I have a question considering a 3D dataset.
I have two different datasets consisting of 3D coordinates, one of these datasets I use to create surfaces in the form of cylinders (lets call it blue for now), from the other dataset I should be able to count the amount of 'points' (x,y,z) that are in this cylinder surface (lets call this dataset orange for now).
I found some code on stackoverflow which I use to create a cylinder in 3D for 2 points out the blue dataset, this all works.
However, now I should classify for every coordinate of the orange dataset if it falls inside this cylinder surface.
This is the code I use to plot the cylinder surface (found here: Plotting a solid cylinder centered on a plane in Matplotlib):
p0 = np.array([-0.0347944, 0.0058072, -0.022887199999999996]) #point at one end
p1 = np.array([-0.0366488, 0.0061488, -0.023424) #point at other end
R = 0.00005
#vector in direction of axis
v = p1 - p0
#find magnitude of vector
mag = norm(v)
#unit vector in direction of axis
v = v / mag
#make some vector not in the same direction as v
not_v = np.array([1, 0, 0])
if (v == not_v).all():
not_v = np.array([0, 1, 0])
#make vector perpendicular to v
n1 = np.cross(v, not_v)
#normalize n1
n1 /= norm(n1)
#make unit vector perpendicular to v and n1
n2 = np.cross(v, n1)
#surface ranges over t from 0 to length of axis and 0 to 2*pi
t = np.linspace(0, mag, 2)
theta = np.linspace(0, 2 * np.pi, 100)
rsample = np.linspace(0, R, 2)
#use meshgrid to make 2d arrays
t, theta2 = np.meshgrid(t, theta)
rsample,theta = np.meshgrid(rsample, theta)
#generate coordinates for surface
# "Tube"
X, Y, Z = [p0[i] + v[i] * t + R * np.sin(theta2) * n1[i] + R * np.cos(theta2) * n2[i] for i in [0, 1, 2]]
# "Bottom"
X2, Y2, Z2 = [p0[i] + rsample[i] * np.sin(theta) * n1[i] + rsample[i] * np.cos(theta) * n2[i] for i in [0, 1, 2]]
# "Top"
X3, Y3, Z3 = [p0[i] + v[i]*mag + rsample[i] * np.sin(theta) * n1[i] + rsample[i] * np.cos(theta) * n2[i] for i in [0, 1, 2]]
ax=plt.subplot(111, projection='3d')
ax.plot_surface(X, Y, Z, color='blue', alpha=0.5)
ax.plot_surface(X2, Y2, Z2, color='blue', alpha=0.5)
ax.plot_surface(X3, Y3, Z3, color='green', alpha=0.7)
plt.show()
Lets now say I need to classify the following points as 'inside' or 'outside' the cylinder surface:
point1 = (-0.0321, 0.003, -0.01) point2 = (-0.5, 0.004, 0.03) point3 = (0.0002, -0.02, 0.00045)
It is important to mention that these points in the orange dataset of which I need to find out whether or not these are inside or outside the cylinder surface, do not have to be points on the top and bottom part enclosing the cylinder surface, these points can be anywhere in a 3D space in and outside the cylinder surface.
The code mentioned here outputs the following result.
Cylinder surface enclosing two point of the blue dataset
UPDATE: Thanks for the help! However, I found the solution here: How to check if a 3D point is inside a cylinder
Your question sounds more about geometry than about coding. What exactly do you need?
Geometrically, if you want to check whether the point (a, b, c) lies inside of a (canonical) cylindrical surface
(x, y, z) such that {x^2 + y^2 = r^2, z in [zi, zf] },
simply check whether a^2 + b^2 < r^2 and c in [zi, zf] is True.
If the axis of your cylinder is not aligned to the z-axis, just bring the point (a, b, c) to a new system where the cylinder is in canonical form. In general, if the cylinder axis lies along the (unit) vector v. the angle with respect to the z-axis is simply beta = arccos(v[2]) (v is already normalized!). Then you want to use Rodrigues' rotation formula with k = v and theta = -beta (note the sign) to transform (a, b, c). You should also check whether the rotated p0 and p1 already lie on the (rotated) z-axis, otherwise you should apply an additional translation to (a, b, c) before making the comparison.
If what you need is help coding this up, well, post your attempt and ask away :)
per wiki, the conversion from barycentric coordinates to Cartesian coordinates is as follow
here is a piece of code come from somewhere else
import numpy as np
import matplotlib.pyplot as plt
# from barycentric coordinates to Cartesian coordinates
a = np.array([0. , 0. , 1. , 0.25, 0.25, 0.5 ])
b = np.array([0. , 1. , 0. , 0.25, 0.5 , 0.25])
c = np.array([1. , 0. , 0. , 0.5 , 0.25, 0.25])
x = 0.5 * ( 2.*b+c ) / ( a+b+c )
y = 0.5*np.sqrt(3) * c / (a+b+c)
plt.scatter(x,y)
plt.show()
it seems that the piece of code is using another formula, if it is, what is the formula?
assume the barycentric coordinates of B is (0,0,1), how to compute its Cartesian coordinates? what lambda_1, lambda_2, lambda_3, x_1, x_2, x_3, y_1, y_2, y_3 are for point B?
