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from __future__ import annotations
import glob
import os
import shutil
import subprocess
import pytest
from cctbx import crystal
from dxtbx.model.experiment_list import ExperimentList, ExperimentListFactory
from dxtbx.serialize import load
from dials.command_line import cluster_unit_cell
def test_dials_cluster_unit_cell_command_line(dials_data, tmp_path):
pytest.importorskip("scipy")
data_dir = dials_data("polyhedra_narrow_wedges", pathlib=True)
experiments = sorted(data_dir.glob("sweep_*_experiments.json"))
result = subprocess.run(
[shutil.which("dials.cluster_unit_cell"), "plot.show=False"] + experiments,
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode
assert tmp_path.joinpath("cluster_unit_cell.png").is_file()
def test_dials_cluster_unit_cell_command_line_output_files(dials_data, tmp_path):
pytest.importorskip("scipy")
data_dir = dials_data("polyhedra_narrow_wedges", pathlib=True)
experiments = sorted(data_dir.glob("sweep_*_experiments.json"))
reflections = sorted(data_dir.glob("sweep_*_reflections.pickle"))
# Combine experiments. Write PHIL file to avoid "command line is too long" error on Windows
with open(tmp_path / "input.phil", "w") as f:
f.writelines(f"input.reflections={i}" + os.linesep for i in reflections)
f.writelines(f"input.experiments={i}" + os.linesep for i in experiments)
result = subprocess.run(
[shutil.which("dials.combine_experiments"), "input.phil"],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode
assert (tmp_path / "combined.refl").is_file()
assert (tmp_path / "combined.expt").is_file()
result = subprocess.run(
[
shutil.which("dials.cluster_unit_cell"),
"plot.show=False",
tmp_path / "combined.refl",
tmp_path / "combined.expt",
"output.clusters=True",
"threshold=40",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode
assert (tmp_path / "cluster_unit_cell.png").is_file()
assert (tmp_path / "cluster_1.refl").is_file()
assert (tmp_path / "cluster_1.expt").is_file()
expts = load.experiment_list(tmp_path / "cluster_1.expt", check_format=False)
assert len(expts) == 101
assert (tmp_path / "cluster_2.refl").is_file()
assert (tmp_path / "cluster_2.expt").is_file()
expts = load.experiment_list(tmp_path / "cluster_2.expt", check_format=False)
assert len(expts) == 1
assert (tmp_path / "cluster_3.refl").is_file()
assert (tmp_path / "cluster_3.expt").is_file()
expts = load.experiment_list(tmp_path / "cluster_3.expt", check_format=False)
assert len(expts) == 1
result = subprocess.run(
[
shutil.which("dials.split_experiments"),
tmp_path / "combined.refl",
tmp_path / "combined.expt",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode
experiments = list(tmp_path.glob("split_*.expt"))
reflections = list(tmp_path.glob("split_*.refl"))
# Write PHIL file to avoid "command line is too long" error on Windows
with open(tmp_path / "input.phil", "w") as f:
f.writelines(f"input.reflections={i}" + os.linesep for i in reflections)
f.writelines(f"input.experiments={i}" + os.linesep for i in experiments)
result = subprocess.run(
[
shutil.which("dials.cluster_unit_cell"),
"output.clusters=True",
"threshold=40",
"plot.show=False",
"input.phil",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode
def test_cluster_unit_cell_api(dials_data):
pytest.importorskip("scipy")
data_dir = dials_data("polyhedra_narrow_wedges", pathlib=True)
experiments = ExperimentList(
[
ExperimentListFactory.from_json_file(expt, check_format=False)[0]
for expt in glob.glob(os.path.join(data_dir, "sweep_*_experiments.json"))
]
)
crystal_symmetries = [
crystal.symmetry(
unit_cell=expt.crystal.get_unit_cell(),
space_group=expt.crystal.get_space_group(),
)
for expt in experiments
]
params = cluster_unit_cell.phil_scope.extract()
params.plot.show = False
params.plot.name = None
clusters = cluster_unit_cell.do_cluster_analysis(crystal_symmetries, params)
assert len(clusters) == 1
cluster = clusters[0]
assert len(cluster) == 40
assert cluster.median_cell == pytest.approx(
[
90.9430182020995,
90.9430182020995,
90.9430182020995,
109.47122063449069,
109.47122063449069,
109.47122063449069,
],
abs=1e-6,
)
assert cluster.cell_std == pytest.approx(
[0.09509739126548639, 0.09509739126548526, 0.0950973912654865, 0, 0, 0],
abs=1e-6,
)
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