def run(args=None):
usage = "dials.cosym [options] models.expt observations.refl"
parser = OptionParser(
usage=usage,
phil=phil_scope,
read_reflections=True,
read_experiments=True,
check_format=False,
epilog=help_message,
)
params, options, args = parser.parse_args(args=args,
show_diff_phil=False,
return_unhandled=True)
# Configure the logging
log.config(verbosity=options.verbose, logfile=params.output.log)
logger.info(dials_version())
# Log the diff phil
diff_phil = parser.diff_phil.as_str()
if diff_phil != "":
logger.info("The following parameters have been modified:\n")
logger.info(diff_phil)
if params.seed is not None:
flex.set_random_seed(params.seed)
np.random.seed(params.seed)
random.seed(params.seed)
if not params.input.experiments or not params.input.reflections:
parser.print_help()
sys.exit()
reflections, experiments = reflections_and_experiments_from_files(
params.input.reflections, params.input.experiments)
reflections = parse_multiple_datasets(reflections)
if len(experiments) != len(reflections):
raise Sorry(
"Mismatched number of experiments and reflection tables found: %s & %s."
% (len(experiments), len(reflections)))
try:
experiments, reflections = assign_unique_identifiers(
experiments, reflections)
cosym_instance = cosym(experiments=experiments,
reflections=reflections,
params=params)
except ValueError as e:
raise Sorry(e)
if params.output.html or params.output.json:
register_default_cosym_observers(cosym_instance)
cosym_instance.run()
cosym_instance.export()
def test_synthetic(
space_group,
unit_cell,
dimensions,
sample_size,
use_known_space_group,
use_known_lattice_group,
tmpdir,
):
os.chdir(tmpdir.strpath)
space_group = sgtbx.space_group_info(space_group).group()
if unit_cell is not None:
unit_cell = uctbx.unit_cell(unit_cell)
experiments, reflections, reindexing_ops = generate_experiments_reflections(
space_group=space_group,
unit_cell=unit_cell,
unit_cell_volume=10000,
sample_size=sample_size,
map_to_p1=True,
d_min=1.5,
)
params = phil_scope.extract()
if use_known_space_group:
params.space_group = space_group.info()
if use_known_lattice_group:
params.lattice_group = space_group.info()
if dimensions is not None:
params.dimensions = dimensions
experiments, reflections = assign_unique_identifiers(
experiments, reflections)
cosym_instance = cosym(experiments, reflections, params=params)
register_default_cosym_observers(cosym_instance)
cosym_instance.run()
cosym_instance.export()
assert os.path.exists(params.output.experiments)
assert os.path.exists(params.output.reflections)
assert os.path.exists(params.output.html)
assert os.path.exists(params.output.json)
cosym_expts = load.experiment_list(params.output.experiments,
check_format=False)
assert len(cosym_expts) == len(experiments)
for expt in cosym_expts:
if unit_cell is not None:
assert expt.crystal.get_unit_cell().parameters() == pytest.approx(
unit_cell.parameters())
assert str(expt.crystal.get_space_group().info()) == str(
space_group.info())
assert expt.crystal.get_space_group() == space_group
