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

Example 11 with PlotWindow

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

the class PsfCreator method plotCumulativeSignal.

/**
 * Show a plot of the cumulative signal vs distance from the centre.
 *
 * @param z The slice to plot
 * @param normalise normalise the sum to 1
 * @param resetScale Reset the y-axis maximum
 * @param distanceThreshold The distance threshold for the cumulative total shown in the plot
 *        label
 */
private void plotCumulativeSignal(int z, boolean normalise, boolean resetScale, double distanceThreshold) {
    final float[] data = (float[]) psf.getProcessor(z).getPixels();
    final int size = psf.getWidth();
    if (indexLookup == null || indexLookup.length != data.length) {
        // Precompute square distances
        final double[] d2 = new double[size];
        for (int y = 0, y2 = -size / 2; y < size; y++, y2++) {
            d2[y] = y2 * y2;
        }
        // Precompute distances
        final double[] d = new double[data.length];
        for (int y = 0, i = 0; y < size; y++) {
            for (int x = 0; x < size; x++, i++) {
                d[i] = Math.sqrt(d2[y] + d2[x]);
            }
        }
        // Sort
        final int[] indices = SimpleArrayUtils.natural(d.length);
        SortUtils.sortData(indices, d, true, false);
        // Store a unique cumulative index for each distance
        double lastD = d[0];
        int lastI = 0;
        int counter = 0;
        final StoredData distance = new StoredData();
        indexLookup = new int[indices.length];
        for (int i = 0; i < indices.length; i++) {
            if (lastD != d[i]) {
                distance.add(lastD * psfNmPerPixel);
                for (int j = lastI; j < i; j++) {
                    indexLookup[indices[j]] = counter;
                }
                lastD = d[i];
                lastI = i;
                counter++;
            }
        }
        // Do the final distance
        distance.add(lastD * psfNmPerPixel);
        for (int j = lastI; j < indices.length; j++) {
            indexLookup[indices[j]] = counter;
        }
        counter++;
        distances = distance.getValues();
    }
    // Get the signal at each distance
    final double[] signal = new double[distances.length];
    for (int i = 0; i < data.length; i++) {
        if (data[i] > 0) {
            signal[indexLookup[i]] += data[i];
        }
    }
    // Get the cumulative signal
    for (int i = 1; i < signal.length; i++) {
        signal[i] += signal[i - 1];
    }
    // Get the total up to the distance threshold
    double sum = 0;
    for (int i = 0; i < signal.length; i++) {
        if (distances[i] > distanceThreshold) {
            break;
        }
        sum = signal[i];
    }
    if (normalise && distanceThreshold > 0) {
        for (int i = 0; i < signal.length; i++) {
            signal[i] /= sum;
        }
    }
    if (resetScale) {
        maxCumulativeSignal = 0;
    }
    maxCumulativeSignal = MathUtils.maxDefault(maxCumulativeSignal, signal);
    final String title = "Cumulative Signal";
    final boolean alignWindows = (WindowManager.getFrame(title) == null);
    final Plot plot = new Plot(title, "Distance (nm)", "Signal");
    plot.addPoints(distances, signal, Plot.LINE);
    plot.setLimits(0, distances[distances.length - 1], 0, maxCumulativeSignal);
    plot.addLabel(0, 0, String.format("Total = %s (@ %s nm). z = %s nm", MathUtils.rounded(sum), MathUtils.rounded(distanceThreshold), MathUtils.rounded((z - zCentre) * settings.getNmPerSlice())));
    plot.setColor(Color.green);
    plot.drawLine(distanceThreshold, 0, distanceThreshold, maxCumulativeSignal);
    plot.setColor(Color.blue);
    final PlotWindow plotWindow = ImageJUtils.display(title, plot);
    if (alignWindows && plotWindow != null) {
        final PlotWindow otherWindow = getPlot(TITLE_PSF_PARAMETERS);
        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 + otherWindow.getHeight();
            plotWindow.setLocation(l);
        }
    }
    // Update the PSF to the correct slice
    if (psfImp != null) {
        psfImp.setSlice(z);
    }
}

Example 12 with PlotWindow

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

the class PsfCreator method showPlots.

