def translation_align_given_rotation_angles(v1, m1, v2, m2, angs):
"""
for each angle, do a translation search
"""
v1f = fftn(v1)
v1f[0, 0, 0] = 0.0
v1f = fftshift(v1f)
a = [{}] * len(angs)
for i, ang in enumerate(angs):
v2r = GR.rotate_pad_mean(v2, angle=ang)
v2rf = fftn(v2r)
v2rf[0, 0, 0] = 0.0
v2rf = fftshift(v2rf)
m2r = GR.rotate_pad_zero(m2, angle=ang)
m1_m2r = m1 * m2
# masked images
v1fm = v1f * m1_m2r
v2rfm = v2rf * m1_m2r
# normalize values
v1fmn = v1fm / N.sqrt(N.square(N.abs(v1fm)).sum())
v2rfmn = v2rfm / N.sqrt(N.square(N.abs(v2rfm)).sum())
lc = translation_align__given_unshifted_fft(ifftshift(v1fmn),
ifftshift(v2rfmn))
a[i] = {'ang': ang, 'loc': lc['loc'], 'score': lc['cor']}
return a
def inv_transform_mask(phi, w, n):
"""
Generates the mask rotated by the angles specified by the inverse of phi
"""
ang = [phi['q_rot'], phi['q_tilt'], phi['q_psi']]
loc = [0.0, 0.0, 0.0]
ang, loc = ang_loc.reverse_transform_ang_loc(ang, loc)
w_rot = rotate.rotate_pad_zero(w, angle=ang, loc_r=loc)
return w_rot
def generate_toy_model(dim_siz=64, model_id=0):
siz = N.array([dim_siz, dim_siz, dim_siz])
mid = siz / 2.0
xg = N.mgrid[0:siz[0], 0:siz[1], 0:siz[2]]
if model_id == 0:
# four gauss functions
short_dia = 0.4
mid_dia = 0.8
long_dia = 1.2
e0 = generate_toy_model__gaussian(
dim_siz=dim_siz,
xg=xg,
xm=(mid + N.array([siz[0] / 4.0, 0.0, 0.0])),
dias=[long_dia, short_dia, short_dia])
e1 = generate_toy_model__gaussian(
dim_siz=dim_siz,
xg=xg,
xm=(mid + N.array([0.0, siz[1] / 4.0, 0.0])),
dias=[short_dia, long_dia, short_dia])
e2 = generate_toy_model__gaussian(
dim_siz=dim_siz,
xg=xg,
xm=(mid + N.array([0.0, 0.0, siz[2] / 4.0])),
dias=[short_dia, short_dia, long_dia])
e3 = GR.rotate_pad_zero(N.array(e0, order='F'),
angle=N.array([N.pi / 4.0, 0.0, 0.0]),
loc_r=N.array([0.0, 0.0, 0.0]))
e = e0 + e1 + e2 + e3
return e
def inv_transform_mask(phi, w, n):
ang = [phi['q_rot'], phi['q_tilt'], phi['q_psi']]
loc = [0.0, 0.0, 0.0]
ang, loc = ang_loc.reverse_transform_ang_loc(ang, loc)
w_rot = rotate.rotate_pad_zero(w, angle=ang, loc_r=loc)
return w_rot