fit a ellipse in Python given a set of points xi=(xi,yi)
I am computing a series of index from a 2D points (x,y). One index is the ratio between minor and major axis. To fit the ellipse i am using the following post
when i run these function the final results looks strange because the center and the axis length are not in scale with the 2D points
center = [ 560415.53298363+0.j 6368878.84576771+0.j]
angle of rotation = (-0.0528033467597-5.55111512313e-17j)
axes = [0.00000000-557.21553487j 6817.76933256 +0.j]
thanks in advance for help
import numpy as np
from numpy.linalg import eig, inv
def fitEllipse(x,y):
x = x[:,np.newaxis]
y = y[:,np.newaxis]
D = np.hstack((x*x, x*y, y*y, x, y, np.ones_like(x)))
S = np.dot(D.T,D)
C = np.zeros([6,6])
C[0,2] = C[2,0] = 2; C[1,1] = -1
E, V = eig(np.dot(inv(S), C))
n = np.argmax(np.abs(E))
a = V[:,n]
return a
def ellipse_center(a):
b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0]
num = b*b-a*c
x0=(c*d-b*f)/num
y0=(a*f-b*d)/num
return np.array([x0,y0])
def ellipse_angle_of_rotation( a ):
b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0]
return 0.5*np.arctan(2*b/(a-c))
def ellipse_axis_length( a ):
b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0]
up = 2*(a*f*f+c*d*d+g*b*b-2*b*d*f-a*c*g)
down1=(b*b-a*c)*( (c-a)*np.sqrt(1+4*b*b/((a-c)*(a-c)))-(c+a))
down2=(b*b-a*c)*( (a-c)*np.sqrt(1+4*b*b/((a-c)*(a-c)))-(c+a))
res1=np.sqrt(up/down1)
res2=np.sqrt(up/down2)
return np.array([res1, res2])
if __name__ == '__main__':
points = [(560036.4495758876, 6362071.890493258),
(560036.4495758876, 6362070.890493258),
(560036.9495758876, 6362070.890493258),
(560036.9495758876, 6362070.390493258),
(560037.4495758876, 6362070.390493258),
(560037.4495758876, 6362064.890493258),
(560036.4495758876, 6362064.890493258),
(560036.4495758876, 6362063.390493258),
(560035.4495758876, 6362063.390493258),
(560035.4495758876, 6362062.390493258),
(560034.9495758876, 6362062.390493258),
(560034.9495758876, 6362061.390493258),
(560032.9495758876, 6362061.390493258),
(560032.9495758876, 6362061.890493258),
(560030.4495758876, 6362061.890493258),
(560030.4495758876, 6362061.390493258),
(560029.9495758876, 6362061.390493258),
(560029.9495758876, 6362060.390493258),
(560029.4495758876, 6362060.390493258),
(560029.4495758876, 6362059.890493258),
(560028.9495758876, 6362059.890493258),
(560028.9495758876, 6362059.390493258),
(560028.4495758876, 6362059.390493258),
(560028.4495758876, 6362058.890493258),
(560027.4495758876, 6362058.890493258),
(560027.4495758876, 6362058.390493258),
(560026.9495758876, 6362058.390493258),
(560026.9495758876, 6362057.890493258),
(560025.4495758876, 6362057.890493258),
(560025.4495758876, 6362057.390493258),
(560023.4495758876, 6362057.390493258),
(560023.4495758876, 6362060.390493258),
(560023.9495758876, 6362060.390493258),
(560023.9495758876, 6362061.890493258),
(560024.4495758876, 6362061.890493258),
(560024.4495758876, 6362063.390493258),
(560024.9495758876, 6362063.390493258),
(560024.9495758876, 6362064.390493258),
(560025.4495758876, 6362064.390493258),
(560025.4495758876, 6362065.390493258),
(560025.9495758876, 6362065.390493258),
(560025.9495758876, 6362065.890493258),
(560026.4495758876, 6362065.890493258),
(560026.4495758876, 6362066.890493258),
(560026.9495758876, 6362066.890493258),
