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

Example 6 with PointRoi

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

the class ImageROIPainter method appendRoi.

/**
	 * Adds a new ROI to the overlay using the coordinates from start to end (non-inclusive)
	 * 
	 * @param x
	 * @param y
	 * @param slice
	 * @param indices
	 * @param o
	 * @param start
	 * @param end
	 */
private void appendRoi(float[] x, float[] y, int[] slice, int[] indices, Overlay o, int start, int end) {
    int p = end - start;
    float[] x2 = new float[p];
    float[] y2 = new float[p];
    for (int j = start, ii = 0; j < end; j++, ii++) {
        x2[ii] = x[indices[j]];
        y2[ii] = y[indices[j]];
    }
    PointRoi roi = new PointRoi(x2, y2, p);
    roi.setPosition(slice[indices[start]]);
    o.add(roi);
}

Example 7 with PointRoi

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

the class GaussianFit method setOverlay.

/**
	 * Show the points as an overlay
	 * 
	 * @param nMaxima
	 * @param xpoints
	 * @param ypoints
	 */
private void setOverlay(int nMaxima, int[] xpoints, int[] ypoints) {
    PointRoi roi = new PointRoi(xpoints, ypoints, nMaxima);
    Color strokeColor = Color.yellow;
    Color fillColor = Color.green;
    roi.setStrokeColor(strokeColor);
    roi.setFillColor(fillColor);
    roi.setShowLabels(false);
    imp.setOverlay(roi, strokeColor, 2, fillColor);
}

Example 8 with PointRoi

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

the class BenchmarkSmartSpotRanking method addToOverlay.

private void addToOverlay(Overlay o, int frame, int[] x, int[] y, int c, Color color) {
    PointRoi roi = new PointRoi(x, y, c);
    roi.setFillColor(color);
    roi.setStrokeColor(color);
    roi.setPosition(frame);
    roi.setShowLabels(false);
    o.add(roi);
}

Example 9 with PointRoi

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

the class PeakFit method addSingleFrameOverlay.

private void addSingleFrameOverlay() {
    // If a single frame was processed add the peaks as an overlay if they are in memory
    ImagePlus imp = this.imp;
    if (fitMaxima && singleFrame > 0) {
        if (source instanceof IJImageSource) {
            String title = source.getName();
            imp = WindowManager.getImage(title);
        }
    }
    if (singleFrame > 0 && imp != null) {
        MemoryPeakResults results = null;
        for (PeakResults r : this.results.toArray()) if (r instanceof MemoryPeakResults) {
            results = (MemoryPeakResults) r;
            break;
        }
        if (results == null || results.size() == 0)
            return;
        ExtendedGenericDialog gd = new ExtendedGenericDialog(TITLE);
        gd.enableYesNoCancel();
        gd.hideCancelButton();
        gd.addMessage("Add the fitted localisations as an overlay?");
        gd.showDialog();
        if (!gd.wasOKed())
            return;
        LUT lut = LUTHelper.createLUT(LutColour.ICE);
        Overlay o = new Overlay();
        ArrayList<PeakResult> list = (ArrayList<PeakResult>) results.getResults();
        for (int i = 0, j = results.size() - 1; i < results.size(); i++, j--) {
            PeakResult r = list.get(i);
            PointRoi roi = new PointRoi(r.getXPosition(), r.getYPosition());
            Color c = LUTHelper.getColour(lut, j, results.size());
            roi.setStrokeColor(c);
            roi.setFillColor(c);
            if (imp.getStackSize() > 1)
                roi.setPosition(singleFrame);
            o.add(roi);
        }
        imp.setOverlay(o);
        imp.getWindow().toFront();
    }
}

Example 10 with PointRoi

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

the class SpotFinderPreview method addRoi.

public static void addRoi(int frame, Overlay o, float[] x, float[] y, int n, Color colour, int pointType) {
    if (n == 0)
        return;
    PointRoi roi = new PointRoi(x, y, n);
    roi.setPointType(pointType);
    roi.setFillColor(colour);
    roi.setStrokeColor(colour);
    if (frame != 0)
        roi.setPosition(frame);
    o.add(roi);
}