def integrate(self, integrator_type):
from dials.algorithms.integration.integrator import IntegratorFactory
from dials.algorithms.integration.integrator import phil_scope as master_phil_scope
from libtbx.phil import parse
import sys
import StringIO
rlist = self.rlist.copy()
output = StringIO.StringIO()
stdout = sys.stdout
sys.stdout = output
try:
phil_scope = parse('''
integration.background.algorithm=null
integration.intensity.algorithm=sum
integration.intensity.sum.integrator=%s
integration.block.size=0.5
integration.profile_fitting=False
''' % integrator_type)
params = master_phil_scope.fetch(source=phil_scope).extract()
integrator = IntegratorFactory.create(params, self.exlist, rlist)
result = integrator.integrate()
except Exception:
print output
raise
sys.stdout = stdout
return result
def test_integrator_3d(dials_data, nproc):
from math import pi
from dxtbx.model.experiment_list import ExperimentListFactory
from dials.algorithms.profile_model.gaussian_rs import Model
from dials.array_family import flex
path = dials_data("centroid_test_data").join("experiments.json").strpath
exlist = ExperimentListFactory.from_json_file(path)
exlist[0].profile = Model(None,
n_sigma=3,
sigma_b=0.024 * pi / 180.0,
sigma_m=0.044 * pi / 180.0)
rlist = flex.reflection_table.from_predictions(exlist[0])
rlist["id"] = flex.int(len(rlist), 0)
rlist.compute_bbox(exlist)
rlist.compute_zeta_multi(exlist)
rlist.compute_d(exlist)
from libtbx.phil import parse
from dials.algorithms.integration.integrator import Integrator3D, phil_scope
params = phil_scope.fetch(
parse("""
integration.block.size=%d
integration.mp.nproc=%d
integration.profile_fitting=False
""" % (5, nproc))).extract()
integrator = Integrator3D(exlist, rlist, params)
integrator.integrate()
def integrate(integrator_type, rlist):
from libtbx.phil import parse
from dials.algorithms.integration.integrator import create_integrator
from dials.algorithms.integration.integrator import (
phil_scope as master_phil_scope,
)
rlist = rlist.copy()
phil_scope = parse(
f"""
integration.background.algorithm=null
integration.intensity.algorithm=sum
integration.intensity.sum.integrator={integrator_type}
integration.block.size=0.5
integration.profile_fitting=False
"""
)
params = master_phil_scope.fetch(source=phil_scope).extract()
integrator = create_integrator(params, exlist, rlist)
result = integrator.integrate()
return result
def run(self):
from dials.algorithms.integration.integrator import Integrator3D
from dials.algorithms.integration.integrator import phil_scope
from dials.algorithms.integration.integrator import Parameters
import StringIO
import sys
from libtbx.phil import parse
params = phil_scope.fetch(
parse('''
integration.block.size=%d
integration.mp.nproc=%d
integration.profile_fitting=False
''' % (5, self.nproc))).extract()
output = StringIO.StringIO()
stdout = sys.stdout
sys.stdout = output
try:
integrator = Integrator3D(self.exlist, self.rlist,
Parameters.from_phil(params.integration))
result = integrator.integrate()
except Exception:
print output
raise
sys.stdout = stdout
print 'OK'
def run(self):
from dials.algorithms.integration.integrator import Integrator3D
from dials.algorithms.integration.integrator import phil_scope
from dials.algorithms.integration.integrator import Parameters
import StringIO
import sys
from libtbx.phil import parse
params = phil_scope.fetch(parse('''
integration.block.size=%d
integration.mp.nproc=%d
integration.profile_fitting=False
''' % (5, self.nproc))).extract()
output = StringIO.StringIO()
stdout = sys.stdout
sys.stdout = output
try:
integrator = Integrator3D(
self.exlist,
self.rlist,
Parameters.from_phil(params.integration))
result = integrator.integrate()
except Exception:
print output
raise
sys.stdout = stdout
print 'OK'
def integrate(integrator_type, rlist):
from dials.algorithms.integration.integrator import IntegratorFactory
from dials.algorithms.integration.integrator import phil_scope as master_phil_scope
from libtbx.phil import parse
rlist = rlist.copy()
phil_scope = parse('''
integration.background.algorithm=null
integration.intensity.algorithm=sum
integration.intensity.sum.integrator=%s
integration.block.size=0.5
integration.profile_fitting=False
''' % integrator_type)
params = master_phil_scope.fetch(source=phil_scope).extract()
integrator = IntegratorFactory.create(params, exlist, rlist)
result = integrator.integrate()
return result
def integrate(self, integrator_type):
from dials.algorithms.integration.integrator import IntegratorFactory
from dials.algorithms.integration.integrator import phil_scope as master_phil_scope
from libtbx.phil import parse
import sys
import StringIO
rlist = self.rlist.copy()
output = StringIO.StringIO()
stdout = sys.stdout
sys.stdout = output
try:
phil_scope = parse('''
integration.background.algorithm=null
integration.intensity.algorithm=sum
integration.intensity.sum.integrator=%s
integration.block.size=0.5
integration.profile_fitting=False
''' % integrator_type)
params = master_phil_scope.fetch(source=phil_scope).extract()
integrator = IntegratorFactory.create(
params,
self.exlist,
rlist)
result = integrator.integrate()
except Exception:
print output
raise
sys.stdout = stdout
return result
rlist = flex.reflection_table.from_predictions(experiments[0])
rlist["id"] = flex.int(len(rlist), 0)
rlist.compute_bbox(experiments, profile_model)
rlist.compute_zeta_multi(experiments)
rlist.compute_d(experiments)
print("")
print("Creating params")
from dials.algorithms.integration.integrator import IntegratorFactory
from dials.algorithms.integration.integrator import phil_scope
from libtbx import phil
user_phil = phil.parse("""
integration {
mp.max_procs = %d
block.size=5
filter.ice_rings.filter=False
intensity.algorithm=sum3d
}
""" % nproc)
working_phil = phil_scope.fetch(source=user_phil)
params = working_phil.extract()
print("Integrating")
integrator = IntegratorFactory.create(params, experiments, profile_model,
rlist)
result = integrator.integrate()
result.as_pickle("temp.pickle")
print "Predicting Reflections"
rlist = flex.reflection_table.from_predictions(experiments[0])
rlist['id'] = flex.int(len(rlist), 0)
rlist.compute_bbox(experiments, profile_model)
rlist.compute_zeta_multi(experiments)
rlist.compute_d(experiments)
print ""
print "Creating params"
from dials.algorithms.integration.integrator import IntegratorFactory
from dials.algorithms.integration.integrator import phil_scope
from libtbx import phil
user_phil = phil.parse('''
integration {
mp.max_procs = %d
block.size=5
filter.ice_rings.filter=False
intensity.algorithm=sum3d
}
''' % nproc)
working_phil = phil_scope.fetch(source=user_phil)
params = working_phil.extract()
print "Integrating"
integrator = IntegratorFactory.create(params, experiments, profile_model, rlist)
result = integrator.integrate()
result.as_pickle("temp.pickle")
