Examples with DBSCANClusterer org.apache.commons.math3.ml.clustering.DBSCANClusterer used on opensource projects

Example 1 with DBSCANClusterer

use of org.apache.commons.math3.ml.clustering.DBSCANClusterer in project chordatlas by twak.

the class Prof method findProfileLines.

/**
 * We find an initial base offset. Then we cluster the start point of all
 * (clean) profiles. If any are a good distance from the initial base, we
 * add those as their own profile lines.
 *
 * The original line is offset by the remaiing data.
 */
public static List<SuperLine> findProfileLines(Collection<Prof> profiles, Line3d line) {
    List<SuperLine> out = new ArrayList();
    // PaintThing.debug.clear();
    SuperLine superLine = new SuperLine(line.start.x, line.start.z, line.end.x, line.end.z);
    double outLen = superLine.length();
    double min = Double.MAX_VALUE, max = -Double.MAX_VALUE;
    Cache<Prof, Double> vLength = new Cache<Prof, Double>() {

        @Override
        public Double create(Prof i) {
            return i.verticalLength(0.5);
        }
    };
    double vLen = profiles.stream().mapToDouble(p -> vLength.get(p)).sum();
    boolean useVertical = vLen / profiles.size() > 1;
    class Wrapper implements Clusterable {

        double[] pt;

        public Wrapper(Point2d pt) {
            this.pt = new double[] { pt.x, pt.y };
        }

        @Override
        public double[] getPoint() {
            return pt;
        }
    }
    List<Wrapper> toCluster = new ArrayList();
    List<Double> baseLineOffset = new ArrayList();
    for (Prof p : profiles) {
        if (// vLen / (5*profiles.size()))
        useVertical && vLength.get(p) < 1)
            continue;
        Prof clean = p.parameterize();
        Point2d pt = clean.get(0);
        Point3d pt3 = clean.to3d(pt);
        double ppram = superLine.findPPram(new Point2d(pt3.x, pt3.z));
        baseLineOffset.add(pt.x);
        toCluster.add(new Wrapper(new Point2d(pt.x, ppram * outLen)));
        min = Math.min(min, ppram);
        max = Math.max(max, ppram);
    }
    if (min == max || toCluster.isEmpty())
        return out;
    if (true) {
        baseLineOffset.sort(Double::compareTo);
        double modeBaselineOffset = baseLineOffset.get(baseLineOffset.size() / 2);
        DBSCANClusterer<Wrapper> cr = new DBSCANClusterer<>(1.5, 0);
        List<Cluster<Wrapper>> results = cr.cluster(toCluster);
        Iterator<Cluster<Wrapper>> cit = results.iterator();
        while (cit.hasNext()) {
            Cluster<Wrapper> cw = cit.next();
            if (cw.getPoints().size() < 2 / TweedSettings.settings.profileHSampleDist) {
                cit.remove();
                double cMeanY = cw.getPoints().stream().mapToDouble(x -> x.pt[1]).average().getAsDouble();
                double bestDist = Double.MAX_VALUE;
                Cluster<Wrapper> bestWrapper = null;
                for (Cluster<Wrapper> near : results) {
                    double meanY = near.getPoints().stream().mapToDouble(x -> x.pt[1]).average().getAsDouble();
                    double dist = Math.abs(meanY - cMeanY);
                    if (dist < bestDist) {
                        bestDist = dist;
                        bestWrapper = near;
                    }
                }
                if (bestWrapper != null)
                    bestWrapper.getPoints().addAll(cw.getPoints());
            }
        }
        {
            baseLineOffset.clear();
            int c = 0;
            for (Cluster<Wrapper> cw : results) {
                double[] minMax = cw.getPoints().stream().map(p -> new double[] { p.pt[1] }).collect(new InAxDoubleArray());
                double[] offsetA = cw.getPoints().stream().mapToDouble(p -> p.pt[0]).sorted().toArray();
                double offset = offsetA[offsetA.length / 2];
                if (offset - modeBaselineOffset < 1) {
                    for (Wrapper w : cw.getPoints()) baseLineOffset.add(w.pt[0]);
                    continue;
                }
                SuperLine sl = new SuperLine(superLine.fromPPram(minMax[0] / outLen), superLine.fromPPram(minMax[1] / outLen));
                sl.moveLeft(offset);
                out.add(sl);
                List<Point2d> pts = cw.getPoints().stream().map(w -> new Point2d(w.pt[0], w.pt[1])).collect(Collectors.toList());
                PaintThing.debug(Rainbow.getColour(c++), 1, pts);
            }
        }
    }
    Point2d nStart = superLine.fromPPram(min), nEnd = superLine.fromPPram(max);
    superLine.start = nStart;
    superLine.end = nEnd;
    baseLineOffset.sort(Double::compare);
    if (!baseLineOffset.isEmpty())
        superLine.moveLeft(baseLineOffset.get(baseLineOffset.size() / 2));
    out.add(0, superLine);
    return out;
}

Example 2 with DBSCANClusterer

use of org.apache.commons.math3.ml.clustering.DBSCANClusterer in project chordatlas by twak.

the class SkelFootprint method findRoofColor.

private static void findRoofColor(HalfMesh2 mesh) {
    class Wrapper implements Clusterable {

        double[] col;

        public Wrapper(float[] col) {
            this.col = new double[] { col[0], col[1], col[2] };
        }

        @Override
        public double[] getPoint() {
            return col;
        }
    }
    for (HalfFace hf : mesh.faces) {
        List<Wrapper> toCluster = new ArrayList();
        SuperFace sf = (SuperFace) hf;
        if (sf.colors == null || sf.colors.isEmpty()) {
            float grey = (float) (Math.random() * 0.3 + 0.2);
            sf.roofColor = new float[] { grey, grey, grey };
            continue;
        }
        for (float[] v : sf.colors) toCluster.add(new Wrapper(v));
        sf.colors = null;
        DBSCANClusterer<Wrapper> cr = new DBSCANClusterer<>(0.2, 5);
        List<Cluster<Wrapper>> results = cr.cluster(toCluster);
        float[] col = new float[] { 0.3f, 0.3f, 0.3f };
        try {
            Cluster<Wrapper> biggest = results.stream().max((a, b) -> Double.compare(a.getPoints().size(), b.getPoints().size())).get();
            col = new float[3];
            for (Wrapper w : biggest.getPoints()) for (int i = 0; i < 3; i++) col[i] += (float) w.col[i];
            int size = biggest.getPoints().size();
            for (int i = 0; i < 3; i++) col[i] /= size;
        } catch (NoSuchElementException e) {
        }
        sf.roofColor = col;
    }
}