javaalgorithmcluster-analysisdistancepoints
Given a set of points in 3d space, find all sets of points within a distance of eachother
I have a set of 3d points S. I need to find the set X of all sets of points in S which are within manhattan distance d of each other.
i.e. for each set Y in X there exists atleast one point in 3d space that is within distance d of all points in Y
The length of set S will never be >20 but I will have to run this analysis on a stream of sets which are being produced at ~10 new sets per second, so whatever solution I use will have to be fairly efficient.
an example to help visualize the problem, given the following:
the output would be ((A,B), (B,C,E), (B,D,E))
we only care about the largest possible sets so the sets (B,C), (B,D), (B,E), (C,E) and (D,E), while within the given parameters, are not in the output given they are subsets of other sets in X
also this I'm doing this in java but any pointers in terms of algorithms or pseudo code would be greatly appreciated, thanks in advance.
Solution
A solution in pseudocode would be:
calculate_intersections(areas):
intersections = calculate every two intersecting areas
combinations = combine_intersections(intersections)
reduced = remove all sets in combinations that are included in bigger sets
combine_intersections(intersections):
do:
combinations = new HashSet
for s1 in intersections:
for s2 in intersections:
diff_1_2 = s1 \ s2
diff_2_1 = s2 \ s1
if diff_1_2.len == 1 && diff_2_1.len == 1:
union = diff_1_2 + diff_2_1
if union in intersections:
union2 = s1 + s2
if !union2 in intersections:
combinations.add(union)
while (combinations not empty)
An implementation in Java could look like this:
import java.util.Arrays;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import org.apache.commons.collections4.SetUtils;
public class IntersectionSetCalculation {
private static class ManhattanDistanceArea {
private String id;
private Vector3D center;
private double distance;
public ManhattanDistanceArea(Vector3D center, double distance, String id) {
this.center = center;
this.distance = distance;
this.id = id;
}
@Override
public String toString() {
return id;
}
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((center == null) ? 0 : center.hashCode());
long temp;
temp = Double.doubleToLongBits(distance);
result = prime * result + (int) (temp ^ (temp >>> 32));
result = prime * result + ((id == null) ? 0 : id.hashCode());
return result;
}
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
ManhattanDistanceArea other = (ManhattanDistanceArea) obj;
if (center == null) {
if (other.center != null)
return false;
}
else if (!center.equals(other.center))
return false;
if (Double.doubleToLongBits(distance) != Double.doubleToLongBits(other.distance))
return false;
if (id == null) {
if (other.id != null)
return false;
}
else if (!id.equals(other.id))
return false;
return true;
}
public boolean intersects(ManhattanDistanceArea other) {
double maxDist = distance + other.distance;
return center.distance(other.center, 1) < maxDist;
}
}
/**
* Calculate the intersection of all areas (maximum of 2 areas in an intersection)
*/
public static Set<Set<ManhattanDistanceArea>> getIntersectingAreas(Set<ManhattanDistanceArea> areas) {
Set<Set<ManhattanDistanceArea>> intersections = new HashSet<Set<ManhattanDistanceArea>>();
for (ManhattanDistanceArea area : areas) {
for (ManhattanDistanceArea area2 : areas) {
if (!area.equals(area2) && area.intersects(area2)) {
HashSet<ManhattanDistanceArea> intersection = new HashSet<ManhattanDistanceArea>();
intersection.add(area);
intersection.add(area2);
intersections.add(intersection);
}
}
}
Set<Set<ManhattanDistanceArea>> combined = combineIntersections(intersections);
Set<Set<ManhattanDistanceArea>> reduced = reduceIntersections(combined);
return reduced;
}
/**
* Combine the small intersections (with a maximum of 2 areas in an intersection) to bigger intersections
*/
public static Set<Set<ManhattanDistanceArea>> combineIntersections(Set<Set<ManhattanDistanceArea>> inters) {
