def xia2_main(stop_after=None):
'''Actually process something...'''
Citations.cite('xia2')
# print versions of related software
from dials.util.version import dials_version
Chatter.write(dials_version())
start_time = time.time()
CommandLine = get_command_line()
start_dir = Flags.get_starting_directory()
# check that something useful has been assigned for processing...
xtals = CommandLine.get_xinfo().get_crystals()
no_images = True
for name in xtals.keys():
xtal = xtals[name]
if not xtal.get_all_image_names():
Chatter.write('-----------------------------------' + \
'-' * len(name))
Chatter.write('| No images assigned for crystal %s |' % name)
Chatter.write('-----------------------------------' + '-' \
* len(name))
else:
no_images = False
args = []
from xia2.Handlers.Phil import PhilIndex
params = PhilIndex.get_python_object()
mp_params = params.xia2.settings.multiprocessing
njob = mp_params.njob
from libtbx import group_args
xinfo = CommandLine.get_xinfo()
if os.path.exists('xia2.json'):
from xia2.Schema.XProject import XProject
xinfo_new = xinfo
xinfo = XProject.from_json(filename='xia2.json')
crystals = xinfo.get_crystals()
crystals_new = xinfo_new.get_crystals()
for crystal_id in crystals_new.keys():
if crystal_id not in crystals:
crystals[crystal_id] = crystals_new[crystal_id]
continue
crystals[crystal_id]._scaler = None # reset scaler
for wavelength_id in crystals_new[crystal_id].get_wavelength_names():
wavelength_new = crystals_new[crystal_id].get_xwavelength(wavelength_id)
if wavelength_id not in crystals[crystal_id].get_wavelength_names():
crystals[crystal_id].add_wavelength(
crystals_new[crystal_id].get_xwavelength(wavelength_new))
continue
wavelength = crystals[crystal_id].get_xwavelength(wavelength_id)
sweeps_new = wavelength_new.get_sweeps()
sweeps = wavelength.get_sweeps()
sweep_names = [s.get_name() for s in sweeps]
sweep_keys = [
(s.get_directory(), s.get_template(), s.get_image_range())
for s in sweeps]
for sweep in sweeps_new:
if ((sweep.get_directory(), sweep.get_template(),
sweep.get_image_range()) not in sweep_keys):
if sweep.get_name() in sweep_names:
i = 1
while 'SWEEEP%i' %i in sweep_names:
i += 1
sweep._name = 'SWEEP%i' %i
break
wavelength.add_sweep(
name=sweep.get_name(),
directory=sweep.get_directory(),
image=sweep.get_image(),
beam=sweep.get_beam_centre(),
reversephi=sweep.get_reversephi(),
distance=sweep.get_distance(),
gain=sweep.get_gain(),
dmin=sweep.get_resolution_high(),
dmax=sweep.get_resolution_low(),
polarization=sweep.get_polarization(),
frames_to_process=sweep.get_frames_to_process(),
user_lattice=sweep.get_user_lattice(),
user_cell=sweep.get_user_cell(),
epoch=sweep._epoch,
ice=sweep._ice,
excluded_regions=sweep._excluded_regions,
)
sweep_names.append(sweep.get_name())
crystals = xinfo.get_crystals()
failover = params.xia2.settings.failover
if njob > 1:
driver_type = mp_params.type
command_line_args = CommandLine.get_argv()[1:]
for crystal_id in crystals.keys():
for wavelength_id in crystals[crystal_id].get_wavelength_names():
wavelength = crystals[crystal_id].get_xwavelength(wavelength_id)
sweeps = wavelength.get_sweeps()
for sweep in sweeps:
sweep._get_indexer()
sweep._get_refiner()
sweep._get_integrater()
args.append((
group_args(
driver_type=driver_type,
stop_after=stop_after,
failover=failover,
command_line_args=command_line_args,
nproc=mp_params.nproc,
crystal_id=crystal_id,
wavelength_id=wavelength_id,
sweep_id=sweep.get_name(),
),))
from xia2.Driver.DriverFactory import DriverFactory
default_driver_type = DriverFactory.get_driver_type()
# run every nth job on the current computer (no need to submit to qsub)
for i_job, arg in enumerate(args):
if (i_job % njob) == 0:
arg[0].driver_type = default_driver_type
if mp_params.type == "qsub":
method = "sge"
else:
method = "multiprocessing"
nproc = mp_params.nproc
qsub_command = mp_params.qsub_command
if not qsub_command:
qsub_command = 'qsub'
qsub_command = '%s -V -cwd -pe smp %d' %(qsub_command, nproc)
from libtbx import easy_mp
results = easy_mp.parallel_map(
process_one_sweep, args, processes=njob,
#method=method,
method="multiprocessing",
qsub_command=qsub_command,
preserve_order=True,
preserve_exception_message=True)
# Hack to update sweep with the serialized indexers/refiners/integraters
i_sweep = 0
for crystal_id in crystals.keys():
for wavelength_id in crystals[crystal_id].get_wavelength_names():
wavelength = crystals[crystal_id].get_xwavelength(wavelength_id)
remove_sweeps = []
sweeps = wavelength.get_sweeps()
for sweep in sweeps:
success, output, xsweep_dict = results[i_sweep]
assert xsweep_dict is not None
if output is not None:
Chatter.write(output)
if not success:
Chatter.write('Sweep failed: removing %s' %sweep.get_name())
remove_sweeps.append(sweep)
else:
Chatter.write('Loading sweep: %s' % sweep.get_name())
from xia2.Schema.XSweep import XSweep
new_sweep = XSweep.from_dict(xsweep_dict)
sweep._indexer = new_sweep._indexer
sweep._refiner = new_sweep._refiner
sweep._integrater = new_sweep._integrater
i_sweep += 1
for sweep in remove_sweeps:
wavelength.remove_sweep(sweep)
sample = sweep.get_xsample()
sample.remove_sweep(sweep)
else:
for crystal_id in crystals.keys():
for wavelength_id in crystals[crystal_id].get_wavelength_names():
wavelength = crystals[crystal_id].get_xwavelength(wavelength_id)
remove_sweeps = []
sweeps = wavelength.get_sweeps()
for sweep in sweeps:
try:
if stop_after == 'index':
sweep.get_indexer_cell()
else:
sweep.get_integrater_intensities()
sweep.serialize()
except Exception, e:
if failover:
Chatter.write('Processing sweep %s failed: %s' % \
(sweep.get_name(), str(e)))
remove_sweeps.append(sweep)
else:
raise
for sweep in remove_sweeps:
wavelength.remove_sweep(sweep)
sample = sweep.get_xsample()
sample.remove_sweep(sweep)
help()
sys.exit()
cwd = os.getcwd()
try:
from xia2_main import xia2_main
xia2_main(stop_after='integrate')
Chatter.write('Status: normal termination')
wd = os.path.join(cwd, 'strategy')
if not os.path.exists(wd):
os.mkdir(wd)
os.chdir(wd)
CommandLine = get_command_line()
xinfo = CommandLine.get_xinfo()
crystals = xinfo.get_crystals()
assert len(crystals) == 1
crystal = crystals.values()[0]
assert len(crystal.get_wavelength_names()) == 1
wavelength = crystal.get_xwavelength(crystal.get_wavelength_names()[0])
sweeps = wavelength.get_sweeps()
from xia2.Handlers.Phil import PhilIndex
params = PhilIndex.get_python_object()
strategy_params = params.strategy
if not len(strategy_params):
strategy_params = [PhilIndex.get_scope_by_name('strategy')[0].extract()]