import numpy as np
import matplotlib.pyplot as plt

size = 1000
sigma_x = 1.
sigma_y = 1.

x = np.linspace(-3, 3, size)
y = np.linspace(-3, 3, size)

xx, yy = np.meshgrid(x, y)
z = (1/(2*np.pi*sigma_x*sigma_y) * np.exp(-(xx**2/(2*sigma_x**2)
     + yy**2/(2*sigma_y**2))))

extent = [x[0], x[-1], y[0], y[-1]]
fig, ax = plt.subplots()
ax.imshow(z, extent=extent)
cs = ax.contour(z, extent=extent, colors='w')
seg1 = cs.allsegs[3][0]
ax.clabel(cs, cs.levels, fmt='%.5f%%', fontsize=15)
seg2 = cs.allsegs[3][0]
plt.show()

fig, (ax1, ax2) = plt.subplots(1, 2, figsize=(6, 3))
ax1.plot(seg1[:, 0], seg1[:, 1], marker='.', ms=1)
ax1.set_title('Before ax.clabel')
ax2.plot(seg2[:, 0], seg2[:, 1], marker='.', ms=1)
ax2.set_title('After ax.clabel')
plt.show()