def create(cls, data, detector_space=False, deconvolution=False):
from dials.algorithms.profile_model.gaussian_rs.algorithm import (
GaussianRSIntensityCalculatorFactory,
)
from dials.algorithms.integration.parallel_integrator import (
GaussianRSReferenceProfileData,
)
from dials.algorithms.integration.parallel_integrator import (
GaussianRSMultiCrystalReferenceProfileData,
)
from dials.algorithms.integration.parallel_integrator import (
ReferenceProfileData,
)
from dials.algorithms.profile_model.modeller import CircleSampler
from dials.algorithms.profile_model.gaussian_rs.transform import TransformSpec
reference = data.reference[0]
experiments = data.experiments
assert len(reference) % 9 == 0
num_scan_points = len(reference) // 9
data_spec = GaussianRSMultiCrystalReferenceProfileData()
for e in experiments:
sampler = CircleSampler(
e.detector[0].get_image_size(),
e.scan.get_array_range(),
num_scan_points,
)
spec = TransformSpec(
e.beam,
e.detector,
e.goniometer,
e.scan,
e.profile.sigma_b(deg=False),
e.profile.sigma_m(deg=False),
e.profile.n_sigma() * 1.5,
5,
)
temp = reference
reference = ReferenceProfileData()
for d, m in temp:
reference.append(d, m)
spec = GaussianRSReferenceProfileData(reference, sampler, spec)
data_spec.append(spec)
return GaussianRSIntensityCalculatorFactory.create(
data_spec, detector_space, deconvolution
)
def create(cls, experiments, reference_profiles, params=None):
"""
Select the intensity calculator
"""
from dials.algorithms.profile_model.gaussian_rs.algorithm import (
GaussianRSIntensityCalculatorFactory,
)
# 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
# Check for detector space
if params.fit_method == "reciprocal_space":
detector_space = False
elif params.fit_method == "detector_space":
detector_space = True
else:
raise RuntimeError("Unknown fit method: %s" % params.fit_method)
# Create the algorithm
algorithm = GaussianRSIntensityCalculatorFactory.create(
reference_profiles,
detector_space=detector_space,
deconvolution=params.detector_space.deconvolution,
)
else:
raise RuntimeError("Unknown profile model algorithm")
# Return the algorithm
return algorithm