def run():
try:
check_environment()
except Exception as e:
traceback.print_exc(file=open('xia2.error', 'w'))
Chatter.write('Status: error "%s"' % str(e))
if len(sys.argv) < 2 or '-help' in sys.argv:
help()
sys.exit()
cwd = os.getcwd()
try:
from xia2.command_line.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()
]
from dxtbx.model import MultiAxisGoniometer
gonio = sweeps[0].get_imageset().get_goniometer()
if (isinstance(gonio, MultiAxisGoniometer)
and len(gonio.get_axes()) == 3 and gonio.get_scan_axis() == 2):
from xia2.Wrappers.Dials.AlignCrystal import AlignCrystal
align_crystal = AlignCrystal()
align_crystal.set_experiments_filename(
sweeps[0]._get_integrater().get_integrated_experiments())
align_crystal.set_working_directory(wd)
auto_logfiler(align_crystal)
align_crystal.set_json_filename('%i_align_crystal.json' %
align_crystal.get_xpid())
align_crystal.run()
Chatter.write("".join(align_crystal.get_all_output()))
results_all = {}
def process_one_strategy(args):
assert len(args) == 4
experiments, reflections, strategy, t_ref = args
from xia2.Wrappers.EMBL import Best
best = Best.BestStrategy()
for isweep, (expt, refl) in enumerate(zip(experiments,
reflections)):
integrater = sweep._get_integrater()
from xia2.Wrappers.Dials.ExportBest import ExportBest
export = ExportBest()
export.set_experiments_filename(expt)
export.set_reflections_filename(refl)
export.set_working_directory(wd)
auto_logfiler(export)
prefix = '%i_best' % export.get_xpid()
export.set_prefix(prefix)
export.run()
if isweep == 0:
imageset = sweep.get_imageset()
scan = imageset.get_scan()
best.set_t_ref(t_ref)
best.set_mos_dat('%s.dat' % prefix)
best.set_mos_par('%s.par' % prefix)
best.add_mos_hkl('%s.hkl' % prefix)
best.set_i2s(strategy.i_over_sigi)
best.set_T_max(strategy.max_total_exposure)
best.set_t_min(strategy.min_exposure)
#best.set_trans_ref(25.0)
best.set_S_max(strategy.max_rotation_speed)
best.set_w_min(strategy.min_oscillation_width)
best.set_M_min(strategy.multiplicity)
best.set_C_min(strategy.completeness)
best.set_GpS(strategy.dose_rate)
best.set_shape(strategy.shape)
best.set_susceptibility(strategy.susceptibility)
best.set_anomalous(strategy.anomalous)
best.set_detector('pilatus6m')
best.set_working_directory(wd)
auto_logfiler(best)
xmlout = '%s/%i_best.xml' % (best.get_working_directory(),
best.get_xpid())
best.set_xmlout(xmlout)
best.strategy()
results = best.get_results_dict()
results['description'] = strategy.description
if 'phi_end' not in results:
results['phi_end'] = str(
float(results['phi_start']) +
float(results['number_of_images']) *
float(results['phi_width']))
from dxtbx.serialize import load
expt = load.experiment_list(experiments[0])[0]
results['spacegroup'] = expt.crystal.get_space_group().type(
).lookup_symbol()
return results
args = []
for istrategy, strategy in enumerate(strategy_params):
imageset = sweeps[0].get_imageset()
scan = imageset.get_scan()
experiments = [
sweep._get_integrater().get_integrated_experiments()
for sweep in sweeps
]
reflections = [
sweep._get_integrater().get_integrated_reflections()
for sweep in sweeps
]
t_ref = scan.get_exposure_times()[0]
args.append((experiments, reflections, strategy, t_ref))
nproc = params.xia2.settings.multiprocessing.nproc
from libtbx import easy_mp
results = easy_mp.parallel_map(process_one_strategy,
args,
processes=nproc,
method='multiprocessing',
preserve_order=True,
preserve_exception_message=True)
for istrategy, (result,
strategy) in enumerate(zip(results, strategy_params)):
name = strategy.name
description = strategy.description
if name is None:
name = 'Strategy%i' % (istrategy + 1)
results_all[name] = result
multiplicity = result['redundancy']
try:
mutiplicity = '%.2f' % multiplicity
except TypeError:
pass
Chatter.write('Strategy %i' % istrategy)
if description is not None:
Chatter.write(description)
Chatter.write('Start / end / width: %.2f/%.2f/%.2f' %
(float(result['phi_start']), float(
result['phi_end']), float(result['phi_width'])))
Chatter.write(
'Completeness / multiplicity / resolution: %.2f/%s/%.2f' %
(float(result['completeness']), multiplicity,
float(result['resolution'])))
Chatter.write('Transmission / exposure %.3f/%.3f' % (float(
result['transmission']), float(result['exposure_time'])))
import json
with open('strategies.json', 'wb') as f:
json.dump(results_all, f, indent=2)
except Exception as e:
traceback.print_exc(file=open(os.path.join(cwd, 'xia2.error'), 'w'))
Chatter.write('Status: error "%s"' % str(e))
os.chdir(cwd)
def run():
try:
check_environment()
except Exception as e:
with open("xia2-error.txt", "w") as fh:
traceback.print_exc(file=fh)
logger.error('Status: error "%s"', str(e))
if len(sys.argv) < 2 or "-help" in sys.argv:
help()
sys.exit()
cwd = os.getcwd()
try:
from .xia2_main import xia2_main
xia2_main(stop_after="integrate")
