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

Example 21 with ExtendedGenericDialog

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

the class DriftCalculator method applyDriftCorrection.

private void applyDriftCorrection(MemoryPeakResults results, double[][] drift) {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Apply drift correction to in-memory results?");
    gd.addChoice("Update_method", UPDATE_METHODS, UPDATE_METHODS[updateMethod]);
    // Option to save the drift unless it was loaded from file
    if (method != DRIFT_FILE)
        gd.addCheckbox("Save_drift", saveDrift);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    updateMethod = gd.getNextChoiceIndex();
    if (method != DRIFT_FILE) {
        saveDrift = gd.getNextBoolean();
        saveDrift(calculatedTimepoints, lastdx, lastdy);
    }
    if (updateMethod == 0)
        return;
    final double[] dx = drift[0];
    final double[] dy = drift[1];
    if (updateMethod == 1) {
        // Update the results in memory
        Utils.log("Applying drift correction to the results set: " + results.getName());
        for (PeakResult r : results) {
            r.params[Gaussian2DFunction.X_POSITION] += dx[r.getFrame()];
            r.params[Gaussian2DFunction.Y_POSITION] += dy[r.getFrame()];
        }
    } else {
        // Create a new set of results
        MemoryPeakResults newResults = new MemoryPeakResults(results.size());
        newResults.copySettings(results);
        newResults.setName(results.getName() + " (Corrected)");
        MemoryPeakResults.addResults(newResults);
        final boolean truncate = updateMethod == 3;
        Utils.log("Creating %sdrift corrected results set: " + newResults.getName(), (truncate) ? "truncated " : "");
        for (PeakResult r : results) {
            if (truncate) {
                if (r.getFrame() < interpolationStart || r.getFrame() > interpolationEnd)
                    continue;
            }
            float[] params = Arrays.copyOf(r.params, r.params.length);
            params[Gaussian2DFunction.X_POSITION] += dx[r.getFrame()];
            params[Gaussian2DFunction.Y_POSITION] += dy[r.getFrame()];
            newResults.addf(r.getFrame(), r.origX, r.origY, r.origValue, r.error, r.noise, params, r.paramsStdDev);
        }
    }
}

Example 22 with ExtendedGenericDialog

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

the class DriftCalculator method showSubImageDialog.

private boolean showSubImageDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Compute the drift using localisation sub-image alignment");
    gd.addNumericField("Frames", frames, 0);
    gd.addSlider("Minimum_localisations", 10, 50, minimimLocalisations);
    gd.addChoice("FFT size", SIZES, reconstructionSize);
    String[] methods = new String[] { AlignImagesFFT.SubPixelMethod.CUBIC.toString(), AlignImagesFFT.SubPixelMethod.GAUSSIAN.toString() };
    gd.addChoice("Sub-pixel_method", methods, subPixelMethod.toString());
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    frames = (int) gd.getNextNumber();
    minimimLocalisations = (int) gd.getNextNumber();
    reconstructionSize = gd.getNextChoice();
    subPixelMethod = (gd.getNextChoiceIndex() == 0) ? AlignImagesFFT.SubPixelMethod.CUBIC : AlignImagesFFT.SubPixelMethod.GAUSSIAN;
    // Check arguments
    try {
        Parameters.isAboveZero("Frames", frames);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    return true;
}

Example 23 with ExtendedGenericDialog

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

the class TraceDiffusion method showDialog.

