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

Example 26 with PlotWindow

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

the class TcPalmAnalysis method runPlot.

/**
 * Create the activations and total activations plots.
 *
 * @param settings the settings
 */
private void runPlot(TcPalmAnalysisSettings settings) {
    final WindowOrganiser wo = new WindowOrganiser();
    String timeLabel = "Time";
    UnaryOperator<float[]> timeConverter;
    double timeScale;
    if (settings.getTimeInSeconds()) {
        timeLabel += " (s)";
        timeScale = 1.0 / results.getCalibration().getTimeCalibration().getExposureTime();
        timeConverter = frames -> {
            SimpleArrayUtils.apply(frames, f -> f *= timeScale);
            return frames;
        };
    } else {
        timeLabel += " (frame)";
        timeConverter = UnaryOperator.identity();
        timeScale = 1;
    }
    final CumulativeCountData data = this.countData;
    String title = TITLE + " Activations vs Time";
    final Plot plot1 = new Plot(title, timeLabel, "Count");
    plot1.addLabel(0, 0, TextUtils.pleural(clusters.size(), "cluster"));
    for (int i = 0; i < data.frames.length; i++) {
        final int t = data.frames[i];
        final int c = data.counts[i];
        plot1.addPoints(timeConverter.apply(new float[] { t, t }), new float[] { 0, c }, Plot.LINE);
    }
    plot1.draw();
    plot1.setLimitsToFit(true);
    if (settings.getFixedTimeAxis()) {
        final double[] limits = plot1.getLimits();
        limits[0] = timeScale * (minT - 1);
        limits[1] = timeScale * (maxT + 1);
        plot1.setLimits(limits);
        plot1.updateImage();
    }
    final PlotWindow pw1 = ImageJUtils.display(title, plot1, ImageJUtils.NO_TO_FRONT, wo);
    title = TITLE + " Total Activations vs Time";
    final Plot plot2 = new Plot(title, timeLabel, "Cumulative count");
    final int localisations = data.counts.length == 0 ? 0 : data.plotCounts[data.plotCounts.length - 1];
    final int clashes = localisations - data.counts.length;
    plot2.addLabel(0, 0, TextUtils.pleural(localisations, "localisation") + " : " + clashes + TextUtils.pleuralise(clashes, " clash", " clashes"));
    plot2.addPoints(timeConverter.apply(SimpleArrayUtils.toFloat(data.plotFrames)), SimpleArrayUtils.toFloat(data.plotCounts), Plot.LINE);
    if (settings.getFixedTimeAxis()) {
        plot2.setLimits(timeScale * (minT - 1), timeScale * (maxT + 1), Double.NaN, Double.NaN);
    }
    final PlotWindow pw2 = ImageJUtils.display(title, plot2, ImageJUtils.NO_TO_FRONT, wo);
    activationsPlotData = new ActivationsPlotData(plot2, timeConverter, data);
    // Simple tile one window above the other only if both are new.
    if (wo.size() == 2) {
        final Point p = pw1.getLocation();
        p.y += pw1.getHeight();
        pw2.setLocation(p);
    }
}

Example 27 with PlotWindow

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

the class DriftCalculator method plotDrift.

private static PlotWindow plotDrift(PlotWindow parent, double[][] interpolated, double[][] original, String name, int index) {
    // Create plot
    final double[] xlimits = MathUtils.limits(interpolated[0]);
    double[] ylimits = MathUtils.limits(original[index]);
    ylimits = MathUtils.limits(ylimits, interpolated[index]);
    final Plot plot = new Plot(name, "Frame", "Drift (px)");
    plot.setLimits(xlimits[0], xlimits[1], ylimits[0], ylimits[1]);
    // De-saturated blue
    plot.setColor(new Color(0, 0, 155));
    plot.addPoints(original[0], original[index], Plot.CROSS);
    plot.setColor(java.awt.Color.RED);
    plot.addPoints(interpolated[0], interpolated[index], Plot.LINE);
    final WindowOrganiser wo = new WindowOrganiser();
    final PlotWindow window = ImageJUtils.display(name, plot, wo);
    if (wo.isNotEmpty() && parent != null) {
        final Point location = parent.getLocation();
        location.y += parent.getHeight();
        window.setLocation(location);
    }
    return window;
}

Example 28 with PlotWindow

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

the class DriftCalculator method plotDrift.

private void plotDrift(int[] limits, double[] dx, double[] dy) {
    if (!settings.plotDrift) {
        return;
    }
    // Build an array of timepoints from the min to the max
    final double[] completeT = new double[limits[1] + 1];
    for (int i = limits[0]; i < completeT.length; i++) {
        completeT[i] = i;
    }
    // Drift should be centred around zero for the calculated points to produce a fair plot
    normalise(lastdx, calculatedTimepoints);
    normalise(lastdy, calculatedTimepoints);
    // Extract the interpolated points and the original drift
    final double[][] interpolated = extractValues(dx, limits[0], limits[1], dx, dy);
    final double[][] original = extractValues(calculatedTimepoints, limits[0], limits[1], lastdx, lastdy);
    final PlotWindow window = plotDrift(null, interpolated, original, "Drift X", 1);
    ploty.set(plotDrift(window, interpolated, original, "Drift Y", 2));
    plotx.set(window);
}