Your formula is correct.
Assuming that the three corners of a triangles are encoded as the columns of the matrix t, here is a simple Python implementation:
import numpy as np
def get_cartesian_from_barycentric(b, t):
return t.dot(b)
b = np.array([0.25,0.3,0.45]) # Barycentric coordinates
t = np.transpose(np.array([[0,0],[1,0],[0,1]])) # Triangle
c = get_cartesian_from_barycentric(b, t)
The formula you found is also calculating Cartesian from barycentric coordinates but uses a predefined regular triangle with the following coordinates:
(x1,y1) = (0,0)
(x2,y2) = (1,0)
(x3,y3) = (1/2,sqrt(3)/2)
In this calculation, the code considers that every column is a point expressed with barycentric coordinates. Thus, it calculates 6 points at once. Furthermore, barycentric coordinates need to be normalized, i.e., lambda1 + lamda2 + lambda3 = 1. This code does not assume normalization, so it needs to divide by the sum of lambdas to ensure this property. Of course, we can see that the sum is always 1 for all 6 points, but the code could be used for lambdas that do not sum to 1.
In the last example you gave, B is a point of the triangle and is not expressed with barycentric coordinates. P is the point that is expressed with barycentric coordinate relative to the point A, B, and C. Let A = (x1,y1), B = (x2,y2), and C = (x3,y3), and that P has barycentric coordinates (l1,l2,l3). Then, the Cartesian coordinates (xp,yp) of P is
xp = l1*x1 + l2*x2 + l3*x3
yp = l1*y1 + l2*y2 + l3*y3
I have this triangle in pygame
triangle = pygame.draw.polygon(window, (210,180,140), [[x, y], [x -10, y -10], [x + 10, y - 10]], 5)
that i need to rotate towards the mouse, very much like the center arrow in this gif: http://i.stack.imgur.com/yxsV1.gif. Pygame doesn't have a built in function for rotating polygons, so I'll need to manually move the three points in a circle, with the lowermost point [x,y] pointing towards the coords of the mouse. The variables I have are:
the distance between the center of the triangle and the circle i want it to rotate along (i.e. the radius)
the distance from the center to the mouse coordinates
the coordinates of the lowermost point of the triangle [x,y] and the other two sides
with this information, how can I use trigonometry to rotate all three sides of the triangle so that the bottom point allways faces the mouse position?
EDIT: this is what I've got so far, but it only manages to move the triangle back and forth along a diagonal instead of rotating.
def draw(self):
curx,cury = cur
#cur is a global var that is mouse coords
angle = math.atan2(self.x - curx, self.y - cury)
distance = math.sqrt(200 - (200 * math.cos(angle)))
x = self.x + distance
y = self.y + distance
triangle = pygame.draw.polygon(window, (210,180,140), [[x, y], [x - 10,y - 10], [x + 10,y - 10]], 5)
Edit: Thinking about this again this morning there's another way to do this since the polygon is a triangle. Also the math is potentially easier to understand, and it requires less calculation for each point.
Let Cx and Cy be the center of the circle inscribing the triangle. We can describe the equation of a circle using the parametric equation:
F(t) = { x = Cx + r * cos(t)
{ y = Cy + r * sin(t)
Where r is the radius of the circle, and t represents the angle along the circle.
Using this equation we can describe the triangle using the points that touch the circle, in this case we'll use t = { 0, 3 * pi / 4, 5 * pi / 4 } as our points.
We also need to calculate the angle that we need to rotate the triangle so that the point that was at t = (0) is on a line from (Cx, Cy) to the mouse location. The angle between two (normalized) vectors can be calculated by:
t = acos(v1 . v2) = acos(<x1, y1> . <x2, y2>) = acos(x1 * x2 + y1 * y2)
where . represents the dot product, and acos is the inverse cosine (arccos or cos^-1).
From these two equations we can easily create a python function which, given the center of the triangle/circle, the radius of the circle, and the location of the mouse, returns a list of tuples representing the x-y coordinates of the triangle. (For the example the center and mouse position are tuples of the form (x, y))
def get_points(center, radius, mouse_position):
# calculate the normalized vector pointing from center to mouse_position
length = math.hypot(mouse_position[0] - center[0], mouse_position[1] - center[1])
# (note we only need the x component since y falls
# out of the dot product, so we won't bother to calculate y)
angle_vector_x = (mouse_position[0] - center[0]) / length
# calculate the angle between that vector and the x axis vector (aka <1,0> or i)
angle = math.acos(angle_vector_x)
# list of un-rotated point locations
triangle = [0, (3 * math.pi / 4), (5 * math.pi / 4)]
result = list()
for t in triangle:
# apply the circle formula
x = center[0] + radius * math.cos(t + angle)
y = center[1] + radius * math.sin(t + angle)
result.append((x, y))
return result
Calling this function like this:
from pprint import pprint
center = (0,0)
radius = 10
mouse_position = (50, 50)
points = get_points(center, radius, mouse_position)
pprint(points)
produces:
[(7.071067811865475, 7.0710678118654755),
(-10.0, 1.2246467991473533e-15),
(-1.8369701987210296e-15, -10.0)]
which is the three points (x, y) of the triangle.
