def set_quad(self, rad):
if self.rad == rad:
print("Using previous quadurature schem")
else:
tic = time.time()
# set slicing interpolation parameters
self.slice_params = {'quad_type': 'sk97'}
self.slice_interp = {'N': self.N, 'kern': 'lanczos', 'kernsize': 6, 'rad': rad, 'zeropad': 0, 'dopremult': True} #, 'onlyRs': True}
# set slicing quadrature
usFactor_R = 1.0
quad_R = quadrature.quad_schemes[('dir', self.slice_params['quad_type'])]
const_quad_rad = 0.45 # adjust quadrature
degree_R, resolution_R = quad_R.compute_degree(self.N, const_quad_rad, usFactor_R)
# print(np.rad2deg(resolution_R))
slice_quad = {}
slice_quad['resolution'] = max(0.5*quadrature.compute_max_angle(self.N, rad), resolution_R)
# slice_quad['resolution'] = np.rad2deg(resolution_R)
slice_quad['dir'], slice_quad['W'] = quad_R.get_quad_points(degree_R, self.is_sym)
self.slice_quad = slice_quad
self.quad_domain_R = quadrature.FixedSphereDomain(slice_quad['dir'], slice_quad['resolution'], sym=self.is_sym)
# generate slicing operators (points on sphere)
self.slice_ops = self.quad_domain_R.compute_operator(self.slice_interp)
self.N_R = len(self.quad_domain_R)
# print(" Slice Ops: %d, resolution: %.2f degree, generated in: %.4f seconds" \
# % (self.N_R, np.rad2deg(self.quad_domain_R.resolution), time.time()-tic))
tic = time.time()
# set inplane interpolation parameters
self.inplane_interp = {'N': self.N, 'kern': 'lanczos', 'kernsize': 6, 'rad': rad, 'zeropad': 0, 'dopremult': True} #, 'onlyRs': True}
# set inplane quadrature
usFactor_I = 1.0
maxAngle = quadrature.compute_max_angle(self.N, const_quad_rad, usFactor_I)
degree_I = np.uint32(np.ceil(2.0 * np.pi / maxAngle))
resolution_I = max(0.5*quadrature.compute_max_angle(self.N, rad), 2.0*np.pi / degree_I)
inplane_quad = {}
inplane_quad['resolution'] = resolution_I
inplane_quad['thetas'] = np.linspace(0, 2.0*np.pi, degree_I, endpoint=False)
# inplane_quad['thetas'] += inplane_quad['thetas'][1]/2.0
inplane_quad['W'] = np.require((2.0*np.pi/float(degree_I))*np.ones((degree_I,)), dtype=np.float32)
self.inplane_quad = inplane_quad
self.quad_domain_I = quadrature.FixedCircleDomain(inplane_quad['thetas'],
inplane_quad['resolution'])
# generate inplane operators
self.inplane_ops = self.quad_domain_I.compute_operator(self.inplane_interp)
self.N_I = len(self.quad_domain_I)
# print(" Inplane Ops: %d, resolution: %.2f degree, generated in: %.4f seconds." \
# % (self.N_I, np.rad2deg(self.quad_domain_I.resolution), time.time()-tic))
transform_change = self.cryodata.interp_params['kern'] != self.inplane_interp['kern'] or \
self.cryodata.interp_params['kernsize'] != self.inplane_interp['kernsize'] or \
self.cryodata.interp_params['zeropad'] != self.inplane_interp['zeropad'] or \
self.cryodata.interp_params['dopremult'] != self.inplane_interp['dopremult']
if transform_change:
self.cryodata.set_transform(self.inplane_interp)
self.rad = rad
def get_quadrature(N=124, const_rad=0.8):
is_sym = None
slice_params = {'quad_type': 'sk97'}
tic = time.time()
# set slicing quadrature
usFactor_R = 1.0
quad_R = quadrature.quad_schemes[('dir', slice_params['quad_type'])]
degree_R, resolution_R = quad_R.compute_degree(N, const_rad, usFactor_R)
# print(np.rad2deg(resolution_R))
slice_quad = {}
slice_quad['resolution'] = max(
0.5 * quadrature.compute_max_angle(N, const_rad), resolution_R)
# slice_quad['resolution'] = np.rad2deg(resolution_R)
slice_quad['dir'], slice_quad['W'] = quad_R.get_quad_points(
degree_R, is_sym)
slice_quad = slice_quad
