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

Example 16 with ExtendedGenericDialog

use of 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
	 */
private void computeRipleysPlot(MemoryPeakResults results) {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Compute Ripley's L(r) - r plot");
    gd.addNumericField("Min_radius", minR, 2);
    gd.addNumericField("Max_radius", maxR, 2);
    gd.addNumericField("Increment", incrementR, 2);
    gd.addCheckbox("Confidence_intervals", confidenceIntervals);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    minR = gd.getNextNumber();
    maxR = gd.getNextNumber();
    incrementR = gd.getNextNumber();
    confidenceIntervals = gd.getNextBoolean();
    if (minR > maxR || incrementR < 0 || gd.invalidNumber()) {
        IJ.error(TITLE, "Invalid radius parameters");
        return;
    }
    DensityManager dm = createDensityManager(results);
    double[][] values = calculateLScores(dm);
    // 99% confidence intervals
    final int iterations = (confidenceIntervals) ? 99 : 0;
    double[] upper = null;
    double[] lower = null;
    Rectangle bounds = results.getBounds();
    // Use a uniform distribution for the coordinates
    HaltonSequenceGenerator dist = new HaltonSequenceGenerator(2);
    dist.skipTo(new Well19937c(System.currentTimeMillis() + System.identityHashCode(this)).nextInt());
    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
        float[] x = new float[results.size()];
        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);
        }
        double[][] values2 = calculateLScores(new DensityManager(x, y, bounds));
        if (upper == null) {
            upper = values2[1];
            lower = new double[upper.length];
            System.arraycopy(upper, 0, lower, 0, upper.length);
        } 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];
            }
        }
    }
    String title = results.getName() + " Ripley's (L(r) - r) / r";
    Plot2 plot = new Plot2(title, "Radius", "(L(r) - r) / r", values[0], values[1]);
    // 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);
    }
    Utils.display(title, plot);
}

Example 17 with ExtendedGenericDialog

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

the class CropResults 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;
    }
    // Show a dialog allowing the results set to be filtered
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addMessage("Select a dataset to crop");
    ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
    gd.showDialog();
    if (gd.wasCanceled())
        return;
    inputOption = ResultsManager.getInputSource(gd);
    results = ResultsManager.loadInputResults(inputOption, false);
    if (results == null || results.size() == 0) {
        IJ.error(TITLE, "No results could be loaded");
        IJ.showStatus("");
        return;
    }
    if (!showDialog())
        return;
    cropResults();
}

Example 18 with ExtendedGenericDialog

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

the class DrawClusters method showDialog.

private boolean showDialog() {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    ArrayList<String> titles = new ArrayList<String>(WindowManager.getImageCount());
    titles.add("[None]");
    int[] idList = WindowManager.getIDList();
    if (idList != null)
        for (int id : idList) {
            ImagePlus imp = WindowManager.getImage(id);
            if (imp != null)
                titles.add(imp.getTitle());
        }
    gd.addMessage("Draw the clusters on an image");
    ResultsManager.addInput(gd, "Input", inputOption, InputSource.MEMORY_CLUSTERED);
    gd.addChoice("Image", titles.toArray(new String[0]), title);
    gd.addNumericField("Image_size", imageSize, 0);
    gd.addCheckbox("Expand_to_singles", expandToSingles);
    gd.addSlider("Min_size", 1, 15, minSize);
    gd.addSlider("Max_size", 0, 20, maxSize);
    gd.addCheckbox("Traces (draw lines)", drawLines);
    gd.addChoice("Sort", sorts, sorts[sort]);
    gd.addCheckbox("Spline_fit (traces only)", splineFit);
    gd.addCheckbox("Use_stack_position", useStackPosition);
    gd.addChoice("LUT", LUTHelper.luts, LUTHelper.luts[lut]);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    inputOption = ResultsManager.getInputSource(gd);
    title = gd.getNextChoice();
    imageSize = (int) Math.abs(gd.getNextNumber());
    expandToSingles = gd.getNextBoolean();
    minSize = (int) Math.abs(gd.getNextNumber());
    maxSize = (int) Math.abs(gd.getNextNumber());
    drawLines = gd.getNextBoolean();
    sort = gd.getNextChoiceIndex();
    splineFit = gd.getNextBoolean();
    useStackPosition = gd.getNextBoolean();
    lut = gd.getNextChoiceIndex();
    return true;
}

