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

Example 51 with Plot

use of ij.gui.Plot in project mcib3d-core by mcib3d.

the class HistogramUtil method plotCumulHistogram.

/**
 * @param title
 */
public void plotCumulHistogram(String title) {
    if (ycumul == null) {
        this.computeCumulHistogram();
    }
    Plot plot = new Plot(title, "values", "nb", xbin, ycumul);
    plot.show();
}

Example 52 with Plot

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

the class SpotInspector method plotScore.

private void plotScore(float[] xValues, float[] yValues, double yMin, double yMax) {
    if (settings.plotScore) {
        final String title = TITLE + " Score";
        final Plot plot = new Plot(title, "Rank", Settings.SORT_ORDER[settings.sortOrderIndex]);
        plot.addPoints(xValues, yValues, Plot.LINE);
        plot.setLimits(1, xValues.length, yMin, yMax);
        ImageJUtils.display(title, plot);
    }
}

Example 53 with Plot

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

the class TcPalmAnalysis method runClusterPlotSelection.

/**
 * Select the data for the first cluster in the provided list on the cumulative activations plot.
 *
 * @param clusters the clusters
 */
private void runClusterPlotSelection(List<ClusterData> clusters) {
    final Plot plot = activationsPlotData.plot;
    // We are expecting only a single cluster
    if (clusters.isEmpty()) {
        plot.getImagePlus().deleteRoi();
        return;
    }
    final int[] plotFrames = activationsPlotData.data.plotFrames;
    final int[] plotCounts = activationsPlotData.data.plotCounts;
    final ClusterData data = clusters.get(0);
    final int is = Arrays.binarySearch(plotFrames, data.start);
    final int ie = Arrays.binarySearch(plotFrames, data.end);
    final int low = plotCounts[is];
    final int high = plotCounts[ie];
    // Pad slightly. This handles the case where start == end to create a width and height
    final float[] x = activationsPlotData.timeConverter.apply(new float[] { data.start - 1, data.end + 1 });
    final double x1 = plot.scaleXtoPxl(x[0]);
    final double x2 = plot.scaleXtoPxl(x[1]);
    final double y1 = plot.scaleYtoPxl(high + 1);
    final double y2 = plot.scaleYtoPxl(low - 1);
    plot.getImagePlus().setRoi(new Roi(x1, y1, x2 - x1, y2 - y1));
}

Example 54 with Plot

use of ij.gui.Plot 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 55 with Plot

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

the class TcPalmAnalysis method createCumulativeCountData.

/**
 * Creates the cumulative count data.
 *
 * @param createPlotData set to true to create the plot data arrays
 * @return the cumulative count data
 */
private CumulativeCountData createCumulativeCountData(LocalList<ClusterData> clusters, boolean createPlotData) {
    final TIntIntHashMap all = new TIntIntHashMap(maxT - minT + 1);
    clusters.forEach(c -> c.results.forEach(peak -> all.adjustOrPutValue(peak.getFrame(), 1, 1)));
    final int[] frames = all.keys();
    final int[] counts = all.values();
    SortUtils.sortData(counts, frames, true, false);
    return new CumulativeCountData(frames, counts, createPlotData);
}