text stringlengths 0 93.6k |
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def load_pkl(pkl): |
with open(pkl, "rb") as f: |
x = pickle.load(f) |
return x |
def save_pkl(data, out_pkl, mode="wb"): |
if mode == "wb" and os.path.exists(out_pkl): |
vlog(f"Warning: {out_pkl} already exists. Overwriting.") |
with open(out_pkl, mode) as f: |
pickle.dump(data, f) |
def R_from_eman(a, b, y): |
a *= np.pi / 180.0 |
b *= np.pi / 180.0 |
y *= np.pi / 180.0 |
ca, sa = np.cos(a), np.sin(a) |
cb, sb = np.cos(b), np.sin(b) |
cy, sy = np.cos(y), np.sin(y) |
Ra = np.array([[ca, -sa, 0], [sa, ca, 0], [0, 0, 1]]) |
Rb = np.array([[1, 0, 0], [0, cb, -sb], [0, sb, cb]]) |
Ry = np.array(([cy, -sy, 0], [sy, cy, 0], [0, 0, 1])) |
R = np.dot(np.dot(Ry, Rb), Ra) |
# handling EMAN convention mismatch for where the origin of an image is (bottom right vs top right) |
R[0, 1] *= -1 |
R[1, 0] *= -1 |
R[1, 2] *= -1 |
R[2, 1] *= -1 |
return R |
def R_from_relion(a, b, y): |
a *= np.pi / 180.0 |
b *= np.pi / 180.0 |
y *= np.pi / 180.0 |
ca, sa = np.cos(a), np.sin(a) |
cb, sb = np.cos(b), np.sin(b) |
cy, sy = np.cos(y), np.sin(y) |
Ra = np.array([[ca, -sa, 0], [sa, ca, 0], [0, 0, 1]]) |
Rb = np.array([[cb, 0, -sb], [0, 1, 0], [sb, 0, cb]]) |
Ry = np.array(([cy, -sy, 0], [sy, cy, 0], [0, 0, 1])) |
R = np.dot(np.dot(Ry, Rb), Ra) |
R[0, 1] *= -1 |
R[1, 0] *= -1 |
R[1, 2] *= -1 |
R[2, 1] *= -1 |
return R |
def R_from_relion_scipy(euler_, degrees=True): |
"""Nx3 array of RELION euler angles to rotation matrix""" |
from scipy.spatial.transform import Rotation as RR |
euler = euler_.copy() |
if euler.shape == (3,): |
euler = euler.reshape(1, 3) |
euler[:, 0] += 90 |
euler[:, 2] -= 90 |
f = np.ones((3, 3)) |
f[0, 1] = -1 |
f[1, 0] = -1 |
f[1, 2] = -1 |
f[2, 1] = -1 |
rot = RR.from_euler("zxz", euler, degrees=degrees).as_matrix() * f |
return rot |
def R_to_relion_scipy(rot, degrees=True): |
"""Nx3x3 rotation matrices to RELION euler angles""" |
from scipy.spatial.transform import Rotation as RR |
if rot.shape == (3, 3): |
rot = rot.reshape(1, 3, 3) |
assert len(rot.shape) == 3, "Input must have dim Nx3x3" |
f = np.ones((3, 3)) |
f[0, 1] = -1 |
f[1, 0] = -1 |
f[1, 2] = -1 |
f[2, 1] = -1 |
euler = RR.from_matrix(rot * f).as_euler("zxz", degrees=True) |
euler[:, 0] -= 90 |
euler[:, 2] += 90 |
euler += 180 |
euler %= 360 |
euler -= 180 |
if not degrees: |
euler *= np.pi / 180 |
return euler |
def xrot(tilt_deg): |
"""Return rotation matrix associated with rotation over the x-axis""" |
theta = tilt_deg * np.pi / 180 |
tilt = np.array( |
[ |
[1.0, 0.0, 0.0], |
[0, np.cos(theta), -np.sin(theta)], |
[0, np.sin(theta), np.cos(theta)], |
] |
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