I'm going to leave the original method below, since it's the way that modern computer graphics systems (OpenGL, DirectX, etc.) do it.
Rotation about the centroid of a arbitrary polygon is a sequence of three distinct matrix operations, Translating the object so that the centroid is at the origin (0,0), applying a rotation, and translating back to the original position.
Calculating the centroid for an arbitrary n-gon is probably outside the scope of an answer here, (Google will reveal many options), but it could be done completely by hand using graph paper. Call that point C.
To simplify operations, and to enable all transformations to be applied using simple matrix multiplications, we use so called Homogeneous coordinates, which are of the form:
[ x ]
p = | y |
[ 1 ]
for 2d coordinates.
Let
[ Cx ]
C = | Cy |
[ 1 ]
The general form of the translation matrix is:
[ 1 0 Vx ]
T = | 0 1 Vy |
[ 0 0 1 ]
Where <Vx, Vy> represents the translation vector. Since the goal of the translation is to move the centroid C to the origin, Vx = -Cx and Vy = -Cy. The inverse translation T' is simply Vx = Cx, Vy = Cy
Next the rotation matrix is needed. Let r be the desired clockwise rotation angle, and R be the general form of the rotation matrix. Then,
[ cos(r) sin(r) 0 ]
R = | -sin(r) cos(r) 0 |
[ 0 0 1 ]
The final transformation matrix is therefore:
[ 1 0 -Cx ] [ cos(r) sin(r) 0 ] [ 1 0 Cx ]
TRT' = | 0 1 -Cy | * | -sin(r) cos(r) 0 | * | 0 1 Cy |
[ 0 0 1 ] [ 0 0 1 ] [ 0 0 1 ]
Which simplifies to:
[ cos(r) sin(r) cos(r)*Cx-Cx+Cy*sin(r) ]
|-sin(r) cos(r) cos(r)*Cy-Cy-Cx*sin(r) |
[ 0 0 1 ]
Applying this to a point p = (x,y) we obtain the following equation:
p' = { x' = Cx*cos(r)-Cx+Cy*sin(r)+x*cos(r)+y*sin(r)
{ y' = -Cx*sin(r)+Cy*cos(r)-Cy-x*sin(r)+y*cos(r)
In Python:
def RotatePoint(c, p, r):
x = c[0]*math.cos(r)-c[0]+c[1]*math.sin(r)+p[0]*math.cos(r)+p[1]*math.sin(r)
y = -c[0]*math.sin(r)+c[1]*math.cos(r)-c[1]-p[0]*math.sin(r)+p[1]*math.cos(r)
return (x, y)
After typing all that I realize that your object may already be centered on the origin, in which case the function above simplifies to x=p[0]*math.cos(r)+p[1]*math.sin(r) and y=p[0]*math.sin(r)+p[1]*math.cos(r)
I put some faith in Wolfram Alpha here, rather than multiplying everything out by hand. If anyone notices any issues, feel free to make the edit.
I have two corresponding 2D arrays, one of velocity, one of intensity. The values of intensity match each of the velocity elements.
I have created another 1d array that that goes from min to max velocity in even bin widths.
How would I sum the intensity values from my 2d array which correspond to my velocity bins in my 1d array.
For example: if I have I = 5 corresponding to velocity = 101km/s, then this is added to the bin 100 - 105 km/s.
Here's my input:
rad = np.linspace(0, 3, 100) # polar coordinates
phi = np.linspace(0, np.pi, 100)
r, theta = np.meshgrid(rad, phi) # 2d arrays of r and theta coordinates
V0 = 225 # Velocity function w/ constants.
rpe = 0.149
alpha = 0.003
Vr = V0 * (1 - np.exp(-r / rpe)) * (1 + (alpha * np.abs(r) / rpe)) # returns 100x100 array of Velocities.
Vlos = Vr * np.cos(theta)# Line of sight velocity assuming the observer is in the plane of the polar disk.
a = (r**2) # intensity as a function of radius
b = (r**2 / 0.23)
I = (3.* np.exp(-1. * a)) - (1.8 * np.exp(-1. * b))
I wish to first create velocity bins from Vmin to Vmax and then sum the intensities over each bin.
My desired out put would be something along the lines of
V_bins = [0, 5, 10,... Vlos.max()]
I_sum = [1.4, 1.1, 1.8, ... 1.2]
plot(V_bins, I_sum)
EDIT: I have come up with temporary solution but perhaps there is a more elegant/efficient method of achieving it?
The two array Vlos and I are both 100 by 100 matrices.
