def create_refiner(params, reflections, experiments):
# Only parameterise the crystal unit cell
det_params = None
beam_params = None
xlo_params = None
xluc_params = []
for crystal in experiments.crystals():
exp_ids = experiments.indices(crystal)
xluc_params.append(
CrystalUnitCellParameterisation(crystal, experiment_ids=exp_ids)
)
# Two theta prediction equation parameterisation
pred_param = TwoThetaPredictionParameterisation(
experiments, det_params, beam_params, xlo_params, xluc_params
)
param_reporter = ParameterReporter(
det_params, beam_params, xlo_params, xluc_params
)
# ReflectionManager, currently without outlier rejection
# Note: If not all reflections are used, then the filtering must be
# communicated to generate_cif/mmcif() to be included in the CIF file!
refman = TwoThetaReflectionManager(
reflections, experiments, outlier_detector=None
)
# Reflection predictor
ref_predictor = TwoThetaExperimentsPredictor(experiments)
# Two theta target
target = TwoThetaTarget(experiments, ref_predictor, refman, pred_param)
# Switch on correlation matrix tracking if a correlation plot is requested
journal = None
if params.output.correlation_plot.filename is not None:
journal = refinery_phil_scope.extract().refinery.journal
journal.track_parameter_correlation = True
# Minimisation engine - hardcoded to LevMar for now.
refinery = Refinery(
target=target,
prediction_parameterisation=pred_param,
log=None,
tracking=journal,
max_iterations=20,
)
# Refiner
refiner = Refiner(
experiments=experiments,
pred_param=pred_param,
param_reporter=param_reporter,
refman=refman,
target=target,
refinery=refinery,
)
return refiner
def create_refiner(params, reflections, experiments):
from dials.algorithms.refinement.parameterisation.crystal_parameters import \
CrystalUnitCellParameterisation
from dials.algorithms.refinement.parameterisation.parameter_report import \
ParameterReporter
from dials.algorithms.refinement.two_theta_refiner import \
TwoThetaReflectionManager, TwoThetaTarget, TwoThetaExperimentsPredictor, \
TwoThetaPredictionParameterisation
verb = params.refinement.verbosity
# Only parameterise the crystal unit cell
det_params = None
beam_params = None
xlo_params = None
xluc_params = []
for icrystal, crystal in enumerate(experiments.crystals()):
exp_ids = experiments.indices(crystal)
xluc_params.append(
CrystalUnitCellParameterisation(crystal,
experiment_ids=exp_ids))
# Two theta prediction equation parameterisation
pred_param = TwoThetaPredictionParameterisation(
experiments, det_params, beam_params, xlo_params, xluc_params)
param_reporter = ParameterReporter(det_params, beam_params, xlo_params,
xluc_params)
# ReflectionManager, currently without outlier rejection
# Note: If not all reflections are used, then the filtering must be
# communicated to generate_cif/mmcif() to be included in the CIF file!
refman = TwoThetaReflectionManager(reflections,
experiments,
outlier_detector=None,
verbosity=verb)
# Reflection predictor
ref_predictor = TwoThetaExperimentsPredictor(experiments)
# Two theta target
target = TwoThetaTarget(experiments, ref_predictor, refman, pred_param)
# Switch on correlation matrix tracking if a correlation plot is requested
journal = None
if params.output.correlation_plot.filename is not None:
from dials.algorithms.refinement.engine import refinery_phil_scope
journal = refinery_phil_scope.extract().refinery.journal
journal.track_parameter_correlation = True
# Minimisation engine - hardcoded to LevMar for now.
from dials.algorithms.refinement.engine \
import LevenbergMarquardtIterations as Refinery
refinery = Refinery(target=target,
prediction_parameterisation=pred_param,
log=None,
verbosity=verb,
tracking=journal,
max_iterations=20)
# Refiner
from dials.algorithms.refinement.refiner import Refiner
refiner = Refiner(reflections=reflections,
experiments=experiments,
pred_param=pred_param,
param_reporter=param_reporter,
refman=refman,
target=target,
refinery=refinery,
verbosity=verb)
return refiner