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Example 1 with ColorPlot

use of org.vcell.imagej.common.gui.ColorPlot in project vcell by virtualcell.

the class PlotROIStats method run.

@Override
public void run() {
    Plot plot = new ColorPlot("ROI Mean Intensity", "Time", "Mean Intensity");
    StringBuilder legendLabels = new StringBuilder();
    for (RandomAccessibleInterval<T> data : datasetROIsMap.keySet()) {
        if (data instanceof Dataset) {
            legendLabels.append(((Dataset) data).getName());
            legendLabels.append(": ");
        }
        List<Overlay> overlays = datasetROIsMap.get(data);
        for (int i = 0; i < overlays.size(); i++) {
            Overlay overlay = overlays.get(i);
            RandomAccessibleInterval<T> cropped = crop(data, overlay);
            Pair<double[], double[]> xyPair = (Pair<double[], double[]>) ops.run("imageStatsForPlotting", ImageStatsForPlotting.MEAN, cropped);
            plot.addPoints(xyPair.getA(), xyPair.getB(), Plot.LINE);
            legendLabels.append("ROI ");
            legendLabels.append(i + 1);
            legendLabels.append("\n");
        }
    }
    plot.addLegend(legendLabels.toString());
    plot.show();
}
Also used : ColorPlot(org.vcell.imagej.common.gui.ColorPlot) Dataset(net.imagej.Dataset) Plot(ij.gui.Plot) ColorPlot(org.vcell.imagej.common.gui.ColorPlot) Overlay(net.imagej.overlay.Overlay) Pair(net.imglib2.util.Pair)

Example 2 with ColorPlot

use of org.vcell.imagej.common.gui.ColorPlot in project vcell by virtualcell.

the class PlotImageStats method run.

@Override
public void run() {
    Plot plot = new ColorPlot("Frame mean intensity", "Time", "Mean intensity");
    StringBuilder legendLabels = new StringBuilder();
    for (int i = 0; i < datasets.size(); i++) {
        RandomAccessibleInterval<T> data = datasets.get(i);
        if (data instanceof Dataset) {
            legendLabels.append(((Dataset) data).getName());
            legendLabels.append(": ");
        }
        Pair<double[], double[]> xyPair = (Pair<double[], double[]>) ops.run("imageStatsForPlotting", ImageStatsForPlotting.MEAN, data, mask);
        plot.addPoints(xyPair.getA(), xyPair.getB(), Plot.LINE);
        legendLabels.append("ROI ");
        legendLabels.append(i + 1);
        legendLabels.append("\n");
    }
    plot.addLegend(legendLabels.toString());
    plot.show();
}
Also used : ColorPlot(org.vcell.imagej.common.gui.ColorPlot) Dataset(net.imagej.Dataset) Plot(ij.gui.Plot) ColorPlot(org.vcell.imagej.common.gui.ColorPlot) Pair(net.imglib2.util.Pair)

Example 3 with ColorPlot

use of org.vcell.imagej.common.gui.ColorPlot in project vcell by virtualcell.

the class PlotCellRegionStats method run.

@Override
public void run() {
    Plot plot = new ColorPlot("Cell region mean intensity", "Time", "Mean intensity");
    StringBuilder legendLabels = new StringBuilder();
    for (int i = 0; i < datasets.size(); i++) {
        RandomAccessibleInterval<T> data = datasets.get(i);
        if (data instanceof Dataset) {
            legendLabels.append(((Dataset) data).getName());
            legendLabels.append(": ");
        }
        RandomAccessibleInterval<T> cropped = ops.transform().crop(data, mask);
        displayService.createDisplay(cropped);
    }
}
Also used : ColorPlot(org.vcell.imagej.common.gui.ColorPlot) Dataset(net.imagej.Dataset) Plot(ij.gui.Plot) ColorPlot(org.vcell.imagej.common.gui.ColorPlot)

Aggregations

Plot (ij.gui.Plot)3 Dataset (net.imagej.Dataset)3 ColorPlot (org.vcell.imagej.common.gui.ColorPlot)3 Pair (net.imglib2.util.Pair)2 Overlay (net.imagej.overlay.Overlay)1