I am trying to sample around 1000 points from a 3-D ellipsoid, uniformly. Is there some way to code it such that we can get points starting from the equation of the ellipsoid?
I want points on the surface of the ellipsoid.
Theory
Using this excellent answer to the MSE question How to generate points uniformly distributed on the surface of an ellipsoid? we can
generate a point uniformly on the sphere, apply the mapping f :
(x,y,z) -> (x'=ax,y'=by,z'=cz) and then correct the distortion
created by the map by discarding the point randomly with some
probability p(x,y,z).
Assuming that the 3 axes of the ellipsoid are named such that
0 < a < b < c
We discard a generated point with
p(x,y,z) = 1 - mu(x,y,y)/mu_max
probability, ie we keep it with mu(x,y,y)/mu_max probability where
mu(x,y,z) = ((acy)^2 + (abz)^2 + (bcx)^2)^0.5
and
mu_max = bc
Implementation
import numpy as np
np.random.seed(42)
# Function to generate a random point on a uniform sphere
# (relying on https://stackoverflow.com/a/33977530/8565438)
def randompoint(ndim=3):
vec = np.random.randn(ndim,1)
vec /= np.linalg.norm(vec, axis=0)
return vec
# Give the length of each axis (example values):
a, b, c = 1, 2, 4
# Function to scale up generated points using the function `f` mentioned above:
f = lambda x,y,z : np.multiply(np.array([a,b,c]),np.array([x,y,z]))
# Keep the point with probability `mu(x,y,z)/mu_max`, ie
def keep(x, y, z, a=a, b=b, c=c):
mu_xyz = ((a * c * y) ** 2 + (a * b * z) ** 2 + (b * c * x) ** 2) ** 0.5
return mu_xyz / (b * c) > np.random.uniform(low=0.0, high=1.0)
# Generate points until we have, let's say, 1000 points:
n = 1000
points = []
while len(points) < n:
[x], [y], [z] = randompoint()
if keep(x, y, z):
points.append(f(x, y, z))
Checks
Check if all points generated satisfy the ellipsoid condition (ie that x^2/a^2 + y^2/b^2 + z^2/c^2 = 1):
for p in points:
pscaled = np.multiply(p,np.array([1/a,1/b,1/c]))
assert np.allclose(np.sum(np.dot(pscaled,pscaled)),1)
Runs without raising any errors. Visualize the points:
import matplotlib.pyplot as plt
fig = plt.figure()
ax = fig.add_subplot(projection="3d")
points = np.array(points)
ax.scatter(points[:, 0], points[:, 1], points[:, 2])
# set aspect ratio for the axes using https://stackoverflow.com/a/64453375/8565438
ax.set_box_aspect((np.ptp(points[:, 0]), np.ptp(points[:, 1]), np.ptp(points[:, 2])))
plt.show()
These points seem evenly distributed.
Problem with currently accepted answer
Generating a point on a sphere and then just reprojecting it without any further corrections to an ellipse will result in a distorted distribution. This is essentially the same as setting this posts's p(x,y,z) to 0. Imagine an ellipsoid where one axis is orders of magnitude bigger than another. This way, it is easy to see, that naive reprojection is not going to work.
Consider using Monte-Carlo simulation: generate a random 3D point; check if the point is inside the ellipsoid; if it is, keep it. Repeat until you get 1,000 points.
P.S. Since the OP changed their question, this answer is no longer valid.
J.F. Williamson, "Random selection of points distributed on curved surfaces", Physics in Medicine & Biology 32(10), 1987, describes a general method of choosing a uniformly random point on a parametric surface. It is an acceptance/rejection method that accepts or rejects each candidate point depending on its stretch factor (norm-of-gradient). To use this method for a parametric surface, several things have to be known about the surface, namely—
x(u, v), y(u, v) and z(u, v), which are functions that generate 3-dimensional coordinates from two dimensional coordinates u and v,
The ranges of u and v,
g(point), the norm of the gradient ("stretch factor") at each point on the surface, and
gmax, the maximum value of g for the entire surface.
