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from __future__ import annotations
from cctbx import miller
from dxtbx.model import ExperimentList
from dials.algorithms.spot_prediction import ScanStaticReflectionPredictor
from dials.util import missing_reflections
def test_connected_components(dials_data):
experiment = ExperimentList.from_file(
dials_data("centroid_test_data", pathlib=True) / "experiments.json"
)[0]
image_ranges = [(1, 9), (1, 100), (1, 1000)]
expected_ms_sizes = [[755], [242, 14, 10, 5, 2, 2, 2], []]
for image_range, expected_sizes in zip(image_ranges, expected_ms_sizes):
experiment.scan.set_image_range(image_range)
predict = ScanStaticReflectionPredictor(experiment, dmin=3, margin=1)
refl = predict.for_ub(experiment.crystal.get_A())
miller_set = miller.set(
experiment.crystal.get_crystal_symmetry(),
refl["miller_index"],
anomalous_flag=False,
)
miller_array = miller_set.d_spacings().resolution_filter(d_min=3)
complete_set, unique_ms = missing_reflections.connected_components(miller_array)
assert len(unique_ms) == len(expected_sizes)
assert [ms.size() for ms in unique_ms] == expected_sizes
# Verify that all the indices reported missing are actually missing from the input
for ms in unique_ms:
assert ms.common_set(miller_array.map_to_asu()).size() == 0
assert complete_set.completeness() == 1
def test_connected_components_centred_cell(dials_data):
experiment = ExperimentList.from_file(
dials_data("insulin_processed", pathlib=True) / "scaled.expt",
check_format=False,
)[0]
experiment.scan.set_image_range((1, 10))
predict = ScanStaticReflectionPredictor(experiment, dmin=3, margin=1)
refl = predict.for_ub(experiment.crystal.get_A())
miller_set = miller.set(
experiment.crystal.get_crystal_symmetry(),
refl["miller_index"],
anomalous_flag=False,
)
miller_array = miller_set.d_spacings().resolution_filter(d_min=3)
complete_set, unique_ms = missing_reflections.connected_components(miller_array)
assert [ms.size() for ms in unique_ms] == [581, 32, 29, 6, 3, 3, 3, 2]
# Verify that all the indices reported missing are actually missing from the input
for ms in unique_ms:
assert ms.common_set(miller_array.map_to_asu()).size() == 0
assert complete_set.completeness() == 1
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