            }
            // Otherwise use the closest failure. 
            if (fitResult == null) {
                final float[] centre = traces[id].getCentroid();
                double minD = Double.POSITIVE_INFINITY;
                for (int n = 0; n < indices.length; n++) {
                    // Since the fit has failed we use the initial parameters
                    final double[] params = job.getFitResult(n).getInitialParameters();
                    final double dx = params[Gaussian2DFunction.X_POSITION] - centre[0];
                    final double dy = params[Gaussian2DFunction.Y_POSITION] - centre[1];
                    final double d = dx * dx + dy * dy;
                    if (minD > d) {
                        minD = d;
                        fitResult = job.getFitResult(n);
                    }
                }
            }
            status = fitResult.getStatus().ordinal();
        } else {
            fitResult = job.getFitResult(0);
            status = fitResult.getStatus().ordinal();
        }
        // All jobs have only one peak
        statusCount[status]++;
        // Debug why any fits failed
        if (fitResult == null || fitResult.getStatus() != FitStatus.OK) {
            refitResults.addAll(trace.getPoints());
            separated += trace.size();
            if (debugFailures) {
                FitStatus s = (fitResult == null) ? FitStatus.UNKNOWN : fitResult.getStatus();
                // Only display the first n per category to limit the number of images
                double[] noise = new double[1];
                if (statusCount[status] <= debugLimit) {
                    Rectangle bounds = new Rectangle();
                    buildCombinedImage(source, trace, fitWidth, bounds, noise, true);
                    float[] centre = trace.getCentroid();
                    Utils.display(String.format("Trace %d (n=%d) : x=%f,y=%f", id, trace.size(), centre[0], centre[1]), slices);
                    switch(s) {
                        case INSUFFICIENT_PRECISION:
                            float precision = (Float) fitResult.getStatusData();
                            IJ.log(String.format("Trace %d (n=%d) : %s = %f", id, trace.size(), names.get(status), precision));
                            break;
                        case INSUFFICIENT_SIGNAL:
                            if (noise[0] == 0)
                                noise[0] = getCombinedNoise(trace);
                            float snr = (Float) fitResult.getStatusData();
                            IJ.log(String.format("Trace %d (n=%d) : %s = %f (noise=%.2f)", id, trace.size(), names.get(status), snr, noise[0]));
                            break;
                        case COORDINATES_MOVED:
                        case OUTSIDE_FIT_REGION:
                        case WIDTH_DIVERGED:
                            float[] shift = (float[]) fitResult.getStatusData();
                            IJ.log(String.format("Trace %d (n=%d) : %s = %.3f,%.3f", id, trace.size(), names.get(status), shift[0], shift[1]));
                            break;
                        default:
                            IJ.log(String.format("Trace %d (n=%d) : %s", id, trace.size(), names.get(status)));
                            break;
                    }
                }
            }
        } else {
            success++;
            if (debugFailures) {
                // Only display the first n per category to limit the number of images
                double[] noise = new double[1];
                if (statusCount[status] <= debugLimit) {
                    Rectangle bounds = new Rectangle();
                    buildCombinedImage(source, trace, fitWidth, bounds, noise, true);
                    float[] centre = trace.getCentroid();
                    Utils.display(String.format("Trace %d (n=%d) : x=%f,y=%f", id, trace.size(), centre[0], centre[1]), slices);
                }
            }
        }
    }
    IJ.log(String.format("Trace fitting : %d singles : %d / %d fitted : %d separated", singles, success, fitted, separated));
    if (separated > 0) {
        IJ.log("Reasons for fit failure :");
        // Start at i=1 to skip FitStatus.OK
        for (int i = 1; i < statusCount.length; i++) {
            if (statusCount[i] != 0)
                IJ.log("  " + names.get(i) + " = " + statusCount[i]);
        }
    }
    refitResults.end();
    MemoryPeakResults.addResults(refitResults);
    source.close();
}

Example 33 with ExtendedGenericDialog

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

the class TraceMolecules method showDialog.