quad_domain_R = quadrature.FixedSphereDomain(slice_quad['dir'],
slice_quad['resolution'],
sym=is_sym)
N_R = len(quad_domain_R)
print(" Slice Ops: %d, resolution: %.2f degree, generated in: %.4f seconds" \
% (N_R, np.rad2deg(quad_domain_R.resolution), time.time()-tic))
tic = time.time()
# set inplane quadrature
usFactor_I = 1.0
maxAngle = quadrature.compute_max_angle(N, const_rad, usFactor_I)
degree_I = np.uint32(np.ceil(2.0 * np.pi / maxAngle))
resolution_I = max(0.5 * quadrature.compute_max_angle(N, const_rad),
2.0 * np.pi / degree_I)
inplane_quad = {}
inplane_quad['resolution'] = resolution_I
inplane_quad['thetas'] = np.linspace(0,
2.0 * np.pi,
degree_I,
endpoint=False)
# inplane_quad['thetas'] += inplane_quad['thetas'][1]/2.0
inplane_quad['W'] = np.require((2.0 * np.pi / float(degree_I)) * np.ones(
(degree_I, )),
dtype=np.float32)
inplane_quad = inplane_quad
quad_domain_I = quadrature.FixedCircleDomain(inplane_quad['thetas'],
inplane_quad['resolution'])
# generate inplane operators
N_I = len(quad_domain_I)
print(" Inplane Ops: %d, resolution: %.2f degree, generated in: %.4f seconds." \
% (N_I, np.rad2deg(quad_domain_I.resolution), time.time()-tic))
return quad_domain_R, quad_domain_I
def set_inplane_quad(self,rad):
# Get (and generate if needed) the quadrature scheme for inplane rotation
params = self.params
tic = time.time()
degree_I = params.get('quad_degree_I','auto')
usFactor_I = params.get('quad_undersample_I',params.get('quad_undersample',1.0))
kern_I = params.get('interp_kernel_I',params.get('interp_kernel',None))
kernsize_I = params.get('interp_kernel_size_I',params.get('interp_kernel_size',None))
zeropad_I = params.get('interp_zeropad_I',params.get('interp_zeropad',0))
dopremult_I = params.get('interp_premult_I',params.get('interp_premult',True))
maxAngle = quadrature.compute_max_angle(self.N,rad,usFactor_I)
if degree_I == 'auto':
degree_I = np.uint32(np.ceil(2.0 * np.pi / maxAngle))
resolution_I = max(0.5*quadrature.compute_max_angle(self.N,rad), 2.0*np.pi / degree_I)
inplane_params = { 'degree':degree_I }
interp_params_I = { 'N':self.N, 'kern':kern_I, 'kernsize':kernsize_I, 'rad':rad, 'zeropad':zeropad_I, 'dopremult':dopremult_I }
domain_change_I = self.inplane_params != inplane_params
interp_change_I = self.inplane_interp != interp_params_I
transform_change = self.inplane_interp is None or \
self.inplane_interp['kern'] != interp_params_I['kern'] or \
self.inplane_interp['kernsize'] != interp_params_I['kernsize'] or \
self.inplane_interp['zeropad'] != interp_params_I['zeropad']
if domain_change_I:
inplane_quad = {}
inplane_quad['resolution'] = resolution_I
inplane_quad['thetas'] = np.linspace(0, 2.0*np.pi, degree_I, endpoint=False)
inplane_quad['thetas'] += inplane_quad['thetas'][1]/2.0
inplane_quad['W'] = np.require((2.0*np.pi/float(degree_I))*np.ones((degree_I,)),dtype=np.float32)
self.quad_domain_I = quadrature.FixedCircleDomain(inplane_quad['thetas'],
inplane_quad['resolution'])
self.N_I = len(self.quad_domain_I)
self.sampler_I.setup(params, self.N_D, self.N_D_Train, self.quad_domain_I)
self.inplane_quad = inplane_quad
self.inplane_params = inplane_params
if domain_change_I or interp_change_I:
print(" Inplane Ops: %d, " % self.N_I); sys.stdout.flush()
if self.N_I < self.otf_thresh_I:
self.using_precomp_inplane = True
print("generated in", end=''); sys.stdout.flush()
self.inplane_ops = self.quad_domain_I.compute_operator(interp_params_I)
print(" {0} secs.".format(time.time() - tic))
else:
self.using_precomp_inplane = False
print("generating OTF.")
