Examples with Plot2 ij.gui.Plot2 used on opensource projects

Example 16 with Plot2

use of ij.gui.Plot2 in project GDSC-SMLM by aherbert.

the class BenchmarkFilterAnalysis method scoreAnalysis.

/**
	 * Score analysis.
	 *
	 * @param allAssignments
	 *            The assignments generated from running the filter (or null)
	 * @param filter
	 *            the filter
	 * @return the assignments
	 */
private ArrayList<FractionalAssignment[]> scoreAnalysis(ArrayList<FractionalAssignment[]> allAssignments, DirectFilter filter) {
    if (!scoreAnalysis)
        return null;
    // Build a histogram of the fitted spots that were available to be scored
    double[] signal = signalFactorStats.getValues();
    double[] distance = distanceStats.getValues();
    double[] limits1;
    if (BenchmarkSpotFit.signalFactor > 0 && upperSignalFactor > 0) {
        double range = BenchmarkSpotFit.signalFactor * upperSignalFactor / 100.0;
        limits1 = new double[] { -range, range };
    } else {
        limits1 = Maths.limits(signal);
        // Prevent the auto-range being too big
        final double bound = 3;
        if (limits1[0] < -bound)
            limits1[0] = -bound;
        if (limits1[1] > bound)
            limits1[1] = bound;
    }
    double[] limits2;
    if (BenchmarkSpotFit.distanceInPixels > 0 && upperMatchDistance > 0) {
        double range = simulationParameters.a * BenchmarkSpotFit.distanceInPixels * upperMatchDistance / 100.0;
        limits2 = new double[] { 0, range };
    } else {
        limits2 = Maths.limits(distance);
    }
    //final int bins = Math.max(10, nActual / 100);
    //final int bins = Utils.getBinsSturges(signal.length);
    final int bins = Utils.getBinsSqrt(signal.length);
    double[][] h1 = Utils.calcHistogram(signal, limits1[0], limits1[1], bins);
    double[][] h2 = Utils.calcHistogram(distance, limits2[0], limits2[1], bins);
    // Run the filter manually to get the results that pass.
    if (allAssignments == null)
        allAssignments = getAssignments(filter);
    double[] signal2 = new double[results.size()];
    double[] distance2 = new double[results.size()];
    int count = 0;
    double sumSignal = 0, sumDistance = 0;
    for (FractionalAssignment[] assignments : allAssignments) {
        if (assignments == null)
            continue;
        for (int i = 0; i < assignments.length; i++) {
            final CustomFractionalAssignment c = (CustomFractionalAssignment) assignments[i];
            sumDistance += distance2[count] = c.d;
            sumSignal += signal2[count] = c.getSignalFactor();
            count++;
        }
    }
    signal2 = Arrays.copyOf(signal2, count);
    distance2 = Arrays.copyOf(distance2, count);
    // Build a histogram using the same limits
    double[][] h1b = Utils.calcHistogram(signal2, limits1[0], limits1[1], bins);
    double[][] h2b = Utils.calcHistogram(distance2, limits2[0], limits2[1], bins);
    // Since the distance and signal factor are computed for all fits (single, multi, doublet)
    // there will be far more of them so we normalise and just plot the histogram profile.
    double s1 = 0, s2 = 0, s1b = 0, s2b = 0;
    for (int i = 0; i < h1b[0].length; i++) {
        s1 += h1[1][i];
        s2 += h2[1][i];
        s1b += h1b[1][i];
        s2b += h2b[1][i];
    }
    for (int i = 0; i < h1b[0].length; i++) {
        h1[1][i] /= s1;
        h2[1][i] /= s2;
        h1b[1][i] /= s1b;
        h2b[1][i] /= s2b;
    }
    // Draw distance histogram first
    String title2 = TITLE + " Distance Histogram";
    Plot2 plot2 = new Plot2(title2, "Distance (nm)", "Frequency");
    plot2.setLimits(limits2[0], limits2[1], 0, Maths.maxDefault(Maths.max(h2[1]), h2b[1]));
    plot2.setColor(Color.black);
    plot2.addLabel(0, 0, String.format("Blue = Fitted (%s); Red = Filtered (%s)", Utils.rounded(distanceStats.getMean()), Utils.rounded(sumDistance / count)));
    plot2.setColor(Color.blue);
    plot2.addPoints(h2[0], h2[1], Plot2.BAR);
    plot2.setColor(Color.red);
    plot2.addPoints(h2b[0], h2b[1], Plot2.BAR);
    PlotWindow pw2 = Utils.display(title2, plot2);
    if (Utils.isNewWindow())
        wo.add(pw2);
    // Draw signal factor histogram
    String title1 = TITLE + " Signal Factor Histogram";
    Plot2 plot1 = new Plot2(title1, "Signal Factor", "Frequency");
    plot1.setLimits(limits1[0], limits1[1], 0, Maths.maxDefault(Maths.max(h1[1]), h1b[1]));
    plot1.setColor(Color.black);
    plot1.addLabel(0, 0, String.format("Blue = Fitted (%s); Red = Filtered (%s)", Utils.rounded(signalFactorStats.getMean()), Utils.rounded(sumSignal / count)));
    plot1.setColor(Color.blue);
    plot1.addPoints(h1[0], h1[1], Plot2.BAR);
    plot1.setColor(Color.red);
    plot1.addPoints(h1b[0], h1b[1], Plot2.BAR);
    PlotWindow pw1 = Utils.display(title1, plot1);
    if (Utils.isNewWindow())
        wo.add(pw1);
    return allAssignments;
}

