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 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 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 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
def test_reindex_experiments():
# See also https://github.com/cctbx/cctbx_project/issues/424
cs = sgtbx.space_group_info("I23").any_compatible_crystal_symmetry(
volume=100000)
B = scitbx.matrix.sqr(
cs.unit_cell().fractionalization_matrix()).transpose()
cryst = Crystal(B, cs.space_group())
n_scan_points = 10
A_at_scan_points = [(1, 0, 0, 0, 1, 0, 0, 0, 1)] * n_scan_points
cryst.set_A_at_scan_points(A_at_scan_points)
groups = metric_subgroups(cs, max_delta=5)
for group in groups.result_groups:
best_subsym = group["best_subsym"]
cb_op = group["cb_op_inp_best"]
expts = ExperimentList([Experiment(crystal=cryst)])
reindexed_expts = reindex_experiments(
experiments=expts,
cb_op=cb_op,
space_group=best_subsym.space_group())
assert (reindexed_expts[0].crystal.get_crystal_symmetry().
is_similar_symmetry(best_subsym))
# Check that the scan-varying A matrices have been copied as well
assert cryst.num_scan_points == n_scan_points
def test_crystal_model():
real_space_a = matrix.col((10, 0, 0))
real_space_b = matrix.col((0, 11, 0))
real_space_c = matrix.col((0, 0, 12))
model = Crystal(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1",
)
# This doesn't work as python class uctbx.unit_cell(uctbx_ext.unit_cell)
# so C++ and python classes are different types
# assert isinstance(model.get_unit_cell(), uctbx.unit_cell)
assert model.get_unit_cell().parameters() == (10.0, 11.0, 12.0, 90.0, 90.0,
90.0)
assert approx_equal(model.get_A(),
(1 / 10, 0, 0, 0, 1 / 11, 0, 0, 0, 1 / 12))
assert approx_equal(
matrix.sqr(model.get_A()).inverse(), (10, 0, 0, 0, 11, 0, 0, 0, 12))
assert approx_equal(model.get_B(), model.get_A())
assert approx_equal(model.get_U(), (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert approx_equal(model.get_real_space_vectors(),
(real_space_a, real_space_b, real_space_c))
assert (model.get_crystal_symmetry().unit_cell().parameters() ==
model.get_unit_cell().parameters())
assert model.get_crystal_symmetry().space_group() == model.get_space_group(
)
model2 = Crystal(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1",
)
assert model == model2
model2a = Crystal(model.get_A(), model.get_space_group())
assert model == model2a
model2b = Crystal(
matrix.sqr(model.get_A()).inverse().elems,
model.get_space_group().type().lookup_symbol(),
reciprocal=False,
)
assert model == model2b
# rotate 45 degrees about x-axis
R1 = matrix.sqr((
1,
0,
0,
0,
math.cos(math.pi / 4),
-math.sin(math.pi / 4),
0,
math.sin(math.pi / 4),
math.cos(math.pi / 4),
))
# rotate 30 degrees about y-axis
R2 = matrix.sqr((
math.cos(math.pi / 6),
0,
math.sin(math.pi / 6),
0,
1,
0,
-math.sin(math.pi / 6),
0,
math.cos(math.pi / 6),
))
# rotate 60 degrees about z-axis
R3 = matrix.sqr((
math.cos(math.pi / 3),
-math.sin(math.pi / 3),
0,
math.sin(math.pi / 3),
math.cos(math.pi / 3),
0,
0,
0,
1,
))
R = R1 * R2 * R3
model.set_U(R)
# B is unchanged
assert approx_equal(model.get_B(),
(1 / 10, 0, 0, 0, 1 / 11, 0, 0, 0, 1 / 12))
assert approx_equal(model.get_U(), R)
assert approx_equal(model.get_A(),
matrix.sqr(model.get_U()) * matrix.sqr(model.get_B()))
a_, b_, c_ = model.get_real_space_vectors()
