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

Example 6 with NonBlockingExtendedGenericDialog

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

Example 7 with NonBlockingExtendedGenericDialog

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

the class AstigmatismModelManager method getRange.

private boolean getRange() {
    minz = 0;
    maxz = z.length - 1;
    final NonBlockingExtendedGenericDialog gd = new NonBlockingExtendedGenericDialog(TITLE);
    gd.addMessage("Select z-range for curve fit.\n" + "Choose a region with a smooth width curve and low XY drift.");
    gd.addSlider("Min_z", minz, maxz, minz);
    gd.addSlider("Max_z", minz, maxz, maxz);
    gd.addMessage("Curve parameter estimation");
    gd.addSlider("Smoothing", 0.05, 0.5, pluginSettings.getSmoothing());
    gd.addCheckbox("Show_estimated_curve", pluginSettings.getShowEstimatedCurve());
    gd.addMessage("Fit options");
    gd.addCheckbox("Weighted_fit", pluginSettings.getWeightedFit());
    gd.addDialogListener(new ZDialogListener());
    gd.addHelp(HelpUrls.getUrl("astigmatism-model-manager-create"));
    gd.showDialog();
    // Save settings
    writeAstigmatismModelManagerSettings(pluginSettings);
    if (gd.wasCanceled()) {
        return false;
    }
    // Ensure there are enough points to fit
    if (maxz - minz < 10) {
        IJ.error(TITLE, "Not enough points for a curve fit");
        return false;
    }
    // Extract data for fit
    fitZ = Arrays.copyOfRange(z, minz, maxz + 1);
    fitSx = Arrays.copyOfRange(sx, minz, maxz + 1);
    fitSy = Arrays.copyOfRange(sy, minz, maxz + 1);
    return true;
}

Example 8 with NonBlockingExtendedGenericDialog

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

the class BackgroundEstimator method showDialog.

@Override
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
    settings = Settings.load();
    // Save now as this just updates the reference held in memory
    settings.save();
    // If using a stack, provide a preview graph of the noise for two methods
    if (imp.getStackSize() > 1) {
        this.pfr = pfr;
        drawPlot();
        final NonBlockingExtendedGenericDialog gd = new NonBlockingExtendedGenericDialog(TITLE);
        gd.addHelp(HelpUrls.getUrl("background-estimator"));
        gd.addSlider("Percential", 0, 100, settings.percentile);
        gd.addChoice("Noise_method", SettingsManager.getNoiseEstimatorMethodNames(), settings.noiseMethod.ordinal());
        // For background based on pixel below a threshold
        final String[] thresholdMethods = AutoThreshold.getMethods(true);
        gd.addChoice("Threshold_method", thresholdMethods, thresholdMethods[settings.thresholdMethod.ordinal() - 1]);
        gd.addSlider("Fraction", 0, 0.999, settings.fraction);
        gd.addNumericField("Histogram_size", settings.histogramSize, 0);
        gd.addDialogListener(this);
        gd.addMessage("Click OK to compute table for all slices");
        gd.showDialog();
        if (gd.wasCanceled() || !dialogItemChanged(gd, null)) {
            return DONE;
        }
    }
    return IJ.setupDialog(imp, FLAGS);
}

Example 9 with NonBlockingExtendedGenericDialog

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

the class SpotFinderPreview method showDialog.

@Override
public int showDialog(ImagePlus imp, String command, PlugInFilterRunner pfr) {
    settings = Settings.load();
    this.overlay = imp.getOverlay();
    this.imp = imp;
    // Saved by reference so do it once now
    settings.save();
    // The image is locked by the PlugInFilterRunner so unlock it to allow scroll.
    // This should be OK as the image data is not modified and only the overlay is
    // adjusted. If another plugin changes the image then the preview should update
    // the overlay and it will be obvious to the user to turn this plugin off.
    imp.unlock();
    config = SettingsManager.readFitEngineConfiguration(0);
    fitConfig = config.getFitConfiguration();
    gd = new NonBlockingExtendedGenericDialog(TITLE);
    gd.addHelp(HelpUrls.getUrl("spot-finder-preview"));
    gd.addMessage("Preview candidate maxima");
    final String[] templates = ConfigurationTemplate.getTemplateNames(true);
    gd.addChoice("Template", templates, templates[0]);
    final String[] models = CameraModelManager.listCameraModels(true);
    gd.addChoice("Camera_model_name", models, fitConfig.getCameraModelName());
    PeakFit.addPsfOptions(gd, (FitConfigurationProvider) () -> fitConfig);
    final PeakFit.SimpleFitEngineConfigurationProvider provider = new PeakFit.SimpleFitEngineConfigurationProvider(config);
    PeakFit.addDataFilterOptions(gd, provider);
    gd.addChoice("Spot_filter_2", SettingsManager.getDataFilterMethodNames(), config.getDataFilterMethod(1, settings.defaultDataFilterMethod).ordinal());
    PeakFit.addRelativeParameterOptions(gd, new RelativeParameterProvider(2.5, 4.5, "Smoothing_2", provider) {

