def main(args):
assert args.cs.endswith('.cs'), "Input file must be a .cs file"
assert args.o.endswith('.pkl'), "Output CTF parameters must be .pkl file"
metadata = np.load(args.cs)
N = len(metadata)
log('{} particles'.format(N))
ctf_params = np.zeros((N, 9))
ctf_params[:,0] = metadata['blob/shape'][0][0]
fields = ('blob/psize_A','ctf/df1_A','ctf/df2_A','ctf/df_angle_rad','ctf/accel_kv','ctf/cs_mm','ctf/amp_contrast','ctf/phase_shift_rad')
for i,f in enumerate(fields):
ctf_params[:,i+1] = metadata[f]
if f in ('ctf/df_angle_rad', 'ctf/phase_shift_rad'): # convert to degrees
ctf_params[:,i+1] *= (180/np.pi)
ctf.print_ctf_params(ctf_params[0])
log('Saving {}'.format(args.o))
with open(args.o,'wb') as f:
pickle.dump(ctf_params.astype(np.float32), f)
if args.png:
import matplotlib.pyplot as plt
ctf.plot_ctf(int(ctf_params[0,0]), ctf_params[0,1], ctf_params[0,2:])
plt.savefig(args.png)
log(args.png)
def main(args):
assert args.star.endswith('.star'), "Input file must be .star file"
assert args.o.endswith('.pkl'), "Output CTF parameters must be .pkl file"
if args.relion31: # TODO: parse the data_optics block
assert args.kv is not None, "--kv must be set manually with RELION 3.1 file format"
assert args.cs is not None, "--cs must be set manually with RELION 3.1 file format"
assert args.w is not None, "-w must be set manually with RELION 3.1 file format"
s = starfile.Starfile.load(args.star, relion31=args.relion31)
N = len(s.df)
log('{} particles'.format(N))
overrides = {}
if args.kv is not None:
log(f'Overriding accerlating voltage with {args.kv} kV')
overrides[HEADERS[3]] = args.kv
if args.cs is not None:
log(f'Overriding spherical abberation with {args.cs} mm')
overrides[HEADERS[4]] = args.cs
if args.w is not None:
log(f'Overriding amplitude contrast ratio with {args.w}')
overrides[HEADERS[5]] = args.w
if args.ps is not None:
log(f'Overriding phase shift with {args.ps}')
overrides[HEADERS[6]] = args.ps
ctf_params = np.zeros((N, 9))
ctf_params[:, 0] = args.D
ctf_params[:, 1] = args.Apix
for i, header in enumerate([
'_rlnDefocusU', '_rlnDefocusV', '_rlnDefocusAngle', '_rlnVoltage',
'_rlnSphericalAberration', '_rlnAmplitudeContrast',
'_rlnPhaseShift'
]):
ctf_params[:, i + 2] = s.df[
header] if header not in overrides else overrides[header]
log('CTF parameters for first particle:')
ctf.print_ctf_params(ctf_params[0])
log('Saving {}'.format(args.o))
with open(args.o, 'wb') as f:
pickle.dump(ctf_params.astype(np.float32), f)
if args.png:
import matplotlib.pyplot as plt
assert args.D, 'Need image size to plot CTF'
ctf.plot_ctf(args.D, args.Apix, ctf_params[0, 2:])
plt.savefig(args.png)
log(args.png)
def main(args):
assert args.cs.endswith('.cs'), "Input file must be a .cs file"
assert args.o.endswith('.pkl'), "Output CTF parameters must be .pkl file"
metadata = np.load(args.cs)
N = len(metadata)
log('{} particles'.format(N))
# sometimes blob/shape, blob/psize_A are missing from the .cs file
try:
D = metadata['blob/shape'][0][0]
Apix = metadata['blob/psize_A']
except ValueError:
assert args.D, "Must provide image size with -D"
assert args.Apix, "Must provide pixel size with --Apix"
D = args.D
Apix = args.Apix
ctf_params = np.zeros((N, 9))
ctf_params[:, 0] = D
ctf_params[:, 1] = Apix
fields = ('ctf/df1_A', 'ctf/df2_A', 'ctf/df_angle_rad', 'ctf/accel_kv',
'ctf/cs_mm', 'ctf/amp_contrast', 'ctf/phase_shift_rad')
for i, f in enumerate(fields):
ctf_params[:, i + 2] = metadata[f]
if f in ('ctf/df_angle_rad',
'ctf/phase_shift_rad'): # convert to degrees
ctf_params[:, i + 2] *= (180 / np.pi)
ctf.print_ctf_params(ctf_params[0])
log('Saving {}'.format(args.o))
with open(args.o, 'wb') as f:
pickle.dump(ctf_params.astype(np.float32), f)
if args.png:
import matplotlib.pyplot as plt
ctf.plot_ctf(int(ctf_params[0, 0]), ctf_params[0, 1], ctf_params[0,
2:])
plt.savefig(args.png)
log(args.png)