The algorithm is then:
Generate a point on the surface, xyz.
If g(xyz) >= RNDU01()*gmax, where RNDU01() is a uniform random variate in [0, 1), accept the point. Otherwise, repeat this process.
Chen and Glotzer (2007) apply the method to the surface of a prolate spheroid (one form of ellipsoid) in "Simulation studies of a phenomenological model for elongated virus capsid formation", Physical Review E 75(5), 051504 (preprint).
Here is a generic function to pick a random point on a surface of a sphere, spheroid or any triaxial ellipsoid with a, b and c parameters. Note that generating angles directly will not provide uniform distribution and will cause excessive population of points along z direction. Instead, phi is obtained as an inverse of randomly generated cos(phi).
import numpy as np
def random_point_ellipsoid(a,b,c):
u = np.random.rand()
v = np.random.rand()
theta = u * 2.0 * np.pi
phi = np.arccos(2.0 * v - 1.0)
sinTheta = np.sin(theta);
cosTheta = np.cos(theta);
sinPhi = np.sin(phi);
cosPhi = np.cos(phi);
rx = a * sinPhi * cosTheta;
ry = b * sinPhi * sinTheta;
rz = c * cosPhi;
return rx, ry, rz
This function is adopted from this post: https://karthikkaranth.me/blog/generating-random-points-in-a-sphere/
One way of doing this whch generalises for any shape or surface is to convert the surface to a voxel representation at arbitrarily high resolution (the higher the resolution the better but also the slower). Then you can easily select the voxels randomly however you want, and then you can select a point on the surface within the voxel using the parametric equation. The voxel selection should be completely unbiased, and the selection of the point within the voxel will suffer the same biases that come from using the parametric equation but if there are enough voxels then the size of these biases will be very small.
You need a high quality cube intersection code but with something like an elipsoid that can optimised quite easily. I'd suggest stepping through the bounding box subdivided into voxels. A quick distance check will eliminate most cubes and you can do a proper intersection check for the ones where an intersection is possible. For the point within the cube I'd be tempted to do something simple like a random XYZ distance from the centre and then cast a ray from the centre of the elipsoid and the selected point is where the ray intersects the surface. As I said above, it will be biased but with small voxels, the bias will probably be small enough.
There are libraries that do convex shape intersection very efficiently and cube/elipsoid will be one of the options. They will be highly optimised but I think the distance culling would probably be worth doing by hand whatever. And you will need a library that differentiates between a surface intersection and one object being totally inside the other.
And if you know your elipsoid is aligned to an axis then you can do the voxel/edge intersection very easily as a stack of 2D square intersection elipse problems with the set of squares to be tested defined as those that are adjacent to those in the layer above. That might be quicker.
One of the things that makes this approach more managable is that you do not need to write all the code for edge cases (it is a lot of work to get around issues with floating point inaccuracies that can lead to missing or doubled voxels at the intersection). That's because these will be very rare so they won't affect your sampling.
It might even be quicker to simply find all the voxels inside the elipse and then throw away all the voxels with 6 neighbours... Lots of options. It all depends how important performance is. This will be much slower than the opther suggestions but if you want ~1000 points then ~100,000 voxels feels about the minimum for the surface, so you probably need ~1,000,000 voxels in your bounding box. However even testing 1,000,000 intersections is pretty fast on modern computers.
Depending on what "uniformly" refers to, different methods are applicable. In any case, we can use the parametric equations using spherical coordinates (from Wikipedia):
where s = 1 refers to the ellipsoid given by the semi-axes a > b > c. From these equations we can derive the relevant volume/area element and generate points such that their probability of being generated is proportional to that volume/area element. This will provide constant volume/area density across the surface of the ellipsoid.
1. Constant volume density
This method generates points on the surface of an ellipsoid such that their volume density across the surface of the ellipsoid is constant. A consequence of this is that the one-dimensional projections (i.e. the x, y, z coordinates) are uniformly distributed; for details see the plot below.
