def create(cls, experiments, params=None):
"""
Select the reference calculator
"""
from dials.algorithms.profile_model.gaussian_rs.algorithm import (
GaussianRSReferenceCalculatorFactory, )
# Get the parameters
if params is None:
from dials.command_line.integrate import phil_scope
params = phil_scope.extract()
# Select the factory function
selection = params.profile.algorithm
if selection == "gaussian_rs":
# Get the parameters
params = params.profile.gaussian_rs.fitting
# Create the algorithm
algorithm = GaussianRSReferenceCalculatorFactory.create(
experiments,
grid_size=params.grid_size,
scan_step=params.scan_step,
grid_method=params.grid_method,
)
else:
raise RuntimeError("Unknown profile model algorithm")
# Return the algorithm
return algorithm
def test_gaussianrs_reference_profile_calculator(data):
from dials.algorithms.profile_model.gaussian_rs.algorithm import (
GaussianRSReferenceCalculatorFactory, )
algorithm = GaussianRSReferenceCalculatorFactory.create(data.experiments)
reflections = flex.reflection_table_to_list_of_reflections(
data.reflections)
count = 0
for r in reflections:
try:
algorithm(r)
except Exception:
count += 1
assert len(reflections) == 15193
assert count == 0
profiles = algorithm.reference_profiles()
count = 0
for i in range(len(profiles)):
p = profiles[i].reference()
for j in range(len(p)):
d = p.data(j)
p.mask(j)
if len(d) != 0:
count += 1
assert count == 9