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from __future__ import annotations
import pickle
import shutil
import subprocess
import pytest
from dials.algorithms.background.gmodel import StaticBackgroundModel
from dials.array_family import flex
@pytest.fixture
def model(tmp_path):
ysize = 2527
xsize = 2463
data = flex.double(flex.grid(ysize, xsize), 1)
model = StaticBackgroundModel()
model.add(data)
model_file = tmp_path / "model.pickle"
with model_file.open("wb") as fh:
pickle.dump(model, fh, pickle.HIGHEST_PROTOCOL)
return model_file
def test_simple(dials_data, model, tmp_path):
experiments = dials_data("centroid_test_data", pathlib=True) / "experiments.json"
reflns_simple = tmp_path / "simple" / "observations.refl"
reflns_g_simple = tmp_path / "gmodel_simple" / "observations.refl"
reflns_simple.parent.mkdir()
reflns_g_simple.parent.mkdir()
result = subprocess.run(
[
shutil.which("dials.integrate"),
"nproc=1",
experiments,
"profile.fitting=False",
"background.algorithm=simple",
"background.simple.outlier.algorithm=null",
f"output.reflections={reflns_simple}",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
assert reflns_simple.is_file()
result = subprocess.run(
[
shutil.which("dials.integrate"),
"nproc=1",
experiments,
"profile.fitting=False",
"background.algorithm=gmodel",
"background.gmodel.robust.algorithm=False",
"background.gmodel.model=model.pickle",
f"output.reflections={reflns_g_simple}",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
assert reflns_g_simple.is_file()
reflections1 = flex.reflection_table.from_file(reflns_simple)
reflections3 = flex.reflection_table.from_file(reflns_g_simple)
assert len(reflections1) == len(reflections3)
flag = flex.reflection_table.flags.integrated_sum
integrated1 = reflections1.select(reflections1.get_flags(flag, all=True))
integrated3 = reflections3.select(reflections3.get_flags(flag, all=True))
assert len(integrated1) > 0
assert len(integrated1) == len(integrated3)
mean_bg1 = integrated1["background.mean"]
mean_bg3 = integrated3["background.mean"]
scale3 = integrated3["background.scale"]
diff1 = flex.abs(mean_bg1 - mean_bg3)
assert (scale3 > 0).count(False) == 0
assert (diff1 < 1e-5).count(False) == 0
def test_robust(dials_data, model, tmp_path):
experiments = dials_data("centroid_test_data", pathlib=True) / "experiments.json"
reflns_robust = tmp_path / "robust" / "observations.refl"
reflns_g_robust = tmp_path / "gmodel_robust" / "observations.refl"
reflns_robust.parent.mkdir()
reflns_g_robust.parent.mkdir()
result = subprocess.run(
[
shutil.which("dials.integrate"),
"nproc=1",
experiments,
"profile.fitting=False",
"background.algorithm=glm",
f"output.reflections={reflns_robust}",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
assert reflns_robust.is_file()
result = subprocess.run(
[
shutil.which("dials.integrate"),
"nproc=1",
experiments,
"profile.fitting=False",
"background.algorithm=gmodel",
"background.gmodel.robust.algorithm=True",
"background.gmodel.model=model.pickle",
f"output.reflections={reflns_g_robust}",
],
cwd=tmp_path,
capture_output=True,
)
assert not result.returncode and not result.stderr
assert reflns_g_robust.is_file()
reflections2 = flex.reflection_table.from_file(reflns_robust)
reflections4 = flex.reflection_table.from_file(reflns_g_robust)
assert len(reflections2) == len(reflections4)
flag = flex.reflection_table.flags.integrated_sum
integrated2 = reflections2.select(reflections2.get_flags(flag, all=True))
integrated4 = reflections4.select(reflections4.get_flags(flag, all=True))
assert len(integrated2) > 0
assert len(integrated2) == len(integrated4)
scale4 = integrated4["background.scale"]
assert (scale4 > 0).count(False) == 0
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