def create(cls, params, experiments, reflections=None):
'''
Compute or load the profile model.
:param params: The input phil parameters
:param experiments: The experiment list
:param reflections: The reflection table
:return: The profile model
'''
from dials.interfaces import ProfileModelIface
Extension = ProfileModelIface.extension(params.profile.algorithm)
Algorithm = Extension().algorithm()
create_profile_model = True
if hasattr(params, 'create_profile_model'):
create_profile_model = params.create_profile_model
if (create_profile_model and reflections is not None
and "shoebox" in reflections):
for expr, indices in reflections.iterate_experiments_and_indices(
experiments):
expr.profile = Algorithm.create(params.profile,
reflections.select(indices),
expr.crystal, expr.beam,
expr.detector, expr.goniometer,
expr.scan)
else:
for expr in experiments:
expr.profile = Algorithm.create(params.profile, None,
expr.crystal, expr.beam,
expr.detector, expr.goniometer,
expr.scan, expr.profile)
return experiments
def generate_phil_scope():
'''
Generate the phil scope for profile model
:return: The phil scope
'''
import dials.extensions
from dials.interfaces import ProfileModelIface
phil_scope = ProfileModelIface.phil_scope()
return phil_scope
def generate_phil_scope(): ''' Generate the phil scope for profile model :return: The phil scope ''' import dials.extensions from dials.interfaces import ProfileModelIface phil_scope = ProfileModelIface.phil_scope() return phil_scope
def tst_after_import_extensions(self):
import dials.extensions # import dependency
from dials.interfaces import ProfileModelIface
from dials.interfaces import SpotFinderThresholdIface
from dials.interfaces import CentroidIface
from dials.interfaces import BackgroundIface
# Should have four interfaces
interfaces = list(Interface.interfaces())
assert (len(interfaces) == 4)
# Check we have the expected number of extensions for each interface
extensions = list(ProfileModelIface.extensions())
assert (len(extensions) > 0)
extensions = list(SpotFinderThresholdIface.extensions())
assert (len(extensions) > 0)
extensions = list(CentroidIface.extensions())
assert (len(extensions) > 0)
extensions = list(BackgroundIface.extensions())
assert (len(extensions) > 0)
# Check the interface contain the expected extensions
from dials.extensions import GaussianRSProfileModelExt
from dials.extensions import KabschSpotFinderThresholdExt
from dials.extensions import SimpleCentroidExt
from dials.extensions import NullBackgroundExt
from dials.extensions import SimpleBackgroundExt
extensions = list(ProfileModelIface.extensions())
assert (GaussianRSProfileModelExt in extensions)
extensions = list(SpotFinderThresholdIface.extensions())
assert (KabschSpotFinderThresholdExt in extensions)
extensions = list(CentroidIface.extensions())
assert (SimpleCentroidExt in extensions)
extensions = list(BackgroundIface.extensions())
assert (NullBackgroundExt in extensions)
assert (SimpleBackgroundExt in extensions)
# Test passed
print 'OK'
def create(cls, params, experiments, reflections):
'''
Compute or load the profile model.
:param params: The input phil parameters
:param experiments: The experiment list
:param reflections: The reflection table
:return: The profile model
'''
from dials.interfaces import ProfileModelIface
Extension = ProfileModelIface.extension(params.profile.algorithm)
Algorithm = Extension().algorithm()
for expr, indices in reflections.iterate_experiments_and_indices(
experiments):
expr.profile = Algorithm.create(params.profile,
reflections.select(indices),
expr.crystal, expr.beam,
expr.detector, expr.goniometer,
expr.scan)
return experiments
def create(cls, params, experiments, reflections):
'''
Compute or load the profile model.
:param params: The input phil parameters
:param experiments: The experiment list
:param reflections: The reflection table
:return: The profile model
'''
from dials.interfaces import ProfileModelIface
Extension = ProfileModelIface.extension(params.profile.algorithm)
Algorithm = Extension().algorithm()
for expr, indices in reflections.iterate_experiments_and_indices(experiments):
expr.profile = Algorithm.create(
params.profile,
reflections.select(indices),
expr.crystal,
expr.beam,
expr.detector,
expr.goniometer,
expr.scan)
return experiments