def max_3D_pixel_error(t1, t2, r=1.0):
"""
Compute maximum pixel error between two sets of orientation parameters
assuming object has radius r, t1 is the projection transformation
of the first projection and t2 of the second one, respectively:
t = Transform({"type":"spider","phi":phi,"theta":theta,"psi":psi})
t.set_trans(Vec2f(-tx, -ty))
Note the function is symmetric in t1, t2.
"""
pass #IMPORTIMPORTIMPORT from EMAN2 import Vec2f
pass #IMPORTIMPORTIMPORT import types
dummy = EMAN2_cppwrap.Transform()
if (type(dummy) != type(t1)):
t = EMAN2_cppwrap.Transform({
"type": "spider",
"phi": t1[0],
"theta": t1[1],
"psi": t1[2]
})
t.set_trans(EMAN2_cppwrap.Vec2f(-t1[3], -t1[4]))
else:
t = t1
if (type(dummy) != type(t2)):
u = EMAN2_cppwrap.Transform({
"type": "spider",
"phi": t2[0],
"theta": t2[1],
"psi": t2[2]
})
u.set_trans(EMAN2_cppwrap.Vec2f(-t2[3], -t2[4]))
else:
u = t2
return EMAN2_cppwrap.EMData().max_3D_pixel_error(t, u, r)
def shc(
data,
refrings,
list_of_reference_angles,
numr,
xrng,
yrng,
step,
an=-1.0,
sym="c1",
finfo=None,
):
number_of_checked_refs = 0
mode = "F"
nx = data.get_xsize()
ny = data.get_ysize()
# center is in SPIDER convention
cnx = old_div(nx, 2) + 1
cny = old_div(ny, 2) + 1
if an >= 0.0:
ant = numpy.cos(numpy.radians(an))
else:
ant = -1.0
# phi, theta, psi, sxo, syo = get_params_proj(data)
t1 = data.get_attr("xform.projection")
dp = t1.get_params("spider")
ou = numr[-3]
sxi = round(-dp["tx"], 2)
syi = round(-dp["ty"], 2)
txrng = search_range(nx, ou, sxi, xrng)
tyrng = search_range(ny, ou, syi, yrng)
if finfo:
finfo.write(
"Old parameters: %9.4f %9.4f %9.4f %9.4f %9.4f\n"
% (dp["phi"], dp["theta"], dp["psi"], -dp["tx"], -dp["ty"])
)
finfo.flush()
z1, z2, z3, z4, z5 = sp_utilities.get_params_proj(data, "xform.anchor")
finfo.write(
"Anc parameters: %9.4f %9.4f %9.4f %9.4f %9.4f\n" % (z1, z2, z3, -z4, -z5)
)
finfo.flush()
previousmax = data.get_attr("previousmax")
[ang, sxs, sys, mirror, iref, peak, checked_refs] = EMAN2_cppwrap.Util.shc(
data,
refrings,
list_of_reference_angles,
txrng,
tyrng,
step,
ant,
mode,
numr,
cnx - sxi,
cny - syi,
sym,
)
iref = int(iref)
number_of_checked_refs += int(checked_refs)
if peak <= previousmax:
return -1.0e23, 0.0, number_of_checked_refs, -1
"""Multiline Comment50"""
else:
# The ormqip returns parameters such that the transformation is applied first, the mirror operation second.
# What that means is that one has to change the the Eulerian angles so they point into mirrored direction: phi+180, 180-theta, 180-psi
if mirror:
phi = (refrings[iref].get_attr("phi") + 540.0) % 360.0
theta = 180.0 - refrings[iref].get_attr("theta")
psi = (540.0 - refrings[iref].get_attr("psi") - ang) % 360.0
else:
phi = refrings[iref].get_attr("phi")
theta = refrings[iref].get_attr("theta")
psi = (360.0 + refrings[iref].get_attr("psi") - ang) % 360.0
s2x = sxs + sxi
s2y = sys + syi
# set_params_proj(data, [phi, theta, psi, s2x, s2y])
t2 = EMAN2_cppwrap.Transform(
{"type": "spider", "phi": phi, "theta": theta, "psi": psi}
)
t2.set_trans(EMAN2_cppwrap.Vec2f(-s2x, -s2y))
data.set_attr("xform.projection", t2)
data.set_attr("previousmax", peak)
# Find the pixel error that is minimum over symmetry transformations
if sym == "nomirror" or sym == "c1":
pixel_error = sp_pixel_error.max_3D_pixel_error(t1, t2, numr[-3])
else:
ts = t2.get_sym_proj(sym)
# only do it if it is not c1
pixel_error = +1.0e23
for ut in ts:
# we do not care which position minimizes the error
pixel_error = min(
sp_pixel_error.max_3D_pixel_error(t1, ut, numr[-3]), pixel_error
)
if finfo:
finfo.write(
"New parameters: %9.4f %9.4f %9.4f %9.4f %9.4f %10.5f %11.3e\n\n"
% (phi, theta, psi, s2x, s2y, peak, pixel_error)
)
finfo.flush()
return peak, pixel_error, number_of_checked_refs, iref