The volume element for a triaxial ellipsoid is given by (see here):
and is thus proportional to sin(theta) (for 0 <= theta <= pi). We can use this as the basis for a probability distribution that indicates "how many" points should be generated for a given value of theta: where the area density is low/high, the probability for generating a corresponding value of theta should be low/high, too.
Hence, we can use the function f(theta) = sin(theta)/2 as our probability distribution on the interval [0, pi]. The corresponding cumulative distribution function is F(theta) = (1 - cos(theta))/2. Now we can use Inverse transform sampling to generate values of theta according to f(theta) from a uniform random distribution. The values of phi can be obtained directly from a uniform distribution on [0, 2*pi].
Example code:
import matplotlib.pyplot as plt
import numpy as np
from numpy import sin, cos, pi
rng = np.random.default_rng(seed=0)
a, b, c = 10, 3, 1
N = 5000
phi = rng.uniform(0, 2*pi, size=N)
theta = np.arccos(1 - 2*rng.random(size=N))
x = a*sin(theta)*cos(phi)
y = b*sin(theta)*sin(phi)
z = c*cos(theta)
fig = plt.figure()
ax = fig.add_subplot(projection='3d')
ax.scatter(x, y, z, s=2)
plt.show()
which produces the following plot:
The following plot shows the one-dimensional projections (i.e. density plots of x, y, z):
import seaborn as sns
sns.kdeplot(data=dict(x=x, y=y, z=z))
plt.show()
2. Constant area density
This method generates points on the surface of an ellipsoid such that their area density is constant across the surface of the ellipsoid.
Again, we start by calculating the corresponding area element. For simplicity we can use SymPy:
from sympy import cos, sin, symbols, Matrix
a, b, c, t, p = symbols('a b c t p')
x = a*sin(t)*cos(p)
y = b*sin(t)*sin(p)
z = c*cos(t)
J = Matrix([
[x.diff(t), x.diff(p)],
[y.diff(t), y.diff(p)],
[z.diff(t), z.diff(p)],
])
print((J.T # J).det().simplify())
This yields
-a**2*b**2*sin(t)**4 + a**2*b**2*sin(t)**2 + a**2*c**2*sin(p)**2*sin(t)**4 - b**2*c**2*sin(p)**2*sin(t)**4 + b**2*c**2*sin(t)**4
and further simplifies to (dividing by (a*b)**2 and taking the sqrt):
sin(t)*np.sqrt(1 + ((c/b)**2*sin(p)**2 + (c/a)**2*cos(p)**2 - 1)*sin(t)**2)
Since for this case the area element is more complex, we can use rejection sampling:
import matplotlib.pyplot as plt
import numpy as np
from numpy import cos, sin
def f_redo(t, p):
return (
sin(t)*np.sqrt(1 + ((c/b)**2*sin(p)**2 + (c/a)**2*cos(p)**2 - 1)*sin(t)**2)
< rng.random(size=t.size)
)
rng = np.random.default_rng(seed=0)
N = 5000
a, b, c = 10, 3, 1
t = rng.uniform(0, np.pi, size=N)
p = rng.uniform(0, 2*np.pi, size=N)
redo = f_redo(t, p)
while redo.any():
t[redo] = rng.uniform(0, np.pi, size=redo.sum())
p[redo] = rng.uniform(0, 2*np.pi, size=redo.sum())
redo[redo] = f_redo(t[redo], p[redo])
x = a*np.sin(t)*np.cos(p)
y = b*np.sin(t)*np.sin(p)
z = c*np.cos(t)
fig = plt.figure()
ax = fig.add_subplot(projection='3d')
ax.scatter(x, y, z, s=2)
plt.show()
which yields the following distribution:
The following plot shows the corresponding one-dimensional projections (x, y, z):
I will have a 3-d grid of points (defined by Cartesian vectors). For any given coordinate within the grid, I wish to find the 8 grid points making the cuboid which surrounds the given coordinate. I also need the distances between the vertices of the cuboid and the given coordinate. I have found a way of doing this for a meshgrid with regular spacings, but not for irregular spacings. I do not yet have an example of the irregularly spaced grid data, I just know that the algorithm will have to deal with them eventually. My solution for the regularly spaced points is based off of this post, Finding index of nearest point in numpy arrays of x and y coordinates and is as follows:
import scipy as sp
import numpy as np
x, y, z = np.mgrid[0:5, 0:10, 0:20]
