def test_choose_initial_scaling_intensities(test_reflections):
"""Test for correct choice of intensities."""
test_refl = test_reflections
intstr = "prf"
new_rt = choose_initial_scaling_intensities(test_refl, intstr)
assert list(new_rt["intensity"]) == list(test_refl["intensity.prf.value"])
assert list(new_rt["variance"]) == list(
test_refl["intensity.prf.variance"])
intstr = "sum" # should apply partiality correction
new_rt = choose_initial_scaling_intensities(test_refl, intstr)
assert list(new_rt["intensity"]) == list(test_refl["intensity.sum.value"] /
test_refl["partiality"])
assert list(new_rt["variance"]) == pytest.approx(
list(test_refl["intensity.sum.variance"] /
flex.pow2(test_refl["partiality"])))
def refine_error_model(params, experiments, reflection_tables):
"""Do error model refinement."""
# prepare relevant data for datastructures
for i, table in enumerate(reflection_tables):
# First get the good data
table = table.select(~table.get_flags(table.flags.bad_for_scaling, all=False))
# Now chose intensities, ideally these two options could be combined
# with a smart refactor
if params.intensity_choice == "combine":
if not params.combine.Imid:
sys.exit("Imid value must be provided if intensity_choice=combine")
table = calculate_prescaling_correction(table) # needed for below.
I, V = combine_intensities(table, params.combine.Imid)
table["intensity"] = I
table["variance"] = V
else:
table = choose_initial_scaling_intensities(
table, intensity_choice=params.intensity_choice
)
reflection_tables[i] = table
space_group = experiments[0].crystal.get_space_group()
Ih_table = IhTable(
reflection_tables, space_group, additional_cols=["partiality"], anomalous=True
)
# now do the error model refinement
model = BasicErrorModel(basic_params=params.basic)
try:
model = run_error_model_refinement(model, Ih_table)
except (ValueError, RuntimeError) as e:
logger.info(e)
else:
return model
def create(cls, params, experiment, reflection_table, for_multi=False):
"""Perform reflection_table preprocessing and create a SingleScaler."""
cls.ensure_experiment_identifier(experiment, reflection_table)
logger.info(
"The scaling model type being applied is %s. \n",
experiment.scaling_model.id_,
)
try:
reflection_table = cls.filter_bad_reflections(
reflection_table,
partiality_cutoff=params.cut_data.partiality_cutoff,
min_isigi=params.cut_data.min_isigi,
intensity_choice=params.reflection_selection.intensity_choice,
)
except ValueError:
raise BadDatasetForScalingException
# combine partial measurements of same reflection, to handle those reflections
# that were split by dials.integrate - changes size of reflection table.
reflection_table = sum_partial_reflections(reflection_table)
if "inverse_scale_factor" not in reflection_table:
reflection_table["inverse_scale_factor"] = flex.double(
reflection_table.size(), 1.0)
elif (reflection_table["inverse_scale_factor"].count(0.0) ==
reflection_table.size()):
reflection_table["inverse_scale_factor"] = flex.double(
reflection_table.size(), 1.0)
reflection_table = choose_initial_scaling_intensities(
reflection_table, params.reflection_selection.intensity_choice)
excluded_for_scaling = reflection_table.get_flags(
reflection_table.flags.excluded_for_scaling)
user_excluded = reflection_table.get_flags(
reflection_table.flags.user_excluded_in_scaling)
reasons = Reasons()
reasons.add_reason("user excluded", user_excluded.count(True))
reasons.add_reason("excluded for scaling",
excluded_for_scaling.count(True))
n_excluded = (excluded_for_scaling | user_excluded).count(True)
if n_excluded == reflection_table.size():
logger.info(
"All reflections were determined to be unsuitable for scaling."
)
logger.info(reasons)
raise BadDatasetForScalingException(
"""Unable to use this dataset for scaling""")
else:
logger.info(
"Excluding %s/%s reflections\n%s",
n_excluded,
reflection_table.size(),
reasons,
)
if params.reflection_selection.method == "intensity_ranges":
reflection_table = quasi_normalisation(reflection_table,
experiment)
if (params.reflection_selection.method
in (None, Auto, "auto", "quasi_random")) or (
experiment.scaling_model.id_ == "physical"
and "absorption" in experiment.scaling_model.components):
if experiment.scan:
reflection_table = calc_crystal_frame_vectors(
reflection_table, experiment)
alignment_axis = (1.0, 0.0, 0.0)
reflection_table["s0c"] = align_axis_along_z(
alignment_axis, reflection_table["s0c"])
reflection_table["s1c"] = align_axis_along_z(
alignment_axis, reflection_table["s1c"])
try:
scaler = SingleScaler(params, experiment, reflection_table,
for_multi)
except BadDatasetForScalingException as e:
raise ValueError(e)
else:
return scaler