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

Example 61 with ExtendedGenericDialog

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

the class FailCountManager method showAnalysisDialog.

private boolean showAnalysisDialog() {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage(TextUtils.wrap("Analysis a set of fail counters on the current pass/fail data.", 80));
    gd.addSlider("Target_pass_fraction", 0.1, 1, settings.getTargetPassFraction());
    gd.addSliderIncludeDefault("Table_top_n", 0, 100, settings.getTableTopN());
    gd.addNumericField("Rolling_counter_min_allowed_failures", settings.getRollingCounterMinAllowedFailures(), 0);
    gd.addNumericField("Rolling_counter_max_allowed_failures", settings.getRollingCounterMaxAllowedFailures(), 0);
    gd.addNumericField("Rolling_counter_min_window", settings.getRollingCounterMinWindow(), 0);
    gd.addNumericField("Rolling_counter_max_window", settings.getRollingCounterMaxWindow(), 0);
    gd.addNumericField("Weighted_counter_min_allowed_failures", settings.getWeightedCounterMinAllowedFailures(), 0);
    gd.addNumericField("Weighted_counter_max_allowed_failures", settings.getWeightedCounterMaxAllowedFailures(), 0);
    gd.addNumericField("Weighted_counter_min_pass_decrement", settings.getWeightedCounterMinPassDecrement(), 0);
    gd.addNumericField("Weighted_counter_max_pass_decrement", settings.getWeightedCounterMaxPassDecrement(), 0);
    gd.addNumericField("Resetting_counter_min_allowed_failures", settings.getResettingCounterMinAllowedFailures(), 0);
    gd.addNumericField("Resetting_counter_max_allowed_failures", settings.getResettingCounterMaxAllowedFailures(), 0);
    gd.addNumericField("Resetting_counter_min_pass_decrement", settings.getResettingCounterMinResetFraction(), 2);
    gd.addNumericField("Resetting_counter_max_pass_decrement", settings.getResettingCounterMaxResetFraction(), 2);
    gd.addNumericField("Resetting_counter_inc_pass_decrement", settings.getResettingCounterIncResetFraction(), 2);
    gd.addNumericField("Pass_rate_counter_min_allowed_failures", settings.getPassRateCounterMinAllowedCounts(), 0);
    gd.addNumericField("Pass_rate_counter_max_allowed_failures", settings.getPassRateCounterMaxAllowedCounts(), 0);
    gd.addNumericField("Pass_rate_counter_min_pass_rate", settings.getPassRateCounterMinPassRate(), 3);
    gd.addNumericField("Pass_rate_counter_max_pass_rate", settings.getPassRateCounterMaxPassRate(), 3);
    gd.addNumericField("Pass_rate_counter_inc_pass_rate", settings.getPassRateCounterIncPassRate(), 3);
    gd.addHelp(HelpUrls.getUrl("fail-count-manager-analysis"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.setTargetPassFraction(gd.getNextNumber());
    settings.setTableTopN((int) gd.getNextNumber());
    settings.setRollingCounterMinAllowedFailures((int) gd.getNextNumber());
    settings.setRollingCounterMaxAllowedFailures((int) gd.getNextNumber());
    settings.setRollingCounterMinWindow((int) gd.getNextNumber());
    settings.setRollingCounterMaxWindow((int) gd.getNextNumber());
    settings.setWeightedCounterMinAllowedFailures((int) gd.getNextNumber());
    settings.setWeightedCounterMaxAllowedFailures((int) gd.getNextNumber());
    settings.setWeightedCounterMinPassDecrement((int) gd.getNextNumber());
    settings.setWeightedCounterMaxPassDecrement((int) gd.getNextNumber());
    settings.setResettingCounterMinAllowedFailures((int) gd.getNextNumber());
    settings.setResettingCounterMaxAllowedFailures((int) gd.getNextNumber());
    settings.setResettingCounterMinResetFraction(gd.getNextNumber());
    settings.setResettingCounterMaxResetFraction(gd.getNextNumber());
    settings.setResettingCounterIncResetFraction(gd.getNextNumber());
    settings.setPassRateCounterMinAllowedCounts((int) gd.getNextNumber());
    settings.setPassRateCounterMaxAllowedCounts((int) gd.getNextNumber());
    settings.setPassRateCounterMinPassRate(gd.getNextNumber());
    settings.setPassRateCounterMaxPassRate(gd.getNextNumber());
    settings.setPassRateCounterIncPassRate(gd.getNextNumber());
    try {
        ParameterUtils.isAboveZero("Target pass fraction", settings.getTargetPassFraction());
        ParameterUtils.isAboveZero("Resetting counter inc pass decrement", settings.getResettingCounterIncResetFraction());
        ParameterUtils.isAboveZero("Pass rate counter inc pass rate", settings.getPassRateCounterIncPassRate());
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    return true;
}

Example 62 with ExtendedGenericDialog

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

the class DensityImage method computeRipleysPlot.

