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from __future__ import annotations
import math
import pytest
from dxtbx.model.experiment_list import ExperimentListFactory
from dials.algorithms.refinement.reflection_manager import ReflectionManager
from dials.array_family import flex
def test_scan_margin(dials_data):
# Use 4 scan data for this test
data_dir = dials_data("l_cysteine_dials_output", pathlib=True)
experiments = ExperimentListFactory.from_json_file(
data_dir / "indexed.expt", check_format=False
)
reflections = flex.reflection_table.from_file(data_dir / "indexed.refl")
orig_phi = reflections["xyzobs.mm.value"].parts()[2]
# Reflection Manager works on predictions, but this dataset has none, so
# need to set the predictions flag
reflections.set_flags(
flex.bool(len(reflections), True), reflections.flags.predicted
)
# Create a reflection manager without trimming scan margins
refman = ReflectionManager(reflections, experiments)
refman.finalise()
refs1 = refman.get_matches()
phi1 = refs1["xyzobs.mm.value"].parts()[2]
# Create a reflection manager with 1 degree width scan margins
margin = 1.0
refman2 = ReflectionManager(reflections, experiments, scan_margin=margin)
refman2.finalise()
refs2 = refman2.get_matches()
phi2 = refs2["xyzobs.mm.value"].parts()[2]
# Check zero scan margins do not trim
assert min(orig_phi) == min(phi1)
assert max(orig_phi) == max(phi1)
# Check 1 degree scan margin trims approximately 1 degree
assert min(phi2) == pytest.approx(min(phi1) + math.radians(margin), abs=1e-3)
assert max(phi2) == pytest.approx(max(phi1) - math.radians(margin), abs=1e-3)
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