assert approx_equal(a_, R * real_space_a)
assert approx_equal(b_, R * real_space_b)
assert approx_equal(c_, R * real_space_c)
assert (str(model).replace("-0.0000", " 0.0000") == """\
Crystal:
Unit cell: (10.000, 11.000, 12.000, 90.000, 90.000, 90.000)
Space group: P 1
U matrix: {{ 0.4330, -0.7500, 0.5000},
{ 0.7891, 0.0474, -0.6124},
{ 0.4356, 0.6597, 0.6124}}
B matrix: {{ 0.1000, 0.0000, 0.0000},
{ 0.0000, 0.0909, 0.0000},
{ 0.0000, 0.0000, 0.0833}}
A = UB: {{ 0.0433, -0.0682, 0.0417},
{ 0.0789, 0.0043, -0.0510},
{ 0.0436, 0.0600, 0.0510}}
""")
model.set_B((1 / 12, 0, 0, 0, 1 / 12, 0, 0, 0, 1 / 12))
assert approx_equal(model.get_unit_cell().parameters(),
(12, 12, 12, 90, 90, 90))
U = matrix.sqr((0.3455, -0.2589, -0.9020, 0.8914, 0.3909, 0.2293, 0.2933,
-0.8833, 0.3658))
B = matrix.sqr((1 / 13, 0, 0, 0, 1 / 13, 0, 0, 0, 1 / 13))
model.set_A(U * B)
assert approx_equal(model.get_A(), U * B)
assert approx_equal(model.get_U(), U, 1e-4)
assert approx_equal(model.get_B(), B, 1e-5)
model3 = Crystal(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group=sgtbx.space_group_info("P 222").group(),
)
assert model3.get_space_group().type().hall_symbol() == " P 2 2"
assert model != model3
#
sgi_ref = sgtbx.space_group_info(number=230)
model_ref = Crystal(
real_space_a=(44, 0, 0),
real_space_b=(0, 44, 0),
real_space_c=(0, 0, 44),
space_group=sgi_ref.group(),
)
assert approx_equal(model_ref.get_U(), (1, 0, 0, 0, 1, 0, 0, 0, 1))
assert approx_equal(model_ref.get_B(),
(1 / 44, 0, 0, 0, 1 / 44, 0, 0, 0, 1 / 44))
assert approx_equal(model_ref.get_A(), model_ref.get_B())
assert approx_equal(model_ref.get_unit_cell().parameters(),
(44, 44, 44, 90, 90, 90))
a_ref, b_ref, c_ref = map(matrix.col, model_ref.get_real_space_vectors())
cb_op_to_primitive = sgi_ref.change_of_basis_op_to_primitive_setting()
model_primitive = model_ref.change_basis(cb_op_to_primitive)
cb_op_to_reference = (model_primitive.get_space_group().info().
change_of_basis_op_to_reference_setting())
a_prim, b_prim, c_prim = map(matrix.col,
model_primitive.get_real_space_vectors())
assert (cb_op_to_primitive.as_abc() ==
"-1/2*a+1/2*b+1/2*c,1/2*a-1/2*b+1/2*c,1/2*a+1/2*b-1/2*c")
assert approx_equal(a_prim, -1 / 2 * a_ref + 1 / 2 * b_ref + 1 / 2 * c_ref)
assert approx_equal(b_prim, 1 / 2 * a_ref - 1 / 2 * b_ref + 1 / 2 * c_ref)
assert approx_equal(c_prim, 1 / 2 * a_ref + 1 / 2 * b_ref - 1 / 2 * c_ref)
assert cb_op_to_reference.as_abc() == "b+c,a+c,a+b"
assert approx_equal(a_ref, b_prim + c_prim)
assert approx_equal(b_ref, a_prim + c_prim)
assert approx_equal(c_ref, a_prim + b_prim)
assert approx_equal(
model_primitive.get_U(),
[
-0.5773502691896258,
0.40824829046386285,
0.7071067811865476,
0.5773502691896257,
-0.4082482904638631,
0.7071067811865476,
0.5773502691896257,
0.8164965809277259,
0.0,
],
)
assert approx_equal(
model_primitive.get_B(),
[
0.0262431940540739,
0.0,
0.0,
0.00927837023781507,
0.02783511071344521,
0.0,
0.01607060866333063,
0.01607060866333063,
0.03214121732666125,
],
)
assert approx_equal(
model_primitive.get_A(),
(0, 1 / 44, 1 / 44, 1 / 44, 0, 1 / 44, 1 / 44, 1 / 44, 0),
)
assert approx_equal(
model_primitive.get_unit_cell().parameters(),
[
38.1051177665153,
38.1051177665153,
38.1051177665153,
109.47122063449069,
109.47122063449069,
109.47122063449069,
],
)
