def create(params, experiments, reflections):
''' Create the integrator from the input configuration. '''
from dials.interfaces import IntensityIface
from dials.interfaces import BackgroundIface
from dials.interfaces import CentroidIface
from dials.array_family import flex
# Initialise the strategy classes
BackgroundAlgorithm = BackgroundIface.extension(
params.integration.background.algorithm)
IntensityAlgorithm = IntensityIface.extension(
params.integration.intensity.algorithm)
CentroidAlgorithm = CentroidIface.extension(
params.integration.centroid.algorithm)
# Set the algorithms in the reflection table
flex.reflection_table._background_algorithm = \
flex.strategy(BackgroundAlgorithm, params)
flex.reflection_table._intensity_algorithm = \
flex.strategy(IntensityAlgorithm, params)
flex.reflection_table._centroid_algorithm = \
flex.strategy(CentroidAlgorithm, params)
# Get the integrator class
IntegratorClass = IntegratorFactory.select_integrator(IntensityAlgorithm)
# Return an instantiation of the class
return IntegratorClass(
experiments=experiments,
reflections=reflections,
block_size=params.integration.block.size,
max_procs=params.integration.mp.max_procs,
mp_method=params.integration.mp.method)
def create(params, experiments, reflections):
"""Create the integrator from the input configuration."""
from dials.interfaces import IntensityIface
from dials.interfaces import BackgroundIface
from dials.interfaces import CentroidIface
from dials.array_family import flex
# Initialise the strategy classes
BackgroundAlgorithm = BackgroundIface.extension(
params.integration.background.algorithm
)
IntensityAlgorithm = IntensityIface.extension(
params.integration.intensity.algorithm
)
CentroidAlgorithm = CentroidIface.extension(
params.integration.centroid.algorithm
)
# Set the algorithms in the reflection table
flex.reflection_table._background_algorithm = flex.strategy(
BackgroundAlgorithm, params
)
flex.reflection_table._intensity_algorithm = flex.strategy(
IntensityAlgorithm, params
)
flex.reflection_table._centroid_algorithm = flex.strategy(
CentroidAlgorithm, params
)
# Get the integrator class
IntegratorClass = IntegratorFactory.select_integrator(IntensityAlgorithm)
# Return an instantiation of the class
return IntegratorClass(
experiments=experiments,
reflections=reflections,
block_size=params.integration.block.size,
max_procs=params.integration.mp.max_procs,
mp_method=params.integration.mp.method,
)
def generate_phil_scope():
''' Generate the phil scope. '''
from dials.interfaces import BackgroundIface
from dials.interfaces import IntensityIface
from dials.interfaces import CentroidIface
phil_scope = phil.parse('''
integration {
include scope dials.data.lookup.phil_scope
mp {
method = *multiprocessing sge lsf pbs
.type = choice
.help = "The multiprocessing method to use"
max_procs = 1
.type = int(value_min=1)
.help = "The number of processes to use."
}
block {
size = 10
.type = float
.help = "The block size in rotation angle (degrees)."
}
shoebox {
n_sigma = 3
.help = "The number of standard deviations of the beam divergence and the"
"mosaicity to use for the bounding box size."
.type = float
sigma_b = None
.help = "The E.S.D. of the beam divergence"
.type = float
sigma_m = None
.help = "The E.S.D. of the reflecting range"
.type = float
}
filter {
min_zeta = 0.05
.help = "Filter the reflections by the value of zeta. A value of less"
"than or equal to zero indicates that this will not be used. A"
"positive value is used as the minimum permissable value."
.type = float
ice_rings {
filter = False
.type = bool
unit_cell = 4.498,4.498,7.338,90,90,120
.type = unit_cell
.help = "The unit cell to generate d_spacings for ice rings."
space_group = 194
.type = space_group
.help = "The space group used to generate d_spacings for ice rings."
d_min = 0
.type = int(value_min=0)
.help = "The minimum resolution to filter ice rings"
width = 0.06
.type = float(value_min=0.0)
.help = "The width of an ice ring (in d-spacing)."
}
}
}
''', process_includes=True)
main_scope = phil_scope.get_without_substitution("integration")
assert(len(main_scope) == 1)
main_scope = main_scope[0]
main_scope.adopt_scope(BackgroundIface.phil_scope())
main_scope.adopt_scope(IntensityIface.phil_scope())
main_scope.adopt_scope(CentroidIface.phil_scope())
return phil_scope
def generate_phil_scope():
"""Generate the phil scope."""
from dials.interfaces import BackgroundIface
from dials.interfaces import IntensityIface
from dials.interfaces import CentroidIface
phil_scope = phil.parse(
"""
integration {
include scope dials.data.lookup.phil_scope
mp {
method = *multiprocessing sge lsf pbs
.type = choice
.help = "The multiprocessing method to use"
max_procs = 1
.type = int(value_min=1)
.help = "The number of processes to use."
}
block {
size = 10
.type = float
.help = "The block size in rotation angle (degrees)."
}
shoebox {
n_sigma = 3
.help = "The number of standard deviations of the beam divergence and the"
"mosaicity to use for the bounding box size."
.type = float
sigma_b = None
.help = "The E.S.D. of the beam divergence"
.type = float
sigma_m = None
.help = "The E.S.D. of the reflecting range"
.type = float
}
filter {
min_zeta = 0.05
.help = "Filter the reflections by the value of zeta. A value of less"
"than or equal to zero indicates that this will not be used. A"
"positive value is used as the minimum permissable value."
.type = float
ice_rings {
filter = False
.type = bool
unit_cell = 4.498,4.498,7.338,90,90,120
.type = unit_cell
.help = "The unit cell to generate d_spacings for ice rings."
space_group = 194
.type = space_group
.help = "The space group used to generate d_spacings for ice rings."
d_min = 0
.type = int(value_min=0)
.help = "The minimum resolution to filter ice rings"
width = 0.06
.type = float(value_min=0.0)
.help = "The width of an ice ring (in d-spacing)."
}
}
}
""",
process_includes=True,
)
main_scope = phil_scope.get_without_substitution("integration")
assert len(main_scope) == 1
main_scope = main_scope[0]
main_scope.adopt_scope(BackgroundIface.phil_scope())
main_scope.adopt_scope(IntensityIface.phil_scope())
main_scope.adopt_scope(CentroidIface.phil_scope())
return phil_scope
