def from_dict(d):
''' Convert the dictionary to a crystal model
Params:
d The dictionary of parameters
Returns:
The crystal model
'''
from dxtbx.model import Crystal
# If None, return None
if d is None:
return None
# Check the version and id
if str(d['__id__']) != "crystal":
raise ValueError("\"__id__\" does not equal \"crystal\"")
# Extract from the dictionary
real_space_a = d['real_space_a']
real_space_b = d['real_space_b']
real_space_c = d['real_space_c']
# str required to force unicode to ascii conversion
space_group = str("Hall:" + d['space_group_hall_symbol'])
xl = Crystal(real_space_a,
real_space_b,
real_space_c,
space_group_symbol=space_group)
# Isoforms used for stills
try:
xl.identified_isoform = d['identified_isoform']
except KeyError:
pass
# Extract scan point setting matrices, if present
try:
A_at_scan_points = d['A_at_scan_points']
xl.set_A_at_scan_points(A_at_scan_points)
except KeyError:
pass
# Extract covariance of B, if present
try:
cov_B = d['B_covariance']
xl.set_B_covariance(cov_B)
except KeyError:
pass
# Extract covariance of B at scan points, if present
cov_B_at_scan_points = d.get('B_covariance_at_scan_points')
if cov_B_at_scan_points is not None:
from scitbx.array_family import flex
cov_B_at_scan_points = flex.double(cov_B_at_scan_points).as_1d()
cov_B_at_scan_points.reshape(flex.grid(xl.num_scan_points, 9, 9))
xl.set_B_covariance_at_scan_points(cov_B_at_scan_points)
return xl
def test_crystal_with_scan_points(example_crystal):
c1 = Crystal(**example_crystal)
A = c1.get_A()
c1.set_A_at_scan_points([A for i in range(5)])
# Set the B covariance. The values are nonsense, just ensure they are
# all different
cov_B = flex.double(range(9 * 9)) * 1e-5
c1.set_B_covariance(cov_B)
cov_B.reshape(flex.grid(1, 9, 9))
cov_B_array = flex.double(flex.grid(5, 9, 9))
for i in range(5):
cov_B_array[i:(i + 1), :, :] = cov_B
c1.set_B_covariance_at_scan_points(cov_B_array)
cov_B = c1.get_B_covariance()
d = c1.to_dict()
c2 = CrystalFactory.from_dict(d)
eps = 1e-9
for Acomp in d["A_at_scan_points"]:
for e1, e2 in zip(A, Acomp):
assert abs(e1 - e2) <= eps
for covBcomp in d["B_covariance_at_scan_points"]:
for e1, e2 in zip(cov_B, covBcomp):
assert abs(e1 - e2) <= eps
assert c1 == c2
def test_crystal_with_scan_points():
from dxtbx.model import Crystal, CrystalFactory
from scitbx import matrix
real_space_a = matrix.col((35.2402102454, -7.60002142787, 22.080026774))
real_space_b = matrix.col((22.659572494, 1.47163505925, -35.6586361881))
real_space_c = matrix.col((5.29417246554, 38.9981792999, 4.97368666613))
c1 = Crystal(
real_space_a=real_space_a,
real_space_b=real_space_b,
real_space_c=real_space_c,
space_group_symbol="P 1 2/m 1",
)
A = c1.get_A()
c1.set_A_at_scan_points([A for i in range(5)])
# Set the B covariance. The values are nonsense, just ensure they are
# all different
from scitbx.array_family import flex
cov_B = flex.double(range((9 * 9))) * 1e-5
c1.set_B_covariance(cov_B)
cov_B.reshape(flex.grid(1, 9, 9))
cov_B_array = flex.double(flex.grid(5, 9, 9))
for i in range(5):
cov_B_array[i : (i + 1), :, :] = cov_B
c1.set_B_covariance_at_scan_points(cov_B_array)
cov_B = c1.get_B_covariance()
d = c1.to_dict()
c2 = CrystalFactory.from_dict(d)
eps = 1e-9
for Acomp in d["A_at_scan_points"]:
for e1, e2 in zip(A, Acomp):
assert abs(e1 - e2) <= eps
for covBcomp in d["B_covariance_at_scan_points"]:
for e1, e2 in zip(cov_B, covBcomp):
assert abs(e1 - e2) <= eps
assert c1 == c2
