data = fp.readlines()
for line in range(len(data)):
if "'psf':" in data[line]:
parameters['psf'] = ast.literal_eval(data[line].strip())['psf']
if "'stem_ref':" in data[line]:
parameters['stem_ref'] = ast.literal_eval(data[line].strip())['stem_ref']
'''
A = ConvStem(parameters=autostemparameters, calc_exp=False)
try:
atoms_ref = inp_out.read_xyz(parameters['stem_ref'], 0)
except KeyError:
atoms_ref = inp_out.read_xyz(
'/home/usitguest/USIT/dropbox_app/STEM_ref', 0)
nk = autostemparameters['Pixels']
A.psf = np.empty([nk, nk], dtype=float)
try:
fileobj = open(parameters['psf'], 'r')
except KeyError:
fileobj = open('/home/usitguest/USIT/dropbox_app/PSF.txt', 'r')
lines = fileobj.readlines()
for x in range(0, nk):
A.psf[x] = lines[x].split()
fileobj.close()
STEM_ref = A.get_image(A.psf, atoms_ref, autostemparameters['Slice size'],
autostemparameters['Pixels'])
parameters['stem_parameters'] = autostemparameters
autostemparameters['Exp_Image'] = STEM_ref
autostemparameters['Grid_sim2exp'] = 1
fp = open('../archive_input_options.txt')
data = fp.readlines()
for line in range(len(data)):
if "'psf':" in data[line]:
parameters['psf'] = ast.literal_eval(data[line].strip())['psf']
if "'stem_ref':" in data[line]:
parameters['stem_ref'] = ast.literal_eval(data[line].strip())['stem_ref']
'''
A = ConvStem(parameters=autostemparameters,calc_exp=False)
try:
atoms_ref=inp_out.read_xyz(parameters['stem_ref'],0)
except KeyError:
atoms_ref=inp_out.read_xyz('/home/usitguest/USIT/dropbox_app/STEM_ref',0)
nk = autostemparameters['Pixels']
A.psf = np.empty([nk,nk],dtype=float)
try:
fileobj = open(parameters['psf'], 'r')
except KeyError:
fileobj = open('/home/usitguest/USIT/dropbox_app/PSF.txt', 'r')
lines = fileobj.readlines()
for x in range(0,nk):
A.psf[x] = lines[x].split()
fileobj.close()
STEM_ref = A.get_image(A.psf, atoms_ref, autostemparameters['Slice size'], autostemparameters['Pixels'])
parameters['stem_parameters']=autostemparameters
autostemparameters['Exp_Image'] = STEM_ref
autostemparameters['Grid_sim2exp'] = 1
autostemparameters['Pixelshift'] = False
