def test_glm_background_calculator():
from dials.algorithms.background.glm.algorithm import GLMBackgroundCalculatorFactory
algorithm = GLMBackgroundCalculatorFactory.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 == 333
def create(cls, experiments, params=None):
"""
Select the background calculator
"""
from dials.algorithms.background.simple.algorithm import (
SimpleBackgroundCalculatorFactory, )
from dials.algorithms.background.glm.algorithm import (
GLMBackgroundCalculatorFactory, )
from dials.algorithms.background.gmodel.algorithm import (
GModelBackgroundCalculatorFactory, )
# 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.integration.background.algorithm
if selection == "simple":
# Get parameters
params = params.integration.background.simple
# Create some keyword parameters
kwargs = {
"model": params.model.algorithm,
"outlier": params.outlier.algorithm,
"min_pixels": params.min_pixels,
}
# Create all the keyword parameters
if params.outlier.algorithm == "null":
pass
elif params.outlier.algorithm == "truncated":
kwargs["lower"] = params.outlier.truncated.lower
kwargs["upper"] = params.outlier.truncated.upper
elif params.outlier.algorithm == "nsigma":
kwargs["lower"] = params.outlier.nsigma.lower
kwargs["upper"] = params.outlier.nsigma.upper
elif params.outlier.algorithm == "normal":
kwargs["min_pixels"] = params.outlier.normal.min_pixels
elif params.outlier.algorithm == "plane":
kwargs["fraction"] = params.outlier.plane.fraction
kwargs["n_sigma"] = params.outlier.plane.n_sigma
elif params.outlier.algorithm == "tukey":
kwargs["lower"] = params.outlier.tukey.lower
kwargs["upper"] = params.outlier.tukey.upper
# Create the algorithm
algorithm = SimpleBackgroundCalculatorFactory.create(
experiments, **kwargs)
elif selection == "glm":
# Get the parameters
params = params.integration.background.glm
# Create the algorithm
algorithm = GLMBackgroundCalculatorFactory.create(
experiments,
model=params.model.algorithm,
tuning_constant=params.robust.tuning_constant,
min_pixels=params.min_pixels,
)
elif selection == "gmodel":
# Get the parameters
params = params.integration.background.gmodel
# Create the algorithm
algorithm = GModelBackgroundCalculatorFactory.create(
experiments,
model=params.model,
robust=params.robust.algorithm,
tuning_constant=params.robust.tuning_constant,
min_pixels=params.min_pixels,
)
else:
raise RuntimeError("Unknown background algorithm")
# Return the background calculator
return algorithm
def create(Class, experiments, params=None):
'''
Select the background calculator
'''
from dials.algorithms.background.simple.algorithm import SimpleBackgroundCalculatorFactory
from dials.algorithms.background.glm.algorithm import GLMBackgroundCalculatorFactory
from dials.algorithms.background.gmodel.algorithm import GModelBackgroundCalculatorFactory
# 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.integration.background.algorithm
if selection == "simple":
# Get parameters
params = params.integration.background.simple
# Create some keyword parameters
kwargs = {
'model' : params.model.algorithm,
'outlier' : params.outlier.algorithm,
'min_pixels' : params.min_pixels
}
# Create all the keyword parameters
if params.outlier.algorithm == 'null':
pass
elif params.outlier.algorithm == 'truncated':
kwargs['lower'] = params.outlier.truncated.lower
kwargs['upper'] = params.outlier.truncated.upper
elif params.outlier.algorithm == 'nsigma':
kwargs['lower'] = params.outlier.nsigma.lower
kwargs['upper'] = params.outlier.nsigma.upper
elif params.outlier.algorithm == 'normal':
kwargs['min_pixels'] = params.outlier.normal.min_pixels
elif params.outlier.algorithm == 'plane':
kwargs['fraction'] = params.outlier.plane.fraction
kwargs['n_sigma'] = params.outlier.plane.n_sigma
elif params.outlier.algorithm == 'tukey':
kwargs['lower'] = params.outlier.tukey.lower
kwargs['upper'] = params.outlier.tukey.upper
# Create the algorithm
algorithm = SimpleBackgroundCalculatorFactory.create(experiments, **kwargs)
elif selection == "glm":
# Get the parameters
params = params.integration.background.glm
# Create the algorithm
algorithm = GLMBackgroundCalculatorFactory.create(
experiments,
model = params.model.algorithm,
tuning_constant = params.robust.tuning_constant,
min_pixels = params.min_pixels)
elif selection == "gmodel":
# Get the parameters
params = params.integration.background.gmodel
# Create the algorithm
algorithm = GModelBackgroundCalculatorFactory.create(
experiments,
model = params.model,
robust = params.robust.algorithm,
tuning_constant = params.robust.tuning_constant,
min_pixels = params.min_pixels)
else:
raise RuntimeError("Unknown background algorithm")
# Return the background calculator
return algorithm