def test_make_cluster_plots():
from xfel.clustering.cluster import Cluster
c1 = Cluster.from_iterable([
(10.0, 10.0, 10.0, 90, 90, 90, "P1"),
(10.1, 10.1, 10.1, 90, 90, 90, "P1"),
(10.2, 10.2, 10.2, 90, 90, 90, "P1"),
])
c2 = Cluster.from_iterable([
(11.0, 11.0, 11.0, 90, 90, 90, "P1"),
(11.1, 11.1, 11.1, 90, 90, 90, "P1"),
(11.2, 11.2, 11.2, 90, 90, 90, "P1"),
(11.3, 11.3, 11.3, 90, 90, 90, "P1"),
])
clusters = [c1, c2]
plots = make_cluster_plots(clusters)
assert "uc_scatter_0" in plots
assert "uc_scatter_1" in plots
assert "uc_hist_0" in plots
assert "uc_hist_1" in plots
print(plots)
assert len(plots["uc_hist_0"]["data"]) == 3
assert len(plots["uc_hist_0"]["data"][0]["x"]) == 3
assert len(plots["uc_hist_1"]["data"][0]["x"]) == 4
assert len(plots["uc_scatter_0"]["data"]) == 3
assert len(plots["uc_scatter_0"]["data"][0]["x"]) == 3
assert len(plots["uc_scatter_1"]["data"][0]["x"]) == 4
def run(self, iterable):
# with Capturing() as junk_output:
errors = []
try:
ucs = Cluster.from_iterable(iterable=iterable)
clusters, _ = ucs.ab_cluster(5000,
log=False,
write_file_lists=False,
schnell=True,
doplot=False)
except Exception as e:
print("IOTA ERROR (CLUSTERING): ", e)
clusters = []
errors.append(str(e))
info = []
if clusters:
for cluster in clusters:
uc_init = unit_cell(cluster.medians)
symmetry = crystal.symmetry(unit_cell=uc_init,
space_group_symbol="P1")
groups = lattice_symmetry.metric_subgroups(
input_symmetry=symmetry, max_delta=3)
top_group = groups.result_groups[0]
best_sg = str(groups.lattice_group_info()).split("(")[0]
best_uc = top_group["best_subsym"].unit_cell().parameters()
uc_no_stdev = ("{:<6.2f} {:<6.2f} {:<6.2f} "
"{:<6.2f} {:<6.2f} {:<6.2f} "
"".format(
best_uc[0],
best_uc[1],
best_uc[2],
best_uc[3],
best_uc[4],
best_uc[5],
))
cluster_info = {
"number": len(cluster.members),
"pg": str(best_sg),
"uc": uc_no_stdev,
}
info.append(cluster_info)
return info, errors
def run(self, iterable):
with Capturing() as junk_output:
try:
ucs = Cluster.from_iterable(iterable=iterable)
clusters, _ = ucs.ab_cluster(5000,
log=False,
write_file_lists=False,
schnell=True,
doplot=False)
except Exception:
clusters = []
if len(clusters) > 0:
info = []
for cluster in clusters:
uc_init = unit_cell(cluster.medians)
symmetry = crystal.symmetry(unit_cell=uc_init,
space_group_symbol='P1')
groups = lattice_symmetry.metric_subgroups(
input_symmetry=symmetry, max_delta=3)
top_group = groups.result_groups[0]
best_uc = top_group['best_subsym'].unit_cell().parameters()
best_sg = top_group['best_subsym'].space_group_info()
uc_no_stdev = "{:<6.2f} {:<6.2f} {:<6.2f} " \
"{:<6.2f} {:<6.2f} {:<6.2f} " \
"".format(best_uc[0], best_uc[1], best_uc[2],
best_uc[3], best_uc[4], best_uc[5])
cluster_info = {
'number': len(cluster.members),
'pg': str(best_sg),
'uc': uc_no_stdev
}
info.append(cluster_info)
else:
info = None
return info
def cluster_unit_cells(self):
input = []
for item in self.spotfinding_info:
if item[4] is not None:
try:
info_line = [float(i) for i in item[4]]
info_line.append(item[3])
input.append(info_line)
except ValueError:
pass
with misc.Capturing() as junk_output:
try:
ucs = Cluster.from_iterable(iterable=input)
clusters, _ = ucs.ab_cluster(5000,
log=False,
write_file_lists=False,
schnell=True,
doplot=False)
except Exception, e:
clusters = []