Example 29 with PlotWindow

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

the class PsfDrift method showHwhm.

private void showHwhm() {
    // Build a list of suitable images
    final List<String> titles = createImageList(false);
    if (titles.isEmpty()) {
        IJ.error(TITLE, "No suitable PSF images");
        return;
    }
    final GenericDialog gd = new GenericDialog(TITLE);
    gd.addMessage("Approximate the volume of the PSF as a Gaussian and\n" + "compute the equivalent Gaussian width.");
    settings = Settings.load();
    gd.addChoice("PSF", titles.toArray(new String[0]), settings.title);
    gd.addCheckbox("Use_offset", settings.useOffset);
    gd.addSlider("Smoothing", 0, 0.5, settings.smoothing);
    gd.addHelp(HelpUrls.getUrl("psf-hwhm"));
    gd.showDialog();
    if (gd.wasCanceled()) {
        return;
    }
    settings.title = gd.getNextChoice();
    settings.useOffset = gd.getNextBoolean();
    settings.smoothing = gd.getNextNumber();
    settings.save();
    imp = WindowManager.getImage(settings.title);
    if (imp == null) {
        IJ.error(TITLE, "No PSF image for image: " + settings.title);
        return;
    }
    psfSettings = getPsfSettings(imp);
    if (psfSettings == null) {
        IJ.error(TITLE, "No PSF settings for image: " + settings.title);
        return;
    }
    final int size = imp.getStackSize();
    final ImagePsfModel psf = createImagePsf(1, size, 1);
    final double[] w0 = psf.getAllHwhm0();
    final double[] w1 = psf.getAllHwhm1();
    // Get current centre
    final int centre = psfSettings.getCentreImage();
    // Extract valid values (some can be NaN)
    double[] sw0 = new double[w0.length];
    double[] sw1 = new double[w1.length];
    final TDoubleArrayList s0 = new TDoubleArrayList(w0.length);
    final TDoubleArrayList s1 = new TDoubleArrayList(w0.length);
    int c0 = 0;
    int c1 = 0;
    for (int i = 0; i < w0.length; i++) {
        if (Double.isFinite(w0[i])) {
            s0.add(i + 1);
            sw0[c0++] = w0[i];
        }
        if (Double.isFinite(w1[i])) {
            s1.add(i + 1);
            sw1[c1++] = w1[i];
        }
    }
    if (c0 == 0 && c1 == 0) {
        IJ.error(TITLE, "No computed HWHM for image: " + settings.title);
        return;
    }
    double[] slice0 = s0.toArray();
    sw0 = Arrays.copyOf(sw0, c0);
    double[] slice1 = s1.toArray();
    sw1 = Arrays.copyOf(sw1, c1);
    // Smooth
    if (settings.smoothing > 0) {
        final LoessInterpolator loess = new LoessInterpolator(settings.smoothing, 1);
        sw0 = loess.smooth(slice0, sw0);
        sw1 = loess.smooth(slice1, sw1);
    }
    final TDoubleArrayList minWx = new TDoubleArrayList();
    final TDoubleArrayList minWy = new TDoubleArrayList();
    for (int i = 0; i < w0.length; i++) {
        double weight = 0;
        if (Double.isFinite(w0[i])) {
            if (Double.isFinite(w1[i])) {
                weight = w0[i] * w1[i];
            } else {
                weight = w0[i] * w0[i];
            }
        } else if (Double.isFinite(w1[i])) {
            weight = w1[i] * w1[i];
        }
        if (weight != 0) {
            minWx.add(i + 1);
            minWy.add(Math.sqrt(weight));
        }
    }
    // Smooth the combined line
    final double[] cx = minWx.toArray();
    double[] cy = minWy.toArray();
    if (settings.smoothing > 0) {
        final LoessInterpolator loess = new LoessInterpolator(settings.smoothing, 1);
        cy = loess.smooth(cx, cy);
    }
    final int newCentre = SimpleArrayUtils.findMinIndex(cy);
    // Convert to FWHM
    final double fwhm = psfSettings.getFwhm();
    // Widths are in pixels
    final String title = TITLE + " HWHM";
    final Plot plot = new Plot(title, "Slice", "HWHM (px)");
    double[] limits = MathUtils.limits(sw0);
    limits = MathUtils.limits(limits, sw1);
    final double maxY = limits[1] * 1.05;
    plot.setLimits(1, size, 0, maxY);
    plot.setColor(Color.red);
    plot.addPoints(slice0, sw0, Plot.LINE);
    plot.setColor(Color.blue);
    plot.addPoints(slice1, sw1, Plot.LINE);
    plot.setColor(Color.magenta);
    plot.addPoints(cx, cy, Plot.LINE);
    plot.setColor(Color.black);
    plot.addLabel(0, 0, "X=red; Y=blue, Combined=Magenta");
    final PlotWindow pw = ImageJUtils.display(title, plot);
    // Show a non-blocking dialog to allow the centre to be updated ...
    // Add a label and dynamically update when the centre is moved.
    final NonBlockingExtendedGenericDialog gd2 = new NonBlockingExtendedGenericDialog(TITLE);
    final double scale = psfSettings.getPixelSize();
    // @formatter:off
    ImageJUtils.addMessage(gd2, "Update the PSF information?\n \n" + "Current z-centre = %d, FHWM = %s px (%s nm)\n", centre, MathUtils.rounded(fwhm), MathUtils.rounded(fwhm * scale));
    // @formatter:on
    gd2.addSlider("z-centre", cx[0], cx[cx.length - 1], newCentre);
    final TextField tf = gd2.getLastTextField();
    gd2.addMessage("");
    gd2.addAndGetButton("Reset", event -> tf.setText(Integer.toString(newCentre)));
    final Label label = gd2.getLastLabel();
    gd2.addCheckbox("Update_centre", settings.updateCentre);
    gd2.addCheckbox("Update_HWHM", settings.updateHwhm);
    gd2.enableYesNoCancel();
    gd2.hideCancelButton();
    final UpdateDialogListener dl = new UpdateDialogListener(cx, cy, maxY, newCentre, scale, pw, label);
    gd2.addDialogListener(dl);
    gd.addHelp(HelpUrls.getUrl("psf-hwhm"));
    gd2.showDialog();
    if (gd2.wasOKed() && (settings.updateCentre || settings.updateHwhm)) {
        final ImagePSF.Builder b = psfSettings.toBuilder();
        if (settings.updateCentre) {
            b.setCentreImage(dl.centre);
        }
        if (settings.updateHwhm) {
            b.setFwhm(dl.getFwhm());
        }
        imp.setProperty("Info", ImagePsfHelper.toString(b));
    }
}