self.inplane_ops = None
self.inplane_interp = interp_params_I
if transform_change:
if dopremult_I:
premult = cryoops.compute_premultiplier(self.N + 2*int(interp_params_I['zeropad']*(self.N/2)),
interp_params_I['kern'],interp_params_I['kernsize'])
premult = premult.reshape((-1,1)) * premult.reshape((1,-1))
else:
premult = None
self.fspace_stack.set_transform(premult,interp_params_I['zeropad'])
def set_slice_quad(self,rad):
# Get (and generate if needed) the quadrature scheme for slicing
params = self.params
tic = time.time()
N = self.N
degree_R = params.get('quad_degree_R','auto')
quad_scheme_R = params.get('quad_type_R','sk97')
sym = get_symmetryop(params.get('symmetry',None)) if params.get('perfect_symmetry',True) else None
usFactor_R = params.get('quad_undersample_R',params.get('quad_undersample',1.0))
kern_R = params.get('interp_kernel_R',params.get('interp_kernel',None))
kernsize_R = params.get('interp_kernel_size_R',params.get('interp_kernel_size',None))
zeropad_R = params.get('interp_zeropad_R',params.get('interp_zeropad',0))
dopremult_R = params.get('interp_premult_R',params.get('interp_premult',True))
quad_R = quadrature.quad_schemes[('dir',quad_scheme_R)]
if degree_R == 'auto':
degree_R,resolution_R = quad_R.compute_degree(N,rad,usFactor_R)
resolution_R = max(0.5*quadrature.compute_max_angle(self.N,rad), resolution_R)
slice_params = { 'quad_type':quad_scheme_R, 'degree':degree_R,
'sym':sym }
interp_params_R = { 'N':self.N, 'kern':kern_R, 'kernsize':kernsize_R, 'rad':rad, 'zeropad':zeropad_R, 'dopremult':dopremult_R }
domain_change_R = slice_params != self.slice_params
interp_change_R = self.slice_interp != interp_params_R
transform_change = self.slice_interp is None or \
self.slice_interp['kern'] != interp_params_R['kern'] or \
self.slice_interp['kernsize'] != interp_params_R['kernsize'] or \
self.slice_interp['zeropad'] != interp_params_R['zeropad']
if domain_change_R:
slice_quad = {}
slice_quad['resolution'] = resolution_R
slice_quad['degree'] = degree_R
slice_quad['symop'] = sym
slice_quad['dir'],slice_quad['W'] = quad_R.get_quad_points(degree_R,slice_quad['symop'])
slice_quad['W'] = np.require(slice_quad['W'], dtype=np.float32)
self.quad_domain_R = quadrature.FixedSphereDomain(slice_quad['dir'],
slice_quad['resolution'],\
sym=sym)
self.N_R = len(self.quad_domain_R)
self.sampler_R.setup(params, self.N_D, self.N_D_Train, self.quad_domain_R)
self.slice_quad = slice_quad
self.slice_params = slice_params
if domain_change_R or interp_change_R:
symorder = 1 if self.slice_quad['symop'] is None else self.slice_quad['symop'].get_order()
print(" Slice Ops: %d, " % self.N_R); sys.stdout.flush()
if self.N_R*symorder < self.otf_thresh_R:
self.using_precomp_slicing = True
print("generated in", end=''); sys.stdout.flush()
self.slice_ops = self.quad_domain_R.compute_operator(interp_params_R)
print(" {0} secs.".format(time.time() - tic))
Gsz = (self.N_R,self.N_T)
self.G = np.empty(Gsz, dtype=self.G_datatype)
self.slices = np.empty(np.prod(Gsz), dtype=np.complex64)
else:
self.using_precomp_slicing = False
print("generating OTF.")
self.slice_ops = None
self.G = np.empty((self.N,self.N,self.N),dtype=self.G_datatype)
self.slices = None
self.slice_interp = interp_params_R
if transform_change:
if dopremult_R:
premult = cryoops.compute_premultiplier(self.N + 2*int(interp_params_R['zeropad']*(self.N/2)),
interp_params_R['kern'],interp_params_R['kernsize'])
premult = premult.reshape((-1,1,1)) * premult.reshape((1,-1,1)) * premult.reshape((1,1,-1))
else:
premult = None
self.slice_premult = premult
self.slice_zeropad = interp_params_R['zeropad']
assert interp_params_R['zeropad'] == 0,'Zero padding for slicing not yet implemented'
def set_proj_quad(self,rad):
# Get (and generate if needed) the quadrature scheme for slicing
params = self.params
tic = time.time()
N = self.N
quad_scheme_R = params.get('quad_type_R','sk97')
quad_R = quadrature.quad_schemes[('dir',quad_scheme_R)]
degree_R = params.get('quad_degree_R','auto')
degree_I = params.get('quad_degree_I','auto')
usFactor_R = params.get('quad_undersample_R',params.get('quad_undersample',1.0))
usFactor_I = params.get('quad_undersample_I',params.get('quad_undersample',1.0))
