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 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'