assert model_ref != model_primitive
model_ref_recycled = model_primitive.change_basis(cb_op_to_reference)
assert approx_equal(model_ref.get_U(), model_ref_recycled.get_U())
assert approx_equal(model_ref.get_B(), model_ref_recycled.get_B())
assert approx_equal(model_ref.get_A(), model_ref_recycled.get_A())
assert approx_equal(
model_ref.get_unit_cell().parameters(),
model_ref_recycled.get_unit_cell().parameters(),
)
assert model_ref == model_ref_recycled
uc = uctbx.unit_cell(
(58.2567, 58.1264, 39.7093, 46.9077, 46.8612, 62.1055))
sg = sgtbx.space_group_info(symbol="P1").group()
cs = crystal.symmetry(unit_cell=uc, space_group=sg)
cb_op_to_minimum = cs.change_of_basis_op_to_minimum_cell()
# the reciprocal matrix
B = matrix.sqr(uc.fractionalization_matrix()).transpose()
U = random_rotation()
direct_matrix = (U * B).inverse()
model = Crystal(direct_matrix[:3],
direct_matrix[3:6],
direct_matrix[6:9],
space_group=sg)
assert uc.is_similar_to(model.get_unit_cell())
uc_minimum = uc.change_basis(cb_op_to_minimum)
model_minimum = model.change_basis(cb_op_to_minimum)
assert uc_minimum.is_similar_to(model_minimum.get_unit_cell())
assert model_minimum != model
model_minimum.update(model)
assert model_minimum == model # lgtm
A_static = matrix.sqr(model.get_A())
A_as_scan_points = [A_static]
num_scan_points = 11
for i in range(num_scan_points - 1):
A_as_scan_points.append(
A_as_scan_points[-1] *
matrix.sqr(euler_angles.xyz_matrix(0.1, 0.2, 0.3)))
model.set_A_at_scan_points(A_as_scan_points)
model_minimum = model.change_basis(cb_op_to_minimum)
assert model.num_scan_points == model_minimum.num_scan_points == num_scan_points
M = matrix.sqr(cb_op_to_minimum.c_inv().r().transpose().as_double())
M_inv = M.inverse()
for i in range(num_scan_points):
A_orig = matrix.sqr(model.get_A_at_scan_point(i))
A_min = matrix.sqr(model_minimum.get_A_at_scan_point(i))
assert approx_equal(A_min, A_orig * M_inv)
assert model.get_unit_cell().parameters() == pytest.approx(
(58.2567, 58.1264, 39.7093, 46.9077, 46.8612, 62.1055))
uc = uctbx.unit_cell((10, 11, 12, 91, 92, 93))
model.set_unit_cell(uc)
assert model.get_unit_cell().parameters() == pytest.approx(uc.parameters())
def test_check_old_vs_new():
from dxtbx.tests.model.crystal_model_old import crystal_model_old
model_1 = Crystal(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1",
)
model_2 = crystal_model_old(
real_space_a=(10, 0, 0),
real_space_b=(0, 11, 0),
real_space_c=(0, 0, 12),
space_group_symbol="P 1",
)
cov_B = matrix.sqr([1] * (9 * 9))
model_1.set_B_covariance(cov_B)
model_2.set_B_covariance(cov_B)
A_list = [model_1.get_A() for i in range(20)]
model_1.set_A_at_scan_points(A_list)
model_2.set_A_at_scan_points(A_list)
A1 = model_1.get_A()
A2 = model_2.get_A()
U1 = model_1.get_U()
U2 = model_2.get_U()
B1 = model_1.get_B()
B2 = model_2.get_B()
UC1 = model_1.get_unit_cell()
UC2 = model_2.get_unit_cell()
RSV1 = model_1.get_real_space_vectors()
RSV2 = model_2.get_real_space_vectors()
SG1 = model_1.get_space_group()
SG2 = model_2.get_space_group()
assert model_1.num_scan_points == model_2.num_scan_points
A_list_1 = [
model_1.get_A_at_scan_point(i)
for i in range(model_1.get_num_scan_points())
]
A_list_2 = [
model_2.get_A_at_scan_point(i)
for i in range(model_1.get_num_scan_points())
]
B_list_1 = [
model_1.get_B_at_scan_point(i)
