org.joml.Vector3d Java Examples

The following examples show how to use org.joml.Vector3d. You can vote up the ones you like or vote down the ones you don't like, and go to the original project or source file by following the links above each example. You may check out the related API usage on the sidebar.

Example #1

Source File: RenderedMap.java From BlockMap with MIT License

6 votes

/** Returns the next Region to render */
protected synchronized RenderedRegion nextRegion() {
	try {
		// In region coordinates
		Vector3d cursorPos = new Vector3d(mouseWorldProperty.get(), 0).div(512).sub(.5, .5, 0);

		Comparator<RenderedRegion> comp = (a, b) -> Double.compare(new Vector3d(a.position.x(), a.position.y(), 0).sub(cursorPos).length(),
				new Vector3d(b.position.x(), b.position.y(), 0).sub(cursorPos).length());
		RenderedRegion min = null;
		for (RenderedRegion r : notRendered)
			if (r.getImage() == null && (min == null || comp.compare(min, r) > 0))
				min = r;
		notRendered.remove(min);
		return min;
	} catch (Throwable e) {
		e.printStackTrace();
		throw new Error(e);
	}
}

Example #2

Source File: VertexUtils.java From AnalyzeSkeleton with GNU General Public License v3.0

6 votes

private static List<Double> getAngles(final Vertex junction) {
	final List<Double> angles = new ArrayList<>();
	final Vector3d centroid = PointUtils.centroid(junction.getPoints());
	final List<Edge> branches = junction.getBranches();
	for (int i = 0; i < branches.size() - 1; i++) {
		for (int j = i + 1; j < branches.size(); j++) {
			final Vector3d endpoint = getOppositeCentroid(junction, centroid,
				branches.get(i));
			final Vector3d endpoint2 = getOppositeCentroid(junction, centroid,
				branches.get(j));
			final double angle = endpoint.angle(endpoint2);
			angles.add(angle);
		}
	}
	return angles;
}

Example #3

Source File: EnergyCalculator.java From OSPREY3 with GNU General Public License v2.0

6 votes

/** calculate the pair energy between position i1 and position i2 */
default double calcEnergyPair(AssignedCoords coords, int posi1, int posi2) {

	double energy = 0.0;

	// TODO: hopefully escape analysis will allocate this on the stack?
	Vector3d pos1 = new Vector3d();
	Vector3d pos2 = new Vector3d();

	int ffi = ffi();
	ConfSpace.IndicesPair indices = coords.getIndices(ffi, posi1, posi2);
	for (int i=0; i<indices.size(); i++) {
		int confAtomi1 = indices.getConfAtom1Index(i);
		int confAtomi2 = indices.getConfAtom2Index(i);
		int paramsi = indices.getParamsIndex(i);
		coords.coords.get(coords.getConfIndex(posi1, confAtomi1), pos1);
		coords.coords.get(coords.getConfIndex(posi2, confAtomi2), pos2);
		double r2 = pos1.distanceSquared(pos2);
		double r = Math.sqrt(r2);
		energy += calcEnergy(r, r2, coords.getParams(ffi, paramsi));
	}

	return energy;
}

Example #4

Source File: EnergyCalculator.java From OSPREY3 with GNU General Public License v2.0

6 votes

/** calculate the pair energy between position i and the static atoms */
default double calcEnergyStatic(AssignedCoords coords, int posi) {

	double energy = 0.0;

	// TODO: hopefully escape analysis will allocate this on the stack?
	Vector3d pos1 = new Vector3d();
	Vector3d pos2 = new Vector3d();

	int ffi = ffi();
	ConfSpace.IndicesSingle indices = coords.getIndices(ffi, posi);
	for (int i=0; i<indices.sizeStatics(); i++) {
		int confAtomi = indices.getStaticConfAtomIndex(i);
		int staticAtomi = indices.getStaticStaticAtomIndex(i);
		int paramsi = indices.getStaticParamsIndex(i);
		coords.coords.get(coords.getConfIndex(posi, confAtomi), pos1);
		coords.coords.get(coords.getStaticIndex(staticAtomi), pos2);
		double r2 = pos1.distanceSquared(pos2);
		double r = Math.sqrt(r2);
		energy += calcEnergy(r, r2, coords.getParams(ffi, paramsi));
	}

	return energy;
}

Example #5

Source File: Quadric.java From imagej-ops with BSD 2-Clause "Simplified" License

6 votes

/**
 * Creates a design matrix used for least squares fitting from a collection of
 * points.
 *
 * @see #solveVector(Collection)
 * @param points points in a 3D space.
 * @return a [points.size()][9] matrix of real values.
 */
private static PrimitiveMatrix createDesignMatrix(
	final Collection<Vector3d> points)
{
	final BasicMatrix.Builder<PrimitiveMatrix> builder = PrimitiveMatrix.FACTORY
		.getBuilder(points.size(), MIN_DATA);
	final Iterator<Vector3d> iterator = points.iterator();
	for (int i = 0; i < points.size(); i++) {
		final Vector3d p = iterator.next();
		builder.set(i, 0, p.x * p.x);
		builder.set(i, 1, p.y * p.y);
		builder.set(i, 2, p.z * p.z);
		builder.set(i, 3, 2 * p.x * p.y);
		builder.set(i, 4, 2 * p.x * p.z);
		builder.set(i, 5, 2 * p.y * p.z);
		builder.set(i, 6, 2 * p.x);
		builder.set(i, 7, 2 * p.y);
		builder.set(i, 8, 2 * p.z);
	}
	return builder.build();
}

Example #6