Set<Set<ManhattanDistanceArea>> intersections = new HashSet<Set<ManhattanDistanceArea>>(inters);
Set<Set<ManhattanDistanceArea>> combinations;
do {
combinations = new HashSet<Set<ManhattanDistanceArea>>();
for (Set<ManhattanDistanceArea> intersecting1 : intersections) {
for (Set<ManhattanDistanceArea> intersecting2 : intersections) {
Set<ManhattanDistanceArea> diff_1_2 = SetUtils.difference(intersecting1, intersecting2);
Set<ManhattanDistanceArea> diff_2_1 = SetUtils.difference(intersecting2, intersecting1);
if (diff_1_2.size() == 1 && diff_2_1.size() == 1) {
Set<ManhattanDistanceArea> union_1_2 = SetUtils.union(diff_1_2, diff_2_1);
if (intersections.contains(union_1_2)) {
Set<ManhattanDistanceArea> union = SetUtils.union(intersecting1, intersecting2);
if (!intersections.contains(union)) {
combinations.add(union);
}
}
}
}
}
intersections.addAll(combinations);
} while (!combinations.isEmpty());
return intersections;
}
/**
* Remove the small intersections that are completely covered by bigger intersections
*/
public static Set<Set<ManhattanDistanceArea>> reduceIntersections(Set<Set<ManhattanDistanceArea>> inters) {
Set<Set<ManhattanDistanceArea>> intersections = new HashSet<Set<ManhattanDistanceArea>>(inters);
Iterator<Set<ManhattanDistanceArea>> iter = intersections.iterator();
while (iter.hasNext()) {
Set<ManhattanDistanceArea> intersection = iter.next();
for (Set<ManhattanDistanceArea> intersection2 : inters) {
if (intersection2.size() > intersection.size() && intersection2.containsAll(intersection)) {
iter.remove();
break;
}
}
}
return intersections;
}
public static void main(String[] args) {
final double dist = 2d;//the manhattan distance d
ManhattanDistanceArea A = new ManhattanDistanceArea(new Vector3D(0, -3, 0), dist, "A");
ManhattanDistanceArea B = new ManhattanDistanceArea(new Vector3D(0, 0, 0), dist, "B");
ManhattanDistanceArea C = new ManhattanDistanceArea(new Vector3D(3.5, 0, 0), dist, "C");
ManhattanDistanceArea D = new ManhattanDistanceArea(new Vector3D(0, 3.5, 0), dist, "D");
ManhattanDistanceArea E = new ManhattanDistanceArea(new Vector3D(1, 1, 0), dist, "E");
ManhattanDistanceArea F = new ManhattanDistanceArea(new Vector3D(-1, 1, 0), dist, "F");
//test the example you provided
Set<ManhattanDistanceArea> abcde = new HashSet<ManhattanDistanceArea>();
abcde.addAll(Arrays.asList(new ManhattanDistanceArea[] {A, B, C, D, E}));
//test another example
Set<ManhattanDistanceArea> abcdef = new HashSet<ManhattanDistanceArea>();
abcdef.addAll(abcde);
abcdef.add(F);
Set<Set<ManhattanDistanceArea>> intersectionsABCDE = getIntersectingAreas(abcde);
Set<Set<ManhattanDistanceArea>> intersectionsABCDEF = getIntersectingAreas(abcdef);
System.out.println(intersectionsABCDE);
System.out.println(intersectionsABCDEF);
//test the runntime for 1000 calculation
double startTime = System.currentTimeMillis();
final int calculations = 1000;
for (int i = 0; i < calculations; i++) {
Set<ManhattanDistanceArea> areas = new HashSet<ManhattanDistanceArea>();
for (int j = 0; j < 20; j++) {
areas.add(new ManhattanDistanceArea(new Vector3D(Math.random() * 10 - 5, Math.random() * 10 - 5, Math.random() * 10 - 5), dist,
"A" + j));
}
getIntersectingAreas(areas);
}
System.out.println("\nTime used for " + calculations + " intersection calculations (with sets of size 20): "
+ (System.currentTimeMillis() - startTime) + "ms");
}
}
For the implementation I used this class Vector3D:
public class Vector3D {
public double x;
public double y;
public double z;
public static final Vector3D NAN_VEC = new Vector3D(Double.NaN, Double.NaN, Double.NaN);
public static final Vector3D NULL_VEC = new Vector3D(0, 0, 0);
public enum Axis {
X, Y, Z;
}
public Vector3D() {
}
/**
* Crate a new Vector2D with x and y components.
*/
public Vector3D(double x, double y, double z) {
this.x = x;
this.y = y;
this.z = z;
}
public Vector3D(double... val) {
x = val[0];
y = val[1];
z = val[2];
}
/**
* Create a Vector3D by two angles (in degree).