for i in range(model_1.get_num_scan_points())
]
B_list_2 = [
model_2.get_B_at_scan_point(i)
for i in range(model_1.get_num_scan_points())
]
U_list_1 = [
model_1.get_U_at_scan_point(i)
for i in range(model_1.get_num_scan_points())
]
U_list_2 = [
model_2.get_U_at_scan_point(i)
for i in range(model_1.get_num_scan_points())
]
assert approx_equal(A1, A2)
assert approx_equal(B1, B2)
assert approx_equal(U1, U2)
assert approx_equal(UC1.parameters(), UC2.parameters())
assert approx_equal(RSV1[0], RSV2[0])
assert approx_equal(RSV1[1], RSV2[1])
assert approx_equal(RSV1[2], RSV2[2])
assert str(SG1.info()) == str(SG2.info())
for i in range(model_1.get_num_scan_points()):
assert approx_equal(A_list_1[i], A_list_2[i])
assert approx_equal(B_list_1[i], B_list_2[i])
assert approx_equal(U_list_1[i], U_list_2[i])
cell_sd_1 = model_1.get_cell_parameter_sd()
cell_sd_2 = model_2.get_cell_parameter_sd()
cell_volume_sd_1 = model_1.get_cell_volume_sd()
cell_volume_sd_2 = model_2.get_cell_volume_sd()
covB1 = model_1.get_B_covariance()
covB2 = model_1.get_B_covariance()
assert approx_equal(covB1, covB2)
assert approx_equal(cell_volume_sd_1, cell_volume_sd_2)
assert approx_equal(cell_sd_1, cell_sd_2)
def load_crystal(entry):
from cctbx import uctbx
from dxtbx.model import Crystal
from scitbx.array_family import flex
# Get the sample
nx_sample = get_nx_sample(entry, "sample")
# Set the space group
space_group_symbol = nx_sample["unit_cell_group"][()]
# Get depends on
if nx_sample["depends_on"][()] != ".":
assert nx_sample["depends_on"][()] == str(
nx_sample["transformations/phi"].name)
# Read the average unit cell data
average_unit_cell = flex.double(np.array(nx_sample["average_unit_cell"]))
assert nx_sample["average_unit_cell"].attrs["angles_units"] == "deg"
assert nx_sample["average_unit_cell"].attrs["length_units"] == "angstrom"
assert len(average_unit_cell.all()) == 1
assert len(average_unit_cell) == 6
average_orientation_matrix = flex.double(
np.array(nx_sample["average_orientation_matrix"]))
assert len(average_orientation_matrix.all()) == 2
assert average_orientation_matrix.all()[0] == 3
assert average_orientation_matrix.all()[1] == 3
# Get the real space vectors
uc = uctbx.unit_cell(tuple(average_unit_cell))
U = matrix.sqr(average_orientation_matrix)
B = matrix.sqr(uc.fractionalization_matrix()).transpose()
A = U * B
A = A.inverse()
real_space_a = A[0:3]
real_space_b = A[3:6]
real_space_c = A[6:9]
# Read the unit cell data
unit_cell = flex.double(np.array(nx_sample["unit_cell"]))
assert nx_sample["unit_cell"].attrs["angles_units"] == "deg"
assert nx_sample["unit_cell"].attrs["length_units"] == "angstrom"
# Read the orientation matrix
orientation_matrix = flex.double(np.array(nx_sample["orientation_matrix"]))
assert len(unit_cell.all()) == 2
assert len(orientation_matrix.all()) == 3
assert unit_cell.all()[0] == orientation_matrix.all()[0]
assert unit_cell.all()[1] == 6
assert orientation_matrix.all()[1] == 3
assert orientation_matrix.all()[2] == 3
# Construct the crystal model
crystal = Crystal(real_space_a, real_space_b, real_space_c,
space_group_symbol)
# Sort out scan points
if unit_cell.all()[0] > 1:
A_list = []
for i in range(unit_cell.all()[0]):
uc = uctbx.unit_cell(tuple(unit_cell[i:i + 1, :]))
U = matrix.sqr(tuple(orientation_matrix[i:i + 1, :, :]))
