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# # ls_ellipsoid and polyToParams3D functions are taken from
# http://www.juddzone.com/ALGORITHMS/least_squares_3D_ellipsoid.html
# # FindBestFittingEllipsoid3D and GetConvexHull3D are adapted from a discussion at
# https://stackoverflow.com/questions/58501545/python-fit-3d-ellipsoid-oblate-prolate-to-3d-points
from scipy.spatial import ConvexHull
import numpy as np
from numpy.linalg import eig, inv
from brick.general.type import site_h, array_t
from brick.component.soma import soma_t
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def ls_ellipsoid(xx, yy, zz): # finds the ellipsoid
# least squares fit to a 3D-ellipsoid
# Ax^2 + By^2 + Cz^2 + Dxy + Exz + Fyz + Gx + Hy + Iz = 1
#
# Note that sometimes it is expressed as a solution to
# Ax^2 + By^2 + Cz^2 + 2Dxy + 2Exz + 2Fyz + 2Gx + 2Hy + 2Iz = 1
# where the last six terms have a factor of 2 in them
# This is in anticipation of forming a matrix with the polynomial coefficients.
# Those terms with factors of 2 are all off diagonal elements. These contribute
# two terms when multiplied out (symmetric) so would need to be divided by two
# change xx from vector of length N to Nx1 matrix so we can use hstack
x = xx[:, np.newaxis]
y = yy[:, np.newaxis]
z = zz[:, np.newaxis]
# Ax^2 + By^2 + Cz^2 + Dxy + Exz + Fyz + Gx + Hy + Iz = 1
J = np.hstack((x * x, y * y, z * z, x * y, x * z, y * z, x, y, z))
K = np.ones_like(x) # column of ones
# np.hstack performs a loop over all samples and creates
# a row in J for each x,y,z sample:
# J[ix,0] = x[ix]*x[ix]
# J[ix,1] = y[ix]*y[ix]
# etc.
JT = J.transpose()
JTJ = np.dot(JT, J)
InvJTJ = np.linalg.inv(JTJ);
ABC = np.dot(InvJTJ, np.dot(JT, K))
# Rearrange, move the 1 to the other side
# Ax^2 + By^2 + Cz^2 + Dxy + Exz + Fyz + Gx + Hy + Iz - 1 = 0
# or
# Ax^2 + By^2 + Cz^2 + Dxy + Exz + Fyz + Gx + Hy + Iz + J = 0
# where J = -1
eansa = np.append(ABC, -1)
return (eansa)
def polyToParams3D(vec, printMe): # gets 3D parameters of an ellipsoid.
# convert the polynomial form of the 3D-ellipsoid to parameters
# center, axes, and transformation matrix
# vec is the vector whose elements are the polynomial
# coefficients A..J
# returns (center, axes, rotation matrix)
# Algebraic form: X.T * Amat * X --> polynomial form
if printMe: print('\npolynomial\n', vec)
Amat = np.array(
[
[vec[0], vec[3] / 2.0, vec[4] / 2.0, vec[6] / 2.0],
[vec[3] / 2.0, vec[1], vec[5] / 2.0, vec[7] / 2.0],
[vec[4] / 2.0, vec[5] / 2.0, vec[2], vec[8] / 2.0],
[vec[6] / 2.0, vec[7] / 2.0, vec[8] / 2.0, vec[9]]
])
if printMe: print('\nAlgebraic form of polynomial\n', Amat)
# See B.Bartoni, Preprint SMU-HEP-10-14 Multi-dimensional Ellipsoidal Fitting
# equation 20 for the following method for finding the center
A3 = Amat[0:3, 0:3]
A3inv = inv(A3)
ofs = vec[6:9] / 2.0
center = -np.dot(A3inv, ofs)
if printMe: print('\nCenter at:', center)
# Center the ellipsoid at the origin
Tofs = np.eye(4)
Tofs[3, 0:3] = center
R = np.dot(Tofs, np.dot(Amat, Tofs.T))
if printMe: print('\nAlgebraic form translated to center\n', R, '\n')
R3 = R[0:3, 0:3]
R3test = R3 / R3[0, 0]
# print('normed \n',R3test)
s1 = -R[3, 3]
R3S = R3 / s1
(el, ec) = eig(R3S)
recip = 1.0 / np.abs(el)
axes = np.sqrt(recip)
if printMe: print('\nAxes are\n', axes, '\n')
inve = inv(ec) # inverse is actually the transpose here
if printMe: print('\nRotation matrix\n', inve)
return (center, axes, inve)
def GetConvexHull3D(soma_sites: site_h) -> array_t:
#
volume = np.stack((soma_sites[0], soma_sites[1], soma_sites[2]), axis=-1)
hull_volume = ConvexHull(volume)
len_hull = len(hull_volume.vertices)
hull = np.zeros((len_hull, 3))
for i in range(len(hull_volume.vertices)):
hull[i] = volume[hull_volume.vertices[i]]
convex_hull = np.transpose(hull)
return convex_hull
def FindBestFittingEllipsoid3D(soma: soma_t) -> tuple:
"""
Find the best fitting ellipsoid for the data points in 3D based on their convex hull.
Return Tuple[ellipsoid coefficients, ellipsoid center, ellipsoid axes, ellipsoid orientation]
"""
# get convex hull
convex_hull = GetConvexHull3D(soma.sites)
# fit ellipsoid on the convex hull
# # get ellipsoid polynomial coefficients
ellipsoid_coef = ls_ellipsoid(convex_hull[0], convex_hull[1], convex_hull[2])
# # get ellipsoid 3D parameters
center, axes, orientation = polyToParams3D(ellipsoid_coef, False)
return ellipsoid_coef, center, axes, orientation