Vlos = array([[ 0., 8.9, 17.44, ..., 238.5],...,
[-0., -8.9, -17.44, ..., -238.5]])
I = random.random((100, 100))
V = np.arange(Vlos.min(), Vlos.max()+5, 5)
bins = np.zeros(len(V))
for i in range(0, len(V)-1):
for j in range(0, len(Vlos)): # horizontal coordinate in matrix
for k in range(0, len(Vlos[0])): # vert coordinate
if Vlos[j,k] >= V[i]and Vlos[j,k] < V[i+1]:
bins[i] = bins[i] + I[j,k]
The result is plotted below.
The overall shape in the histogram is to be expected, however I don't understand the spike in the curve at V = 0. As far as I can tell this isn't there in the data which leads me to question my method.
Any further help would be appreciated.
import numpy as np
bins = np.arange(100,120,5)
velocities = np.array([101, 111, 102, 112])
intensities = np.array([1,2,3,4])
h = np.histogram(velocities, bins, weights=intensities)
print h
Output:
(array([4, 0, 6]), array([100, 105, 110, 115]))
I'm trying to work out how best to locate the centroid of an arbitrary shape draped over a unit sphere, with the input being ordered (clockwise or anti-cw) vertices for the shape boundary. The density of vertices is irregular along the boundary, so the arc-lengths between them are not generally equal. Because the shapes may be very large (half a hemisphere) it is generally not possible to simply project the vertices to a plane and use planar methods, as detailed on Wikipedia (sorry I'm not allowed more than 2 hyperlinks as a newcomer). A slightly better approach involves the use of planar geometry manipulated in spherical coordinates, but again, with large polygons this method fails, as nicely illustrated here. On that same page, 'Cffk' highlighted this paper which describes a method for calculating the centroid of spherical triangles. I've tried to implement this method, but without success, and I'm hoping someone can spot the problem?
I have kept the variable definitions similar to those in the paper to make it easier to compare. The input (data) is a list of longitude/latitude coordinates, converted to [x,y,z] coordinates by the code. For each of the triangles I have arbitrarily fixed one point to be the +z-pole, the other two vertices being composed of a pair of neighboring points along the polygon boundary. The code steps along the boundary (starting at an arbitrary point), using each boundary segment of the polygon as a triangle side in turn. A sub-centroid is determined for each of these individual spherical triangles and they are weighted according to triangle area and added to calculate the total polygon centroid. I don't get any errors when running the code, but the total centroids returned are clearly wrong (I have run some very basic shapes where the centroid location is unambiguous). I haven't found any sensible pattern in the location of the centroids returned...so at the moment I'm not sure what is going wrong, either in the math or code (although, the suspicion is the math).
The code below should work copy-paste as is if you would like to try it. If you have matplotlib and numpy installed, it will plot the results (it will ignore plotting if you don't). You just have to put the longitude/latitude data below the code into a text file called example.txt.
from math import *
try:
import matplotlib as mpl
import matplotlib.pyplot
from mpl_toolkits.mplot3d import Axes3D
import numpy
plotting_enabled = True
except ImportError:
plotting_enabled = False
def sph_car(point):
if len(point) == 2:
point.append(1.0)
rlon = radians(float(point[0]))
rlat = radians(float(point[1]))
x = cos(rlat) * cos(rlon) * point[2]
y = cos(rlat) * sin(rlon) * point[2]
z = sin(rlat) * point[2]
return [x, y, z]
def xprod(v1, v2):
x = v1[1] * v2[2] - v1[2] * v2[1]
y = v1[2] * v2[0] - v1[0] * v2[2]
z = v1[0] * v2[1] - v1[1] * v2[0]
return [x, y, z]
def dprod(v1, v2):
dot = 0
for i in range(3):
dot += v1[i] * v2[i]
return dot
def plot(poly_xyz, g_xyz):
fig = mpl.pyplot.figure()
ax = fig.add_subplot(111, projection='3d')
# plot the unit sphere
u = numpy.linspace(0, 2 * numpy.pi, 100)
v = numpy.linspace(-1 * numpy.pi / 2, numpy.pi / 2, 100)
x = numpy.outer(numpy.cos(u), numpy.sin(v))
y = numpy.outer(numpy.sin(u), numpy.sin(v))
z = numpy.outer(numpy.ones(numpy.size(u)), numpy.cos(v))
ax.plot_surface(x, y, z, rstride=4, cstride=4, color='w', linewidth=0,
alpha=0.3)
# plot 3d and flattened polygon
x, y, z = zip(*poly_xyz)
ax.plot(x, y, z)
ax.plot(x, y, zs=0)
# plot the alleged 3d and flattened centroid
x, y, z = g_xyz
ax.scatter(x, y, z, c='r')
ax.scatter(x, y, 0, c='r')
# display
ax.set_xlim3d(-1, 1)
ax.set_ylim3d(-1, 1)
ax.set_zlim3d(0, 1)
mpl.pyplot.show()
lons, lats, v = list(), list(), list()
# put the two-column data at the bottom of the question into a file called
# example.txt in the same directory as this script
with open('example.txt') as f:
for line in f.readlines():
sep = line.split()
lons.append(float(sep[0]))
lats.append(float(sep[1]))
# convert spherical coordinates to cartesian
for lon, lat in zip(lons, lats):
v.append(sph_car([lon, lat, 1.0]))
# z unit vector/pole ('north pole'). This is an arbitrary point selected to act as one
#(fixed) vertex of the summed spherical triangles. The other two vertices of any
#triangle are composed of neighboring vertices from the polygon boundary.