        @Override
        void setAbsolute(boolean absolute) {
            final FitEngineConfiguration c = fitEngineConfigurationProvider.getFitEngineConfiguration();
            final DataFilterMethod m = c.getDataFilterMethod(1, settings.defaultDataFilterMethod);
            final double smooth = c.getDataFilterParameterValue(1, settings.defaultSmooth);
            c.setDataFilter(m, smooth, absolute, 1);
        }

        @Override
        boolean isAbsolute() {
            return fitEngineConfigurationProvider.getFitEngineConfiguration().getDataFilterParameterAbsolute(1, false);
        }

        @Override
        double getValue() {
            return fitEngineConfigurationProvider.getFitEngineConfiguration().getDataFilterParameterValue(1, settings.defaultSmooth);
        }
    });
    PeakFit.addSearchOptions(gd, provider);
    PeakFit.addBorderOptions(gd, provider);
    // Find if this image was created with ground truth data
    if (imp.getID() == CreateData.getImageId()) {
        final MemoryPeakResults results = CreateData.getResults();
        if (results != null) {
            gd.addSlider("Match_distance", 0, 2.5, settings.distance);
            gd.addSlider("Lower_match_distance (%)", 0, 100, settings.lowerDistance);
            gd.addCheckbox("Multiple_matches", settings.multipleMatches);
            gd.addCheckbox("Show_TP", settings.showTP);
            gd.addCheckbox("Show_FP", settings.showFP);
            gd.addMessage("");
            label = (Label) gd.getMessage();
            final boolean integerCoords = false;
            actualCoordinates = ResultsMatchCalculator.getCoordinates(results, integerCoords);
        }
    }
    if (label == null) {
        // If no ground truth data add options to show the spots by their rank
        // and number of neighbours
        gd.addSlider("Top_N", 0, 100, settings.topN);
        topNScrollBar = gd.getLastScrollbar();
        gd.addSlider("Select", 0, 100, settings.select);
        selectScrollBar = gd.getLastScrollbar();
        gd.addSlider("Neigbour_radius", 0, 10, settings.neighbourRadius);
    }
    ImageListener imageListener = null;
    if (ImageJUtils.isShowGenericDialog()) {
        // Listen for changes in the dialog options
        gd.addOptionCollectedListener(event -> {
            // Just run on the current processor
            if (preview) {
                run(imp.getProcessor());
            }
        });
        // Listen for changes to an image
        imageListener = new ImageAdapter() {

            @Override
            public void imageUpdated(ImagePlus imp) {
                if (SpotFinderPreview.this.imp.getID() == imp.getID() && preview && imp.getCurrentSlice() != currentSlice && filter != null) {
                    run(imp.getProcessor(), filter);
                }
            }
        };
        ImagePlus.addImageListener(imageListener);
        // Support template settings
        final Vector<TextField> numerics = gd.getNumericFields();
        final Vector<Choice> choices = gd.getChoices();
        final Iterator<TextField> nu = numerics.iterator();
        final Iterator<Choice> ch = choices.iterator();
        final Choice textTemplate = ch.next();
        textTemplate.removeItemListener(gd);
        textTemplate.removeKeyListener(gd);
        textTemplate.addItemListener(this::itemStateChanged);
        textCameraModelName = ch.next();
        textPsf = ch.next();
        textDataFilterType = ch.next();
        textDataFilterMethod = ch.next();
        textSmooth = nu.next();
        textDataFilterMethod2 = ch.next();
        textSmooth2 = nu.next();
        textSearch = nu.next();
        textBorder = nu.next();
    }
    gd.addPreviewCheckbox(pfr);
    gd.addDialogListener(this::dialogItemChanged);
    gd.setOKLabel("Save");
    gd.setCancelLabel("Close");
    gd.showDialog();
    if (imageListener != null) {
        ImagePlus.removeImageListener(imageListener);
    }
    if (!gd.wasCanceled() && !SettingsManager.writeSettings(config, SettingsManager.FLAG_SILENT)) {
        IJ.error(TITLE, "Failed to save settings");
    }
    // Reset
    imp.setOverlay(overlay);
    return DONE;
}

Example 10 with NonBlockingExtendedGenericDialog

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

the class TraceLengthAnalysis method run.

