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

Example 11 with Plot

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

the class PSFCreator method subtractBackgroundAndWindow.

/**
	 * Subtract the background from the spot, compute the intensity within half the box region distance from the centre
	 * and smooth the intensity profile. In interactive mode the user must choose to accept the profile or reject.
	 * If accepted the smoothed profile is user to normalise the image and then the image is rolled off to zero
	 * using a Tukey window function.
	 * 
	 * @param spot
	 * @param background
	 *            The minimum level, all below this is background and set to zero
	 * @param spotWidth
	 * @param spotHeight
	 * @param n
	 *            The spot number
	 * @param loess
	 *            The smoothing interpolator
	 * @return True if accepted
	 */
private boolean subtractBackgroundAndWindow(float[][] spot, final float background, final int spotWidth, final int spotHeight, double[] centre, LoessInterpolator loess) {
    //ImageWindow imageWindow = new ImageWindow();
    for (int i = 0; i < spot.length; i++) {
        for (int j = 0; j < spot[i].length; j++) spot[i][j] = FastMath.max(spot[i][j] - background, 0);
    }
    // Create a distance map from the centre
    if (lastWidth != spotWidth || lastHeight != spotHeight) {
        final double cx = spotWidth * 0.5;
        final double cy = spotHeight * 0.5;
        minx = FastMath.max(0, (int) (cx - boxRadius * 0.5));
        maxx = FastMath.min(spotWidth, (int) Math.ceil(cx + boxRadius * 0.5));
        miny = FastMath.max(0, (int) (cy - boxRadius * 0.5));
        maxy = FastMath.min(spotHeight, (int) Math.ceil(cy + boxRadius * 0.5));
        // Precompute square distances
        double[] dx2 = new double[maxx - minx + 1];
        for (int x = minx, i = 0; x < maxx; x++, i++) {
            // Use pixel centres with 0.5 offset
            final double dx = x + 0.5 - cx;
            dx2[i] = dx * dx;
        }
        dmap = new boolean[dx2.length * (maxy - miny + 1)];
        final double d2 = boxRadius * boxRadius / 4;
        for (int y = miny, j = 0; y < maxy; y++) {
            final double dy = (y + 0.5 - cy);
            final double dy2 = dy * dy;
            final double limit = d2 - dy2;
            for (int x = minx, i = 0; x < maxx; x++, i++, j++) {
                dmap[j] = (dx2[i] < limit);
            }
        }
        lastWidth = spotWidth;
        lastHeight = spotHeight;
    }
    // Calculate the intensity profile within half the box radius from the centre
    double[] xValues = new double[spot.length];
    double[] yValues = new double[spot.length];
    for (int i = 0; i < spot.length; i++) {
        xValues[i] = i + 1;
        double sum = 0;
        for (int y = miny, j = 0; y < maxy; y++) {
            int index = y * spotWidth + minx;
            for (int x = minx; x < maxx; x++, index++, j++) if (dmap[j])
                sum += spot[i][index];
        }
        yValues[i] = sum;
    }
    double[] newY = loess.smooth(xValues, yValues);
    // falls towards zero at the ends)
    for (int i = 0; i < newY.length; i++) if (newY[i] < 0)
        newY[i] = yValues[i];
    if (interactiveMode) {
        Utils.hide(TITLE_AMPLITUDE);
        Utils.hide(TITLE_PSF_PARAMETERS);
        final int n = (int) centre[4];
        String title = TITLE_INTENSITY;
        Plot plot = new Plot(title, "Slice", "Sum", xValues, yValues);
        plot.setColor(Color.red);
        plot.addPoints(xValues, newY, Plot.LINE);
        plot.setColor(Color.green);
        double[] limits = Maths.limits(yValues);
        plot.drawLine(centre[2], limits[0], centre[2], limits[1]);
        plot.setColor(Color.black);
        plot.addLabel(0, 0, "Spot " + n);
        Utils.display(title, plot);
        GenericDialog gd = new GenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage(String.format("Add spot %d to the PSF?\n(The intensity profile is the sum within half the box region)", n));
        if (yesNoPosition != null) {
            gd.centerDialog(false);
            gd.setLocation(yesNoPosition);
        }
        gd.showDialog();
        yesNoPosition = gd.getLocation();
        if (!gd.wasOKed())
            return false;
    }
    for (int i = 0; i < spot.length; i++) {
        // Normalise
        final float scale = (float) (newY[i] / yValues[i]);
        for (int j = 0; j < spot[i].length; j++) spot[i][j] *= scale;
        // Use a Tukey window to roll-off the image edges
        //spot[i] = imageWindow.applySeperable(spot[i], spotWidth, spotHeight, ImageWindow.WindowFunction.Tukey);
        spot[i] = ImageWindow.applyWindow(spot[i], spotWidth, spotHeight, ImageWindow.WindowFunction.TUKEY);
    }
    return true;
}

Example 12 with Plot

use of ij.gui.Plot 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);
    }
}