def run_strategies(strategies):
# starting from scratch
observed_hkls = {}
total_score = 0.0
degrees = 0
from itertools import izip, count
for (run, strategy) in izip(count(1), strategies):
print
print "Sweep %d:" % run
evaluation_function = evaluation_function_factory(possible_hkl, observed_hkls, map_hkl_to_symmhkl, map_symmhkl_to_hkl)
goniometer = goniometer_factory.make_kappa_goniometer(alpha=54.7,
kappa=strategy['kappa'],
phi=strategy['phi'],
omega=strategy['omega'],
direction="-y",
scan_axis=strategy['scan_axis'])
degrees += strategy['scan']
from math import radians
if strategy['scan_axis'] == 'omega':
oscillation_range = (radians(strategy['omega']), radians(strategy['omega'] + strategy['scan']))
else:
oscillation_range = (radians(strategy['phi']), radians(strategy['phi'] + strategy['scan']))
# repeat sweep: expt.goniometer
proposed_hkls = calculate_observations(expt.detector, goniometer, oscillation_range)
strategy_results = evaluate_concrete_strategy(proposed_hkls, evaluation_function)
combined_observations = self.add_seen_multiplicity(observed_hkls, proposed_hkls)
num_observed_hkls = len(set([map_hkl_to_symmhkl[hkl] for hkl in combined_observations.keys()]))
count_hkl_observations = sum(combined_observations.values())
completeness = 100 * num_observed_hkls / completeness_limit
multiplicity = count_hkl_observations / num_observed_hkls
total_score += strategy_results['score']
print "Estimated total completeness: %5.1f %% total multiplicity : %.1f total score: %.1f" %\
(completeness, multiplicity, total_score)
# keep the repeat sweep and continue
observed_hkls = combined_observations
export_mtz(observed_hkls, expt, "mtzout.mtz")
return {'completeness': completeness, 'multiplicity': multiplicity, 'score': total_score, 'degrees': degrees}
def calculate_miller_rings(detector):
import time
t = time.clock()
mrings = {}
for scan_axis in ["phi", "omega"]:
mrings[scan_axis] = {}
for other_axis in range(0, 360, 10):
gonio = goniometer_factory.make_kappa_goniometer(
alpha=54.7356, # fixed magic angle
kappa=0, # fixed 0 kappa
phi=0 if scan_axis == "phi" else other_axis,
omega=0 if scan_axis == "omega" else other_axis,
direction="-y",
scan_axis=scan_axis,
)
ring = tools.determine_miller_ring_sectors(
detector, gonio, s0, possible_hkl_flex, crystal_A)
mrings[scan_axis][other_axis] = ring
print(time.clock() - t)
print(list(mrings.iterkeys()))
print([list(x.iterkeys()) for x in mrings.itervalues()])
t = time.clock()
sc = scorings
all_scorings = {
"%s:%s:%s" % (scan, str(x1), str(x2)): tools.geometric_scoring(
[hkl_to_id[hkl] for hkl in mrings[scan][x1][x2]],
sc)["total"]
for scan in mrings.iterkeys()
for x1 in mrings[scan].iterkeys() for x2 in range(0, 36)
}
# print list(all_scorings.itervalues())
print(
len(list(all_scorings.itervalues())),
min(all_scorings.itervalues()),
max(all_scorings.itervalues()),
sum(all_scorings.itervalues()) /
len(list(all_scorings.itervalues())),
)
print(time.clock() - t)
sys.exit(0)
def calculate_miller_rings(detector):
import time
t = time.clock()
mrings = {}
for scan_axis in ['phi', 'omega']:
mrings[scan_axis] = {}
for other_axis in range(0, 360, 10):
gonio = goniometer_factory.make_kappa_goniometer(alpha=54.7356, # fixed magic angle
kappa=0, # fixed 0 kappa
phi=0 if scan_axis == "phi" else other_axis,
omega=0 if scan_axis == "omega" else other_axis,
direction="-y",
scan_axis=scan_axis)
ring = tools.determine_miller_ring_sectors(detector, gonio, s0, possible_hkl_flex, crystal_A)
mrings[scan_axis][other_axis] = ring
print time.clock() - t
print list(mrings.iterkeys())
print [ list(x.iterkeys()) for x in mrings.itervalues() ]
def run_strategies(strategies):
# starting from scratch
observed_hkls = {}
total_score = 0.0
degrees = 0
from itertools import izip, count
for (run, strategy) in izip(count(1), strategies):
print()
print("Sweep %d:" % run)
evaluation_function = evaluation_function_factory(
possible_hkl, observed_hkls, map_hkl_to_symmhkl,
map_symmhkl_to_hkl)
goniometer = goniometer_factory.make_kappa_goniometer(
alpha=54.7,
kappa=strategy["kappa"],
phi=strategy["phi"],
omega=strategy["omega"],
direction="-y",
scan_axis=strategy["scan_axis"],
)
degrees += strategy["scan"]
from math import radians
if strategy["scan_axis"] == "omega":
oscillation_range = (
radians(strategy["omega"]),
radians(strategy["omega"] + strategy["scan"]),
)
else:
oscillation_range = (
radians(strategy["phi"]),
radians(strategy["phi"] + strategy["scan"]),
)
# repeat sweep: expt.goniometer
proposed_hkls = calculate_observations(expt.detector,
goniometer,
oscillation_range)
strategy_results = evaluate_concrete_strategy(
proposed_hkls, evaluation_function)
combined_observations = self.add_seen_multiplicity(
observed_hkls, proposed_hkls)
num_observed_hkls = len(
set([
map_hkl_to_symmhkl[hkl]
for hkl in combined_observations.keys()
]))
count_hkl_observations = sum(combined_observations.values())
completeness = 100 * num_observed_hkls / completeness_limit
multiplicity = count_hkl_observations / num_observed_hkls
total_score += strategy_results["score"]
print(
"Estimated total completeness: %5.1f %% total multiplicity : %.1f total score: %.1f"
% (completeness, multiplicity, total_score))
# keep the repeat sweep and continue
observed_hkls = combined_observations
export_mtz(observed_hkls, expt, "mtzout.mtz")
return {
"completeness": completeness,
"multiplicity": multiplicity,
"score": total_score,
"degrees": degrees,
}
