def test_dials_cluster_unit_cell_command_line(dials_regression, tmpdir):
pytest.importorskip("scipy")
data_dir = os.path.join(dials_regression, 'refinement_test_data',
'multi_narrow_wedges')
import glob
experiments = glob.glob(
os.path.join(data_dir, 'data/sweep_*/experiments.json'))
tmpdir.chdir()
import procrunner
result = procrunner.run_process(
command=['dials.cluster_unit_cell', 'plot.show=False'] + experiments,
print_stdout=False,
)
assert not result['exitcode']
#print result
assert os.path.exists('cluster_unit_cell.png')
from dxtbx.model.experiment_list import ExperimentList, ExperimentListFactory
from dials.command_line import cluster_unit_cell
experiments = ExperimentList([
ExperimentListFactory.from_json_file(expt, check_format=False)[0]
for expt in experiments
])
from cctbx import crystal
crystal_symmetries = [
crystal.symmetry(unit_cell=expt.crystal.get_unit_cell(),
space_group=expt.crystal.get_space_group())
for expt in experiments
]
params = cluster_unit_cell.phil_scope.extract()
params.plot.show = False
params.plot.name = None
clusters = cluster_unit_cell.do_cluster_analysis(crystal_symmetries,
params)
assert len(clusters) == 1
cluster = clusters[0]
assert len(cluster.members) == 40
assert cluster.medians == pytest.approx([
90.9430182020995, 90.9430182020995, 90.9430182020995,
109.47122063449069, 109.47122063449069, 109.47122063449069
],
abs=1e-6)
assert cluster.stdevs == pytest.approx([
0.09509739126548639, 0.09509739126548526, 0.0950973912654865, 0, 0, 0
],
abs=1e-6)
def test_cluster_unit_cell_api(dials_regression):
pytest.importorskip("scipy")
pytest.importorskip("xfel")
data_dir = os.path.join(dials_regression, "refinement_test_data",
"multi_narrow_wedges")
experiments = ExperimentList([
ExperimentListFactory.from_json_file(expt, check_format=False)[0]
for expt in glob.glob(
os.path.join(data_dir, "data/sweep_*/experiments.json"))
])
crystal_symmetries = [
crystal.symmetry(
unit_cell=expt.crystal.get_unit_cell(),
space_group=expt.crystal.get_space_group(),
) for expt in experiments
]
params = cluster_unit_cell.phil_scope.extract()
params.plot.show = False
params.plot.name = None
clusters = cluster_unit_cell.do_cluster_analysis(crystal_symmetries,
params)
assert len(clusters) == 1
cluster = clusters[0]
assert len(cluster.members) == 40
assert cluster.medians == pytest.approx(
[
90.9430182020995,
90.9430182020995,
90.9430182020995,
109.47122063449069,
109.47122063449069,
109.47122063449069,
],
abs=1e-6,
)
assert cluster.stdevs == pytest.approx(
[
0.09509739126548639, 0.09509739126548526, 0.0950973912654865, 0, 0,
0
],
abs=1e-6,
)