/**
 * Compute the Ripley's L-function for user selected radii and show it on a plot.
 *
 * @param results the results
 */
private void computeRipleysPlot(MemoryPeakResults results) {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Compute Ripley's L(r) - r plot");
    gd.addNumericField("Min_radius", settings.minR, 2);
    gd.addNumericField("Max_radius", settings.maxR, 2);
    gd.addNumericField("Increment", settings.incrementR, 2);
    gd.addCheckbox("Confidence_intervals", settings.confidenceIntervals);
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    settings.minR = gd.getNextNumber();
    settings.maxR = gd.getNextNumber();
    settings.incrementR = gd.getNextNumber();
    settings.confidenceIntervals = gd.getNextBoolean();
    if (settings.minR > settings.maxR || settings.incrementR < 0 || gd.invalidNumber()) {
        IJ.error(TITLE, "Invalid radius parameters");
        return;
    }
    final DensityManager dm = createDensityManager(results);
    final double[][] values = calculateLScores(dm);
    // 99% confidence intervals
    final int iterations = (settings.confidenceIntervals) ? 99 : 0;
    double[] upper = null;
    double[] lower = null;
    final Rectangle bounds = results.getBounds();
    final double area = (double) bounds.width * bounds.height;
    // Use a uniform distribution for the coordinates
    final HaltonSequenceGenerator dist = new HaltonSequenceGenerator(2);
    dist.skipTo(SeedFactory.createInt());
    for (int i = 0; i < iterations; i++) {
        IJ.showProgress(i, iterations);
        IJ.showStatus(String.format("L-score confidence interval %d / %d", i + 1, iterations));
        // Randomise coordinates
        final float[] x = new float[results.size()];
        final float[] y = new float[x.length];
        for (int j = x.length; j-- > 0; ) {
            final double[] d = dist.nextVector();
            x[j] = (float) (d[0] * bounds.width);
            y[j] = (float) (d[1] * bounds.height);
        }
        final double[][] values2 = calculateLScores(new DensityManager(x, y, area));
        if (upper == null || lower == null) {
            upper = values2[1];
            lower = upper.clone();
        } else {
            for (int m = upper.length; m-- > 0; ) {
                if (upper[m] < values2[1][m]) {
                    upper[m] = values2[1][m];
                }
                if (lower[m] > values2[1][m]) {
                    lower[m] = values2[1][m];
                }
            }
        }
    }
    final String title = results.getName() + " Ripley's (L(r) - r) / r";
    final Plot plot = new Plot(title, "Radius", "(L(r) - r) / r");
    plot.addPoints(values[0], values[1], Plot.LINE);
    // Get the limits
    double yMin = min(0, values[1]);
    double yMax = max(0, values[1]);
    if (iterations > 0) {
        yMin = min(yMin, lower);
        yMax = max(yMax, upper);
    }
    plot.setLimits(0, values[0][values[0].length - 1], yMin, yMax);
    if (iterations > 0) {
        plot.setColor(Color.BLUE);
        plot.addPoints(values[0], upper, 1);
        plot.setColor(Color.RED);
        plot.addPoints(values[0], lower, 1);
        plot.setColor(Color.BLACK);
    }
    ImageJUtils.display(title, plot);
}

Example 63 with ExtendedGenericDialog

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

the class DensityImage method showDialog.