private boolean showDialog() {
    TITLE = outputName + " Molecules";
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
    globalSettings = SettingsManager.loadSettings();
    settings = globalSettings.getClusteringSettings();
    gd.addNumericField("Distance_Threshold (nm)", settings.distanceThreshold, 2);
    gd.addNumericField("Distance_Exclusion (nm)", settings.distanceExclusion, 2);
    gd.addNumericField("Time_Threshold", settings.getTimeThreshold(), 2);
    String[] timeUnits = SettingsManager.getNames((Object[]) ClusteringSettings.TimeUnit.values());
    gd.addChoice("Time_unit", timeUnits, timeUnits[settings.getTimeUnit().ordinal()]);
    String[] traceModes = SettingsManager.getNames((Object[]) TraceManager.TraceMode.values());
    gd.addChoice("Trace_mode", traceModes, traceModes[settings.getTraceMode().ordinal()]);
    gd.addNumericField("Pulse_interval (frames)", settings.pulseInterval, 0);
    gd.addNumericField("Pulse_window (frames)", settings.pulseWindow, 0);
    gd.addCheckbox("Split_pulses", settings.splitPulses);
    gd.addCheckbox("Optimise", settings.optimise);
    gd.addCheckbox("Save_traces", settings.saveTraces);
    gd.addCheckbox("Show_histograms", settings.showHistograms);
    gd.addCheckbox("Save_trace_data", settings.saveTraceData);
    gd.addCheckbox("Refit_option", settings.refitOption);
    if (altKeyDown) {
        gd.addCheckbox("Debug", inputDebugMode);
    }
    gd.showDialog();
    if (gd.wasCanceled() || !readDialog(gd))
        return false;
    // Update the settings
    SettingsManager.saveSettings(globalSettings);
    // Load the results
    results = ResultsManager.loadInputResults(inputOption, true);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        IJ.showStatus("");
        return false;
    }
    // Store exposure time in seconds
    exposureTime = results.getCalibration().getExposureTime() / 1000;
    return true;
}

Example 34 with ExtendedGenericDialog

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

the class TraceMolecules method readDialog.

private boolean readDialog(ExtendedGenericDialog gd) {
    inputOption = ResultsManager.getInputSource(gd);
    settings.distanceThreshold = gd.getNextNumber();
    settings.distanceExclusion = gd.getNextNumber();
    settings.setTimeThreshold(gd.getNextNumber());
    settings.setTimeUnit(gd.getNextChoiceIndex());
    settings.setTraceMode(gd.getNextChoiceIndex());
    settings.pulseInterval = (int) gd.getNextNumber();
    settings.pulseWindow = (int) gd.getNextNumber();
    settings.splitPulses = gd.getNextBoolean();
    settings.optimise = gd.getNextBoolean();
    settings.saveTraces = gd.getNextBoolean();
    settings.showHistograms = gd.getNextBoolean();
    settings.saveTraceData = gd.getNextBoolean();
    settings.refitOption = gd.getNextBoolean();
    if (altKeyDown) {
        debugMode = inputDebugMode = gd.getNextBoolean();
    }
    if (gd.invalidNumber())
        return false;
    if (settings.showHistograms) {
        gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("Select the histograms to display");
        gd.addCheckbox("Remove_outliers", settings.removeOutliers);
        gd.addNumericField("Histogram_bins", settings.histogramBins, 0);
        for (int i = 0; i < displayHistograms.length; i++) gd.addCheckbox(NAMES[i].replace(' ', '_'), displayHistograms[i]);
        gd.showDialog();
        if (gd.wasCanceled())
            return false;
        settings.removeOutliers = gd.getNextBoolean();
        settings.histogramBins = (int) Math.abs(gd.getNextNumber());
        for (int i = 0; i < displayHistograms.length; i++) displayHistograms[i] = gd.getNextBoolean();
    }
    // Check arguments
    try {
        Parameters.isAboveZero("Distance threshold", settings.distanceThreshold);
        Parameters.isAboveZero("Time threshold", settings.getTimeThreshold());
        Parameters.isPositive("Pulse interval", settings.pulseInterval);
        Parameters.isPositive("Pulse window", settings.pulseWindow);
        Parameters.isAboveZero("Histogram bins", settings.histogramBins);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    return true;
}

Example 35 with ExtendedGenericDialog

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

the class CalibrateResults method showInputDialog.

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