def get_subset_for_symmetry(experiments,
reflection_tables,
exclude_images=None):
"""Select an image range for symmetry analysis, or just select
the first 360 degrees of data."""
refls_for_sym = []
if exclude_images:
experiments = exclude_image_ranges_from_scans(reflection_tables,
experiments,
exclude_images)
for refl, exp in zip(reflection_tables, experiments):
sel = get_selection_for_valid_image_ranges(refl, exp)
refls_for_sym.append(refl.select(sel))
else:
for expt, refl in zip(experiments, reflection_tables):
sel = get_selection_for_valid_image_ranges(refl, expt)
if not sel.count(False):
# Use first 360 degrees if <360 deg i.e. first measured data,
# but only if no reflections have been exlicitly excluded
# already
scan_end = int(
math.ceil(360 / abs(expt.scan.get_oscillation()[1])))
if scan_end < len(expt.scan):
sel = refl["xyzobs.px.value"].parts()[2] <= scan_end
refls_for_sym.append(refl.select(sel))
return refls_for_sym
def test_exclude_image_ranges_from_scans():
"""Test for namesake function"""
explist = ExperimentList(
[make_scan_experiment(expid="0"),
make_scan_experiment(expid="1")])
exclude_images = [["0:81:100"], ["1:61:80"]]
r1 = flex.reflection_table()
r1.experiment_identifiers()[1] = "1"
r0 = flex.reflection_table()
r0.experiment_identifiers()[0] = "0"
tables = [r0, r1]
explist = exclude_image_ranges_from_scans(tables, explist, exclude_images)
assert list(explist[0].scan.get_valid_image_ranges("0")) == [(1, 80)]
assert list(explist[1].scan.get_valid_image_ranges("1")) == [(1, 60),
(81, 100)]
# Try excluding a range that already has been excluded
explist = exclude_image_ranges_from_scans(tables, explist, [["1:70:80"]])
assert list(explist[0].scan.get_valid_image_ranges("0")) == [(1, 80)]
assert list(explist[1].scan.get_valid_image_ranges("1")) == [(1, 60),
(81, 100)]
scanlessexplist = ExperimentList([make_scanless_experiment()])
with pytest.raises(ValueError):
_ = exclude_image_ranges_from_scans(tables, scanlessexplist,
[["0:1:100"]])
# Now try excluding everything, should set an empty array
explist = exclude_image_ranges_from_scans(tables, explist, [["1:1:100"]])
assert list(explist[0].scan.get_valid_image_ranges("0")) == [(1, 80)]
assert list(explist[1].scan.get_valid_image_ranges("1")) == []
## test what happens if a single image is left within the scan
explist = ExperimentList(
[make_scan_experiment(expid="0"),
make_scan_experiment(expid="1")])
exclude_images = [["0:81:100"], ["1:76:79"], ["1:81:99"]]
r1 = flex.reflection_table()
r1.experiment_identifiers()[1] = "1"
r0 = flex.reflection_table()
r0.experiment_identifiers()[0] = "0"
tables = [r0, r1]
explist = exclude_image_ranges_from_scans(tables, explist, exclude_images)
assert list(explist[0].scan.get_valid_image_ranges("0")) == [(1, 80)]
assert list(explist[1].scan.get_valid_image_ranges("1")) == [
(1, 75),
(80, 80),
(100, 100),
]
def test_exclude_image_ranges_from_scans():
"""Test for namesake function"""
explist = ExperimentList(
[make_scan_experiment(expid="0"),
make_scan_experiment(expid="1")])
exclude_images = [["0:81:100"], ["1:61:80"]]
explist = exclude_image_ranges_from_scans(explist, exclude_images)
assert list(explist[0].scan.get_valid_image_ranges("0")) == [(1, 80)]
assert list(explist[1].scan.get_valid_image_ranges("1")) == [(1, 60),
(81, 100)]
# Try excluding a range that already has been excluded
explist = exclude_image_ranges_from_scans(explist, [["1:70:80"]])
assert list(explist[0].scan.get_valid_image_ranges("0")) == [(1, 80)]
assert list(explist[1].scan.get_valid_image_ranges("1")) == [(1, 60),
(81, 100)]
scanlessexplist = ExperimentList([make_scanless_experiment()])
with pytest.raises(ValueError):
_ = exclude_image_ranges_from_scans(scanlessexplist, [["0:1:100"]])
# Now try excluding everything, should set an empty array
explist = exclude_image_ranges_from_scans(explist, [["1:1:100"]])
assert list(explist[0].scan.get_valid_image_ranges("0")) == [(1, 80)]
assert list(explist[1].scan.get_valid_image_ranges("1")) == []
def test_get_subset_for_symmetry_prior_image_range():
"""Test that first 360 degrees are selected from each sweep with an exclude
images command."""
exclude_images, expts, tables = _make_input_for_exclude_tests(exclude_images=True)
# Explicitly exclude a different image range
expts = exclude_image_ranges_from_scans(tables, expts, [["0:1:360"], ["1:1:360"]])
refls = get_subset_for_symmetry(expts, tables)
assert refls[0]["i"].all_eq(1)
assert refls[1]["i"].all_eq(1)
# Exclude_images should be cumulative, i.e. the range exclude above should
# be excluded in addition to the new range provided explicitly to the
# function
refls = get_subset_for_symmetry(expts, tables, exclude_images)
assert len(refls[0]) == 0
assert len(refls[1]) == 0
