1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
|
from __future__ import annotations
import pickle
import shutil
import subprocess
import pytest
from dxtbx.model import ExperimentList
from scitbx.array_family import flex
def test_model_background(dials_data, tmp_path):
# Use a data set from a P2M for speed (small detector).
data_dir = dials_data("l_cysteine_dials_output", pathlib=True)
result = subprocess.run(
[shutil.which("dials.model_background"), data_dir / "11_integrated.expt"],
cwd=tmp_path,
capture_output=True,
)
print(result.stderr.decode())
result.check_returncode()
assert not result.stderr
for filename in (
"background.pickle",
"mean_0.png",
"variance_0.png",
"dispersion_0.png",
"mask_0.png",
"min_0.png",
"max_0.png",
"model_0.png",
):
assert (tmp_path / filename).is_file()
with open((tmp_path / "background.pickle"), "rb") as f:
background = pickle.load(f)
panel = 0
data = background.data(panel)
assert data.all() == (1679, 1475)
min_max_mean = flex.min_max_mean_double(data.as_1d())
assert min_max_mean.max == pytest.approx(0.1800928143817288)
assert min_max_mean.min == 0.0
assert min_max_mean.mean == pytest.approx(0.020816338853321865)
# Test integration using this background model. It turns out that 11_integrated.{expt,refl}
# can't be passed to dials.integrate, so we will make our own input from the
# indexed.{expt,refl}. This has 4 experiments and 1700 images, and we'll take just the first
# experiment and 10 images for this test.
subprocess.run(
[
shutil.which("dials.split_experiments"),
data_dir / "indexed.expt",
data_dir / "indexed.refl",
],
cwd=tmp_path,
capture_output=True,
)
expts = ExperimentList.from_file(tmp_path / "split_0.expt")
expts[0].scan.set_image_range((1, 10))
expts.as_file(tmp_path / "modified.expt")
# Test integration using the background model, with robust.algorithm=(True|False)
result = subprocess.run(
[
shutil.which("dials.integrate"),
tmp_path / "modified.expt",
tmp_path / "split_0.refl",
"background.algorithm=gmodel",
"gmodel.robust.algorithm=False",
"gmodel.model=background.pickle",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
result = subprocess.run(
[
shutil.which("dials.integrate"),
tmp_path / "modified.expt",
tmp_path / "split_0.refl",
"background.algorithm=gmodel",
"gmodel.robust.algorithm=True",
"gmodel.model=background.pickle",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
|
