def _reindex_experiments_reflections(experiments, reflections, space_group, cb_op):
"""Reindex the input data."""
reindexed_experiments = reindex_experiments(
experiments, cb_op, space_group=space_group
)
reindexed_reflections = flex.reflection_table()
for i in range(len(reindexed_experiments)):
reindexed_refl = copy.deepcopy(reflections[i])
reindexed_refl["miller_index"] = cb_op.apply(reindexed_refl["miller_index"])
reindexed_reflections.extend(reindexed_refl)
return reindexed_experiments, [reindexed_reflections]
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
