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from __future__ import annotations
import shutil
import subprocess
import pytest
from dxtbx.serialize import load
from dials.array_family import flex
def test_slice_sequence_and_compare_with_expected_results(dials_data, tmp_path):
data_dir = dials_data("refinement_test_data", pathlib=True)
experiments_path = data_dir / "i04-weak.json"
pickle_path = data_dir / "i04-weak.pickle"
assert experiments_path.is_file()
assert pickle_path.is_file()
result = subprocess.run(
[
shutil.which("dials.slice_sequence"),
experiments_path,
pickle_path,
"image_range=1 20",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
# load results
sliced_exp = load.experiment_list(
tmp_path / "i04-weak_1_20.expt", check_format=False
)[0]
sliced_refs = flex.reflection_table.from_file(tmp_path / "i04-weak_1_20.refl")
# simple test of results
assert sliced_exp.scan.get_image_range() == (1, 20)
assert len(sliced_refs) == 3672
def test_slice_sequence_with_first_images_missing(dials_data, tmp_path):
"""Test slicing where scan image range does not start at 1, exercising
a case that exposed a bug"""
data_dir = dials_data("refinement_test_data", pathlib=True)
experiments_path = data_dir / "i04-weak.json"
# first slice
result = subprocess.run(
[shutil.which("dials.slice_sequence"), experiments_path, "image_range=5,20"],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
# second slice
result = subprocess.run(
[
shutil.which("dials.slice_sequence"),
"i04-weak_5_20.expt",
"image_range=10,20",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
sliced_exp = load.experiment_list(
tmp_path / "i04-weak_5_20_10_20.expt", check_format=False
)[0]
assert sliced_exp.scan.get_image_range() == (10, 20)
assert sliced_exp.scan.get_array_range() == (9, 20)
assert sliced_exp.scan.get_oscillation()[0] == pytest.approx(83.35)
def test_slice_sequence_to_degree_blocks(dials_data, tmp_path):
"""Slice data into 10 degree blocks i.e. 17 datasets"""
expt = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True) / "scaled_30.expt"
refl = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True) / "scaled_30.refl"
subprocess.run(
[
shutil.which("dials.slice_sequence"),
"block_size=10",
"output.experiments=sliced.expt",
"output.reflections=sliced.refl",
expt,
refl,
],
cwd=tmp_path,
capture_output=True,
)
sliced_expts = load.experiment_list(tmp_path / "sliced.expt", check_format=False)
assert len(sliced_expts) == 17
sliced_refl = flex.reflection_table.from_file(tmp_path / "sliced.refl")
assert len(set(sliced_refl.experiment_identifiers().values())) == 17
sliced_refl.assert_experiment_identifiers_are_consistent(sliced_expts)
def test_slice_sequence_with_scan_varying_crystal(dials_data, tmp_path):
"""test slicing keeps a scan-varying crystal"""
expt = dials_data("l_cysteine_4_sweeps_scaled", pathlib=True) / "scaled_30.expt"
subprocess.run(
[
shutil.which("dials.slice_sequence"),
"image_range=10,20",
"output.experiments=sliced.expt",
expt,
],
cwd=tmp_path,
capture_output=True,
)
orig = load.experiment_list(expt, check_format=False)[0]
sliced = load.experiment_list(tmp_path / "sliced.expt", check_format=False)[0]
assert sliced.crystal.num_scan_points == 12
orig_UB = [
orig.crystal.get_A_at_scan_point(i) for i in range(orig.crystal.num_scan_points)
]
sliced_UB = [
sliced.crystal.get_A_at_scan_point(i)
for i in range(sliced.crystal.num_scan_points)
]
for a, b in zip(orig_UB[9:21], sliced_UB):
assert a == pytest.approx(b)
def test_slice_sequence_exclude_images_multiple(dials_data, tmp_path):
data_dir = dials_data("refinement_test_data", pathlib=True)
experiments_path = data_dir / "i04-weak.json"
pickle_path = data_dir / "i04-weak.pickle"
assert experiments_path.is_file()
assert pickle_path.is_file()
result = subprocess.run(
[
shutil.which("dials.slice_sequence"),
experiments_path,
pickle_path,
"exclude_images_multiple=40",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
# load results
sliced_expts = load.experiment_list(
tmp_path / "i04-weak_sliced.expt", check_format=False
)
sliced_refls = flex.reflection_table.from_file(tmp_path / "i04-weak_sliced.refl")
# simple test of results
assert len(sliced_expts) == 14
assert len(sliced_refls) == 100397
image_ranges = [e.scan.get_image_range() for e in sliced_expts]
assert image_ranges == [
(1, 39),
(41, 79),
(81, 119),
(121, 159),
(161, 199),
(201, 239),
(241, 279),
(281, 319),
(321, 359),
(361, 399),
(401, 439),
(441, 479),
(481, 519),
(521, 540),
]
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