def random_pattern(symmetry, k):
"""Creates a random pattern of some symmetry at some k
Parameters
---------------
symmetry: int
The symmetry of the cluster
k: float
The inverse spacing of the cluster nm^-1
Returns
------------
k:array-like
The
"""
angle = (2 * np.pi) / symmetry
k = k # +np.random.randn()/10 # normal distribution about k
k = [[np.cos(angle * i) * k, np.sin(angle * i) * k]
for i in range(symmetry)]
rotation_vector, theta = random_rotation()
rand_angle = np.random.rand() * np.pi * 2
k = [list(rotate(x, y, rand_angle)) + [0] for x, y in k]
s = [
sg(acc_voltage=200,
rotation_vector=rotation_vector,
theta=theta,
k0=speckle) for speckle in k
]
observed_intensity = [100 * shape_function(r=1, s=dev) for dev in s]
return k, observed_intensity
def simulate_symmetry(symmetry=4, I=1, k=4, r=1, iterations=1000):
"""Simulates the intensities of some symmetry for a random rotation.
Assumes a spherical cluster of randius r and spots appearing at k and an Intensity of I (if the deviation parameter
"s" is zero)
Parameters
---------------
symmetry: int
The symmetry of the clusters
I: float
Intensity with deviation parameter of zero
k: float
The inverse spacing of the clusters nm^-1
r: float
The radius of the cluster.
Returns
------------
observed_int:list
The intensities of the speckles described.
"""
angle = (2 * np.pi) / symmetry
k = [[np.cos(angle * i) * k,
np.sin(angle * i) * k, 0] for i in range(symmetry)]
observed_int = np.zeros(shape=(iterations, symmetry * 4))
for i in range(iterations):
rotation_vector, theta = random_rotation()
for j, speckle in enumerate(k):
s = sg(acc_voltage=200,
rotation_vector=rotation_vector,
theta=theta,
k0=speckle)
observed_int[i, j * 4] = I * shape_function(r=r, s=s)
observed_int[i, j * 4 + 1] = I * shape_function(r=r, s=s)
return observed_int
def test_shape_function(self):
plt.plot([shape_function(1, (i / 100) + .00001) for i in range(100)])
plt.show()