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from __future__ import annotations
import shutil
import subprocess
import pytest
from dials.array_family import flex
def test_against_dials_integrate(dials_data, tmp_path):
## ensure insulin folder exists
dials_data("insulin", pathlib=True)
# Run as a single job to avoid splitting reflections
subprocess.run(
(
shutil.which("dials.integrate"),
dials_data("insulin_processed", pathlib=True) / "refined.expt",
dials_data("insulin_processed", pathlib=True) / "refined.refl",
"mp.njobs=1",
"mp.nproc=1",
"scan_range=1,2",
),
cwd=tmp_path,
capture_output=True,
).check_returncode()
subprocess.run(
(
shutil.which("dev.dials.simple_integrate"),
dials_data("insulin_processed", pathlib=True) / "refined.expt",
dials_data("insulin_processed", pathlib=True) / "refined.refl",
"scan_range=1,2",
),
cwd=tmp_path,
capture_output=True,
).check_returncode()
simple_refl = flex.reflection_table.from_file(tmp_path / "simple_integrated.refl")
dials_refl = flex.reflection_table.from_file(tmp_path / "integrated.refl")
matches = dials_refl.match_with_reference(simple_refl)[0]
dials_refl = dials_refl.select(matches)
assert len(simple_refl) == len(dials_refl)
assert sum(
simple_refl["intensity.sum.value"] - dials_refl["intensity.sum.value"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(
simple_refl["intensity.prf.value"] - dials_refl["intensity.prf.value"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(
simple_refl["background.sum.value"] - dials_refl["background.sum.value"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(
simple_refl["background.mean"] - dials_refl["background.mean"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(
simple_refl["background.dispersion"] - dials_refl["background.dispersion"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(
simple_refl["background.mse"] - dials_refl["background.mse"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(
simple_refl["background.sum.variance"] - dials_refl["background.sum.variance"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(
simple_refl["intensity.prf.variance"] - dials_refl["intensity.prf.variance"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(
simple_refl["intensity.sum.variance"] - dials_refl["intensity.sum.variance"]
) == pytest.approx(0.0, abs=1e-7)
assert sum(simple_refl["lp"] - dials_refl["lp"]) == pytest.approx(0.0, abs=1e-7)
assert sum(simple_refl["zeta"] - dials_refl["zeta"]) == pytest.approx(0.0, abs=1e-7)
assert sum(simple_refl["d"] - dials_refl["d"]) == pytest.approx(0.0, abs=1e-7)
assert sum(simple_refl["partiality"] - dials_refl["partiality"]) == pytest.approx(
0.0, abs=1e-7
)
assert (
simple_refl["num_pixels.foreground"] == dials_refl["num_pixels.foreground"]
).count(True) == len(simple_refl)
assert (
simple_refl["num_pixels.background"] == dials_refl["num_pixels.background"]
).count(True) == len(simple_refl)
assert (simple_refl["num_pixels.valid"] == dials_refl["num_pixels.valid"]).count(
True
) == len(simple_refl)
assert (
simple_refl["num_pixels.background_used"]
== dials_refl["num_pixels.background_used"]
).count(True) == len(simple_refl)
assert sum(
simple_refl["profile.correlation"] - dials_refl["profile.correlation"]
) == pytest.approx(0.0, abs=1e-7)
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