(560026.9495758876, 6362068.390493258),
(560027.4495758876, 6362068.390493258),
(560027.4495758876, 6362068.890493258),
(560027.9495758876, 6362068.890493258),
(560027.9495758876, 6362069.390493258),
(560028.4495758876, 6362069.390493258),
(560028.4495758876, 6362069.890493258),
(560033.4495758876, 6362069.890493258),
(560033.4495758876, 6362070.390493258),
(560033.9495758876, 6362070.390493258),
(560033.9495758876, 6362070.890493258),
(560034.4495758876, 6362070.890493258),
(560034.4495758876, 6362071.390493258),
(560034.9495758876, 6362071.390493258),
(560034.9495758876, 6362071.890493258),
(560036.4495758876, 6362071.890493258)]
a_points = np.array(points)
x = a_points[:, 0]
y = a_points[:, 1]
from pylab import *
plot(x,y)
show()
a = fitEllipse(x,y)
center = ellipse_center(a)
phi = ellipse_angle_of_rotation(a)
axes = ellipse_axis_length(a)
print "center = ", center
print "angle of rotation = ", phi
print "axes = ", axes
from pylab import *
plot(x,y)
plot(center[0:1],center[1:], color = 'red')
show()
each vertex is a xi,y,i point
plot of 2D point and center of fit ellipse
using OpenCV i have the following result:
import cv
PointArray2D32f = cv.CreateMat(1, len(points), cv.CV_32FC2)
for (i, (x, y)) in enumerate(points):
PointArray2D32f[0, i] = (x, y)
# Fits ellipse to current contour.
(center, size, angle) = cv.FitEllipse2(PointArray2D32f)
(center, size, angle)
((560030.625, 6362066.5),(10.480490684509277, 17.20206642150879),144.34889221191406)
Answer
The calculation for fitEllipse is returning bogus results because the values for x and y are very large compared to the variation between the values. If you try printing out the eigenvalues E for example, you see
array([ 0.00000000e+00 +0.00000000e+00j,
0.00000000e+00 +0.00000000e+00j,
0.00000000e+00 +0.00000000e+00j,
-1.36159790e-12 +8.15049878e-12j,
-1.36159790e-12 -8.15049878e-12j, 1.18685632e-11 +0.00000000e+00j])
They are all practically zero! Clearly there is some kind of numerical inaccuracy here.
You can fix the problem by moving the mean of your data closer to zero so that the values are more "normal"-sized and the variation between the numbers becomes more significant.
x = a_points[:, 0]
y = a_points[:, 1]
xmean = x.mean()
ymean = y.mean()
x = x-xmean
y = y-ymean
You can then successfully find the center, phi and axes, and then re-shift the center back to (xmean, ymean):
center = ellipse_center(a)
center[0] += xmean
center[1] += ymean
import numpy as np
import numpy.linalg as linalg
import matplotlib.pyplot as plt
def fitEllipse(x,y):
x = x[:,np.newaxis]
y = y[:,np.newaxis]
D = np.hstack((x*x, x*y, y*y, x, y, np.ones_like(x)))
S = np.dot(D.T,D)
C = np.zeros([6,6])
C[0,2] = C[2,0] = 2; C[1,1] = -1
E, V = linalg.eig(np.dot(linalg.inv(S), C))
n = np.argmax(np.abs(E))
a = V[:,n]
return a
def ellipse_center(a):
b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0]
num = b*b-a*c
x0=(c*d-b*f)/num
y0=(a*f-b*d)/num
return np.array([x0,y0])
def ellipse_angle_of_rotation( a ):
b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0]
return 0.5*np.arctan(2*b/(a-c))
def ellipse_axis_length( a ):
b,c,d,f,g,a = a[1]/2, a[2], a[3]/2, a[4]/2, a[5], a[0]
up = 2*(a*f*f+c*d*d+g*b*b-2*b*d*f-a*c*g)
down1=(b*b-a*c)*( (c-a)*np.sqrt(1+4*b*b/((a-c)*(a-c)))-(c+a))