Example 30 with PlotWindow

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

the class PsfCreator method plotSignalAtSpecifiedSd.

/**
 * Show a plot of the amount of signal within N x SD for each z position. This indicates how much
 * the PSF has spread from the original Gaussian shape.
 *
 * @param psf The PSF
 * @param fittedSd The width of the PSF (in pixels)
 * @param factor The factor to use
 * @param slice The slice used to create the label
 */
private void plotSignalAtSpecifiedSd(ImageStack psf, double fittedSd, double factor, int slice) {
    if (signalZ == null) {
        // Get the bounds
        final int radius = (int) Math.round(fittedSd * factor);
        final int min = Math.max(0, psf.getWidth() / 2 - radius);
        final int max = Math.min(psf.getWidth() - 1, psf.getWidth() / 2 + radius);
        // Create a circle mask of the PSF projection
        final ByteProcessor circle = new ByteProcessor(max - min + 1, max - min + 1);
        circle.setColor(255);
        circle.fillOval(0, 0, circle.getWidth(), circle.getHeight());
        final byte[] mask = (byte[]) circle.getPixels();
        // Sum the pixels within the mask for each slice
        signalZ = new double[psf.getSize()];
        signal = new double[psf.getSize()];
        for (int i = 0; i < psf.getSize(); i++) {
            double sum = 0;
            final float[] data = (float[]) psf.getProcessor(i + 1).getPixels();
            for (int y = min, ii = 0; y <= max; y++) {
                int index = y * psf.getWidth() + min;
                for (int x = min; x <= max; x++, ii++, index++) {
                    if (mask[ii] != 0 && data[index] > 0) {
                        sum += data[index];
                    }
                }
            }
            double total = 0;
            for (final float f : data) {
                if (f > 0) {
                    total += f;
                }
            }
            signalZ[i] = i + 1;
            signal[i] = 100 * sum / total;
        }
        signalTitle = String.format("%% PSF signal at %s x SD", MathUtils.rounded(factor, 3));
        signalLimits = MathUtils.limits(signal);
    }
    // Plot the sum
    final boolean alignWindows = (WindowManager.getFrame(signalTitle) == null);
    final double total = signal[slice - 1];
    final Plot plot = new Plot(signalTitle, "z", "Signal");
    plot.addPoints(signalZ, signal, Plot.LINE);
    plot.addLabel(0, 0, String.format("Total = %s. z = %s nm", MathUtils.rounded(total), MathUtils.rounded((slice - zCentre) * settings.getNmPerSlice())));
    plot.setColor(Color.green);
    plot.drawLine(slice, signalLimits[0], slice, signalLimits[1]);
    plot.setColor(Color.blue);
    final PlotWindow plotWindow = ImageJUtils.display(signalTitle, plot);
    if (alignWindows && plotWindow != null) {
        final PlotWindow otherWindow = getPlot(TITLE_AMPLITUDE);
        if (otherWindow != null) {
            // Put the two plots tiled together so both are visible
            final Point l = plotWindow.getLocation();
            l.x = otherWindow.getLocation().x + otherWindow.getWidth();
            l.y = otherWindow.getLocation().y;
            plotWindow.setLocation(l);
        }
    }
}