def calculate_animation(self, dt):
'''
based on the assumption that dt goes from 0 to 1
'''
if dt > 1: raise
if self.angle != 0:
t1 = dt * self.angle
t2 = self.angle - t1
next = old_div(
(sin(t2) * self.start_point + sin(t1) * self.end_point),
self.sinangle)
else:
T = Transform()
d = {"type": "spin"}
d["omega"] = dt * 360
d["n1"] = self.rot_vec[0]
d["n2"] = self.rot_vec[1]
d["n3"] = self.rot_vec[2]
T.set_rotation(d)
next = T * self.start_point
#next = Vec3f(self.start_point[0],self.start_point[1],self.start_point[2])
self.arc_points[self.stage].append(self.radius * next)
self.target.arc_animation_update(self.arc_points)
def __establish_sphere_points(self, stage):
self.start_point = self.transforms[stage].transpose() * self.z_point
self.end_point = self.transforms[stage + 1].transpose() * self.z_point
if self.start_point != self.end_point:
self.angle = acos(self.start_point.dot(self.end_point))
self.omega = 1
else:
self.angle = 0
normal = Vec3f(-self.start_point[2], 0, -self.start_point[0])
normal.normalize()
T = Transform()
d = {"type": "spin"}
d["omega"] = self.omega
d["n1"] = normal[0]
d["n2"] = normal[1]
d["n3"] = normal[2]
T.set_rotation(d)
self.rot_vec = self.start_point
p = self.start_point
self.start_point = T * self.rot_vec
self.end_point = T * self.rot_vec
self.omega += 1
self.sinangle = sin(self.angle)
self.arc_points.append([])
def calculate_animation(self, dt):
"""
based on the assumption that dt goes from 0 to 1
"""
if dt > 1:
raise
if self.angle != 0:
t1 = dt * self.angle
t2 = self.angle - t1
next = (sin(t2) * self.start_point + sin(t1) * self.end_point) / self.sinangle
else:
T = Transform()
d = {"type": "spin"}
d["omega"] = dt * 360
d["n1"] = self.rot_vec[0]
d["n2"] = self.rot_vec[1]
d["n3"] = self.rot_vec[2]
T.set_rotation(d)
next = T * self.start_point
# next = Vec3f(self.start_point[0],self.start_point[1],self.start_point[2])
self.arc_points[self.stage].append(self.radius * next)
self.target.arc_animation_update(self.arc_points)
def __establish_sphere_points(self, stage):
self.start_point = self.transforms[stage].transpose() * self.z_point
self.end_point = self.transforms[stage + 1].transpose() * self.z_point
if self.start_point != self.end_point:
self.angle = acos(self.start_point.dot(self.end_point))
self.omega = 1
else:
self.angle = 0
normal = Vec3f(-self.start_point[2], 0, -self.start_point[0])
normal.normalize()
T = Transform()
d = {"type": "spin"}
d["omega"] = self.omega
d["n1"] = normal[0]
d["n2"] = normal[1]
d["n3"] = normal[2]
T.set_rotation(d)
self.rot_vec = self.start_point
p = self.start_point
self.start_point = T * self.rot_vec
self.end_point = T * self.rot_vec
self.omega += 1
self.sinangle = sin(self.angle)
self.arc_points.append([])
def transform_com(com, ptcl):
t = Transform()
if len(com) == 3:
t.set_rotation({'psi': meta.psi, 'phi': meta.phi, 'theta': meta.theta, 'type': 'spider'})
else:
t.set_rotation({'psi': meta.psi})
shift = t.transform(com)
# The change in the origin is the projection of the transformed difference vector on the new xy plane.
return shift[0], shift[1]
def subtract(particle,
dens,
sub_dens,
recenter=None,
no_frc=False,
low_cutoff=0.0,
high_cutoff=0.7071):
"""
Perform projection subtraction on one particle image.
:param particle: Tuple holding original (particle EMData, particle MetaData)
:param dens: Whole density map
:param sub_dens: Subtraction density map
:param recenter: Vector between CoM before and after subtraction, or None to skip recenter operation (default None)
:param no_frc: Skip FRC normalization (default False)
:param low_cutoff: Low cutoff frequency in FRC normalization (default 0.0)
:param high_cutoff: High cutoff frequency in FRC normalization (default 0.7071)
:return: Result object
"""
ptcl, meta = particle[0], particle[1]
ctfproj = make_proj(dens, meta)
ctfproj_sub = make_proj(sub_dens, meta)
if no_frc: # Direct subtraction only.
ptcl_sub = ptcl - ctfproj_sub
else: # Per-particle FRC normalization.
ptcl_sub = ptcl.process(
"math.sub.optimal", {
"ref": ctfproj,
"actual": ctfproj_sub,
"low_cutoff_frequency": low_cutoff,
"high_cutoff_frequency": high_cutoff
})
ptcl_norm_sub = ptcl_sub.process("normalize")
if recenter is not None:
# Rotate the coordinate frame of the CoM difference vector by the Euler angles.
t = Transform()
t.set_rotation({
'psi': meta.psi,
'phi': meta.phi,
'theta': meta.theta,
'type': 'spider'
})
shift = t.transform(recenter)
# The change in the origin is the projection of the transformed difference vector on the new xy plane.
meta.x_origin += shift[0]
meta.y_origin += shift[1]
return Result(ptcl, meta, ctfproj, ctfproj_sub, ptcl_sub, ptcl_norm_sub)
def make_proj(dens, meta):
"""
Project and CTF filter density according to particle metadata.
:param dens: EMData density
:param meta: Particle metadata (Euler angles and CTF parameters)
:return: CTF-filtered projection
"""
t = Transform()
t.set_rotation({'psi': meta.psi, 'phi': meta.phi, 'theta': meta.theta, 'type': 'spider'})
t.set_trans(-meta.x_origin, -meta.y_origin)
proj = dens.project("standard", t)
ctf = generate_ctf(meta.ctf_params)
ctf_proj = filt_ctf(proj, ctf)
return ctf_proj
