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 tst_crystal_with_scan_points(self):
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)])
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)
assert (c1 == c2)
print 'OK'
def tst_crystal(self):
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")
c1.set_mosaicity(0.1)
d = c1.to_dict()
c2 = CrystalFactory.from_dict(d)
eps = 1e-7
assert (abs(matrix.col(d['real_space_a']) - real_space_a) <= eps)
assert (abs(matrix.col(d['real_space_b']) - real_space_b) <= eps)
assert (abs(matrix.col(d['real_space_c']) - real_space_c) <= eps)
assert (d['space_group_hall_symbol'] == "-P 2y")
assert (d['mosaicity'] == 0.1)
assert (c1 == c2)
print 'OK'
def test_crystal(mosaic):
from dxtbx.model import 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))
if mosaic:
from dxtbx.model import MosaicCrystalKabsch2010
c1 = MosaicCrystalKabsch2010(
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")
c1.set_mosaicity(0.1)
else:
from dxtbx.model import Crystal
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")
d = c1.to_dict()
c2 = CrystalFactory.from_dict(d)
eps = 1e-7
assert abs(matrix.col(d['real_space_a']) - real_space_a) <= eps
assert abs(matrix.col(d['real_space_b']) - real_space_b) <= eps
assert abs(matrix.col(d['real_space_c']) - real_space_c) <= eps
assert d['space_group_hall_symbol'] == "-P 2y"
if mosaic:
assert d['mosaicity'] == 0.1
assert c1 == c2
def test_crystal(example_crystal):
c1 = Crystal(**example_crystal)
d = c1.to_dict()
c2 = CrystalFactory.from_dict(d)
for direction in ("real_space_a", "real_space_b", "real_space_c"):
assert abs(matrix.col(d[direction]) - example_crystal[direction]) <= 1e-7
assert d["space_group_hall_symbol"] == "-P 2y"
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