down2=(b*b-a*c)*( (a-c)*np.sqrt(1+4*b*b/((a-c)*(a-c)))-(c+a))
res1=np.sqrt(up/down1)
res2=np.sqrt(up/down2)
return np.array([res1, res2])
def find_ellipse(x, y):
xmean = x.mean()
ymean = y.mean()
x -= xmean
y -= ymean
a = fitEllipse(x,y)
center = ellipse_center(a)
center[0] += xmean
center[1] += ymean
phi = ellipse_angle_of_rotation(a)
axes = ellipse_axis_length(a)
x += xmean
y += ymean
return center, phi, axes
if __name__ == '__main__':
points = [(560036.4495758876, 6362071.890493258),
(560036.4495758876, 6362070.890493258),
(560036.9495758876, 6362070.890493258),
(560036.9495758876, 6362070.390493258),
(560037.4495758876, 6362070.390493258),
(560037.4495758876, 6362064.890493258),
(560036.4495758876, 6362064.890493258),
(560036.4495758876, 6362063.390493258),
(560035.4495758876, 6362063.390493258),
(560035.4495758876, 6362062.390493258),
(560034.9495758876, 6362062.390493258),
(560034.9495758876, 6362061.390493258),
(560032.9495758876, 6362061.390493258),
(560032.9495758876, 6362061.890493258),
(560030.4495758876, 6362061.890493258),
(560030.4495758876, 6362061.390493258),
(560029.9495758876, 6362061.390493258),
(560029.9495758876, 6362060.390493258),
(560029.4495758876, 6362060.390493258),
(560029.4495758876, 6362059.890493258),
(560028.9495758876, 6362059.890493258),
(560028.9495758876, 6362059.390493258),
(560028.4495758876, 6362059.390493258),
(560028.4495758876, 6362058.890493258),
(560027.4495758876, 6362058.890493258),
(560027.4495758876, 6362058.390493258),
(560026.9495758876, 6362058.390493258),
(560026.9495758876, 6362057.890493258),
(560025.4495758876, 6362057.890493258),
(560025.4495758876, 6362057.390493258),
(560023.4495758876, 6362057.390493258),
(560023.4495758876, 6362060.390493258),
(560023.9495758876, 6362060.390493258),
(560023.9495758876, 6362061.890493258),
(560024.4495758876, 6362061.890493258),
(560024.4495758876, 6362063.390493258),
(560024.9495758876, 6362063.390493258),
(560024.9495758876, 6362064.390493258),
(560025.4495758876, 6362064.390493258),
(560025.4495758876, 6362065.390493258),
(560025.9495758876, 6362065.390493258),
(560025.9495758876, 6362065.890493258),
(560026.4495758876, 6362065.890493258),
(560026.4495758876, 6362066.890493258),
(560026.9495758876, 6362066.890493258),
(560026.9495758876, 6362068.390493258),
(560027.4495758876, 6362068.390493258),
(560027.4495758876, 6362068.890493258),
(560027.9495758876, 6362068.890493258),
(560027.9495758876, 6362069.390493258),
(560028.4495758876, 6362069.390493258),
(560028.4495758876, 6362069.890493258),
(560033.4495758876, 6362069.890493258),
(560033.4495758876, 6362070.390493258),
(560033.9495758876, 6362070.390493258),
(560033.9495758876, 6362070.890493258),
(560034.4495758876, 6362070.890493258),
(560034.4495758876, 6362071.390493258),
(560034.9495758876, 6362071.390493258),
(560034.9495758876, 6362071.890493258),
(560036.4495758876, 6362071.890493258)]
fig, axs = plt.subplots(2, 1, sharex = True, sharey = True)
a_points = np.array(points)
x = a_points[:, 0]
y = a_points[:, 1]
axs[0].plot(x,y)
center, phi, axes = find_ellipse(x, y)
print "center = ", center
print "angle of rotation = ", phi
print "axes = ", axes
axs[1].plot(x, y)
axs[1].scatter(center[0],center[1], color = 'red', s = 100)
axs[1].set_xlim(x.min(), x.max())
axs[1].set_ylim(y.min(), y.max())
plt.show()
