def test_integrated(dials_data, capsys, run_in_tmpdir):
expts_file = dials_data("insulin_processed") / "integrated.expt"
refl_file = dials_data("insulin_processed") / "integrated.refl"
refl = flex.reflection_table.from_file(refl_file)
z = refl["xyzobs.px.value"].parts()[2]
sel = z < 40
refl_subset = refl.select(sel)
refl_subset["intensity.prf.value"].set_selected(
z.select(sel) < 10, refl_subset["intensity.prf.value"] * 0.05)
refl_subset.as_file("mod.refl")
detect_blanks.run(
[expts_file.strpath, "mod.refl", "output.json=detect_blanks.json"])
captured = capsys.readouterr()
assert ("""\
Analysis of 18171 strong reflections:
Potential blank images: 41 -> 45
Analysis of 18171 indexed reflections:
Potential blank images: 41 -> 45
Analysis of 44340 integrated reflections:
Potential blank images: 1 -> 9
Potential blank images: 41 -> 45
""" in captured.out)
json_file = run_in_tmpdir / "detect_blanks.json"
assert json_file.check(file=1)
with json_file.open() as fh:
d = json.load(fh)
assert d["strong"]["blank_regions"] == [[40, 45]]
assert d["indexed"]["blank_regions"] == [[40, 45]]
assert d["integrated"]["blank_regions"] == [[0, 9], [40, 45]]
def test_strong(dials_data, capsys, run_in_tmpdir):
expts_file = dials_data("insulin_processed") / "imported.expt"
refl_file = dials_data("insulin_processed") / "strong.refl"
refl = flex.reflection_table.from_file(refl_file)
z = refl["xyzobs.px.value"].parts()[2]
refl_subset = refl.select((z < 10) | (z > 20))
refl_subset.as_file("mod.refl")
detect_blanks.run([expts_file.strpath, "mod.refl"])
captured = capsys.readouterr()
assert "Potential blank images: 11 -> 21" in captured.out
json_file = run_in_tmpdir / "blanks.json"
assert json_file.check(file=1)
with json_file.open() as fh:
d = json.load(fh)
assert d["strong"]["blank_regions"] == [[10, 21]]
assert not d["indexed"]
assert not d["integrated"]
def test_still_raises_sysexit(dials_data, run_in_tmpdir):
path = dials_data("thaumatin_grid_scan")
# Import the data
result = procrunner.run(
["dials.import", "output.experiments=imported.expt"] + path.listdir("*.cbf*")
)
assert not result.returncode and not result.stderr
expts_file = run_in_tmpdir.join("imported.expt")
assert expts_file.check(file=1)
# Find the spots
result = procrunner.run(["dials.find_spots", "imported.expt", "min_spot_size=3"],)
assert not result.returncode and not result.stderr
refl_file = run_in_tmpdir.join("strong.refl")
assert refl_file.check(file=1)
# Now test that passing stills raises a sys.exit
with pytest.raises(SystemExit):
detect_blanks.run([expts_file.strpath, refl_file.strpath])