private boolean showDialog() {
    settings = Settings.load();
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("density-image"));
    // Build a list of all images with a region ROI
    final List<String> titles = new LinkedList<>();
    for (final int imageId : ImageJUtils.getIdList()) {
        final ImagePlus imp = WindowManager.getImage(imageId);
        if (imp != null && imp.getRoi() != null && imp.getRoi().isArea()) {
            titles.add(imp.getTitle());
        }
    }
    gd.addMessage("Show an image using the localisation density");
    ResultsManager.addInput(gd, settings.inputOption, InputSource.MEMORY);
    gd.addNumericField("Radius", settings.radius, 3);
    if (!titles.isEmpty()) {
        gd.addCheckbox((titles.size() == 1) ? "Use_ROI" : "Choose_ROI", settings.chooseRoi);
    }
    gd.addCheckbox("Adjust_for_border", settings.adjustForBorder);
    gd.addSlider("Image_Scale", 1, 15, settings.imageScale);
    gd.addCheckbox("Cumulative_image", settings.cumulativeImage);
    gd.addCheckbox("Use_square_approx", settings.useSquareApproximation);
    gd.addNumericField("Square_resolution", settings.resolution, 0);
    gd.addChoice("Score", Settings.scoreMethods, settings.scoreMethodIndex);
    gd.addMessage("Filter localisations using the L-score / Relative density.\n" + "Filtered results will be added to memory:");
    gd.addCheckbox("Filter_localisations", settings.filterLocalisations);
    gd.addNumericField("Filter_threshold", settings.filterThreshold, 2);
    gd.addCheckbox("Compute_Ripleys_L_plot", settings.computeRipleysPlot);
    gd.showDialog();
    if (gd.wasCanceled()) {
        return false;
    }
    settings.inputOption = ResultsManager.getInputSource(gd);
    settings.radius = (float) gd.getNextNumber();
    if (!titles.isEmpty()) {
        settings.chooseRoi = gd.getNextBoolean();
    }
    settings.adjustForBorder = gd.getNextBoolean();
    settings.imageScale = (int) gd.getNextNumber();
    settings.cumulativeImage = gd.getNextBoolean();
    settings.useSquareApproximation = gd.getNextBoolean();
    settings.resolution = (int) gd.getNextNumber();
    settings.scoreMethodIndex = gd.getNextChoiceIndex();
    settings.filterLocalisations = gd.getNextBoolean();
    settings.filterThreshold = gd.getNextNumber();
    settings.computeRipleysPlot = gd.getNextBoolean();
    settings.save();
    // Check arguments
    try {
        ParameterUtils.isAboveZero("Radius", settings.radius);
        ParameterUtils.isAboveZero("Image scale", settings.imageScale);
        ParameterUtils.isAboveZero("Resolution", settings.resolution);
    } catch (final IllegalArgumentException ex) {
        IJ.error(TITLE, ex.getMessage());
        return false;
    }
    if (!titles.isEmpty() && settings.chooseRoi) {
        if (titles.size() == 1) {
            settings.roiImage = titles.get(0);
            Recorder.recordOption("Image", settings.roiImage);
        } else {
            final String[] items = titles.toArray(new String[0]);
            gd = new ExtendedGenericDialog(TITLE);
            gd.addMessage("Select the source image for the ROI");
            gd.addChoice("Image", items, settings.roiImage);
            gd.showDialog();
            if (gd.wasCanceled()) {
                return false;
            }
            settings.roiImage = gd.getNextChoice();
        }
        final ImagePlus imp = WindowManager.getImage(settings.roiImage);
        roiBounds = imp.getRoi().getBounds();
        roiImageWidth = imp.getWidth();
        roiImageHeight = imp.getHeight();
    } else {
        roiBounds = null;
    }
    return true;
}

Example 64 with ExtendedGenericDialog

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

the class DriftCalculator method applyDriftCorrection.