Example 17 with Plot2

use of ij.gui.Plot2 in project GDSC-SMLM by aherbert.

the class BackgroundEstimator method plot.

private void plot(WindowOrganiser wo, double[] xValues, double[] data1, double[] data2, double[] data3, String title, String title1, String title2, String title3) {
    // Get limits
    double[] a = Maths.limits(xValues);
    double[] b = Maths.limits(data1);
    b = Maths.limits(b, data2);
    if (data3 != null)
        b = Maths.limits(b, data3);
    title = imp.getTitle() + " " + title;
    Plot2 plot = new Plot2(title, "Slice", title);
    double range = b[1] - b[0];
    if (range == 0)
        range = 1;
    plot.setLimits(a[0], a[1], b[0] - 0.05 * range, b[1] + 0.05 * range);
    plot.setColor(Color.blue);
    plot.addPoints(xValues, data1, Plot2.LINE);
    plot.draw();
    Statistics stats = new Statistics(data1);
    String label = String.format("%s (Blue) = %s +/- %s", title1, Utils.rounded(stats.getMean()), Utils.rounded(stats.getStandardDeviation()));
    plot.setColor(Color.red);
    plot.addPoints(xValues, data2, Plot2.LINE);
    stats = new Statistics(data2);
    label += String.format(", %s (Red) = %s +/- %s", title2, Utils.rounded(stats.getMean()), Utils.rounded(stats.getStandardDeviation()));
    if (data3 != null) {
        plot.setColor(Color.green);
        plot.addPoints(xValues, data3, Plot2.LINE);
        stats = new Statistics(data3);
        label += String.format(", %s (Green) = %s +/- %s", title3, Utils.rounded(stats.getMean()), Utils.rounded(stats.getStandardDeviation()));
    }
    plot.setColor(Color.black);
    plot.addLabel(0, 0, label);
    PlotWindow pw = Utils.display(title, plot);
    if (Utils.isNewWindow())
        wo.add(pw);
}

Example 18 with Plot2

use of ij.gui.Plot2 in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method runCrosstalkAnalysis.

private void runCrosstalkAnalysis() {
    if (!showCrossTalkAnalysisDialog())
        return;
    double[] crosstalk = computeCrosstalk(count, targetChannel - 1);
    // Store the cross talk.
    // Crosstalk from M into N is defined as the number of times the molecule that should be 
    // activated by a pulse from channel M is activated by a pulse from channel N.
    // targetChannel = M
    // activationChannel = N
    int index1, index2 = -1;
    if (channels == 2) {
        if (targetChannel == 1)
            index1 = setCrosstalk(C12, crosstalk[1]);
        else
            index1 = setCrosstalk(C21, crosstalk[0]);
    } else {
        // 3-channel
        if (targetChannel == 1) {
            index1 = setCrosstalk(C12, crosstalk[1]);
            index2 = setCrosstalk(C13, crosstalk[2]);
        } else if (targetChannel == 2) {
            index1 = setCrosstalk(C21, crosstalk[0]);
            index2 = setCrosstalk(C23, crosstalk[2]);
        } else {
            index1 = setCrosstalk(C31, crosstalk[0]);
            index2 = setCrosstalk(C32, crosstalk[1]);
        }
    }
    // Show fraction activations histogram. So we have to set the sum to 1
    double sum = Maths.sum(crosstalk);
    for (int i = 0; i < crosstalk.length; i++) crosstalk[i] /= sum;
    // Plot a histogram
    double[] x = Utils.newArray(channels, 0.5, 1);
    double[] y = crosstalk;
    Plot2 plot = new Plot2(TITLE, "Channel", "Fraction activations");
    plot.setLimits(0, channels + 1, 0, 1);
    plot.setXMinorTicks(false);
    plot.addPoints(x, y, Plot2.BAR);
    String label = String.format("Crosstalk %s = %s", ctNames[index1], Maths.round(ct[index1]));
    if (index2 > -1)
        label += String.format(", %s = %s", ctNames[index2], Maths.round(ct[index2]));
    plot.addLabel(0, 0, label);
    Utils.display(TITLE, plot);
}

Example 19 with Plot2

use of ij.gui.Plot2 in project GDSC-SMLM by aherbert.

the class BenchmarkSpotFilter method showFailuresPlot.