np = [0.0, 0.0, 1.0]
# Gx,Gy,Gz are the cartesian coordinates of the calculated centroid
Gx, Gy, Gz = 0.0, 0.0, 0.0
for i in range(-1, len(v) - 1):
# cycle through the boundary vertices of the polygon, from 0 to n
if all((v[i][0] != v[i+1][0],
v[i][1] != v[i+1][1],
v[i][2] != v[i+1][2])):
# this just ignores redundant points which are common in my larger input files
# A,B,C are the internal angles in the triangle: 'np-v[i]-v[i+1]-np'
A = asin(sqrt((dprod(np, xprod(v[i], v[i+1])))**2
/ ((1 - (dprod(v[i+1], np))**2) * (1 - (dprod(np, v[i]))**2))))
B = asin(sqrt((dprod(v[i], xprod(v[i+1], np)))**2
/ ((1 - (dprod(np , v[i]))**2) * (1 - (dprod(v[i], v[i+1]))**2))))
C = asin(sqrt((dprod(v[i + 1], xprod(np, v[i])))**2
/ ((1 - (dprod(v[i], v[i+1]))**2) * (1 - (dprod(v[i+1], np))**2))))
# A/B/Cbar are the vertex angles, such that if 'O' is the sphere center, Abar
# is the angle (v[i]-O-v[i+1])
Abar = acos(dprod(v[i], v[i+1]))
Bbar = acos(dprod(v[i+1], np))
Cbar = acos(dprod(np, v[i]))
# e is the 'spherical excess', as defined on wikipedia
e = A + B + C - pi
# mag1/2/3 are the magnitudes of vectors np,v[i] and v[i+1].
mag1 = 1.0
mag2 = float(sqrt(v[i][0]**2 + v[i][1]**2 + v[i][2]**2))
mag3 = float(sqrt(v[i+1][0]**2 + v[i+1][1]**2 + v[i+1][2]**2))
# vec1/2/3 are cross products, defined here to simplify the equation below.
vec1 = xprod(np, v[i])
vec2 = xprod(v[i], v[i+1])
vec3 = xprod(v[i+1], np)
# multiplying vec1/2/3 by e and respective internal angles, according to the
#posted paper
for x in range(3):
vec1[x] *= Cbar / (2 * e * mag1 * mag2
* sqrt(1 - (dprod(np, v[i])**2)))
vec2[x] *= Abar / (2 * e * mag2 * mag3
* sqrt(1 - (dprod(v[i], v[i+1])**2)))
vec3[x] *= Bbar / (2 * e * mag3 * mag1
* sqrt(1 - (dprod(v[i+1], np)**2)))
Gx += vec1[0] + vec2[0] + vec3[0]
Gy += vec1[1] + vec2[1] + vec3[1]
Gz += vec1[2] + vec2[2] + vec3[2]
approx_expected_Gxyz = (0.78, -0.56, 0.27)
print('Approximate Expected Gxyz: {0}\n'
' Actual Gxyz: {1}'
''.format(approx_expected_Gxyz, (Gx, Gy, Gz)))
if plotting_enabled:
plot(v, (Gx, Gy, Gz))
Thanks in advance for any suggestions or insight.
EDIT: Here is a figure that shows a projection of the unit sphere with a polygon and the resulting centroid I calculate from the code. Clearly, the centroid is wrong as the polygon is rather small and convex but yet the centroid falls outside its perimeter.
EDIT: Here is a highly-similar set of coordinates to those above, but in the original [lon,lat] format I normally use (which is now converted to [x,y,z] by the updated code).
-39.366295 -1.633460
-47.282630 -0.740433
-53.912136 0.741380
-59.004217 2.759183
-63.489005 5.426812
-68.566001 8.712068
-71.394853 11.659135
-66.629580 15.362600
-67.632276 16.827507
-66.459524 19.069327
-63.819523 21.446736
-61.672712 23.532143
-57.538431 25.947815
-52.519889 28.691766
-48.606227 30.646295
-45.000447 31.089437
-41.549866 32.139873
-36.605156 32.956277
-32.010080 34.156692
-29.730629 33.756566
-26.158767 33.714080
-25.821513 34.179648
-23.614658 36.173719
-20.896869 36.977645
-17.991994 35.600074
-13.375742 32.581447
-9.554027 28.675497
-7.825604 26.535234
-7.825604 26.535234
-9.094304 23.363132
-9.564002 22.527385
-9.713885 22.217165
-9.948596 20.367878
-10.496531 16.486580
-11.151919 12.666850
-12.350144 8.800367
-15.446347 4.993373
-20.366139 1.132118
-24.784805 -0.927448
-31.532135 -1.910227
-39.366295 -1.633460
EDIT: A couple more examples...with 4 vertices defining a perfect square centered at [1,0,0] I get the expected result:
However, from a non-symmetric triangle I get a centroid that is nowhere close...the centroid actually falls on the far side of the sphere (here projected onto the front side as the antipode):
Interestingly, the centroid estimation appears 'stable' in the sense that if I invert the list (go from clockwise to counterclockwise order or vice-versa) the centroid correspondingly inverts exactly.