# Example 3-d grid of points.
b = np.dstack((x.ravel(), y.ravel(), z.ravel()))[0]
tree = sp.spatial.cKDTree(b)
example_coord = np.array([1.5, 3.5, 5.5])
d, i = tree.query((example_coord), 8)
# i being the indices of the closest grid points, d being their distance from the
# given coordinate, example_coord
b[i[0]], d[0]
# This gives one of the points of the surrounding cuboid and its distance from
# example_coord
I am looking to make this algorithm run as efficiently as possible as it will need to be run a lot. Thanks in advance for your help.
I would like to be able to plot two lines using direction and distance. It is a Drillhole trace, so I have the data in this format right now,
The depth is actually distance down the hole, not vertical depth. Azimuth is from magnetic north. Dip is based on 0 being horizontal. I want to plot two lines from the same point (0,0,0 is fine) and see how they differ, based on this kind of info.
I have no experience with Matplotlib but am comfortable with Python and would like to get to know this plotting tool. I have found this page and it helped to understand the framework, but I still can't figure out how to plot lines with 3d vectors. Can someone give me some pointers on how to do this or where to find the directions I need? Thank you
A script converting your coordinates to cartesian and plotting it with matplotlib with the comments included:
import numpy as np
import matplotlib.pyplot as plt
# import for 3d plot
from mpl_toolkits.mplot3d import Axes3D
# initializing 3d plot
fig = plt.figure()
ax = fig.add_subplot(111, projection = '3d')
# several data points
r = np.array([0, 14, 64, 114])
# get lengths of the separate segments
r[1:] = r[1:] - r[:-1]
phi = np.array([255.6, 255.6, 261.7, 267.4])
theta = np.array([-79.5, -79.5, -79.4, -78.8])
# convert to radians
phi = phi * 2 * np.pi / 360.
# in spherical coordinates theta is measured from zenith down; you are measuring it from horizontal plane up
theta = (90. - theta) * 2 * np.pi / 360.
# get x, y, z from known formulae
x = r*np.cos(phi)*np.sin(theta)
y = r*np.sin(phi)*np.sin(theta)
z = r*np.cos(theta)
# np.cumsum is employed to gradually sum resultant vectors
ax.plot(np.cumsum(x),np.cumsum(y),np.cumsum(z))
For a drillhole with 500 m you may use minimum curvature method, otherwise the position error will be really large. I implemented this in a python module for geostatistics (PyGSLIB). An example showing a complete desurvey process for a real drillhole database, including positions at assay/lithology intervals is shown at:
http://nbviewer.ipython.org/github/opengeostat/pygslib/blob/master/pygslib/Ipython_templates/demo_1.ipynb
This also shows how to export drillholes in VTK format to lad it in paraview.
Results shown in Paraview
The code in Cython to desurvey one interval is as follows:
cpdef dsmincurb( float len12,
float azm1,
float dip1,
float azm2,
float dip2):
"""
dsmincurb(len12, azm1, dip1, azm2, dip2)
Desurvey one interval with minimum curvature
Given a line with length ``len12`` and endpoints p1,p2 with
direction angles ``azm1, dip1, azm2, dip2``, this function returns
the differences in coordinate ``dz,dn,de`` of p2, assuming
p1 with coordinates (0,0,0)
Parameters
----------
len12, azm1, dip1, azm2, dip2: float
len12 is the length between a point 1 and a point 2.
azm1, dip1, azm2, dip2 are direction angles azimuth, with 0 or
360 pointing north and dip angles measured from horizontal
surface positive downward. All these angles are in degrees.
Returns
-------
out : tuple of floats, ``(dz,dn,de)``
Differences in elevation, north coordinate (or y) and
east coordinate (or x) in an Euclidean coordinate system.
