Examples with CoordinatePredicate uk.ac.sussex.gdsc.core.ij.roi.CoordinatePredicate used on opensource projects

Example 1 with CoordinatePredicate

use of uk.ac.sussex.gdsc.core.ij.roi.CoordinatePredicate in project GDSC-SMLM by aherbert.

the class TcPalmAnalysis method createSelectionFilter.

/**
 * Creates the selection filter to identify all cluster groups using a custom filter.
 *
 * @param roi the roi
 * @param settings the settings
 * @return the bi predicate
 */
private BiPredicate<ClusterData, Rectangle2D> createSelectionFilter(final Roi roi, final TcPalmAnalysisSettings settings) {
    // Filter on time first as this is simple.
    BiPredicate<ClusterData, Rectangle2D> test = null;
    if (settings.getMinFrame() > minT) {
        final int min = settings.getMinFrame();
        test = (c, r) -> c.start >= min;
    }
    if (settings.getMaxFrame() < maxT) {
        final int max = settings.getMaxFrame();
        test = and(test, (c, r) -> c.end <= max);
    }
    // Add square bounds check
    test = and(test, settings.getIntersects() ? ClusterData::intersects : ClusterData::isWithin);
    // -- Check if the cluster is inside the ROI using a CoordinatePredicate
    if (roi.getType() != Roi.RECTANGLE || roi.getCornerDiameter() != 0) {
        final CoordinatePredicate pred = CoordinatePredicateUtils.createContainsPredicate(roi);
        if (settings.getIntersects()) {
            test = and(test, (c, r) -> c.intersects(pred, image::mapX, image::mapY));
        } else {
            test = and(test, (c, r) -> c.isWithin(pred, image::mapX, image::mapY));
        }
    }
    return test;
}

Example 2 with CoordinatePredicate

use of uk.ac.sussex.gdsc.core.ij.roi.CoordinatePredicate in project GDSC-SMLM by aherbert.

the class CropResults method roiCropResults.

private void roiCropResults() {
    final MemoryPeakResults newResults = createNewResults();
    // These bounds are integer. But this is because the results are meant to come from an image.
    final Rectangle integerBounds = results.getBounds(true);
    final ImagePlus imp = WindowManager.getImage(settings.getRoiImage());
    if (imp == null) {
        IJ.error(TITLE, "No ROI image: " + settings.getRoiImage());
        return;
    }
    final CoordinatePredicate roiTest = CoordinatePredicateUtils.createContainsPredicate(imp.getRoi());
    if (roiTest == null) {
        IJ.error(TITLE, "Not an area ROI");
        return;
    }
    // Scale the results to the size of the image with the ROI
    final int roiImageWidth = imp.getWidth();
    final int roiImageHeight = imp.getHeight();
    final double ox = integerBounds.getX();
    final double oy = integerBounds.getY();
    final double xscale = roiImageWidth / integerBounds.getWidth();
    final double yscale = roiImageHeight / integerBounds.getHeight();
    final Predicate<PeakResult> testZ = getZFilter();
    results.forEach(DistanceUnit.PIXEL, (XyrResultProcedure) (x, y, result) -> {
        if (roiTest.test((x - ox) * xscale, (y - oy) * yscale) && testZ.test(result)) {
            newResults.add(result);
        }
    });
    if (settings.getPreserveBounds()) {
        newResults.setBounds(integerBounds);
    } else {
        newResults.setBounds(null);
        newResults.getBounds(true);
    }
    IJ.showStatus(newResults.size() + " Cropped localisations");
}