Anybody finding this, make sure to check Don Hatch's answer which is probably better.
I think this will do it. You should be able to reproduce this result by just copy-pasting the code below.
You will need to have the latitude and longitude data in a file called longitude and latitude.txt. You can copy-paste the original sample data which is included below the code.
If you have mplotlib it will additionally produce the plot below
For non-obvious calculations, I included a link that explains what is going on
In the graph below, the reference vector is very short (r = 1/10) so that the 3d-centroids are easier to see. You can easily remove the scaling to maximize accuracy.
Note to op: I rewrote almost everything so I'm not sure exactly where the original code was not working. However, at least I think it was not taking into consideration the need to handle clockwise / counterclockwise triangle vertices.
Legend:
(black line) reference vector
(small red dots) spherical triangle 3d-centroids
(large red / blue / green dot) 3d-centroid / projected to the surface / projected to the xy plane
(blue / green lines) the spherical polygon and the projection onto the xy plane
from math import *
try:
import matplotlib as mpl
import matplotlib.pyplot
from mpl_toolkits.mplot3d import Axes3D
import numpy
plotting_enabled = True
except ImportError:
plotting_enabled = False
def main():
# get base polygon data based on unit sphere
r = 1.0
polygon = get_cartesian_polygon_data(r)
point_count = len(polygon)
reference = ok_reference_for_polygon(polygon)
# decompose the polygon into triangles and record each area and 3d centroid
areas, subcentroids = list(), list()
for ia, a in enumerate(polygon):
# build an a-b-c point set
ib = (ia + 1) % point_count
b, c = polygon[ib], reference
if points_are_equivalent(a, b, 0.001):
continue # skip nearly identical points
# store the area and 3d centroid
areas.append(area_of_spherical_triangle(r, a, b, c))
tx, ty, tz = zip(a, b, c)
subcentroids.append((sum(tx)/3.0,
sum(ty)/3.0,
sum(tz)/3.0))
# combine all the centroids, weighted by their areas
total_area = sum(areas)
subxs, subys, subzs = zip(*subcentroids)
_3d_centroid = (sum(a*subx for a, subx in zip(areas, subxs))/total_area,
sum(a*suby for a, suby in zip(areas, subys))/total_area,
sum(a*subz for a, subz in zip(areas, subzs))/total_area)
# shift the final centroid to the surface
surface_centroid = scale_v(1.0 / mag(_3d_centroid), _3d_centroid)
plot(polygon, reference, _3d_centroid, surface_centroid, subcentroids)
def get_cartesian_polygon_data(fixed_radius):
cartesians = list()
with open('longitude and latitude.txt') as f:
for line in f.readlines():
spherical_point = [float(v) for v in line.split()]
if len(spherical_point) == 2:
spherical_point.append(fixed_radius)
cartesians.append(degree_spherical_to_cartesian(spherical_point))
return cartesians
def ok_reference_for_polygon(polygon):
point_count = len(polygon)
# fix the average of all vectors to minimize float skew
polyx, polyy, polyz = zip(*polygon)
# /10 is for visualization. Remove it to maximize accuracy
return (sum(polyx)/(point_count*10.0),
sum(polyy)/(point_count*10.0),
sum(polyz)/(point_count*10.0))
def points_are_equivalent(a, b, vague_tolerance):
# vague tolerance is something like a percentage tolerance (1% = 0.01)
(ax, ay, az), (bx, by, bz) = a, b
return all(((ax-bx)/ax < vague_tolerance,
(ay-by)/ay < vague_tolerance,
(az-bz)/az < vague_tolerance))
def degree_spherical_to_cartesian(point):
rad_lon, rad_lat, r = radians(point[0]), radians(point[1]), point[2]
x = r * cos(rad_lat) * cos(rad_lon)
y = r * cos(rad_lat) * sin(rad_lon)
z = r * sin(rad_lat)
return x, y, z
def area_of_spherical_triangle(r, a, b, c):
# points abc
# build an angle set: A(CAB), B(ABC), C(BCA)
# http://math.stackexchange.com/a/66731/25581
A, B, C = surface_points_to_surface_radians(a, b, c)
E = A + B + C - pi # E is called the spherical excess
area = r**2 * E
# add or subtract area based on clockwise-ness of a-b-c
# http://stackoverflow.com/a/10032657/377366
if clockwise_or_counter(a, b, c) == 'counter':
area *= -1.0
return area
def surface_points_to_surface_radians(a, b, c):
"""build an angle set: A(cab), B(abc), C(bca)"""
points = a, b, c
angles = list()
for i, mid in enumerate(points):
start, end = points[(i - 1) % 3], points[(i + 1) % 3]
x_startmid, x_endmid = xprod(start, mid), xprod(end, mid)
ratio = (dprod(x_startmid, x_endmid)
/ ((mag(x_startmid) * mag(x_endmid))))
angles.append(acos(ratio))
return angles
def clockwise_or_counter(a, b, c):
ab = diff_cartesians(b, a)
bc = diff_cartesians(c, b)
x = xprod(ab, bc)
if x < 0:
return 'clockwise'
elif x > 0:
return 'counter'
else:
raise RuntimeError('The reference point is in the polygon.')