private void showFailuresPlot(BenchmarkFilterResult filterResult) {
    double[][] h = filterResult.cumul;
    StoredData data = filterResult.stats;
    String xTitle = "Failures";
    final int id = Utils.showHistogram(TITLE, data, xTitle, 1, 0, 0);
    if (Utils.isNewWindow())
        windowOrganiser.add(id);
    String title = TITLE + " " + xTitle + " Cumulative";
    Plot2 plot = new Plot2(title, xTitle, "Frequency");
    double xMin = (data.size() == 0) ? 1 : h[0][0];
    double xMax = (data.size() == 0) ? 1 : h[0][h[0].length - 1] + 1;
    double xPadding = 0.05 * (xMax - xMin);
    plot.setLimits(xMin - xPadding, xMax, 0, 1.05);
    plot.setColor(Color.blue);
    plot.addPoints(h[0], h[1], Plot2.BAR);
    PlotWindow pw = Utils.display(title, plot);
    if (Utils.isNewWindow())
        windowOrganiser.add(pw);
}

Example 20 with Plot2

use of ij.gui.Plot2 in project GDSC-SMLM by aherbert.

the class BenchmarkSpotFilter method showPlot.

private void showPlot(BenchmarkFilterResult filterResult) {
    double[] r = filterResult.r;
    double[] p = filterResult.p;
    double[] j = filterResult.j;
    double[] c = filterResult.c;
    int fractionIndex = filterResult.fractionIndex;
    int maxIndex = filterResult.maxIndex;
    double auc = filterResult.auc;
    double auc2 = filterResult.auc2;
    double slope = filterResult.slope;
    double[] i1 = filterResult.i1;
    double[] i2 = filterResult.i2;
    double[] intensity = filterResult.intensity;
    double[] rank = new double[intensity.length];
    final double topIntensity = (intensity.length == 1) ? 0 : intensity[1];
    for (int i = 1; i < rank.length; i++) {
        if (rankByIntensity)
            rank[i] = topIntensity - intensity[i];
        else
            rank[i] = i;
    }
    String title = TITLE + " Performance";
    Plot2 plot = new Plot2(title, (rankByIntensity) ? "Relative Intensity" : "Spot Rank", "");
    double[] limits = Maths.limits(rank);
    plot.setLimits(limits[0], limits[1], 0, 1.05);
    plot.setColor(Color.blue);
    plot.addPoints(rank, p, Plot2.LINE);
    //plot.addPoints(rank, maxp, Plot2.DOT);
    plot.setColor(Color.red);
    plot.addPoints(rank, r, Plot2.LINE);
    plot.setColor(Color.black);
    plot.addPoints(rank, j, Plot2.LINE);
    // Plot correlation - update the scale to be 0-1?
    plot.setColor(Color.yellow);
    plot.addPoints(rank, c, Plot2.LINE);
    plot.setColor(Color.magenta);
    plot.drawLine(rank[fractionIndex], 0, rank[fractionIndex], Maths.max(p[fractionIndex], r[fractionIndex], j[fractionIndex], c[fractionIndex]));
    plot.setColor(Color.pink);
    plot.drawLine(rank[maxIndex], 0, rank[maxIndex], Maths.max(p[maxIndex], r[maxIndex], j[maxIndex], c[maxIndex]));
    plot.setColor(Color.black);
    plot.addLabel(0, 0, "Precision=Blue, Recall=Red, Jaccard=Black, Correlation=Yellow");
    PlotWindow pw = Utils.display(title, plot);
    if (Utils.isNewWindow())
        windowOrganiser.add(pw);
    title = TITLE + " Precision-Recall";
    plot = new Plot2(title, "Recall", "Precision");
    plot.setLimits(0, 1, 0, 1.05);
    plot.setColor(Color.red);
    plot.addPoints(r, p, Plot2.LINE);
    //plot.setColor(Color.magenta);
    //plot.addPoints(r, maxp, Plot2.LINE);
    plot.drawLine(r[r.length - 1], p[r.length - 1], r[r.length - 1], 0);
    plot.setColor(Color.black);
    plot.addLabel(0, 0, "AUC = " + Utils.rounded(auc) + ", AUC2 = " + Utils.rounded(auc2));
    PlotWindow pw2 = Utils.display(title, plot);
    if (Utils.isNewWindow())
        windowOrganiser.add(pw2);
    title = TITLE + " Intensity";
    plot = new Plot2(title, "Candidate", "Spot");
    double[] limits1 = Maths.limits(i1);
    double[] limits2 = Maths.limits(i2);
    plot.setLimits(limits1[0], limits1[1], limits2[0], limits2[1]);
    plot.addLabel(0, 0, String.format("Correlation=%s; Slope=%s", Utils.rounded(c[c.length - 1]), Utils.rounded(slope)));
    plot.setColor(Color.red);
    plot.addPoints(i1, i2, Plot.DOT);
    if (slope > 1)
        plot.drawLine(limits1[0], limits1[0] * slope, limits1[1], limits1[1] * slope);
    else
        plot.drawLine(limits2[0] / slope, limits2[0], limits2[1] / slope, limits2[1]);
    PlotWindow pw3 = Utils.display(title, plot);
    if (Utils.isNewWindow())
        windowOrganiser.add(pw3);
}