B = matrix.sqr(uc.fractionalization_matrix()).transpose()
A_list.append(U * B)
crystal.set_A_at_scan_points(A_list)
else:
assert unit_cell.all_eq(average_unit_cell)
assert orientation_matrix.all_eq(average_orientation_matrix)
# Return the crystal
return crystal
def run(args):
import libtbx.load_env
from dials.util import Sorry
usage = "dials.reindex [options] indexed.expt indexed.refl"
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_reflections=True,
read_experiments=True,
check_format=False,
epilog=help_message,
)
params, options = parser.parse_args(show_diff_phil=True)
reflections = flatten_reflections(params.input.reflections)
experiments = flatten_experiments(params.input.experiments)
if len(experiments) == 0 and len(reflections) == 0:
parser.print_help()
return
if params.change_of_basis_op is None:
raise Sorry("Please provide a change_of_basis_op.")
reference_crystal = None
if params.reference.experiments is not None:
from dxtbx.serialize import load
reference_experiments = load.experiment_list(
params.reference.experiments, check_format=False)
assert len(reference_experiments.crystals()) == 1
reference_crystal = reference_experiments.crystals()[0]
if params.reference.reflections is not None:
# First check that we have everything as expected for the reference reindexing
# Currently only supports reindexing one dataset at a time
if params.reference.experiments is None:
raise Sorry(
"""For reindexing against a reference dataset, a reference
experiments file must also be specified with the option: reference= """)
if not os.path.exists(params.reference.reflections):
raise Sorry("Could not locate reference dataset reflection file")
if len(experiments) != 1 or len(reflections) != 1:
raise Sorry(
"Only one dataset can be reindexed to a reference at a time")
reference_reflections = flex.reflection_table().from_file(
params.reference.reflections)
test_reflections = reflections[0]
if (reference_crystal.get_space_group().type().number() !=
experiments.crystals()[0].get_space_group().type().number()):
raise Sorry("Space group of input does not match reference")
# Set some flags to allow filtering, if wanting to reindex against
# reference with data that has not yet been through integration
if (test_reflections.get_flags(
test_reflections.flags.integrated_sum).count(True) == 0):
assert (
"intensity.sum.value"
in test_reflections), "No 'intensity.sum.value' in reflections"
test_reflections.set_flags(
flex.bool(test_reflections.size(), True),
test_reflections.flags.integrated_sum,
)
if (reference_reflections.get_flags(
reference_reflections.flags.integrated_sum).count(True) == 0):
assert ("intensity.sum.value" in test_reflections
), "No 'intensity.sum.value in reference reflections"
reference_reflections.set_flags(
flex.bool(reference_reflections.size(), True),
reference_reflections.flags.integrated_sum,
)
# Make miller array of the two datasets
try:
test_miller_set = filtered_arrays_from_experiments_reflections(
experiments, [test_reflections])[0]
except ValueError:
raise Sorry(
"No reflections remain after filtering the test dataset")
try:
reference_miller_set = filtered_arrays_from_experiments_reflections(
reference_experiments, [reference_reflections])[0]
except ValueError:
raise Sorry(
"No reflections remain after filtering the reference dataset")