def diff_cartesians(positive, negative):
return tuple(p - n for p, n in zip(positive, negative))
def xprod(v1, v2):
x = v1[1] * v2[2] - v1[2] * v2[1]
y = v1[2] * v2[0] - v1[0] * v2[2]
z = v1[0] * v2[1] - v1[1] * v2[0]
return [x, y, z]
def dprod(v1, v2):
dot = 0
for i in range(3):
dot += v1[i] * v2[i]
return dot
def mag(v1):
return sqrt(v1[0]**2 + v1[1]**2 + v1[2]**2)
def scale_v(scalar, v):
return tuple(scalar * vi for vi in v)
def plot(polygon, reference, _3d_centroid, surface_centroid, subcentroids):
fig = mpl.pyplot.figure()
ax = fig.add_subplot(111, projection='3d')
# plot the unit sphere
u = numpy.linspace(0, 2 * numpy.pi, 100)
v = numpy.linspace(-1 * numpy.pi / 2, numpy.pi / 2, 100)
x = numpy.outer(numpy.cos(u), numpy.sin(v))
y = numpy.outer(numpy.sin(u), numpy.sin(v))
z = numpy.outer(numpy.ones(numpy.size(u)), numpy.cos(v))
ax.plot_surface(x, y, z, rstride=4, cstride=4, color='w', linewidth=0,
alpha=0.3)
# plot 3d and flattened polygon
x, y, z = zip(*polygon)
ax.plot(x, y, z, c='b')
ax.plot(x, y, zs=0, c='g')
# plot the 3d centroid
x, y, z = _3d_centroid
ax.scatter(x, y, z, c='r', s=20)
# plot the spherical surface centroid and flattened centroid
x, y, z = surface_centroid
ax.scatter(x, y, z, c='b', s=20)
ax.scatter(x, y, 0, c='g', s=20)
# plot the full set of triangular centroids
x, y, z = zip(*subcentroids)
ax.scatter(x, y, z, c='r', s=4)
# plot the reference vector used to findsub centroids
x, y, z = reference
ax.plot((0, x), (0, y), (0, z), c='k')
ax.scatter(x, y, z, c='k', marker='^')
# display
ax.set_xlim3d(-1, 1)
ax.set_ylim3d(-1, 1)
ax.set_zlim3d(0, 1)
mpl.pyplot.show()
# run it in a function so the main code can appear at the top
main()
Here is the longitude and latitude data you can paste into longitude and latitude.txt
-39.366295 -1.633460
-47.282630 -0.740433
-53.912136 0.741380
-59.004217 2.759183
-63.489005 5.426812
-68.566001 8.712068
-71.394853 11.659135
-66.629580 15.362600
-67.632276 16.827507
-66.459524 19.069327
-63.819523 21.446736
-61.672712 23.532143
-57.538431 25.947815
-52.519889 28.691766
-48.606227 30.646295
-45.000447 31.089437
-41.549866 32.139873
-36.605156 32.956277
-32.010080 34.156692
-29.730629 33.756566
-26.158767 33.714080
-25.821513 34.179648
-23.614658 36.173719
-20.896869 36.977645
-17.991994 35.600074
-13.375742 32.581447
-9.554027 28.675497
-7.825604 26.535234
-7.825604 26.535234
-9.094304 23.363132
-9.564002 22.527385
-9.713885 22.217165
-9.948596 20.367878
-10.496531 16.486580
-11.151919 12.666850
-12.350144 8.800367
-15.446347 4.993373
-20.366139 1.132118
-24.784805 -0.927448
-31.532135 -1.910227
-39.366295 -1.633460
To clarify: the quantity of interest is the projection of the true 3d centroid
(i.e. 3d center-of-mass, i.e. 3d center-of-area) onto the unit sphere.
Since all you care about is the direction from the origin to the 3d centroid,
you don't need to bother with areas at all;
it's easier to just compute the moment (i.e. 3d centroid times area).
The moment of the region to the left of a closed path on the unit sphere
is half the integral of the leftward unit vector as you walk around the path.
This follows from a non-obvious application of Stokes' theorem; see Frank Jones's vector calculus book, chapter 13 Problem 13-12.
In particular, for a spherical polygon, the moment is half the sum of
(a x b) / ||a x b|| * (angle between a and b) for each pair of consecutive vertices a,b.
(That's for the region to the left of the path;
negate it for the region to the right of the path.)
(And if you really did want the 3d centroid, just compute the area and divide the moment by it. Comparing areas might also be useful in choosing which of the two regions to call "the polygon".)