*
* The first angle is in XY direction. The second angle is the Z direction.
*
* An angle (XY) of 0° results in (x, y) = (1, 0); 90° in (x, y) = (0, 1); ... An angle (Z) of 0° results in (x, y, z) = (x, y, 0); 90° in (x, y,
* z) = (x, y, 1); -90° in (x, y, z) = (x, y, -1)
*
* The resulting vector has a length of 1.
*
* @param angleXY
* The angle of the new vector (in degree) for the XY direction (from 0 to 360).
*
* @param angleZ
* The angle of the new vector (in degree) for the Z direction (from -90 to 90).
*/
public Vector3D(double angleXY, double angleZ) {
x = Math.cos(angleXY * Math.PI / 180) * Math.cos(angleZ * Math.PI / 180);
y = Math.sin(angleXY * Math.PI / 180) * Math.cos(angleZ * Math.PI / 180);
z = Math.sin(angleZ * Math.PI / 180);
double len = length();
x /= len;
y /= len;
z /= len;
}
private Vector3D(Vector3D clone) {
this.x = clone.x;
this.y = clone.y;
}
@Override
public Vector3D clone() {
return new Vector3D(this);
}
@Override
public String toString() {
return "Vector3D[x: " + x + " y: " + y + " z:" + z + "]";
}
@Override
public boolean equals(Object obj) {
if (obj instanceof Vector3D) {
Vector3D v = (Vector3D) obj;
return Math.abs(x - v.x) < 1e-8 && Math.abs(y - v.y) < 1e-8 && Math.abs(z - v.z) < 1e-8;
}
return false;
}
/**
* Get this vector as 3D-Array.
*/
public double[] asArray() {
return new double[] {x, y, z};
}
/**
* The (euclidean) length of the Vector.
*/
public double length() {
return Math.sqrt(Math.pow(x, 2) + Math.pow(y, 2) + Math.pow(z, 2));
}
/**
* The length of this vector in a given norm.
*
* @param norm
* The norm of the vector length.
*
* @return The length of this vector in the given norm.
*/
public double length(int norm) {
if (norm == Integer.MAX_VALUE) {
return Math.max(Math.max(x, y), z);
}
return Math.pow(Math.pow(x, norm) + Math.pow(y, norm) + Math.pow(z, norm), 1.0 / norm);
}
/**
* Rotate this vector an angle (in degrees) around an axis resulting in a new Vector that is returned.
*
* @param degrees
* The angle to return the vector.
*
* @param axis
* The axis around which the vector is rotated.
*
* @return The new created vector.
*/
public Vector3D rotate(double degrees, Axis axis) {
double cos = Math.cos(degrees * Math.PI / 180);
double sin = Math.sin(degrees * Math.PI / 180);
switch (axis) {
case X:
return new Vector3D(x, cos * y - sin * z, sin * y + cos * z);
case Y:
return new Vector3D(cos * x + sin * z, y, -sin * x + cos * z);
case Z:
return new Vector3D(cos * x - sin * y, sin * x + cos * y, z);
default:
return null;
}
}
/**
* Project the vector given as parameter on this vector.
*
* @param vec
* The vector that is to be projected on this vector.
*
* @return The projected vector.
*/
public Vector3D project(Vector3D vec) {
return mult(scalar(vec) / Math.pow(length(), 2));
}
/**
* Add another Vector3D to this vector resulting in a new Vector that is returned.
*
* @param vec
* The vector added to this vector.
*
* @return The new created vector.
*/
public Vector3D add(Vector3D vec) {
return new Vector3D(x + vec.x, y + vec.y, z + vec.z);
}
/**
* Subtract another Vector3D from this vector resulting in a new Vector that is returned.
*
* @param vec
* The vector subtracted from this vector.
*
* @return The new created vector.
*/
public Vector3D sub(Vector3D vec) {
return new Vector3D(x - vec.x, y - vec.y, z - vec.z);
}
/**
* Multiply this vector with a scalar resulting in a new Vector that is returned.
*
* @param scalar
* The scalar to multiply this vector with.
*
* @return The new created vector.
*/
public Vector3D mult(double scalar) {
return new Vector3D(x * scalar, y * scalar, z * scalar);
}
/**
* Check whether this vector is linearly dependent to the parameter vector.
*
* @param vec
* The checked vector.
*
* @return True if the vectors are linearly dependent. False otherwise.