logger.info("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 = list(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()
]
from dxtbx.model import MultiAxisGoniometer
gonio = sweeps[0].get_imageset().get_goniometer()
if (isinstance(gonio, MultiAxisGoniometer)
and len(gonio.get_axes()) == 3 and gonio.get_scan_axis() == 2):
from xia2.Wrappers.Dials.AlignCrystal import AlignCrystal
align_crystal = AlignCrystal()
align_crystal.set_experiments_filename(
sweeps[0]._get_integrater().get_integrated_experiments())
align_crystal.set_working_directory(wd)
auto_logfiler(align_crystal)
align_crystal.set_json_filename("%i_align_crystal.json" %
align_crystal.get_xpid())
align_crystal.run()
logger.info("".join(align_crystal.get_all_output()))
results_all = {}
def process_one_strategy(args):
assert len(args) == 4
experiments, reflections, strategy, t_ref = args
from xia2.Wrappers.EMBL import Best
best = Best.BestStrategy()
for isweep, (expt, refl) in enumerate(zip(experiments,
reflections)):
from xia2.Wrappers.Dials.ExportBest import ExportBest
export = ExportBest()
export.set_experiments_filename(expt)
export.set_reflections_filename(refl)
export.set_working_directory(wd)
auto_logfiler(export)
prefix = "%i_best" % export.get_xpid()
export.set_prefix(prefix)
export.run()
if isweep == 0:
best.set_t_ref(t_ref)
best.set_mos_dat("%s.dat" % prefix)
best.set_mos_par("%s.par" % prefix)
best.add_mos_hkl("%s.hkl" % prefix)
best.set_i2s(strategy.i_over_sigi)
best.set_T_max(strategy.max_total_exposure)
best.set_t_min(strategy.min_exposure)
# best.set_trans_ref(25.0)
best.set_S_max(strategy.max_rotation_speed)
best.set_w_min(strategy.min_oscillation_width)
best.set_M_min(strategy.multiplicity)
best.set_C_min(strategy.completeness)
best.set_GpS(strategy.dose_rate)
best.set_shape(strategy.shape)
best.set_susceptibility(strategy.susceptibility)
best.set_anomalous(strategy.anomalous)
best.set_detector("pilatus6m")
best.set_working_directory(wd)
auto_logfiler(best)
xmlout = os.path.join(best.get_working_directory(),
"%i_best.xml" % best.get_xpid())
best.set_xmlout(xmlout)
best.strategy()
results = best.get_results_dict()
results["description"] = strategy.description
if "phi_end" not in results:
results["phi_end"] = str(
float(results["phi_start"]) +
float(results["number_of_images"]) *
float(results["phi_width"]))
from dxtbx.serialize import load
expt = load.experiment_list(experiments[0])[0]
results["spacegroup"] = (
expt.crystal.get_space_group().type().lookup_symbol())
return results
args = []
for istrategy, strategy in enumerate(strategy_params):
imageset = sweeps[0].get_imageset()
scan = imageset.get_scan()
experiments = [
sweep._get_integrater().get_integrated_experiments()
for sweep in sweeps
]
reflections = [
sweep._get_integrater().get_integrated_reflections()
for sweep in sweeps
]
t_ref = scan.get_exposure_times()[0]
args.append((experiments, reflections, strategy, t_ref))
nproc = params.xia2.settings.multiprocessing.nproc
from libtbx import easy_mp
results = easy_mp.parallel_map(
process_one_strategy,
args,
processes=nproc,
method="multiprocessing",
preserve_order=True,
preserve_exception_message=True,
)
for istrategy, (result,
strategy) in enumerate(zip(results, strategy_params)):
name = strategy.name
description = strategy.description
if name is None:
name = "Strategy%i" % (istrategy + 1)
results_all[name] = result
multiplicity = result["redundancy"]
try:
multiplicity = "%.2f" % multiplicity
except TypeError:
pass
logger.info("Strategy %i", istrategy)
if description is not None:
logger.info(description)
logger.info(
"Start / end / width: %.2f/%.2f/%.2f",
float(result["phi_start"]),
float(result["phi_end"]),
float(result["phi_width"]),
)
logger.info(
"Completeness / multiplicity / resolution: %.2f/%s/%.2f",
float(result["completeness"]),
multiplicity,
float(result["resolution"]),
)
logger.info(
"Transmission / exposure %.3f/%.3f",
float(result["transmission"]),
float(result["exposure_time"]),
)
with open("strategies.json", "wb") as f:
json.dump(results_all, f, indent=2)
except Exception as e:
with open(os.path.join(cwd, "xia2-error.txt"), "w") as fh:
traceback.print_exc(file=fh)
logger.error('Status: error "%s"', str(e))
os.chdir(cwd)
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()]
from dxtbx.model import MultiAxisGoniometer
gonio = sweeps[0].get_imageset().get_goniometer()
if (isinstance(gonio, MultiAxisGoniometer) and
len(gonio.get_axes()) == 3 and gonio.get_scan_axis() == 2):
from xia2.Wrappers.Dials.AlignCrystal import AlignCrystal
align_crystal = AlignCrystal()
align_crystal.set_experiments_filename(
sweeps[0]._get_integrater().get_integrated_experiments())
align_crystal.set_working_directory(wd)
auto_logfiler(align_crystal)
align_crystal.set_json_filename(
'%i_align_crystal.json' %align_crystal.get_xpid())
align_crystal.run()
Chatter.write("".join(align_crystal.get_all_output()))