@Override
public void run(String arg) {
    SmlmUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "No localisations in memory");
        return;
    }
    if (!showDialog()) {
        return;
    }
    // Load the results
    MemoryPeakResults results = ResultsManager.loadInputResults(settings.inputOption, false, null, null);
    if (MemoryPeakResults.isEmpty(results)) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    try {
        distanceConverter = results.getDistanceConverter(DistanceUnit.UM);
        timeConverter = results.getTimeConverter(TimeUnit.SECOND);
    } catch (final Exception ex) {
        IJ.error(TITLE, "Cannot convert units to um or seconds: " + ex.getMessage());
        return;
    }
    // Get the localisation error (4s^2) in raw units^2
    double precision = 0;
    try {
        final PrecisionResultProcedure p = new PrecisionResultProcedure(results);
        p.getPrecision();
        // Precision in nm using the median
        precision = new Percentile().evaluate(p.precisions, 50);
        // Convert from nm to um to raw units
        final double rawPrecision = distanceConverter.convertBack(precision / 1e3);
        // Get the localisation error (4s^2) in units^2
        error = 4 * rawPrecision * rawPrecision;
    } catch (final Exception ex) {
        ImageJUtils.log(TITLE + " - Unable to compute precision: " + ex.getMessage());
    }
    // Analyse the track lengths
    results = results.copy();
    results.sort(IdFramePeakResultComparator.INSTANCE);
    // Ensure the first result triggers an id change
    lastid = results.getFirst().getId() - 1;
    results.forEach(this::processTrackLength);
    // For the final track
    store();
    msds = msdList.toArray();
    lengths = lengthList.toArray();
    ids = idList.toArray();
    final int[] limits = MathUtils.limits(lengths);
    h1 = new int[limits[1] + 1];
    h2 = new int[h1.length];
    x1 = SimpleArrayUtils.newArray(h1.length, 0, 1f);
    y1 = new float[x1.length];
    y2 = new float[x1.length];
    // Sort by MSD
    final int[] indices = SimpleArrayUtils.natural(msds.length);
    SortUtils.sortIndices(indices, msds, false);
    final double[] msds2 = msds.clone();
    final int[] lengths2 = lengths.clone();
    final int[] ids2 = ids.clone();
    for (int i = 0; i < indices.length; i++) {
        msds[i] = msds2[indices[i]];
        lengths[i] = lengths2[indices[i]];
        ids[i] = ids2[indices[i]];
    }
    // Interactive analysis
    final NonBlockingExtendedGenericDialog gd = new NonBlockingExtendedGenericDialog(TITLE);
    ImageJUtils.addMessage(gd, "Split traces into fixed or moving using the track diffusion coefficient (D).\n" + "Localisation error has been subtracted from jumps (%s nm).", MathUtils.rounded(precision));
    final Statistics s = Statistics.create(msds);
    final double av = s.getMean();
    final String msg = String.format("Average D per track = %s um^2/s", MathUtils.rounded(av));
    gd.addMessage(msg);
    // Histogram the diffusion coefficients
    final WindowOrganiser wo = new WindowOrganiser();
    final HistogramPlot histogramPlot = new HistogramPlotBuilder("Trace diffusion coefficient", StoredData.create(msds), "D (um^2/s)").setRemoveOutliersOption(1).setPlotLabel(msg).build();
    histogramPlot.show(wo);
    final double[] xvalues = histogramPlot.getPlotXValues();
    final double min = xvalues[0];
    final double max = xvalues[xvalues.length - 1];
    // see if we can build a nice slider range from the histogram limits
    if (max - min < 5) {
        // Because sliders are used when the range is <5 and floating point
        gd.addSlider("D_threshold", min, max, settings.msdThreshold);
    } else {
        gd.addNumericField("D_threshold", settings.msdThreshold, 2, 6, "um^2/s");
    }
    gd.addCheckbox("Normalise", settings.normalise);
    gd.addDialogListener((gd1, event) -> {
        settings.msdThreshold = gd1.getNextNumber();
        settings.normalise = gd1.getNextBoolean();
        update();
        return true;
    });
    if (ImageJUtils.isShowGenericDialog()) {
        draw(wo);
        wo.tile();
    }
    gd.setOKLabel("Save datasets");
    gd.setCancelLabel("Close");
    gd.addHelp(HelpUrls.getUrl("trace-length-analysis"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    // Sort by ID
    final PeakResult[] list = results.toArray();
    Arrays.sort(list, IdFramePeakResultComparator.INSTANCE);
    createResults(results, "Fixed", 0, lastIndex, list);
    createResults(results, "Moving", lastIndex, msds.length, list);
}