Example 19 with ExtendedGenericDialog

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

the class DriftCalculator method showStackDialog.

private ImageStack showStackDialog(String[] stackTitles) {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Compute the drift using a reference stack alignment");
    gd.addChoice("Stack_image", stackTitles, stackTitle);
    gd.addMessage("Frame = previous + spacing");
    gd.addNumericField("Start_frame", startFrame, 0);
    gd.addSlider("Frame_spacing", 1, 20, frameSpacing);
    String[] methods = ImageProcessor.getInterpolationMethods();
    gd.addChoice("Interpolation_method", methods, methods[interpolationMethod]);
    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 null;
    stackTitle = gd.getNextChoice();
    startFrame = (int) gd.getNextNumber();
    frameSpacing = (int) gd.getNextNumber();
    interpolationMethod = gd.getNextChoiceIndex();
    subPixelMethod = (gd.getNextChoiceIndex() == 0) ? AlignImagesFFT.SubPixelMethod.CUBIC : AlignImagesFFT.SubPixelMethod.GAUSSIAN;
    try {
        Parameters.isAboveZero("Start frame", startFrame);
        Parameters.isAboveZero("Frame spacing", frameSpacing);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return null;
    }
    ImagePlus imp = WindowManager.getImage(stackTitle);
    if (imp != null && imp.getStackSize() > 1)
        return imp.getImageStack();
    return null;
}

Example 20 with ExtendedGenericDialog

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

the class DriftCalculator method showDialog.

private boolean showDialog(Roi[] rois, String[] stackTitles) {
    ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
    gd.addHelp(About.HELP_URL);
    gd.addMessage("Correct the drift in localisation results");
    ResultsManager.addInput(gd, inputOption, InputSource.MEMORY);
    ArrayList<String> methods = new ArrayList<String>(4);
    methods.add(SUB_IMAGE_ALIGNMENT);
    methods.add(DRIFT_FILE);
    if (rois != null)
        methods.add(MARKED_ROIS);
    if (stackTitles != null)
        methods.add(STACK_ALIGNMENT);
    String[] items = methods.toArray(new String[methods.size()]);
    gd.addChoice("Method", items, method);
    gd.addMessage("Stopping criteria");
    gd.addSlider("Max_iterations", 0, 100, maxIterations);
    gd.addNumericField("Relative_error", relativeError, 3);
    gd.addMessage("LOESS smoothing parameters");
    gd.addSlider("Smoothing", 0.001, 1, smoothing);
    gd.addCheckbox("Limit_smoothing", limitSmoothing);
    gd.addSlider("Min_smoothing_points", 5, 50, minSmoothingPoints);
    gd.addSlider("Max_smoothing_points", 5, 50, maxSmoothingPoints);
    gd.addSlider("Smoothing_iterations", 1, 10, iterations);
    gd.addCheckbox("Plot_drift", plotDrift);
    gd.showDialog();
    if (gd.wasCanceled())
        return false;
    inputOption = ResultsManager.getInputSource(gd);
    method = gd.getNextChoice();
    maxIterations = (int) gd.getNextNumber();
    relativeError = gd.getNextNumber();
    smoothing = gd.getNextNumber();
    limitSmoothing = gd.getNextBoolean();
    minSmoothingPoints = (int) gd.getNextNumber();
    maxSmoothingPoints = (int) gd.getNextNumber();
    iterations = (int) gd.getNextNumber();
    plotDrift = gd.getNextBoolean();
    // Check arguments
    try {
        Parameters.isPositive("Max iterations", maxIterations);
        Parameters.isAboveZero("Relative error", relativeError);
        Parameters.isPositive("Smoothing", smoothing);
        if (limitSmoothing) {
            Parameters.isEqualOrAbove("Min smoothing points", minSmoothingPoints, 3);
            Parameters.isEqualOrAbove("Max smoothing points", maxSmoothingPoints, 3);
            Parameters.isEqualOrAbove("Max smoothing points", maxSmoothingPoints, minSmoothingPoints);
        }
        Parameters.isEqualOrBelow("Smoothing", smoothing, 1);
        Parameters.isPositive("Smoothing iterations", iterations);
    } catch (IllegalArgumentException e) {
        IJ.error(TITLE, e.getMessage());
        return false;
    }
    return true;
}