private void showPlots(final double[] z, final double[] a, final double[] smoothAz, final double[] smoothA, final double[] xCoord, final double[] yCoord, final double[] sd, final double[] newZ, final double[] smoothX, final double[] smoothY, double[] smoothSd, final int cz) {
    PlotWindow amplitudeWindow = null;
    // Draw a plot of the amplitude
    if (a != null) {
        final Plot plot = new Plot(TITLE_AMPLITUDE, "z", "Amplitude");
        plot.addPoints(smoothAz, smoothA, Plot.LINE);
        final double[] limits2 = MathUtils.limits(MathUtils.limits(a), smoothA);
        plot.setLimits(z[0], z[z.length - 1], limits2[0], limits2[1]);
        plot.addPoints(z, a, Plot.CIRCLE);
        // Add a line for the z-centre
        plot.setColor(Color.GREEN);
        plot.addPoints(new double[] { cz, cz }, limits2, Plot.LINE);
        plot.setColor(Color.BLACK);
        double amplitude = Double.NaN;
        for (int i = 0; i < smoothAz.length; i++) {
            if (smoothAz[i] == cz) {
                amplitude = smoothA[i];
                break;
            }
        }
        double maxAmplitude = Double.NaN;
        for (int i = 0; i < smoothAz.length; i++) {
            if (smoothAz[i] == zCentre) {
                maxAmplitude = smoothA[i];
                break;
            }
        }
        plot.addLabel(0, 0, String.format("Amplitude = %s (%sx). z = %s nm", MathUtils.rounded(amplitude), MathUtils.rounded(amplitude / maxAmplitude), MathUtils.rounded((slice - zCentre) * settings.getNmPerSlice())));
        amplitudeWindow = ImageJUtils.display(TITLE_AMPLITUDE, plot);
    }
    // Show plot of width, X centre, Y centre
    if (xCoord != null) {
        final Plot plot = new Plot(TITLE_PSF_PARAMETERS, "z", "px");
        plot.addPoints(newZ, smoothSd, Plot.LINE);
        // Get the limits
        final double[] sd2 = invert(sd);
        final double[] limits = MathUtils.limits(MathUtils.limits(MathUtils.limits(MathUtils.limits(xCoord), yCoord), sd), sd2);
        plot.setLimits(z[0], z[z.length - 1], limits[0], limits[1]);
        plot.addPoints(newZ, invert(smoothSd), Plot.LINE);
        plot.addPoints(z, sd, Plot.DOT);
        plot.addPoints(z, sd2, Plot.DOT);
        plot.setColor(Color.BLUE);
        plot.addPoints(z, xCoord, Plot.DOT);
        plot.addPoints(newZ, smoothX, Plot.LINE);
        plot.setColor(Color.RED);
        plot.addPoints(z, yCoord, Plot.DOT);
        plot.addPoints(newZ, smoothY, Plot.LINE);
        // Add a line for the z-centre
        plot.setColor(Color.GREEN);
        plot.addPoints(new double[] { cz, cz }, limits, Plot.LINE);
        plot.setColor(Color.BLACK);
        double width = Double.NaN;
        for (int i = 0; i < smoothSd.length; i++) {
            if (newZ[i] == cz) {
                width = smoothSd[i];
                break;
            }
        }
        plot.addLabel(0, 0, String.format("Width = %s nm (%sx). z = %s nm", MathUtils.rounded(width * nmPerPixel), MathUtils.rounded(width * nmPerPixel / psfWidth), MathUtils.rounded((slice - zCentre) * settings.getNmPerSlice())));
        // Check if the window will need to be aligned
        final boolean alignWindows = (WindowManager.getFrame(TITLE_PSF_PARAMETERS) == null);
        final PlotWindow psfWindow = ImageJUtils.display(TITLE_PSF_PARAMETERS, plot);
        if (alignWindows && psfWindow != null && amplitudeWindow != null) {
            // Put the two plots tiled together so both are visible
            final Point l = psfWindow.getLocation();
            l.x = amplitudeWindow.getLocation().x;
            l.y = amplitudeWindow.getLocation().y + amplitudeWindow.getHeight();
            psfWindow.setLocation(l);
        }
    }
}

Example 13 with PlotWindow

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

the class FilterAnalysis method showPlots.

private void showPlots() {
    if (plots.isEmpty()) {
        return;
    }
    // Display the top N plots
    final int[] list = new int[plots.size()];
    int index = 0;
    for (final NamedPlot p : plots) {
        final Plot plot = new Plot(p.name, p.xAxisName, "Jaccard");
        plot.addPoints(p.xValues, p.yValues, Plot.LINE);
        plot.setLimits(p.xValues[0], p.xValues[p.xValues.length - 1], 0, 1);
        plot.setColor(Color.RED);
        plot.draw();
        plot.setColor(Color.BLUE);
        plot.addPoints(p.xValues, p.yValues, Plot.CROSS);
        final PlotWindow plotWindow = ImageJUtils.display(p.name, plot);
        list[index++] = plotWindow.getImagePlus().getID();
    }
    WindowOrganiser.tileWindows(list);
}

Example 14 with PlotWindow

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

the class EmGainAnalysis method plotPmf.

