def test_local_multiple_rotations(dials_data):
"""Test the fix for https://github.com/dials/dials/issues/1458"""
experiments = load.experiment_list(
dials_data("insulin_processed").join("indexed.expt"),
check_format=False,
)
# Override the scan range to ensure we have 4 full rotations
experiments[0].scan.set_image_range((1, 1440))
# Generate some predicted reflections
reflections = flex.reflection_table.from_predictions(experiments[0],
dmin=4)
reflections["imageset_id"] = flex.int(len(reflections), 0)
reflections["id"] = flex.int(len(reflections), -1)
reflections["xyzobs.px.value"] = reflections["xyzcal.px"]
reflections["xyzobs.mm.value"] = reflections["xyzcal.mm"]
predicted_miller_indices = reflections["miller_index"]
# Prepare reflections for indexing
reflections.centroid_px_to_mm(experiments)
reflections.map_centroids_to_reciprocal_space(experiments)
# Reset miller indices to ensure they are reindexed
reflections["miller_index"] = flex.miller_index(len(reflections),
(0, 0, 0))
# Assign indices with the correct scan oscillation
AssignIndicesLocal()(reflections, experiments)
# Assert we have correctly indexed all reflections
assert (reflections["miller_index"] == (0, 0, 0)).count(True) == 0
assert (reflections["miller_index"] == predicted_miller_indices
).count(False) == 0
# Modify the scan oscillation such that we are out by 1 degree per rotation
experiments[0].scan.set_oscillation((0, 1 - 1 / 360), deg=True)
# Reset miller indices and re-map to reciprocal space
reflections["miller_index"] = flex.miller_index(len(reflections),
(0, 0, 0))
reflections["id"] = flex.int(len(reflections), -1)
reflections.centroid_px_to_mm(experiments)
reflections.map_centroids_to_reciprocal_space(experiments)
# Assign indices, this time with the incorrect scan oscillation
AssignIndicesLocal()(reflections, experiments)
# Assert that most reflections have been indexed
indexed_sel = reflections["miller_index"] == (0, 0, 0)
assert indexed_sel.count(True) < 10
# Assert that all indexed miller indices are correct
assert ((reflections["miller_index"] != predicted_miller_indices)
& ~indexed_sel).count(True) == 0
def __init__(self, experiment, reflections, expected_miller_indices):
index_reflections_global = AssignIndicesGlobal()
index_reflections_local = AssignIndicesLocal()
# index reflections using simple "global" method
self.reflections_global = copy.deepcopy(reflections)
self.reflections_global["id"] = flex.int(len(self.reflections_global), -1)
self.reflections_global["imageset_id"] = flex.int(
len(self.reflections_global), 0
)
index_reflections_global(self.reflections_global, ExperimentList([experiment]))
non_zero_sel = self.reflections_global["miller_index"] != (0, 0, 0)
assert self.reflections_global["id"].select(~non_zero_sel).all_eq(-1)
self.misindexed_global = (
(expected_miller_indices == self.reflections_global["miller_index"])
.select(non_zero_sel)
.count(False)
)
self.correct_global = (
expected_miller_indices == self.reflections_global["miller_index"]
).count(True)
# index reflections using xds-style "local" method
self.reflections_local = copy.deepcopy(reflections)
self.reflections_local["id"] = flex.int(len(self.reflections_local), -1)
index_reflections_local(self.reflections_local, ExperimentList([experiment]))
non_zero_sel = self.reflections_local["miller_index"] != (0, 0, 0)
assert self.reflections_local["id"].select(~non_zero_sel).all_eq(-1)
self.misindexed_local = (
(expected_miller_indices == self.reflections_local["miller_index"])
.select(non_zero_sel)
.count(False)
)
self.correct_local = (
expected_miller_indices == self.reflections_local["miller_index"]
).count(True)
print(
"Global misindexed: %d, correct: %d, total: %d"
% (
self.misindexed_global,
self.correct_global,
len(self.reflections_global),
)
)
print(
" Local misindexed: %d, correct: %d, total: %d"
% (self.misindexed_local, self.correct_local, len(self.reflections_local))
)