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from __future__ import annotations
import shutil
import subprocess
from dials.array_family import flex
def test_sort_intensities(dials_data, tmp_path):
result = subprocess.run(
[
shutil.which("dials.sort_reflections"),
dials_data("centroid_test_data", pathlib=True) / "integrated.pickle",
"key=intensity.sum.value",
"output=sorted1.refl",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
assert tmp_path.joinpath("sorted1.refl").is_file()
data = flex.reflection_table.from_file(tmp_path / "sorted1.refl")
assert_sorted(data["intensity.sum.value"])
def test_reverse_sort_intensities(dials_data, tmp_path):
result = subprocess.run(
[
shutil.which("dials.sort_reflections"),
dials_data("centroid_test_data", pathlib=True) / "integrated.pickle",
"output=sorted2.refl",
"key=intensity.sum.value",
"reverse=True",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
assert tmp_path.joinpath("sorted2.refl").is_file()
data = flex.reflection_table.from_file(tmp_path / "sorted2.refl")
assert_sorted(data["intensity.sum.value"], reverse=True)
def test_default_sort_on_miller_index(dials_data, tmp_path):
result = subprocess.run(
[
shutil.which("dials.sort_reflections"),
dials_data("centroid_test_data", pathlib=True) / "integrated.pickle",
"output=sorted3.refl",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
assert tmp_path.joinpath("sorted3.refl").is_file()
data = flex.reflection_table.from_file(tmp_path / "sorted3.refl")
mi1 = data["miller_index"]
orig = flex.reflection_table.from_file(
dials_data("centroid_test_data", pathlib=True) / "integrated.pickle"
)
mi2 = flex.miller_index(sorted(orig["miller_index"]))
assert mi1.all_eq(mi2)
def test_default_sort_on_miller_index_verbose(dials_data, tmp_path):
result = subprocess.run(
[
shutil.which("dials.sort_reflections"),
dials_data("centroid_test_data", pathlib=True) / "integrated.pickle",
"output=sorted4.refl",
"-v",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
assert tmp_path.joinpath("sorted4.refl").is_file()
assert b"Head of sorted list miller_index:" in result.stdout
def assert_sorted(data, reverse=False):
assert len(data) > 0
elem = data[0]
for x in data:
if reverse is True:
assert x <= elem
else:
assert x >= elem
elem = x
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