from dials.algorithms.symmetry.reindex_to_reference import (
determine_reindex_operator_against_reference, )
change_of_basis_op = determine_reindex_operator_against_reference(
test_miller_set, reference_miller_set)
elif len(experiments) and params.change_of_basis_op is libtbx.Auto:
if reference_crystal is not None:
if len(experiments.crystals()) > 1:
raise Sorry("Only one crystal can be processed at a time")
from dials.algorithms.indexing.compare_orientation_matrices import (
difference_rotation_matrix_axis_angle, )
cryst = experiments.crystals()[0]
R, axis, angle, change_of_basis_op = difference_rotation_matrix_axis_angle(
cryst, reference_crystal)
print("Change of basis op: %s" % change_of_basis_op)
print("Rotation matrix to transform input crystal to reference::")
print(R.mathematica_form(format="%.3f", one_row_per_line=True))
print(
"Rotation of %.3f degrees" % angle,
"about axis (%.3f, %.3f, %.3f)" % axis,
)
elif len(reflections):
assert len(reflections) == 1
# always re-map reflections to reciprocal space
refl_copy = flex.reflection_table()
for i, imageset in enumerate(experiments.imagesets()):
if "imageset_id" in reflections[0]:
sel = reflections[0]["imageset_id"] == i
else:
sel = reflections[0]["id"] == i
refl = reflections[0].select(sel)
refl.centroid_px_to_mm(imageset.get_detector(),
imageset.get_scan())
refl.map_centroids_to_reciprocal_space(
imageset.get_detector(),
imageset.get_beam(),
imageset.get_goniometer(),
)
refl_copy.extend(refl)
# index the reflection list using the input experiments list
refl_copy["id"] = flex.int(len(refl_copy), -1)
index = AssignIndicesGlobal(tolerance=0.2)
index(refl_copy, experiments)
hkl_expt = refl_copy["miller_index"]
hkl_input = reflections[0]["miller_index"]
change_of_basis_op = derive_change_of_basis_op(hkl_input, hkl_expt)
# reset experiments list since we don't want to reindex this
experiments = []
else:
change_of_basis_op = sgtbx.change_of_basis_op(
params.change_of_basis_op)
if len(experiments):
for crystal in experiments.crystals():
cryst_orig = copy.deepcopy(crystal)
cryst_reindexed = cryst_orig.change_basis(change_of_basis_op)
if params.space_group is not None:
a, b, c = cryst_reindexed.get_real_space_vectors()
A_varying = [
cryst_reindexed.get_A_at_scan_point(i)
for i in range(cryst_reindexed.num_scan_points)
]
cryst_reindexed = Crystal(
a, b, c, space_group=params.space_group.group())
cryst_reindexed.set_A_at_scan_points(A_varying)
crystal.update(cryst_reindexed)
print("Old crystal:")
print(cryst_orig)
print()
print("New crystal:")
print(cryst_reindexed)
print()
print("Saving reindexed experimental models to %s" %
params.output.experiments)
experiments.as_file(params.output.experiments)
if len(reflections):
assert len(reflections) == 1
reflections = reflections[0]
miller_indices = reflections["miller_index"]
if params.hkl_offset is not None:
h, k, l = miller_indices.as_vec3_double().parts()
h += params.hkl_offset[0]
k += params.hkl_offset[1]
l += params.hkl_offset[2]
miller_indices = flex.miller_index(h.iround(), k.iround(),
l.iround())
non_integral_indices = change_of_basis_op.apply_results_in_non_integral_indices(
miller_indices)
if non_integral_indices.size() > 0:
print(
"Removing %i/%i reflections (change of basis results in non-integral indices)"
% (non_integral_indices.size(), miller_indices.size()))
