Examples with XyrResultProcedure uk.ac.sussex.gdsc.smlm.results.procedures.XyrResultProcedure used on opensource projects

Example 11 with XyrResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.XyrResultProcedure in project GDSC-SMLM by aherbert.

the class PcPalmMolecules method cropToRoi.

private MemoryPeakResults cropToRoi(MemoryPeakResults results) {
    final Rectangle bounds = results.getBounds(true);
    settings.area = (bounds.width * bounds.height * results.getNmPerPixel() * results.getNmPerPixel()) / 1e6;
    if (roiBounds == null) {
        return results;
    }
    // Adjust bounds relative to input results image
    final double xscale = (double) roiImageWidth / bounds.width;
    final double yscale = (double) roiImageHeight / bounds.height;
    final float minX = (float) Math.floor(roiBounds.x / xscale);
    final float maxX = (float) Math.ceil((roiBounds.x + roiBounds.width) / xscale);
    final float minY = (float) Math.floor(roiBounds.y / yscale);
    final float maxY = (float) Math.ceil((roiBounds.y + roiBounds.height) / yscale);
    // Update the area with the cropped region
    settings.area *= (maxX - minX) / bounds.width;
    settings.area *= (maxY - minY) / bounds.height;
    // Create a new set of results within the bounds
    final MemoryPeakResults newResults = new MemoryPeakResults();
    newResults.begin();
    results.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (x, y, result) -> {
        if (x >= minX && x <= maxX && y >= minY && y <= maxY) {
            newResults.add(result);
        }
    });
    newResults.end();
    newResults.copySettings(results);
    newResults.setBounds(new Rectangle((int) minX, (int) minY, (int) (maxX - minX), (int) (maxY - minY)));
    return newResults;
}

Example 12 with XyrResultProcedure

use of uk.ac.sussex.gdsc.smlm.results.procedures.XyrResultProcedure in project GDSC-SMLM by aherbert.

the class PulseActivationAnalysis method drawLoop.

private void drawLoop(ImagePlus imp, Roi roi, int number) {
    if (!roi.isArea()) {
        return;
    }
    // Map the ROI to a crop of the results set
    final Rectangle roiBounds = roi.getBounds();
    final Rectangle resultsBounds = results.getBounds(true);
    // @formatter:off
    final Rectangle2D.Double r = new Rectangle2D.Double(resultsBounds.width * (double) roiBounds.x / imp.getWidth(), resultsBounds.height * (double) roiBounds.y / imp.getHeight(), // Since we output pixels map the width/height to the nearest pixel
    Math.ceil(resultsBounds.width * (double) roiBounds.width / imp.getWidth()), Math.ceil(resultsBounds.height * (double) roiBounds.height / imp.getHeight()));
    // @formatter:on
    final double x = r.getX();
    final double y = r.getY();
    final int magnification = getMagnification();
    // For each result set crop out the localisation and construct an overlay
    final Overlay o = new Overlay();
    for (int i = 0; i < output.length; i++) {
        final Color color = Settings.colors[i];
        // The first result is the memory results
        final MemoryPeakResults localResults = (MemoryPeakResults) output[i].getOutput(0);
        localResults.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (xx, yy, result) -> {
            if (r.contains(xx, yy)) {
                add(o, (xx - x) * magnification, (yy - y) * magnification, color);
            }
        });
    }
    // This results in a change of shape depending on where the roi is positioned
    int width = (int) r.getWidth();
    int height = (int) r.getHeight();
    width *= magnification;
    height *= magnification;
    final ImageProcessor ip = new ByteProcessor(width, height);
    final String loopTitle = imp.getTitle() + " Loop " + number;
    imp = WindowManager.getImage(loopTitle);
    if (imp == null) {
        imp = new ImagePlus(loopTitle, ip);
        imp.show();
    } else {
        imp.setProcessor(ip);
        imp.getWindow().toFront();
    }
    imp.setOverlay(o);
}