kern_R = params.get('interp_kernel_R',params.get('interp_kernel',None))
kernsize_R = params.get('interp_kernel_size_R',params.get('interp_kernel_size',None))
zeropad_R = params.get('interp_zeropad_R',params.get('interp_zeropad',0))
dopremult_R = params.get('interp_premult_R',params.get('interp_premult',True))
sym = get_symmetryop(params.get('symmetry',None)) if params.get('perfect_symmetry',True) else None
maxAngle = quadrature.compute_max_angle(self.N,rad,usFactor_I)
if degree_I == 'auto':
degree_I = np.uint32(np.ceil(2.0 * np.pi / maxAngle))
if degree_R == 'auto':
degree_R,resolution_R = quad_R.compute_degree(N,rad,usFactor_R)
resolution_R = max(0.5*quadrature.compute_max_angle(self.N,rad), resolution_R)
resolution_I = max(0.5*quadrature.compute_max_angle(self.N,rad), 2.0*np.pi / degree_I)
slice_params = { 'quad_type':quad_scheme_R, 'degree':degree_R,
'sym':sym }
inplane_params = { 'degree':degree_I }
proj_params = { 'quad_type_R':quad_scheme_R, 'degree_R':degree_R,
'sym':sym, 'degree_I':degree_I }
interp_params_RI = { 'N':self.N, 'kern':kern_R, 'kernsize':kernsize_R, 'rad':rad, 'zeropad':zeropad_R, 'dopremult':dopremult_R }
interp_change_RI = self.proj_interp != interp_params_RI
transform_change = self.slice_interp is None or \
self.slice_interp['kern'] != interp_params_RI['kern'] or \
self.slice_interp['kernsize'] != interp_params_RI['kernsize'] or \
self.slice_interp['zeropad'] != interp_params_RI['zeropad']
domain_change_R = self.slice_params != slice_params
domain_change_I = self.inplane_params != inplane_params
domain_change_RI = self.proj_params != proj_params
if domain_change_RI:
proj_quad = {}
proj_quad['resolution'] = max(resolution_R,resolution_I)
proj_quad['degree_R'] = degree_R
proj_quad['degree_I'] = degree_I
proj_quad['symop'] = sym
proj_quad['dir'],proj_quad['W_R'] = quad_R.get_quad_points(degree_R,proj_quad['symop'])
proj_quad['W_R'] = np.require(proj_quad['W_R'], dtype=np.float32)
proj_quad['thetas'] = np.linspace(0, 2.0*np.pi, degree_I, endpoint=False)
proj_quad['thetas'] += proj_quad['thetas'][1]/2.0
proj_quad['W_I'] = np.require((2.0*np.pi/float(degree_I))*np.ones((degree_I,)),dtype=np.float32)
self.quad_domain_RI = quadrature.FixedSO3Domain( proj_quad['dir'],
-proj_quad['thetas'],
proj_quad['resolution'],
sym=sym)
self.N_RI = len(self.quad_domain_RI)
self.proj_quad = proj_quad
self.proj_params = proj_params
if domain_change_R:
self.quad_domain_R = quadrature.FixedSphereDomain(proj_quad['dir'],
proj_quad['resolution'],
sym=sym)
self.N_R = len(self.quad_domain_R)
self.sampler_R.setup(params, self.N_D, self.N_D_Train, self.quad_domain_R)
self.slice_params = slice_params
if domain_change_I:
self.quad_domain_I = quadrature.FixedCircleDomain(proj_quad['thetas'],
proj_quad['resolution'])
self.N_I = len(self.quad_domain_I)
self.sampler_I.setup(params, self.N_D, self.N_D_Train, self.quad_domain_I)
self.inplane_params = inplane_params
if domain_change_RI or interp_change_RI:
symorder = 1 if self.proj_quad['symop'] is None else self.proj_quad['symop'].get_order()
print(" Projection Ops: %d (%d slice, %d inplane), " % (self.N_RI, self.N_R, self.N_I)); sys.stdout.flush()
if self.N_RI*symorder < self.otf_thresh_RI:
self.using_precomp_slicing = True
print("generated in", end=''); sys.stdout.flush()
self.slice_ops = self.quad_domain_RI.compute_operator(interp_params_RI)
print(" {0} secs.".format(time.time() - tic))
Gsz = (self.N_RI,self.N_T)
self.G = np.empty(Gsz, dtype=self.G_datatype)
self.slices = np.empty(np.prod(Gsz), dtype=np.complex64)
else:
self.using_precomp_slicing = False
print("generating OTF.")
self.slice_ops = None
self.G = np.empty((N,N,N),dtype=self.G_datatype)
self.slices = None
self.using_precomp_inplane = False
self.inplane_ops = None
self.proj_interp = interp_params_RI
if transform_change:
if dopremult_R:
premult = cryoops.compute_premultiplier(self.N + 2*int(interp_params_RI['zeropad']*(self.N/2)),
interp_params_RI['kern'],interp_params_RI['kernsize'])
premult = premult.reshape((-1,1,1)) * premult.reshape((1,-1,1)) * premult.reshape((1,1,-1))
else:
premult = None
self.slice_premult = premult
self.slice_zeropad = interp_params_RI['zeropad']
assert interp_params_RI['zeropad'] == 0,'Zero padding for slicing not yet implemented'