def check_scatter_consistancy(value):
atoms, exp = value[0:2]
proc, alg = value[-1]
scat = ElasticScatter(exp_dict=exp, verbose=True)
scat.set_processor(proc, alg)
ans = scat.get_pdf(atoms)
ans1 = scat.get_fq(atoms)
print(len(ans1))
print(scat.get_scatter_vector().shape)
ans2 = scat.get_sq(atoms)
print(len(ans2))
ans3 = scat.get_iq(atoms)
def test_consistency2():
outs = [[] for i in range(len(test_atoms))]
s = ElasticScatter(verbose=True)
for i, atoms in enumerate(test_data):
stru = convert_atoms_to_stru(atoms)
srfit_calc = DebyePDFCalculator()
srfit_calc.qmin = s.exp['qmin']
srfit_calc.qmax = s.exp['qmax']
srfit_calc.qstep = s.exp['qbin']
srfit_calc(stru)
stats_check(s.get_scatter_vector(), srfit_calc.qgrid)
fq = srfit_calc.fq
outs[i % len(test_atoms)].append(fq)
for j in range(len(test_atoms)):
for a, b in permutations(outs[j], 2):
stats_check(a, b)
def test_consistency2():
outs = [[] for i in range(len(test_atoms))]
s = ElasticScatter(verbose=True)
for i, atoms in enumerate(test_data):
stru = convert_atoms_to_stru(atoms)
srfit_calc = DebyePDFCalculator()
srfit_calc.qmin = s.exp['qmin']
srfit_calc.qmax = s.exp['qmax']
srfit_calc.qstep = s.exp['qbin']
srfit_calc(stru)
stats_check(s.get_scatter_vector(), srfit_calc.qgrid)
fq = srfit_calc.fq
outs[i % len(test_atoms)].append(fq)
for j in range(len(test_atoms)):
for a, b in permutations(outs[j], 2):
stats_check(a, b)
def test_fq_against_srfit():
# unpack the atoms and experiment
atoms = local_test_atoms
exp = None
# get the pyIID F(Q)
s = ElasticScatter(exp)
# s.set_processor('CPU', 'nxn')
# get the SrFit F(Q)
stru = convert_atoms_to_stru(atoms)
srfit_calc = DebyePDFCalculator()
srfit_calc.qmin = s.exp['qmin']
srfit_calc.qmax = s.exp['qmax']
srfit_calc.qstep = s.exp['qbin']
srfit_calc(stru)
stats_check(s.get_scatter_vector(), srfit_calc.qgrid)
ans1 = s.get_fq(atoms)
ans2 = srfit_calc.fq
stats_check(ans1, ans2, rtol=1e-4, atol=5e-6)
del srfit_calc
stats_check(ans1, ans2, rtol=1e-4, atol=5e-6)
import numpy as np
from ase.atoms import Atoms
from pyiid.experiments.elasticscatter import ElasticScatter
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
import ase.io
__author__ = 'christopher'
# atoms = Atoms('Au4', [[0, 0, 0], [3, 0, 0], [0, 3, 0], [3, 3, 0]])
atoms = ase.io.read('/mnt/work-data/dev/IID_data/db_test/PDF_LAMMPS_587.traj')
scat = ElasticScatter()
scat.update_experiment({'qmax': 8, 'qmin': .5})
s = scat.get_scatter_vector()
k = 100
i_max, j_max = k, k
pixel_array = np.zeros((i_max, j_max))
for i in range(i_max):
for j in range(j_max):
pixel_array[i, j] = np.sqrt(i**2 + j**2)
pixel_array /= np.max(pixel_array)
pixel_array *= np.max(s)
img = scat.get_2d_scatter(atoms, pixel_array)
print img.shape
# plt.imshow(pixel_array)
print np.max(img), np.min(img)
plt.imshow(img, aspect='auto')
import numpy as np
from ase.atoms import Atoms
from pyiid.experiments.elasticscatter import ElasticScatter
import matplotlib.pyplot as plt
from matplotlib.colors import LogNorm
import ase.io
__author__ = 'christopher'
# atoms = Atoms('Au4', [[0, 0, 0], [3, 0, 0], [0, 3, 0], [3, 3, 0]])
atoms = ase.io.read('/mnt/work-data/dev/IID_data/db_test/PDF_LAMMPS_587.traj')
scat = ElasticScatter()
scat.update_experiment({'qmax': 8, 'qmin': .5})
s = scat.get_scatter_vector()
k = 100
i_max, j_max = k, k
pixel_array = np.zeros((i_max, j_max))
for i in range(i_max):
for j in range(j_max):
pixel_array[i, j] = np.sqrt(i ** 2 + j ** 2)
pixel_array /= np.max(pixel_array)
pixel_array *= np.max(s)
img = scat.get_2d_scatter(atoms, pixel_array)
print img.shape
# plt.imshow(pixel_array)
print np.max(img), np.min(img)