See Also
--------
ang2cart,
Notes
-----
The equations were derived from the paper:
http://www.cgg.com/data//1/rec_docs/2269_MinimumCurvatureWellPaths.pdf
The minimum curvature is a weighted mean based on the
dog-leg (dl) value and a Ratio Factor (rf = 2*tan(dl/2)/dl )
if dl is zero we assign rf = 1, which is equivalent to balanced
tangential desurvey method. The dog-leg is zero if the direction
angles at the endpoints of the desurvey intervals are equal.
Example
--------
>>> dsmincurb(len12=10, azm1=45, dip1=75, azm2=90, dip2=20)
(7.207193374633789, 1.0084573030471802, 6.186459064483643)
"""
# output
cdef:
float dz
float dn
float de
# internal
cdef:
float i1
float a1
float i2
float a2
float DEG2RAD
float rf
float dl
DEG2RAD=3.141592654/180.0
i1 = (90 - dip1) * DEG2RAD
a1 = azm1 * DEG2RAD
i2 = (90 - dip2) * DEG2RAD
a2 = azm2 * DEG2RAD
# calculate the dog-leg (dl) and the Ratio Factor (rf)
dl = acos(cos(i2-i1)-sin(i1)*sin(i2)*(1-cos(a2-a1)))
if dl!=0.:
rf = 2*tan(dl/2)/dl # minimum curvature
else:
rf=1 # balanced tangential
dz = 0.5*len12*(cos(i1)+cos(i2))*rf
dn = 0.5*len12*(sin(i1)*cos(a1)+sin(i2)*cos(a2))*rf
de = 0.5*len12*(sin(i1)*sin(a1)+sin(i2)*sin(a2))*rf
return dz,dn,de
I have a set of GPS coordinates in decimal notation, and I'm looking for a way to find the coordinates in a circle with variable radius around each location.
Here is an example of what I need. It is a circle with 1km radius around the coordinate 47,11.
What I need is the algorithm for finding the coordinates of the circle, so I can use it in my kml file using a polygon. Ideally for python.
see also Adding distance to a GPS coordinate for simple relations between lat/lon and short-range distances.
this works:
import math
# inputs
radius = 1000.0 # m - the following code is an approximation that stays reasonably accurate for distances < 100km
centerLat = 30.0 # latitude of circle center, decimal degrees
centerLon = -100.0 # Longitude of circle center, decimal degrees
# parameters
N = 10 # number of discrete sample points to be generated along the circle
# generate points
circlePoints = []
for k in xrange(N):
# compute
angle = math.pi*2*k/N
dx = radius*math.cos(angle)
dy = radius*math.sin(angle)
point = {}
point['lat']=centerLat + (180/math.pi)*(dy/6378137)
point['lon']=centerLon + (180/math.pi)*(dx/6378137)/math.cos(centerLat*math.pi/180)
# add to list
circlePoints.append(point)
print circlePoints
Use the formula for "Destination point given distance and bearing from start point" here:
http://www.movable-type.co.uk/scripts/latlong.html
with your centre point as start point, your radius as distance, and loop over a number of bearings from 0 degrees to 360 degrees. That will give you the points on a circle, and will work at the poles because it uses great circles everywhere.
It is a simple trigonometry problem.
Set your coordinate system XOY at your circle centre. Start from y = 0 and find your x value with x = r. Then just rotate your radius around origin by angle a (in radians). You can find the coordinates of your next point on the circle with Xi = r * cos(a), Yi = r * sin(a). Repeat the last 2 * Pi / a times.
That's all.
UPDATE
Taking the comment of #poolie into account, the problem can be solved in the following way (assuming the Earth being the right sphere). Consider a cross section of the Earth with its largest diameter D through our point (call it L). The diameter of 1 km length of our circle then becomes a chord (call it AB) of the Earth cross section circle. So, the length of the arc AB becomes (AB) = D * Theta, where Theta = 2 * sin(|AB| / 2). Further, it is easy to find all other dimensions.