*/
public boolean isLinearlyDependent(Vector3D vec) {
double t1 = (x == 0 ? 0 : vec.x / x);
double t2 = (y == 0 ? 0 : vec.y / y);
double t3 = (z == 0 ? 0 : vec.z / z);
return Math.abs(t1 - t2) < 1e-5 && Math.abs(t1 - t3) < 1e-5 && t1 != 0;//all parameters t are equal and != 0
}
/**
* Calculate the scalar product of this vector and the parameter vector.
*
* @param vec
* The vector to calculate the scalar with this vector.
*
* @return The scalar of the vectors.
*/
public double scalar(Vector3D vec) {
return this.x * vec.x + this.y * vec.y + this.z * vec.z;
}
/**
* Calculate the cross product of this vector with another vector (resulting vector = this X parameter vector)
*
* @param vec
* The second vector for the cross product calculation.
*
* @return The cross product vector of the two vectors.
*/
public Vector3D cross(Vector3D vec) {
return new Vector3D(y * vec.z - z * vec.y, z * vec.x - x * vec.z, x * vec.y - y * vec.x);
}
/**
* Create a new vector with the same direction but a different length as this vector.
*
* @param length
* The length of the new vector.
*
* @return The new vector with a new length.
*/
public Vector3D setLength(double length) {
double len = length();
return new Vector3D(x * length / len, y * length / len, z * length / len);
}
/**
* Get the distance of this point's position vector to another point's position vector.
*
* @param p
* The second point's position vector.
*
* @return The distance between the points.
*/
public double distance(Vector3D p) {
return Math.sqrt((this.x - p.x) * (this.x - p.x) + (this.y - p.y) * (this.y - p.y) + (this.z - p.z) * (this.z - p.z));
}
/**
* Get the distance of this point's position vector to another point's position vector in a given norm.
*
* @param p
* The second point's position vector.
*
* @param norm
* The norm in which the distance is calculated (1 -> manhattan, 2 -> euclide, ...)
*
* @return The distance between the points in the given norm.
*/
public double distance(Vector3D p, int norm) {
return Math.pow((Math.pow(Math.abs(this.x - p.x), norm) + Math.pow(Math.abs(this.y - p.y), norm) + Math.pow(Math.abs(this.z - p.z), norm)),
1d / norm);
}
/**
* Change this vector to the new coordinates.
*/
public void move(double x, double y, double z) {
this.x = x;
this.y = y;
this.z = z;
}
/**
* Move a point's position vector in a direction (by a vector) and a distance.
*
* @param p
* The direction vector.
*
* @param distance
* The distance to move the new vector
*
* @return The new created vector.
*/
public Vector3D moveTo(Vector3D p, double distance) {
double d = distance(p);
double dx = p.x - x;
double dy = p.y - y;
double dz = p.z - z;
double coef = distance / d;
return new Vector3D(x + dx * coef, y + dy * coef, z + dz * coef);
}
/**
* Get the angle difference of this vector to another vector.
*
* @param vec
* The other vector.
*
* @return The angle difference of the two vectors (from 0° to 180°).
*/
public double getAngleTo(Vector3D vec) {
double angle = Math.acos(scalar(vec) / (length() * vec.length())) * 180 / Math.PI;
if (angle > 180) {
angle = 360 - angle;
}
return angle;
}
/**
* Get the vector from this point to another.
*
* @param vec
* The point to which the vector is calculated.
*
* @return The vector from this points position vector to the other point.
*/
public Vector3D vectorTo(Vector3D vec) {
return new Vector3D(vec.x - x, vec.y - y, vec.z - z);
}
/**
* Checks whether a point (by its position vector) is in a given range of this point.
*
* @param p
* The point that is checked.
*
* @param range
* The range used for the check.
*
* @return True if the point is in the range of this point (distance <= range).
*/
public boolean isInRange(Vector3D p, double range) {
return p != this && distance(p) <= range;
}
}
and the class SetUtils from the apache commons lib.
I also added some tests:
- the test from your question
- another test with a bigger intersection set
- a test for the runtime
The results are:
[[A, B], [B, E, C], [B, E, D]]
[[A, B], [B, E, C], [D, E, F, B]]
Time used for 1000 intersection calculations (with sets of size 20): 791.0ms
So the results seem to be correct and you can calculate more than 1000 intersections in a second.
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