@SuppressWarnings("unused")
private void plotPmf() {
    if (!showPmfDialog()) {
        return;
    }
    final double step = getStepSize(settings.settingPhotons, settings.settingGain, settings.settingNoise);
    final Pdf pdf = pdf(0, step, settings.settingPhotons, settings.settingGain, settings.settingNoise);
    double[] pmf = pdf.probability;
    double yMax = MathUtils.max(pmf);
    // Get the approximation
    LikelihoodFunction fun;
    switch(settings.approximationType) {
        case 3:
            fun = new PoissonFunction(1.0 / settings.settingGain);
            break;
        case 2:
            // Use adaptive normalisation
            fun = PoissonGaussianFunction2.createWithStandardDeviation(1.0 / settings.settingGain, settings.settingNoise);
            break;
        case 1:
            // Create Poisson-Gamma (no Gaussian noise)
            fun = createPoissonGammaGaussianFunction(0);
            break;
        case 0:
        default:
            fun = createPoissonGammaGaussianFunction(settings.settingNoise);
    }
    double expected = settings.settingPhotons;
    if (settings.settingOffset != 0) {
        expected += settings.settingOffset * expected / 100.0;
    }
    // Normalise
    final boolean normalise = false;
    if (normalise) {
        final double sum = MathUtils.sum(pmf);
        for (int i = pmf.length; i-- > 0; ) {
            pmf[i] /= sum;
        }
    }
    // Get CDF
    double sum = 0;
    double sum2 = 0;
    double[] x = pdf.x;
    double[] fvalues = new double[x.length];
    double[] cdf1 = new double[pmf.length];
    double[] cdf2 = new double[pmf.length];
    for (int i = 0; i < cdf1.length; i++) {
        sum += pmf[i] * step;
        cdf1[i] = sum;
        fvalues[i] = fun.likelihood(x[i], expected);
        sum2 += fvalues[i] * step;
        cdf2[i] = sum2;
    }
    // Truncate x for plotting
    int max = 0;
    double plimit = 1 - settings.tail;
    while (sum < plimit && max < pmf.length) {
        sum += pmf[max] * step;
        if (sum > 0.5 && pmf[max] == 0) {
            break;
        }
        max++;
    }
    int min = pmf.length;
    sum = 0;
    plimit = 1 - settings.head;
    while (sum < plimit && min > 0) {
        min--;
        sum += pmf[min] * step;
        if (sum > 0.5 && pmf[min] == 0) {
            break;
        }
    }
    pmf = Arrays.copyOfRange(pmf, min, max);
    x = Arrays.copyOfRange(x, min, max);
    fvalues = Arrays.copyOfRange(fvalues, min, max);
    if (settings.showApproximation) {
        yMax = MathUtils.maxDefault(yMax, fvalues);
    }
    final String label = String.format("Gain=%s, noise=%s, photons=%s", MathUtils.rounded(settings.settingGain), MathUtils.rounded(settings.settingNoise), MathUtils.rounded(settings.settingPhotons));
    final Plot plot = new Plot("PMF", "ADUs", "p");
    plot.setLimits(x[0], x[x.length - 1], 0, yMax);
    plot.setColor(Color.red);
    plot.addPoints(x, pmf, Plot.LINE);
    if (settings.showApproximation) {
        plot.setColor(Color.blue);
        plot.addPoints(x, fvalues, Plot.LINE);
    }
    plot.setColor(Color.magenta);
    plot.drawLine(settings.settingPhotons * settings.settingGain, 0, settings.settingPhotons * settings.settingGain, yMax);
    plot.setColor(Color.black);
    plot.addLabel(0, 0, label);
    final PlotWindow win1 = ImageJUtils.display("PMF", plot);
    // Plot the difference between the actual and approximation
    final double[] delta = new double[fvalues.length];
    for (int i = 0; i < fvalues.length; i++) {
        if (pmf[i] == 0 && fvalues[i] == 0) {
            continue;
        }