Here's some code; it's really simple:
#!/usr/bin/python
import math
def plus(a,b): return [x+y for x,y in zip(a,b)]
def minus(a,b): return [x-y for x,y in zip(a,b)]
def cross(a,b): return [a[1]*b[2]-a[2]*b[1], a[2]*b[0]-a[0]*b[2], a[0]*b[1]-a[1]*b[0]]
def dot(a,b): return sum([x*y for x,y in zip(a,b)])
def length(v): return math.sqrt(dot(v,v))
def normalized(v): l = length(v); return [1,0,0] if l==0 else [x/l for x in v]
def addVectorTimesScalar(accumulator, vector, scalar):
for i in xrange(len(accumulator)): accumulator[i] += vector[i] * scalar
def angleBetweenUnitVectors(a,b):
# https://www.plunk.org/~hatch/rightway.html
if dot(a,b) < 0:
return math.pi - 2*math.asin(length(plus(a,b))/2.)
else:
return 2*math.asin(length(minus(a,b))/2.)
def sphericalPolygonMoment(verts):
moment = [0.,0.,0.]
for i in xrange(len(verts)):
a = verts[i]
b = verts[(i+1)%len(verts)]
addVectorTimesScalar(moment, normalized(cross(a,b)),
angleBetweenUnitVectors(a,b) / 2.)
return moment
if __name__ == '__main__':
import sys
def lonlat_degrees_to_xyz(lon_degrees,lat_degrees):
lon = lon_degrees*(math.pi/180)
lat = lat_degrees*(math.pi/180)
coslat = math.cos(lat)
return [coslat*math.cos(lon), coslat*math.sin(lon), math.sin(lat)]
verts = [lonlat_degrees_to_xyz(*[float(v) for v in line.split()])
for line in sys.stdin.readlines()]
#print "verts = "+`verts`
moment = sphericalPolygonMoment(verts)
print "moment = "+`moment`
print "centroid unit direction = "+`normalized(moment)`
For the example polygon, this gives the answer (unit vector):
[-0.7644875430808217, 0.579935445918147, -0.2814847687566214]
This is roughly the same as, but more accurate than, the answer computed by #KobeJohn's code, which uses rough tolerances and planar approximations to the sub-centroids:
[0.7628095787179151, -0.5977153368303585, 0.24669398601094406]
The directions of the two answers are roughly opposite (so I guess KobeJohn's code
decided to take the region to the right of the path in this case).
I think a good approximation would be to compute the center of mass using weighted cartesian coordinates and projecting the result onto the sphere (supposing the origin of coordinates is (0, 0, 0)^T).
Let be (p[0], p[1], ... p[n-1]) the n points of the polygon. The approximative (cartesian) centroid can be computed by:
c = 1 / w * (sum of w[i] * p[i])
whereas w is the sum of all weights and whereas p[i] is a polygon point and w[i] is a weight for that point, e.g.
w[i] = |p[i] - p[(i - 1 + n) % n]| / 2 + |p[i] - p[(i + 1) % n]| / 2
whereas |x| is the length of a vector x.
I.e. a point is weighted with half the length to the previous and half the length to the next polygon point.
This centroid c can now projected onto the sphere by:
c' = r * c / |c|
whereas r is the radius of the sphere.
To consider orientation of polygon (ccw, cw) the result may be
c' = - r * c / |c|.
Sorry I (as a newly registered user) had to write a new post instead of just voting/commenting on the above answer by Don Hatch. Don's answer, I think, is the best and most elegant. It is mathematically rigorous in computing the center of mass (first moment of mass) in a simple way when applying to the spherical polygon.
Kobe John's answer is a good approximation but only satisfactory for smaller areas. I also noticed a few glitches in the code. Firstly, the reference point should be projected to the spherical surface to compute the actual spherical area. Secondly, function points_are_equivalent() might need to be refined to avoid divided-by-zero.
The approximation error in Kobe's method lies in the calculation of the centroid of spherical triangles. The sub-centroid is NOT the center of mass of the spherical triangle but the planar one. This is not an issue if one is to determine that single triangle (sign may flip, see below). It is also not an issue if triangles are small (e.g. a dense triangulation of the polygon).
A few simple tests could illustrate the approximation error. For example if we use just four points:
10 -20
10 20
-10 20
-10 -20
The exact answer is (1,0,0) and both methods are good. But if you throw in a few more points along one edge (e.g. add {10,-15},{10,-10}... to the first edge), you'll see the results from Kobe's method start to shift. Further more, if you increase the longitude from [10,-10] to [100,-100], you'll see Kobe's result flips the direction. A possible improvement might be to add another level(s) for sub-centroid calculation (basically refine/reduce sizes of triangles).
For our application, the spherical area boundary is composed of multiple arcs and thus not polygon (i.e. the arc is not part of great circle). But this will just be a little more work to find the n-vector in the curve integration.
EDIT: Replacing the subcentroid calculation with the one given in Brock's paper should fix Kobe's method. But I did not try though.