Examples with Polygon2D net.imglib2.roi.geom.real.Polygon2D used on opensource projects

Example 11 with Polygon2D

use of net.imglib2.roi.geom.real.Polygon2D in project imagej-ops by imagej.

the class DefaultSmallestEnclosingRectangle method calculate.

@Override
public Polygon2D calculate(final Polygon2D input) {
    Polygon2D ch = convexHullFunc.calculate(input);
    RealLocalizable cog = centroidFunc.calculate(ch);
    Polygon2D minBounds = input;
    double minArea = Double.POSITIVE_INFINITY;
    // for each edge (i.e. line from P(i-1) to P(i)
    for (int i = 1; i < ch.numVertices() - 1; i++) {
        final double angle = Math.atan2(ch.vertex(i).getDoublePosition(1) - ch.vertex(i - 1).getDoublePosition(1), ch.vertex(i).getDoublePosition(0) - ch.vertex(i - 1).getDoublePosition(0));
        // rotate the polygon in such a manner that the line has an angle of 0
        final Polygon2D rotatedPoly = rotate(ch, -angle, cog);
        // get the bounds
        final Polygon2D bounds = boundingBoxFunc.calculate(rotatedPoly);
        // calculate the area of the bounds
        final double area = areaFunc.calculate(bounds).get();
        // original polygon and save it.
        if (area < minArea) {
            minArea = area;
            minBounds = rotate(bounds, angle, cog);
        }
    }
    // edge (n-1) to 0
    final double angle = Math.atan2(ch.vertex(0).getDoublePosition(1) - ch.vertex(ch.numVertices() - 1).getDoublePosition(1), ch.vertex(0).getDoublePosition(0) - ch.vertex(ch.numVertices() - 1).getDoublePosition(0));
    // rotate the polygon in such a manner that the line has an angle of 0
    final Polygon2D rotatedPoly = rotate(ch, -angle, cog);
    // get the bounds
    final Polygon2D bounds = boundingBoxFunc.calculate(rotatedPoly);
    // calculate the area of the bounds
    final double area = areaFunc.calculate(bounds).get();
    // original polygon and save it.
    if (area < minArea) {
        minArea = area;
        minBounds = rotate(bounds, angle, cog);
    }
    return minBounds;
}

Example 12 with Polygon2D

use of net.imglib2.roi.geom.real.Polygon2D in project imagej-ops by imagej.

the class DefaultContour method calculate.

@Override
public Polygon2D calculate(final RandomAccessibleInterval<B> input) {
    List<RealPoint> p = new ArrayList<>();
    final B var = Util.getTypeFromInterval(input).createVariable();
    final RandomAccess<B> raInput = Views.extendValue(input, var).randomAccess();
    final Cursor<B> cInput = Views.flatIterable(input).cursor();
    final ClockwiseMooreNeighborhoodIterator<B> cNeigh = new ClockwiseMooreNeighborhoodIterator<>(raInput);
    double[] position = new double[2];
    double[] startPos = new double[2];
    // find first true pixel
    while (cInput.hasNext()) {
        // we are looking for a true pixel
        if (cInput.next().get()) {
            raInput.setPosition(cInput);
            raInput.localize(startPos);
            // add to polygon
            p.add(new RealPoint(startPos[0], startPos[1]));
            // backtrack:
            raInput.move(-1, 0);
            cNeigh.reset();
            while (cNeigh.hasNext()) {
                if (cNeigh.next().get()) {
                    boolean specialBacktrack = false;
                    raInput.localize(position);
                    if (startPos[0] == position[0] && startPos[1] == position[1]) {
                        // startPoint was found.
                        if (useJacobs) {
                            // Jacobs stopping criteria
                            final int index = cNeigh.getIndex();
                            if (index == 1 || index == 0) {
                                // Jonathans refinement to
                                // non-terminating jacobs criteria
                                specialBacktrack = true;
                            } else if (index == 2 || index == 3) {
                                // way.
                                break;
                            }
                        // else criteria not fulfilled, continue.
                        } else {
                            break;
                        }
                    }
                    // add found point to polygon
                    p.add(new RealPoint(position[0], position[1]));
                    if (specialBacktrack) {
                        cNeigh.backtrackSpecial();
                    } else {
                        cNeigh.backtrack();
                    }
                }
            }
            // we only need to extract one contour.
            break;
        }
    }
    return new DefaultWritablePolygon2D(p);
}

Example 13 with Polygon2D

use of net.imglib2.roi.geom.real.Polygon2D in project imagej-ops by imagej.

the class DefaultConvexHull2D method calculate.

@Override
public Polygon2D calculate(final Polygon2D input) {
    // create a copy of points because se will get resorted, etc.
    List<? extends RealLocalizable> RealPoints = new ArrayList<>(GeomUtils.vertices(input));
    // Sort RealPoints of P by x-coordinate (in case of a tie, sort by
    // y-coordinate).
    Collections.sort(RealPoints, new Comparator<RealLocalizable>() {