        if (settings.relativeDelta) {
            delta[i] = DoubleEquality.relativeError(fvalues[i], pmf[i]) * Math.signum(fvalues[i] - pmf[i]);
        } else {
            delta[i] = fvalues[i] - pmf[i];
        }
    }
    final Plot plot2 = new Plot("PMF delta", "ADUs", (settings.relativeDelta) ? "Relative delta" : "delta");
    final double[] limits = MathUtils.limits(delta);
    plot2.setLimits(x[0], x[x.length - 1], limits[0], limits[1]);
    plot2.setColor(Color.red);
    plot2.addPoints(x, delta, Plot.LINE);
    plot2.setColor(Color.magenta);
    plot2.drawLine(settings.settingPhotons * settings.settingGain, limits[0], settings.settingPhotons * settings.settingGain, limits[1]);
    plot2.setColor(Color.black);
    plot2.addLabel(0, 0, label + ((settings.settingOffset == 0) ? "" : ", expected = " + MathUtils.rounded(expected / settings.settingGain)));
    final WindowOrganiser wo = new WindowOrganiser();
    final PlotWindow win2 = ImageJUtils.display("PMF delta", plot2, wo);
    if (wo.isNotEmpty()) {
        final Point p2 = win1.getLocation();
        p2.y += win1.getHeight();
        win2.setLocation(p2);
    }
    // Plot the CDF of each distribution.
    // Compute the Kolmogorov distance as the supremum (maximum)
    // difference between the two cumulative probability distributions.
    // https://en.wikipedia.org/wiki/Kolmogorov%E2%80%93Smirnov_test
    double kolmogorovDistance = 0;
    double xd = x[0];
    for (int i = 0; i < cdf1.length; i++) {
        final double dist = Math.abs(cdf1[i] - cdf2[i]);
        if (kolmogorovDistance < dist) {
            kolmogorovDistance = dist;
            xd = pdf.x[i];
        }
    }
    cdf1 = Arrays.copyOfRange(cdf1, min, max);
    cdf2 = Arrays.copyOfRange(cdf2, min, max);
    final Plot plot3 = new Plot("CDF", "ADUs", "p");
    yMax = 1.05;
    plot3.setLimits(x[0], x[x.length - 1], 0, yMax);
    plot3.setColor(Color.red);
    plot3.addPoints(x, cdf1, Plot.LINE);
    plot3.setColor(Color.blue);
    plot3.addPoints(x, cdf2, Plot.LINE);
    plot3.setColor(Color.magenta);
    plot3.drawLine(settings.settingPhotons * settings.settingGain, 0, settings.settingPhotons * settings.settingGain, yMax);
    plot3.drawDottedLine(xd, 0, xd, yMax, 2);
    plot3.setColor(Color.black);
    plot3.addLabel(0, 0, label + ", Kolmogorov distance = " + MathUtils.rounded(kolmogorovDistance) + " @ " + xd);
    plot3.addLegend("CDF\nApprox");
    final int size = wo.size();
    final PlotWindow win3 = ImageJUtils.display("CDF", plot3, wo);
    if (size != wo.size()) {
        final Point p2 = win1.getLocation();
        p2.x += win1.getWidth();
        win3.setLocation(p2);
    }
}

Example 15 with PlotWindow

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

the class BenchmarkFilterAnalysis method showPlots.

private void showPlots() {
    if (filterAnalysisResult.plots.isEmpty()) {
        return;
    }
    // Display the top N plots
    final int[] list = new int[filterAnalysisResult.plots.size()];
    int index = 0;
    for (final NamedPlot p : filterAnalysisResult.plots) {
        final Plot plot = new Plot(p.name, p.xAxisName, Settings.COLUMNS[settings.scoreIndex]);
        plot.setLimits(p.xValues[0], p.xValues[p.xValues.length - 1], 0, 1);
        plot.setColor(Color.RED);
        plot.addPoints(p.xValues, p.yValues, Plot.LINE);
        plot.setColor(Color.BLUE);
        plot.addPoints(p.xValues, p.yValues, Plot.CROSS);
        final PlotWindow plotWindow = ImageJUtils.display(p.name, plot);
        list[index++] = plotWindow.getImagePlus().getID();
    }
    WindowOrganiser.tileWindows(list);
}