def __init__(self):
from dials.util.options import OptionParser
self.params = self.parser = None
if COMM.rank == 0:
self.parser = OptionParser(
usage="", # stage 1 (per-shot) diffBragg refinement",
sort_options=True,
phil=phil_scope,
read_experiments=True,
read_reflections=True,
check_format=False,
epilog="PyCuties")
self.params, _ = self.parser.parse_args(show_diff_phil=True)
assert self.params.outdir is not None
self.params = COMM.bcast(self.params)
if COMM.rank == 0:
if not os.path.exists(self.params.outdir):
utils.safe_makedirs(self.params.outdir)
COMM.barrier()
if self.params.logging.logname is None:
self.params.logging.logname = "main_stage1.log"
if self.params.profile_name is None:
self.params.profile_name = "prof_stage1.log"
from simtbx.diffBragg import mpi_logger
mpi_logger.setup_logging_from_params(self.params)
def __init__(self):
from dials.util.options import ArgumentParser
self.params = None
if COMM.rank == 0:
self.parser = ArgumentParser(
usage="", # stage 1 (per-shot) diffBragg refinement",
sort_options=True,
phil=phil_scope,
read_experiments=True,
read_reflections=True,
check_format=False,
epilog="PyCuties")
self.params, _ = self.parser.parse_args(show_diff_phil=True)
assert self.params.outdir is not None
utils.safe_makedirs(self.params.outdir)
ts = time.strftime("%Y%m%d-%H%M%S")
diff_phil_outname = os.path.join(self.params.outdir,
"diff_phil_run_at_%s.txt" % ts)
with open(diff_phil_outname, "w") as o:
o.write("command line:\n%s\n" % (" ".join(sys.argv)))
o.write("workding directory: \n%s\n" % os.getcwd())
o.write("diff phil:\n")
o.write(self.parser.diff_phil.as_str())
self.params = COMM.bcast(self.params)
if self.params.logging.logname is None:
self.params.logging.logname = "main_stage1.log"
if self.params.profile_name is None:
self.params.profile_name = "prof_stage1.log"
from simtbx.diffBragg import mpi_logger
mpi_logger.setup_logging_from_params(self.params)
lp.add_function(stage_two_refiner.StageTwoRefiner._mpi_aggregation)
lp.add_function(stage_two_refiner.StageTwoRefiner._setup)
lp.add_function(hopper_utils.DataModeler.GatherFromExperiment)
RUN = lp(script.run)
if script.params.outdir is None:
od = script.params.refiner.io.output_dir
script.params.outdir = od if od is not None else '.'
if script.params.logging.logname is None:
script.params.logging.logname = "main_stage2.log"
if script.params.profile_name is None:
script.params.profile_name = "prof_stage2.log"
if script.params.logging.disable:
logging.disable(
level=logging.CRITICAL) # disables CRITICAL and below
else:
mpi_logger.setup_logging_from_params(script.params)
RUN()
if lp is not None:
stats = lp.get_stats()
from simtbx.diffBragg import hopper_utils
hopper_utils.print_profile(stats, [
"launch_refiner", "_compute_functional_and_gradients",
"_run_diffBragg_current", "_update_Fcell", "_scale_pixel_data",
"_Fcell_derivatives", "_mpi_aggregation",
"GatherFromExperiment", "_setup"
])