private boolean showDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    globalSettings = SettingsManager.loadSettings();
    settings = globalSettings.getClusteringSettings();
    gd.addCheckbox("Truncate_traces", settings.truncate);
    gd.addCheckbox("Internal_distances", settings.internalDistances);
    //gd.addCheckbox("Sub-sample_distances", settings.subSampledDistances);
    gd.addSlider("Fit_length", 2, 20, settings.fitLength);
    gd.addCheckbox("MSD_correction", settings.msdCorrection);
    gd.addCheckbox("Precision_correction", settings.precisionCorrection);
    gd.addCheckbox("Maximum_likelihood", settings.mle);
    gd.addSlider("Fit_restarts", 0, 10, settings.fitRestarts);
    gd.addSlider("Jump_distance", 1, 20, settings.jumpDistance);
    gd.addSlider("Minimum_difference", 0, 10, minDifference);
    gd.addSlider("Minimum_fraction", 0, 1, minFraction);
    if (extraOptions)
        gd.addSlider("Minimum_N", 1, 10, minN);
    gd.addSlider("Maximum_N", 2, 10, maxN);
    gd.addCheckbox("Debug_fitting", debugFitting);
    gd.addCheckbox("Save_trace_distances", saveTraceDistances);
    gd.addCheckbox("Save_raw_data", saveRawData);
    gd.addCheckbox("Show_histograms", settings.showHistograms);
    gd.addStringField("Title", title);
    gd.showDialog();
    if (gd.wasCanceled() || !readDialog(gd))
        return false;
    // Update the settings
    SettingsManager.saveSettings(globalSettings);
    return true;
}

Example 24 with ExtendedGenericDialog

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

the class SplitResults method run.

/*
	 * (non-Javadoc)
	 * 
	 * @see ij.plugin.PlugIn#run(java.lang.String)
	 */
public void run(String arg) {
    SMLMUsageTracker.recordPlugin(this.getClass(), arg);
    if (MemoryPeakResults.isMemoryEmpty()) {
        IJ.error(TITLE, "There are no fitting results in memory");
        return;
    }
    String[] items = Utils.getImageList(Utils.GREY_8_16);
    if (items.length == 0) {
        IJ.error(TITLE, "There are no suitable mask images");
        return;
    }
    // Show a dialog allowing the results set to be filtered
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Select a dataset to split");
    ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
    gd.addChoice("Object_mask", items, objectMask);
    gd.addCheckbox("Show_object_mask", showObjectMask);
    gd.addCheckbox("Non_mask_dataset", nonMaskDataset);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    inputOption = ResultsManager.getInputSource(gd);
    objectMask = gd.getNextChoice();
    showObjectMask = gd.getNextBoolean();
    nonMaskDataset = gd.getNextBoolean();
    MemoryPeakResults results = ResultsManager.loadInputResults(inputOption, false);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        return;
    }
    ImagePlus imp = WindowManager.getImage(objectMask);
    if (imp == null) {
        IJ.error(TITLE, "No object mask could be found");
        return;
    }
    splitResults(results, imp.getProcessor());
}

Example 25 with ExtendedGenericDialog

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

the class TraceDiffusion method calculatePrecision.

/**
	 * Calculate the average precision of localisation in the traces
	 * 
	 * @param traces
	 * @param multi
	 */
private void calculatePrecision(Trace[] traces, boolean multi) {
    // Check the diffusion simulation for a precision
    if (DiffusionRateTest.isSimulated(results.getName()) && !multi) {
        precision = DiffusionRateTest.lastSimulatedPrecision;
    } else {
        // Get the average precision of the localisations
        precision = 0;
        final double nmPerPixel = results.getNmPerPixel();
        final double gain = results.getGain();
        final boolean emCCD = results.isEMCCD();
        int n = 0;
        for (Trace trace : traces) {
            for (PeakResult r : trace.getPoints()) precision += r.getPrecision(nmPerPixel, gain, emCCD);
            n += trace.size();
        }
        precision /= n;
    }
    if (precision > 100) {
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.addMessage("The average precision of the traced results is " + Utils.rounded(precision, 4) + " nm.\nPlease verify the precision.");
        gd.addSlider("Precision (nm)", 5, 100, precision);
        gd.showDialog();
        if (!(gd.wasCanceled() || gd.invalidNumber())) {
            precision = Math.abs(gd.getNextNumber());
        }
    }
}