sel = flex.bool(miller_indices.size(), True)
sel.set_selected(non_integral_indices, False)
miller_indices_reindexed = change_of_basis_op.apply(
miller_indices.select(sel))
reflections["miller_index"].set_selected(sel, miller_indices_reindexed)
reflections["miller_index"].set_selected(~sel, (0, 0, 0))
print("Saving reindexed reflections to %s" % params.output.reflections)
easy_pickle.dump(params.output.reflections, reflections)
def load_crystal(entry):
from dxtbx.model import Crystal
from scitbx.array_family import flex
from scitbx import matrix
from cctbx import uctbx
import numpy
# Get the sample
nx_sample = get_nx_sample(entry, "sample")
# Set the space group
space_group_symbol = nx_sample['unit_cell_group'].value
# Get depends on
if nx_sample['depends_on'].value != '.':
assert (nx_sample['depends_on'].value == str(
nx_sample['transformations/phi'].name))
# Read the average unit cell data
average_unit_cell = flex.double(numpy.array(
nx_sample['average_unit_cell']))
assert (nx_sample['average_unit_cell'].attrs['angles_units'] == 'deg')
assert (nx_sample['average_unit_cell'].attrs['length_units'] == 'angstrom')
assert (len(average_unit_cell.all()) == 1)
assert (len(average_unit_cell) == 6)
average_orientation_matrix = flex.double(
numpy.array(nx_sample['average_orientation_matrix']))
assert (len(average_orientation_matrix.all()) == 2)
assert (average_orientation_matrix.all()[0] == 3)
assert (average_orientation_matrix.all()[1] == 3)
# Get the real space vectors
uc = uctbx.unit_cell(tuple(average_unit_cell))
U = matrix.sqr(average_orientation_matrix)
B = matrix.sqr(uc.fractionalization_matrix()).transpose()
A = U * B
A = A.inverse()
real_space_a = A[0:3]
real_space_b = A[3:6]
real_space_c = A[6:9]
# Read the unit cell data
unit_cell = flex.double(numpy.array(nx_sample['unit_cell']))
assert (nx_sample['unit_cell'].attrs['angles_units'] == 'deg')
assert (nx_sample['unit_cell'].attrs['length_units'] == 'angstrom')
# Read the orientation matrix
orientation_matrix = flex.double(
numpy.array(nx_sample['orientation_matrix']))
assert (len(unit_cell.all()) == 2)
assert (len(orientation_matrix.all()) == 3)
assert (unit_cell.all()[0] == orientation_matrix.all()[0])
assert (unit_cell.all()[1] == 6)
assert (orientation_matrix.all()[1] == 3)
assert (orientation_matrix.all()[2] == 3)
# Construct the crystal model
crystal = Crystal(real_space_a, real_space_b, real_space_c,
space_group_symbol)
# Sort out scan points
if unit_cell.all()[0] > 1:
A_list = []
for i in range(unit_cell.all()[0]):
uc = uctbx.unit_cell(tuple(unit_cell[i:i + 1, :]))
U = matrix.sqr(tuple(orientation_matrix[i:i + 1, :, :]))
B = matrix.sqr(uc.fractionalization_matrix()).transpose()
A_list.append(U * B)
crystal.set_A_at_scan_points(A_list)
else:
assert (unit_cell.all_eq(average_unit_cell))
assert (orientation_matrix.all_eq(average_orientation_matrix))
# Return the crystal
return crystal
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)
# New parameters for maximum likelihood values
try:
xl._ML_half_mosaicity_deg = d['ML_half_mosaicity_deg']
except KeyError:
pass
try:
xl._ML_domain_size_ang = d['ML_domain_size_ang']
except KeyError:
pass
# 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 mosaicity, if present
try:
mosaicity = d['mosaicity']
xl.set_mosaicity(mosaicity)
except KeyError:
pass
return xl
