I have two arrays of values of angles in radians. The two arrays are symmetrical with respect to a known constant angle. The arrays are shown in the figure:

The example values are following:
one = [ 2.98153965 -1.33298928 2.94993567 -1.39909924 2.99214403 3.00138863
3.04390642 -1.59098448 -1.65660299 -1.73146174 -1.8166248 -2.85595599
-2.02035274 -2.64530394 -2.26451127 -2.3982946 -2.52735954 -2.17570346
-2.77544658 -2.88566686 -1.84913768 -3.07261908 -1.66738719 -1.6029932
-1.54596053 -1.50177363 -1.46133745 -1.42288915 -1.38241718 2.79925996
-1.30775884 -1.27309395 2.72153718 -1.20592812 -1.18113435 -1.15029987]
two = [-1.30507254 2.9385436 -1.36415496 2.95897805 -1.43845065 -1.48295087
-1.53346541 3.09685482 -3.11358085 -3.0466034 -2.95794156 -1.9128659
-2.75067133 -2.13826992 -2.51567194 -2.39565127 -2.28148844 -2.65519436
-2.05312249 -1.95523663 -2.98473857 -1.75415233 3.13322155 3.06539723
3.00595703 2.95378704 2.90786779 2.86730208 2.831318 -1.34113191
2.77057495 2.74479777 -1.23620286 2.70046364 2.68129889 2.66380717]
It can be seen that the values are "following" two symmetrical arctan lines, my question is how do I distinguish between the two of them, and get something like this:

I've tried several approaches but can't come up with a universal one which will work in all cases, there is often a misinterpreted section assigned to the wrong array.
Any ideas are welcome! Thanks!
Here is a solution that minimizes the distance between consecutive points and also the change in slope (weighted by parameter lam). Distance alone fails at the crossover point. 
import numpy as np
one = list(map(float, """ 2.98153965 -1.33298928 2.94993567 -1.39909924 2.99214403 3.00138863
3.04390642 -1.59098448 -1.65660299 -1.73146174 -1.8166248 -2.85595599
-2.02035274 -2.64530394 -2.26451127 -2.3982946 -2.52735954 -2.17570346
-2.77544658 -2.88566686 -1.84913768 -3.07261908 -1.66738719 -1.6029932
-1.54596053 -1.50177363 -1.46133745 -1.42288915 -1.38241718 2.79925996
-1.30775884 -1.27309395 2.72153718 -1.20592812 -1.18113435 -1.15029987""".split()))
two = list(map(float, """-1.30507254 2.9385436 -1.36415496 2.95897805 -1.43845065 -1.48295087
-1.53346541 3.09685482 -3.11358085 -3.0466034 -2.95794156 -1.9128659
-2.75067133 -2.13826992 -2.51567194 -2.39565127 -2.28148844 -2.65519436
-2.05312249 -1.95523663 -2.98473857 -1.75415233 3.13322155 3.06539723
3.00595703 2.95378704 2.90786779 2.86730208 2.831318 -1.34113191
2.77057495 2.74479777 -1.23620286 2.70046364 2.68129889 2.66380717""".split()))
data = np.array([one, two])
dd = (data[[[0, 1], [1, 0]], 1:] - data[:, None, :-1] + np.pi)%(2*np.pi) - np.pi
dde2 = np.einsum('ijk,ijk->jk', dd, dd)
xovr1 = np.argmin(dde2, axis=0)
pick1 = np.r_[0, np.cumsum(xovr1) & 1]
d2d = dd[:, :, None, 1:] - dd[[[1, 0], [0, 1]], :, :-1]
d2de2 = np.r_['2', np.zeros((2, 2, 1)), np.einsum('ijkl,ijkl->jkl', d2d, d2d)]
lam = 0.5
e2 = (dde2[:, None, :] + lam * d2de2).reshape(4, -1)
xovr2 = np.argmin(e2, axis=0)>>1
pick2 = np.r_[0, np.cumsum(xovr2) & 1]
print('by position only')
print(data[pick1, np.arange(data.shape[1])])
print(data[1-pick1, np.arange(data.shape[1])])
print('by position and slope')
print(data[pick2, np.arange(data.shape[1])])
print(data[1-pick2, np.arange(data.shape[1])])
# by position only
# [ 2.98153965 2.9385436 2.94993567 2.95897805 2.99214403 3.00138863
# 3.04390642 3.09685482 -3.11358085 -3.0466034 -2.95794156 -2.85595599
# -2.75067133 -2.64530394 -2.51567194 -2.3982946 -2.52735954 -2.65519436
# -2.77544658 -2.88566686 -2.98473857 -3.07261908 3.13322155 3.06539723
# 3.00595703 2.95378704 2.90786779 2.86730208 2.831318 2.79925996
# 2.77057495 2.74479777 2.72153718 2.70046364 2.68129889 2.66380717]
# [-1.30507254 -1.33298928 -1.36415496 -1.39909924 -1.43845065 -1.48295087
# -1.53346541 -1.59098448 -1.65660299 -1.73146174 -1.8166248 -1.9128659
# -2.02035274 -2.13826992 -2.26451127 -2.39565127 -2.28148844 -2.17570346
# -2.05312249 -1.95523663 -1.84913768 -1.75415233 -1.66738719 -1.6029932
# -1.54596053 -1.50177363 -1.46133745 -1.42288915 -1.38241718 -1.34113191
# -1.30775884 -1.27309395 -1.23620286 -1.20592812 -1.18113435 -1.15029987]
# by position and slope
# [ 2.98153965 2.9385436 2.94993567 2.95897805 2.99214403 3.00138863
# 3.04390642 3.09685482 -3.11358085 -3.0466034 -2.95794156 -2.85595599
# -2.75067133 -2.64530394 -2.51567194 -2.39565127 -2.28148844 -2.17570346
# -2.05312249 -1.95523663 -1.84913768 -1.75415233 -1.66738719 -1.6029932
# -1.54596053 -1.50177363 -1.46133745 -1.42288915 -1.38241718 -1.34113191
# -1.30775884 -1.27309395 -1.23620286 -1.20592812 -1.18113435 -1.15029987]
# [-1.30507254 -1.33298928 -1.36415496 -1.39909924 -1.43845065 -1.48295087
# -1.53346541 -1.59098448 -1.65660299 -1.73146174 -1.8166248 -1.9128659
# -2.02035274 -2.13826992 -2.26451127 -2.3982946 -2.52735954 -2.65519436
# -2.77544658 -2.88566686 -2.98473857 -3.07261908 3.13322155 3.06539723
# 3.00595703 2.95378704 2.90786779 2.86730208 2.831318 2.79925996
# 2.77057495 2.74479777 2.72153718 2.70046364 2.68129889 2.66380717]
The difficulty come from the 2 pi jump, which can be resolved by :
def transform(x):
return x+2*pi*(x<0)
This function transform the arrays in continuous ones. You must first turn your lists in ndarrays.
then :
t=arange(one.size)
tone = transform(one)
ttwo = transform(two)
maxi=np.maximum(tone,ttwo)
subplot(211)
plot(t,tone,'o',t,ttwo,'o',maxi)
induces what to do :
i=maxi.argmin()
dicrease = np.choose(np.logical_xor(tone>ttwo,t<i),[tone,ttwo])
increase = np.choose(np.logical_xor(tone>ttwo,t<i),[ttwo,tone])
subplot(212)
plot(t,dicrease,label='dicrease')
plot(t,increase,label='increase')
legend()
for

You can if necessary turn back in [-pi,pi[ by x -> (x + pi) % (2*pi) - pi .
EDIT
for a less ad hoc transform, I propose this other, which will probably solve more cases :
def transform2(y,gap):
breaks=np.diff(y)**2>gap**2/2
signs=np.sign(np.diff(y))
offset=np.concatenate(([0],(breaks*signs).cumsum()))*gap
return y-offset
and an noisy example :

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