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from __future__ import annotations
import os
import shutil
import subprocess
import pytest
from dxtbx.serialize import load
from dials.array_family import flex
from dials.command_line.damage_analysis import PychefRunner, phil_scope, run
def test_damage_analysis_on_scaled_data(dials_data, run_in_tmp_path):
location = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True)
refls = str(location / "scaled_20_25.refl")
expts = str(location / "scaled_20_25.expt")
args = [
str(refls),
str(expts),
"min_completeness=0.4",
"-v",
"json=dials.damage_analysis.json",
]
run(args)
assert run_in_tmp_path.joinpath("dials.damage_analysis.html").is_file()
assert run_in_tmp_path.joinpath("dials.damage_analysis.json").is_file()
def test_damage_analysis_damage_series(dials_data, run_in_tmp_path):
location = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True)
refls = location / "scaled_20_25.refl"
expts = location / "scaled_20_25.expt"
args = [
str(refls),
str(expts),
"min_completeness=0.4",
"-v",
"json=dials.damage_analysis.json",
"dose_group_size=500",
"output.damage_series=True",
"output.accumulation_series=True",
]
run(args)
assert os.path.isfile("dials.damage_analysis.html")
assert os.path.isfile("dials.damage_analysis.json")
expected_series = [
"0_500",
"500_1000",
"1000_1500",
"1500_2000",
"0_1000",
"0_1500",
"0_2000",
]
for e in expected_series:
assert os.path.isfile(f"damage_series_{e}.refl")
assert os.path.isfile(f"damage_series_{e}.expt")
def test_setup_from_dials_data(dials_data):
"""Test dials.damage_analysis on scaled data."""
location = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True)
refls = location / "scaled_20_25.refl"
expts = location / "scaled_20_25.expt"
table = flex.reflection_table.from_file(refls)
experiments = load.experiment_list(expts, check_format=False)
params = phil_scope.extract()
params.dose.experiments.shared_crystal = True
params.dose.experiments.dose_per_image = [1.0, 2.0]
# First experiment is images 1>1800, second 1>1700 (i.e. dose spans 1>5200)
runner = PychefRunner.from_dials_data_files(params, experiments, table)
assert max(runner.dose) == 5198 # last reflection measured not quite at end
assert min(runner.dose) == 2
# Now try again in 'standard' mode i.e. not shared crystal, and set a
# starting dose
params.dose.experiments.shared_crystal = False
params.dose.experiments.dose_per_image = [1.0]
params.dose.experiments.starting_doses = [10, 10]
runner = PychefRunner.from_dials_data_files(params, experiments, table)
assert max(runner.dose) == 1800 + 10
assert min(runner.dose) == 2 + 10
def test_damage_analysis_on_scaled_mtz(dials_data, run_in_tmp_path):
location = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True)
refls = str(location / "scaled_20_25.refl")
expts = str(location / "scaled_20_25.expt")
# First export the data
command = [shutil.which("dials.export"), refls, expts]
result = subprocess.run(command, cwd=run_in_tmp_path, capture_output=True)
assert not result.returncode and not result.stderr
assert os.path.isfile("scaled.mtz")
args = [
str(run_in_tmp_path / "scaled.mtz"),
"anomalous=True",
"json=dials.damage_analysis.json",
]
run(args)
assert run_in_tmp_path.joinpath("dials.damage_analysis.html").is_file()
assert run_in_tmp_path.joinpath("dials.damage_analysis.json").is_file()
def test_damage_analysis_mtz_damage_series(dials_data, run_in_tmp_path):
"""Test dials.damage_analysis on scaled data."""
location = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True)
refls = location / "scaled_20_25.refl"
expts = location / "scaled_20_25.expt"
# First export the data
command = [shutil.which("dials.export"), refls, expts]
result = subprocess.run(command, cwd=run_in_tmp_path, capture_output=True)
assert not result.returncode and not result.stderr
assert os.path.isfile("scaled.mtz")
args = [
str(run_in_tmp_path / "scaled.mtz"),
"anomalous=True",
"json=dials.damage_analysis.json",
"dose_group_size=500",
"output.damage_series=True",
"output.accumulation_series=True",
]
run(args)
assert os.path.isfile("dials.damage_analysis.html")
assert os.path.isfile("dials.damage_analysis.json")
expected_series = [
"0_500",
"500_1000",
"1000_1500",
"1500_2000",
"0_1000",
"0_1500",
"0_2000",
]
for e in expected_series:
assert os.path.isfile(f"damage_series_{e}.mtz")
def test_damage_analysis_input_handling(dials_data, run_in_tmp_path):
"""Test that errors are handled if more than one refl file, no refl/expt
file or unscaled data."""
location = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True)
refls = str(location / "scaled_20_25.refl")
expts = str(location / "scaled_20_25.expt")
# Too many refl files
args = [refls, expts, refls]
with pytest.raises(SystemExit):
run(args)
# No refl file
args = [expts]
with pytest.raises(SystemExit):
run(args)
# No expt file
args = [refls]
with pytest.raises(SystemExit):
run(args)
def test_damage_analysis_fails_on_unscaled_data(dials_data, run_in_tmp_path):
location = dials_data("l_cysteine_dials_output", pathlib=True)
refls = str(location / "20_integrated.pickle")
expts = str(location / "20_integrated_experiments.json")
args = [refls, expts]
with pytest.raises(SystemExit):
run(args)
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