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

Example 1 with XyzResultProcedure

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

the class ImageJ3DResultsViewer method getPoints.

/**
 * Gets the points.
 *
 * @param results the results
 * @param settings the settings
 * @return the points
 */
static LocalList<Point3f> getPoints(MemoryPeakResults results, ImageJ3DResultsViewerSettingsOrBuilder settings) {
    final LocalList<Point3f> points = new LocalList<>(results.size());
    if (results.is3D()) {
        results.forEach(DistanceUnit.NM, (XyzResultProcedure) (x, y, z) -> {
            points.push(new Point3f(x, y, z));
        });
    } else {
        results.forEach(DistanceUnit.NM, (XyResultProcedure) (x, y) -> {
            points.push(new Point3f(x, y, 0));
        });
        final double range = settings.getDepthRange();
        if (range > 0 && results.size() > 1) {
            final DepthMode mode = DepthMode.forNumber(settings.getDepthMode());
            final double min = -settings.getDepthRange() / 2;
            switch(mode) {
                case DITHER:
                    final SplitMix r = SplitMix.new64(settings.getDitherSeed());
                    for (int i = points.size(); i-- > 0; ) {
                        points.unsafeGet(i).z += (min + r.nextDouble() * range);
                    }
                    break;
                case INTENSITY:
                    // Rank by intensity, highest first
                    final StandardResultProcedure p = new StandardResultProcedure(results);
                    p.getI();
                    final int[] indices = SimpleArrayUtils.natural(results.size());
                    SortUtils.sortIndices(indices, p.intensity, true);
                    final double inc = range / indices.length;
                    for (int i = 0; i < indices.length; i++) {
                        // The standard rendering has +z going away so put the highest rank at min
                        points.unsafeGet(indices[i]).z += (min + i * inc);
                    }
                    break;
                case NONE:
                    break;
                default:
                    throw new IllegalStateException("Unknown depth mode: " + mode);
            }
        }
    }
    return points;
}