private void applyDriftCorrection(MemoryPeakResults results, double[][] drift) {
    final ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Apply drift correction to in-memory results?");
    gd.addChoice("Update_method", Settings.UPDATE_METHODS, settings.updateMethod);
    // Option to save the drift unless it was loaded from file
    if (!Settings.DRIFT_FILE.equals(settings.method)) {
        gd.addCheckbox("Save_drift", settings.saveDrift);
    }
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    settings.updateMethod = gd.getNextChoiceIndex();
    if (!Settings.DRIFT_FILE.equals(settings.method)) {
        settings.saveDrift = gd.getNextBoolean();
        saveDrift(calculatedTimepoints, lastdx, lastdy);
    }
    if (settings.updateMethod == 0) {
        return;
    }
    final double[] dx = drift[0];
    final double[] dy = drift[1];
    if (settings.updateMethod == 1) {
        // Update the results in memory
        ImageJUtils.log("Applying drift correction to the results set: " + results.getName());
        results.forEach((PeakResultProcedure) result -> {
            result.setXPosition((float) (result.getXPosition() + dx[result.getFrame()]));
            result.setYPosition((float) (result.getYPosition() + dy[result.getFrame()]));
        });
    } else {
        // Create a new set of results
        final MemoryPeakResults newResults = new MemoryPeakResults(results.size());
        newResults.copySettings(results);
        newResults.setName(results.getName() + " (Corrected)");
        MemoryPeakResults.addResults(newResults);
        final boolean truncate = settings.updateMethod == 3;
        ImageJUtils.log("Creating %sdrift corrected results set: " + newResults.getName(), (truncate) ? "truncated " : "");
        results.forEach((PeakResultProcedure) result -> {
            if (truncate && (result.getFrame() < interpolationStart || result.getFrame() > interpolationEnd)) {
                return;
            }
            result.setXPosition((float) (result.getXPosition() + dx[result.getFrame()]));
            result.setYPosition((float) (result.getYPosition() + dy[result.getFrame()]));
            newResults.add(result);
        });
    }
}

Example 65 with ExtendedGenericDialog

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

the class CameraModelAnalysis method showDialog.

@Override
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
    settings = SettingsManager.readCameraModelAnalysisSettings(0).toBuilder();
    gd = new NonBlockingExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("camera-model-analysis"));
    gd.addMessage("Simulate on-chip camera applification.");
    gd.addNumericField("Photons", settings.getPhotons(), 2);
    gd.addChoice("Mode", MODE, settings.getMode(), new OptionListener<Integer>() {

        @Override
        public boolean collectOptions(Integer value) {
            settings.setMode(value);
            return collectOptions(false);
        }

        @Override
        public boolean collectOptions() {
            return collectOptions(true);
        }

        private boolean collectOptions(boolean silent) {
            final int mode = settings.getMode();
            final ExtendedGenericDialog egd = new ExtendedGenericDialog(TITLE);
            if (mode == MODE_CCD) {
                egd.addNumericField("Gain", settings.getGain(), 2, 6, "Count/electrons");
                egd.addNumericField("Noise", settings.getNoise(), 2, 6, "Count");
            } else if (mode == MODE_EM_CCD) {
                egd.addNumericField("Gain", settings.getEmGain(), 2, 6, "Count/electrons");
                egd.addNumericField("Noise", settings.getEmNoise(), 2, 6, "Count");
                egd.addNumericField("EM_samples", settings.getEmSamples(), 0);
            } else if (mode == MODE_SCMOS) {
                egd.addNumericField("Gain", settings.getCmosGain(), 2, 6, "Count/electrons");
                egd.addNumericField("Noise", settings.getCmosNoise(), 2, 6, "Count");
            } else {
                throw new IllegalStateException();
            }
            egd.setSilent(silent);
            egd.showDialog(true, gd);
            if (egd.wasCanceled()) {
                return false;
            }
            if (mode == MODE_CCD) {
                settings.setGain(egd.getNextNumber());
                settings.setNoise(egd.getNextNumber());
            } else if (mode == MODE_EM_CCD) {
                settings.setEmGain(egd.getNextNumber());
                settings.setEmNoise(egd.getNextNumber());
                settings.setEmSamples(Math.max(1, (int) egd.getNextNumber()));
            } else {
                // MODE_SCMOS
                settings.setCmosGain(egd.getNextNumber());
                settings.setCmosNoise(egd.getNextNumber());
            }
            return true;
        }
    });
    if (extraOptions) {
        gd.addNumericField("Seed", settings.getSeed(), 0);
    }
    gd.addNumericField("Samples", settings.getSamples(), 0);
    gd.addNumericField("Noise_samples", settings.getNoiseSamples(), 0);
    gd.addCheckbox("Round_down", settings.getRoundDown());
    gd.addChoice("Model", MODEL, settings.getModel());
    gd.addCheckbox("Full_integration", settings.getSimpsonIntegration());
    gd.addOptionCollectedListener(this::optionCollected);
    gd.addDialogListener(this::dialogItemChanged);
    gd.addPreviewCheckbox(pfr);
    gd.showDialog();
    SettingsManager.writeSettings(settings);
    if (!gd.wasCanceled() && dirty) {
        execute();
    }
    return DONE;
}