import matplotlib.pyplot as plt
import matplotlib.cm as cm
from MAST.structopt_stem.tools.StemCalc import ConvStem
from MAST.structopt_stem.generate.gen_pop_box import gen_pop_box as gpb
from MAST.structopt_stem import Optimizer
import numpy
size = 10.0
Au1 = gpb([('Au',10,0,0),('Cu',10,0,0)],size)
aber=[[0,0],[0,0],[22.56,-20.1],[22.08,-7.5],[0.1198,0],[0.9018,-170.1],[0.04964,20.9],[28.43,-120.6],[11.84,153.8],[8.456,76.1],[0.622,0],[2.811,-125.5]]
autostemparameters={'Electron energy': 200,'Spherical aberration': 1.4,'Defocus':0,'Aperture semiangle': 24.5,'Source size': 0.882,'Slice size': 20.0,'Pixels':800,'aber':aber,'Scale Factor':0.00570113}
A = ConvStem(parameters=autostemparameters,calc_exp=False)
#fig = plt.figure()
#ax = fig.add_subplot(111)
#psf = numpy.fft.fftshift(A.psf)
#ax.imshow(psf,cmap=cm.hot)
#plt.show()
imAu1 = A.get_image(A.psf, Au1, autostemparameters['Slice size'], autostemparameters['Pixels'], 1)
#fig2 = plt.figure()
#ax2 = fig2.add_subplot(111)
#ax2.imshow(imAu1,cmap=cm.hot)
#plt.show()
autostemparameters['Exp_Image'] = imAu1
optparameters = {'structure': 'Cluster', 'optimizer_type': 'BH', 'size':10,'atomlist': [('Au', 10, 0, 0), ('Cu', 10, 0, 0)],'FIT_SCHEME':'STEM_Cost','STEM_Parameters':autostemparameters}
B = Optimizer(optparameters)
B.algorithm_serial()
'Spherical aberration': 1.4,
'Defocus': 0,
'Aperture semiangle': 24.5,
'Source size': 0.882,
'Slice size': 20.0,
'Pixels': 800,
'aber': aber,
'Scale Factor': 0.00570113
}
A = ConvStem(parameters=autostemparameters, calc_exp=False)
#fig = plt.figure()
#ax = fig.add_subplot(111)
#psf = numpy.fft.fftshift(A.psf)
#ax.imshow(psf,cmap=cm.hot)
#plt.show()
imAu1 = A.get_image(A.psf, Au1, autostemparameters['Slice size'],
autostemparameters['Pixels'], 1)
#fig2 = plt.figure()
#ax2 = fig2.add_subplot(111)
#ax2.imshow(imAu1,cmap=cm.hot)
#plt.show()
autostemparameters['Exp_Image'] = imAu1
optparameters = {
'structure': 'Cluster',
'optimizer_type': 'BH',
'size': 10,
'atomlist': [('Au', 10, 0, 0), ('Cu', 10, 0, 0)],
'FIT_SCHEME': 'STEM_Cost',
'STEM_Parameters': autostemparameters
}
B = Optimizer(optparameters)
B.algorithm_serial()
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
else:
parameters = None
parameters = MPI.COMM_WORLD.bcast(parameters, root=0)
C = Optimizer(parameters)
C.run()
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
else:
parameters=None
parameters = MPI.COMM_WORLD.bcast(parameters,root=0)
C = Optimizer(parameters)
C.run()