        @Override
        public int compare(final RealLocalizable o1, final RealLocalizable o2) {
            final Double o1x = new Double(o1.getDoublePosition(0));
            final Double o2x = new Double(o2.getDoublePosition(0));
            final int result = o1x.compareTo(o2x);
            if (result == 0) {
                return new Double(o1.getDoublePosition(1)).compareTo(new Double(o2.getDoublePosition(1)));
            }
            return result;
        }
    });
    // Initialize U and L as empty lists.
    // lists will hold vertices of upper and lower hulls
    // respectively.
    final List<RealLocalizable> U = new ArrayList<>();
    final List<RealLocalizable> L = new ArrayList<>();
    // build lower hull
    for (final RealLocalizable p : RealPoints) {
        // turn: remove last RealPoint from L
        while (L.size() >= 2 && ccw(L.get(L.size() - 2), L.get(L.size() - 1), p) <= 0) {
            L.remove(L.size() - 1);
        }
        L.add(p);
    }
    // build upper hull
    Collections.reverse(RealPoints);
    for (final RealLocalizable p : RealPoints) {
        // turn: remove last RealPoint from U
        while (U.size() >= 2 && ccw(U.get(U.size() - 2), U.get(U.size() - 1), p) <= 0) {
            U.remove(U.size() - 1);
        }
        U.add(p);
    }
    // Remove last RealPoint of each list (it's same as first
    // RealPoint
    // of or list).
    L.remove(L.size() - 1);
    U.remove(U.size() - 1);
    // concatenate L and U
    L.addAll(U);
    return new DefaultWritablePolygon2D(L);
}

Example 14 with Polygon2D

use of net.imglib2.roi.geom.real.Polygon2D in project imagej-ops by imagej.

the class DefaultElongation method compute.

@Override
public void compute(final Polygon2D input, final DoubleType output) {
    final List<? extends RealLocalizable> minBB = GeomUtils.vertices(minimumBoundingBoxFunc.calculate(input));
    final RealLocalizable p1 = minBB.get(0);
    final RealLocalizable p2 = minBB.get(1);
    final RealLocalizable p3 = minBB.get(2);
    double width = Math.sqrt(Math.pow(p1.getDoublePosition(0) - p2.getDoublePosition(0), 2) + Math.pow(p1.getDoublePosition(1) - p2.getDoublePosition(1), 2));
    double length = Math.sqrt(Math.pow(p2.getDoublePosition(0) - p3.getDoublePosition(0), 2) + Math.pow(p2.getDoublePosition(1) - p3.getDoublePosition(1), 2));
    if (width > length) {
        final double tmp = width;
        width = length;
        length = tmp;
    }
    output.set(1d - (width / length));
}

Example 15 with Polygon2D

use of net.imglib2.roi.geom.real.Polygon2D in project imagej-ops by imagej.

the class DefaultMinimumFeret method calculate.

@Override
public Pair<RealLocalizable, RealLocalizable> calculate(Polygon2D input) {
    final List<? extends RealLocalizable> points = GeomUtils.vertices(function.calculate(input));
    double distance = Double.POSITIVE_INFINITY;
    RealLocalizable p0 = points.get(0);
    RealLocalizable p1 = points.get(0);
    double tmpDist = 0;
    RealLocalizable tmpP0 = p0;
    RealLocalizable tmpP1 = p1;
    for (int i = 0; i < points.size() - 2; i++) {
        final RealLocalizable lineStart = points.get(i);
        final RealLocalizable lineEnd = points.get(i + 1);
        tmpDist = 0;
        final Line l = new Line(new Vector2D(lineStart.getDoublePosition(0), lineStart.getDoublePosition(1)), new Vector2D(lineEnd.getDoublePosition(0), lineEnd.getDoublePosition(1)), 10e-12);
        for (int j = 0; j < points.size(); j++) {
            if (j != i && j != i + 1) {
                final RealLocalizable ttmpP0 = points.get(j);
                final double tmp = l.distance(new Vector2D(ttmpP0.getDoublePosition(0), ttmpP0.getDoublePosition(1)));
                if (tmp > tmpDist) {
                    tmpDist = tmp;
                    final Vector2D vp = (Vector2D) l.project(new Vector2D(ttmpP0.getDoublePosition(0), ttmpP0.getDoublePosition(1)));
                    tmpP0 = new RealPoint(vp.getX(), vp.getY());
                    tmpP1 = ttmpP0;
                }
            }
        }
        if (tmpDist < distance) {
            distance = tmpDist;
            p0 = tmpP0;
            p1 = tmpP1;
        }
    }
    final RealLocalizable lineStart = points.get(points.size() - 1);
    final RealLocalizable lineEnd = points.get(0);
    final Line l = new Line(new Vector2D(lineStart.getDoublePosition(0), lineStart.getDoublePosition(1)), new Vector2D(lineEnd.getDoublePosition(0), lineEnd.getDoublePosition(1)), 10e-12);
    tmpDist = 0;
    for (int j = 0; j < points.size(); j++) {
        if (j != points.size() - 1 && j != 0 + 1) {
            final RealLocalizable ttmpP0 = points.get(j);
            final double tmp = l.distance(new Vector2D(ttmpP0.getDoublePosition(0), ttmpP0.getDoublePosition(1)));
            if (tmp > tmpDist) {
                tmpDist = tmp;
                final Vector2D vp = (Vector2D) l.project(new Vector2D(ttmpP0.getDoublePosition(0), ttmpP0.getDoublePosition(1)));
                tmpP0 = new RealPoint(vp.getX(), vp.getY());
                tmpP1 = ttmpP0;
            }
        }
    }
    if (tmpDist < distance) {
        distance = tmpDist;
        p0 = tmpP0;
        p1 = tmpP1;
    }
    return new ValuePair<>(p0, p1);
}