def create_trial(self, d_min = 1.5, n_bins = 10, **kwargs):
# d_min and n_bins only used if isoforms are in this trial
trial = Trial(self, d_min = d_min, **kwargs)
if trial.target_phil_str is not None:
from iotbx.phil import parse
backend = ['labelit', 'dials'][['cxi.xtc_process', 'cctbx.xfel.xtc_process'].index(self.params.dispatcher)]
if backend == 'labelit':
from spotfinder.applications.xfel import cxi_phil
trial_params = cxi_phil.cxi_versioned_extract().persist.phil_scope.fetch(parse(trial.target_phil_str)).extract()
isoforms = trial_params.isoforms
elif backend == 'dials':
from xfel.command_line.xtc_process import phil_scope
trial_params = phil_scope.fetch(parse(trial.target_phil_str)).extract()
isoforms = trial_params.indexing.stills.isoforms
else:
assert False
if len(isoforms) > 0:
for isoform in isoforms:
print "Creating isoform", isoform.name
db_isoform = Isoform(self,
name = isoform.name,
trial_id = trial.id)
a, b, c, alpha, beta, gamma = isoform.cell.parameters()
cell = self.create_cell(cell_a = a, cell_b = b, cell_c = c,
cell_alpha = alpha, cell_beta = beta, cell_gamma = gamma,
lookup_symbol = isoform.lookup_symbol,
isoform_id = db_isoform.id)
from cctbx.crystal import symmetry
cs = symmetry(unit_cell = isoform.cell,space_group_symbol=str(isoform.lookup_symbol))
mset = cs.build_miller_set(anomalous_flag=False, d_min=d_min)
binner = mset.setup_binner(n_bins=n_bins)
for i in binner.range_used():
d_max, d_min = binner.bin_d_range(i)
Bin(self, number = i, d_min = d_min, d_max = d_max,
total_hkl = binner.counts_complete()[i], cell_id = cell.id)
elif backend == 'labelit':
pass # TODO: labelit target
elif backend == 'dials':
if trial_params.indexing.known_symmetry.unit_cell is not None and \
trial_params.indexing.known_symmetry.space_group is not None:
print "Creating target cell"
unit_cell = trial_params.indexing.known_symmetry.unit_cell
symbol = str(trial_params.indexing.known_symmetry.space_group)
a, b, c, alpha, beta, gamma = unit_cell.parameters()
cell = self.create_cell(cell_a = a, cell_b = b, cell_c = c,
cell_alpha = alpha, cell_beta = beta, cell_gamma = gamma,
lookup_symbol = symbol,
trial_id = trial.id)
from cctbx.crystal import symmetry
cs = symmetry(unit_cell = unit_cell, space_group_symbol = symbol)
mset = cs.build_miller_set(anomalous_flag=False, d_min=d_min)
binner = mset.setup_binner(n_bins=n_bins)
for i in binner.range_used():
d_max, d_min = binner.bin_d_range(i)
Bin(self, number = i, d_min = d_min, d_max = d_max,
total_hkl = binner.counts_complete()[i], cell_id = cell.id)
return trial
def get_trial(self, trial_id = None, trial_number = None):
assert [trial_id, trial_number].count(None) == 1
if trial_id is None:
trials = [t for t in self.get_all_trials() if t.trial == trial_number]
assert len(trials) == 1
return trials[0]
else:
return Trial(self, trial_id)
def __init__(self, params, composite_tag=None, rank=0):
super(DialsProcessorWithLogging,
self).__init__(params, composite_tag, rank)
self.tt_low = None
self.tt_high = None
if self.params.experiment_tag is None:
return
assert params.db.logging_batch_size >= 1
from libtbx.mpi4py import MPI
comm = MPI.COMM_WORLD
self.queries = []
self.rank = rank
if comm.size > 1:
if rank == 0:
db_app = dxtbx_xfel_db_application(params,
cache_connection=False,
mode='cache_commits')
run = db_app.get_run(run_number=self.params.input.run_num)
run_id = run.id
rund = run._db_dict
trial = db_app.get_trial(trial_number=params.input.trial)
trial_id = trial.id
triald = trial._db_dict
else:
db_app = None
run_id = None
rund = None
trial_id = None
triald = None
self.db_app, run_id, rund, trial_id, triald = comm.bcast(
(db_app, run_id, rund, trial_id, triald), root=0)
self.run = Run(self.db_app, run_id=run_id, **rund)
self.trial = Trial(self.db_app, trial_id=trial_id, **triald)
else:
self.db_app = dxtbx_xfel_db_application(params,
cache_connection=False,
mode='cache_commits')
self.run = self.db_app.get_run(
run_number=self.params.input.run_num)
self.trial = self.db_app.get_trial(trial_number=params.input.trial)
self.n_strong = None