def subtract(p1, submap_ft, refmap_ft, sx, sy, s, a, apix, def1, def2, angast,
phase, kv, ac, cs, az, el, sk, xshift, yshift, coefs_method, r,
nr, pfac):
c = ctf.eval_ctf(s / apix,
a,
def1,
def2,
angast,
phase,
kv,
ac,
cs,
bf=0,
lp=2 * apix)
orient = euler2rot(np.deg2rad(az), np.deg2rad(el), np.deg2rad(sk))
pshift = np.exp(-2 * np.pi * 1j * (-xshift * sx + -yshift * sy))
p2 = vop.interpolate_slice_numba(submap_ft, orient, pfac=pfac)
p2 *= pshift
if coefs_method < 1:
# p1s = p1 - p2 * c
p1s = p2 * c
elif coefs_method == 1:
p3 = vop.interpolate_slice_numba(refmap_ft, orient, pfac=pfac)
p3 *= pshift
frc = np.abs(algo.bincorr_nb(p1, p3 * c, r, nr))
coefs = np.take(frc, r)
# p1s = p1 - p2 * c * coefs
p1s = p2 * c * coefs
return p1s
def project(f3d,
p,
s,
sx,
sy,
a,
apply_ctf=False,
size=None,
flip_phase=False):
orient = util.euler2rot(np.deg2rad(p[star.Relion.ANGLEROT]),
np.deg2rad(p[star.Relion.ANGLETILT]),
np.deg2rad(p[star.Relion.ANGLEPSI]))
pshift = np.exp(
-2 * np.pi * 1j *
(-p[star.Relion.ORIGINX] * sx + -p[star.Relion.ORIGINY] * sy))
f2d = vop.interpolate_slice_numba(f3d, orient, size=size)
f2d *= pshift
if apply_ctf or flip_phase:
apix = star.calculate_apix(p)
c = ctf.eval_ctf(s / apix,
a,
p[star.Relion.DEFOCUSU],
p[star.Relion.DEFOCUSV],
p[star.Relion.DEFOCUSANGLE],
p[star.Relion.PHASESHIFT],
p[star.Relion.VOLTAGE],
p[star.Relion.AC],
p[star.Relion.CS],
bf=0,
lp=2 * apix)
if flip_phase:
c = np.sign(c)
f2d *= c
return f2d
def particle_xcorr(ptcl, refmap_ft):
r = util.euler2rot(*np.deg2rad(ptcl[star.Relion.ANGLES]))
proj = vop.interpolate_slice_numba(refmap_ft, r)
c = ctf.eval_ctf(s / apix,
a,
def1[i],
def2[i],
angast[i],
phase[i],
kv[i],
ac[i],
cs[i],
bf=0,
lp=2 * apix)
pshift = np.exp(-2 * np.pi * 1j * (-xshift[i] * sx + -yshift * sy))
proj_ctf = proj * pshift * c
with mrc.ZSliceReader(ptcl[star.Relion.IMAGE_NAME]) as f:
exp_image_fft = rfft2(fftshift(f.read(i)))
xcor_fft = exp_image_fft * proj_ctf
xcor = fftshift(irfft2(xcor_fft))
return xcor
