def tilt_mask(size,
tilt_ang1,
tilt_ang2=None,
tilt_axis=1,
light_axis=2,
sphere_mask=True):
"""wedge mask defined using tilt angles light axis is the direction of electrons"""
assert tilt_axis != light_axis
if tilt_ang2 is None:
tilt_ang2 = float(N.abs(tilt_ang1))
tilt_ang1 = -tilt_ang2
else:
assert tilt_ang1 < 0
assert tilt_ang2 > 0
tilt_ang1 = (tilt_ang1 / 180.0) * N.pi
tilt_ang2 = (tilt_ang2 / 180.0) * N.pi
g = AIVU.grid_displacement_to_center(size=size,
mid_co=IVU.fft_mid_co(siz=size))
plane_axis = set([0, 1, 2])
plane_axis.difference_update([light_axis, tilt_axis])
assert len(plane_axis) == 1
plane_axis = list(plane_axis)[0]
x_light = g[light_axis]
x_plane = g[plane_axis]
m = N.zeros(size, dtype=float)
m[N.logical_and(x_light <= (N.tan(tilt_ang1) * x_plane), x_light >=
(N.tan(tilt_ang2) * x_plane))] = 1.0
m[N.logical_and(x_light >= (N.tan(tilt_ang1) * x_plane), x_light <=
(N.tan(tilt_ang2) * x_plane))] = 1.0
if sphere_mask:
m *= MU.sphere_mask(m.shape)
return m
def tilt_mask(size,
tilt_ang1,
tilt_ang2=None,
tilt_axis=1,
light_axis=2,
sphere_mask_bool=True):
assert tilt_axis != light_axis
if tilt_ang2 is None:
tilt_ang2 = float(N.abs(tilt_ang1))
tilt_ang1 = -tilt_ang2
else:
assert tilt_ang1 < 0
assert tilt_ang2 > 0
tilt_ang1 = (tilt_ang1 / 180.0) * N.pi
tilt_ang2 = (tilt_ang2 / 180.0) * N.pi
g = IVU.grid_displacement_to_center(size=size,
mid_co=IVU.fft_mid_co(siz=size))
plane_axis = {0, 1, 2}
plane_axis.difference_update([light_axis, tilt_axis])
assert len(plane_axis) == 1
plane_axis = list(plane_axis)[0]
x_light = g[light_axis]
x_plane = g[plane_axis]
m = N.zeros(size, dtype=float)
m[N.logical_and(x_light <= (N.tan(tilt_ang1) * x_plane), x_light >=
(N.tan(tilt_ang2) * x_plane))] = 1.0
m[N.logical_and(x_light >= (N.tan(tilt_ang1) * x_plane), x_light <=
(N.tan(tilt_ang2) * x_plane))] = 1.0
if sphere_mask_bool:
m *= MU.sphere_mask(m.shape)
return m
def model_based_align_help(img_db_path, d, A_k, n, i, k):
X = get_image_db(img_db_path)
v1 = inv_fourier_transform(X[d['v']])
m1 = X[d['m']]
v2 = inv_fourier_transform(A_k)
m2 = TMU.sphere_mask([n, n, n])
transforms = fast_align(v1, m1, v2, m2)
result = []
for item in transforms:
phi = dict()
phi['q_rot'] = item['ang'][0]
phi['q_tilt'] = item['ang'][1]
phi['q_psi'] = item['ang'][2]
phi['q_x'] = item['loc'][0]
phi['q_y'] = item['loc'][1]
phi['q_z'] = item['loc'][2]
result.append(phi)
return {'i': i, 'k': k, 'transforms':result}
def align_vols_no_mask(v1, v2, L=36):
m = MU.sphere_mask(v1.shape)
return align_vols(v1=v1, m1=m, v2=v2, m2=m, L=L)
