def run():
if os.path.exists('xia2-working.phil'):
sys.argv.append('xia2-working.phil')
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()
wd = os.getcwd()
try:
multi_crystal_analysis()
Chatter.write('Status: normal termination')
except Exception as e:
traceback.print_exc(file=open(os.path.join(wd, 'xia2.error'), 'w'))
Chatter.write('Status: error "%s"' % str(e))
Chatter.write(
'Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:'
)
Chatter.write('*****@*****.**')
sys.exit(1)
def run():
try:
check_environment()
except Exception as e:
with open("xia2-error.txt", "w") as fh:
traceback.print_exc(file=fh)
logger.info('Status: error "%s"', str(e))
if len(sys.argv) < 2 or "-help" in sys.argv:
help()
sys.exit()
wd = os.getcwd()
try:
# xia2_index()
from .xia2_main import xia2_main
xia2_main(stop_after="index")
logger.info("Status: normal termination")
except Exception as e:
with open(os.path.join(wd, "xia2-error.txt"), "w") as fh:
traceback.print_exc(file=fh)
logger.error('Status: error "%s"', str(e))
def run():
try:
check_environment()
except Exception as e:
with open("xia2.error", "w") as fh:
traceback.print_exc(file=fh)
Chatter.write('Status: error "%s"' % str(e))
sys.exit(1)
if len(sys.argv) < 2 or "-help" in sys.argv:
help()
sys.exit()
wd = os.getcwd()
try:
from xia2.command_line.xia2_main import xia2_main
xia2_main(stop_after="integrate")
Chatter.write("Status: normal termination")
except Exception as e:
with open(os.path.join(wd, "xia2.error"), "w") as fh:
traceback.print_exc(file=fh)
Chatter.write('Status: error "%s"' % str(e))
sys.exit(1)
def run():
if os.path.exists("xia2-working.phil"):
sys.argv.append("xia2-working.phil")
try:
check_environment()
except Exception as e:
traceback.print_exc(file=open("xia2.error", "w"))
Chatter.write('Status: error "%s"' % str(e))
# print the version
Chatter.write(Version)
Citations.cite("xia2")
start_time = time.time()
assert os.path.exists("xia2.json")
from xia2.Schema.XProject import XProject
xinfo = XProject.from_json(filename="xia2.json")
crystals = xinfo.get_crystals()
for crystal_id, crystal in crystals.iteritems():
# cwd = os.path.abspath(os.curdir)
from libtbx import Auto
scale_dir = PhilIndex.params.xia2.settings.scale.directory
if scale_dir is Auto:
scale_dir = "scale"
i = 0
while os.path.exists(os.path.join(crystal.get_name(), scale_dir)):
i += 1
scale_dir = "scale%i" % i
PhilIndex.params.xia2.settings.scale.directory = scale_dir
working_directory = Environment.generate_directory(
[crystal.get_name(), scale_dir])
# os.chdir(working_directory)
crystals[crystal_id]._scaler = None # reset scaler
scaler = crystal._get_scaler()
Chatter.write(xinfo.get_output())
crystal.serialize()
duration = time.time() - start_time
# write out the time taken in a human readable way
Chatter.write("Processing took %s" %
time.strftime("%Hh %Mm %Ss", time.gmtime(duration)))
# delete all of the temporary mtz files...
cleanup()
write_citations()
xinfo.as_json(filename="xia2.json")
Environment.cleanup()
def run():
if os.path.exists("xia2-working.phil"):
sys.argv.append("xia2-working.phil")
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))
# print the version
logger.info(Version)
Citations.cite("xia2")
start_time = time.time()
assert os.path.exists("xia2.json")
from xia2.Schema.XProject import XProject
xinfo = XProject.from_json(filename="xia2.json")
with cleanup(xinfo.path):
crystals = xinfo.get_crystals()
for crystal_id, crystal in crystals.items():
scale_dir = PhilIndex.params.xia2.settings.scale.directory
if scale_dir is Auto:
scale_dir = "scale"
i = 0
while os.path.exists(os.path.join(crystal.get_name(), scale_dir)):
i += 1
scale_dir = "scale%i" % i
PhilIndex.params.xia2.settings.scale.directory = scale_dir
# reset scaler
crystals[crystal_id]._scaler = None
crystal._get_scaler()
logger.info(xinfo.get_output())
crystal.serialize()
duration = time.time() - start_time
# write out the time taken in a human readable way
logger.info(
"Processing took %s", time.strftime("%Hh %Mm %Ss", time.gmtime(duration))
)
write_citations()
xinfo.as_json(filename="xia2.json")
def run():
if len(sys.argv) < 2 or "-help" in sys.argv or "--help" in sys.argv:
help()
sys.exit()
if "-version" in sys.argv or "--version" in sys.argv:
print(xia2.XIA2Version.Version)
print(dials_version())
ccp4_version = get_ccp4_version()
if ccp4_version:
print("CCP4 %s" % ccp4_version)
sys.exit()
xia2.Handlers.Streams.setup_logging(logfile="xia2.txt",
debugfile="xia2-debug.txt")
try:
check_environment()
except Exception as e:
traceback.print_exc(file=open("xia2-error.txt", "w"))
logger.debug(traceback.format_exc())
logger.error("Error setting up xia2 environment: %s" % str(e))
logger.warning(
"Please send the contents of xia2.txt, xia2-error.txt and xia2-debug.txt to:"
)
logger.warning("*****@*****.**")
sys.exit(1)
wd = os.getcwd()
try:
xia2_main()
logger.debug("\nTiming report:")
logger.debug("\n".join(xia2.Driver.timing.report()))
logger.info("Status: normal termination")
return
except Sorry as s:
logger.error("Error: %s", str(s))
sys.exit(1)
except Exception as e:
with open(os.path.join(wd, "xia2-error.txt"), "w") as fh:
traceback.print_exc(file=fh)
logger.debug(traceback.format_exc())
logger.error("Error: %s", str(e))
logger.warning(
"Please send the contents of xia2.txt, xia2-error.txt and xia2-debug.txt to:"
)
logger.warning("*****@*****.**")
sys.exit(1)
def run():
from libtbx.utils import Sorry
if len(sys.argv) < 2 or '-help' in sys.argv or '--help' in sys.argv:
help()
sys.exit()
if '-version' in sys.argv or '--version' in sys.argv:
import xia2.XIA2Version
print xia2.XIA2Version.Version
print dials_version()
ccp4_version = get_ccp4_version()
if ccp4_version is not None:
print 'CCP4 %s' % ccp4_version
sys.exit()
try:
check_environment()
except Exception as e:
traceback.print_exc(file=open('xia2.error', 'w'))
Chatter.write('Error setting up xia2 environment: %s' % str(e))
Chatter.write(
'Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:'
)
Chatter.write('*****@*****.**')
sys.exit(1)
wd = os.getcwd()
try:
xinfo = xia2_main()
Chatter.write('Status: normal termination')
Debug.write('\n------\nTiming summary:')
import xia2.Driver.DefaultDriver
xia2.Driver.DefaultDriver.output_timing_information()
return xinfo
except Sorry as s:
Chatter.write('Error: %s' % str(s))
sys.exit(1)
except Exception as e:
traceback.print_exc(file=open(os.path.join(wd, 'xia2.error'), 'w'))
Chatter.write('Error: %s' % str(e))
Chatter.write(
'Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:'
)
Chatter.write('*****@*****.**')
sys.exit(1)
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()
wd = os.getcwd()
try:
from xia2.command_line.xia2_main import xia2_main
xia2_main(stop_after='integrate')
Chatter.write('Status: normal termination')
except Exception as e:
traceback.print_exc(file = open(os.path.join(wd, 'xia2.error'), 'w'))
Chatter.write('Status: error "%s"' % str(e))
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)
def run():
if len(sys.argv) < 2 or "-help" in sys.argv or "--help" in sys.argv:
help()
sys.exit()
if "-version" in sys.argv or "--version" in sys.argv:
print(xia2.XIA2Version.Version)
print(dials_version())
ccp4_version = get_ccp4_version()
if ccp4_version is not None:
print("CCP4 %s" % ccp4_version)
sys.exit()
xia2.Handlers.Streams.setup_logging(logfile="xia2.txt", debugfile="xia2-debug.txt")
xia2.Handlers.Streams.reconfigure_streams_to_logging()
try:
check_environment()
except Exception as e:
traceback.print_exc(file=open("xia2.error", "w"))
Debug.write(traceback.format_exc(), strip=False)
Chatter.write("Error setting up xia2 environment: %s" % str(e))
Chatter.write(
"Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:"
)
Chatter.write("*****@*****.**")
sys.exit(1)
wd = os.getcwd()
# Temporarily patch os.chdir() to help identify source of #214
origpid = os.getpid()
origchdir = os.chdir
def chdir_override(arg):
if os.getpid() != origpid:
return origchdir(arg)
# Try to determine the name of the calling module.
# Use exception trick to pick up the current frame.
try:
raise Exception()
except Exception:
f = sys.exc_info()[2].tb_frame.f_back
Debug.write(
"Directory change to %r in %s:%d" % (arg, f.f_code.co_filename, f.f_lineno)
)
return origchdir(arg)
os.chdir = chdir_override
try:
xia2_main()
Debug.write("\nTiming report:")
for line in xia2.Driver.timing.report():
Debug.write(line, strip=False)
Chatter.write("Status: normal termination")
return
except Sorry as s:
Chatter.write("Error: %s" % str(s))
sys.exit(1)
except Exception as e:
traceback.print_exc(file=open(os.path.join(wd, "xia2.error"), "w"))
Debug.write(traceback.format_exc(), strip=False)
Chatter.write("Error: %s" % str(e))
Chatter.write(
"Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:"
)
Chatter.write("*****@*****.**")
sys.exit(1)
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():
from libtbx.utils import Sorry
if len(sys.argv) < 2 or '-help' in sys.argv or '--help' in sys.argv:
help()
sys.exit()
if '-version' in sys.argv or '--version' in sys.argv:
import xia2.XIA2Version
print(xia2.XIA2Version.Version)
print(dials_version())
ccp4_version = get_ccp4_version()
if ccp4_version is not None:
print('CCP4 %s' % ccp4_version)
sys.exit()
try:
check_environment()
except Exception as e:
traceback.print_exc(file=open('xia2.error', 'w'))
Chatter.write('Error setting up xia2 environment: %s' % str(e))
Chatter.write(
'Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:'
)
Chatter.write('*****@*****.**')
sys.exit(1)
wd = os.getcwd()
# Temporarily patch os.chdir() to help identify source of #214
pid = os.getpid()
origchdir = os.chdir
def chdir_override(arg):
if os.getpid() != pid:
return origchdir(arg)
# Try to determine the name of the calling module.
# Use exception trick to pick up the current frame.
try:
raise Exception()
except Exception:
f = sys.exc_info()[2].tb_frame.f_back
Debug.write('Directory change to %r in %s:%d' %
(arg, f.f_code.co_filename, f.f_lineno))
return origchdir(arg)
os.chdir = chdir_override
try:
xinfo = xia2_main()
Chatter.write('Status: normal termination')
Debug.write('\n------\nTiming summary:')
import xia2.Driver.DefaultDriver
xia2.Driver.DefaultDriver.output_timing_information()
return xinfo
except Sorry as s:
Chatter.write('Error: %s' % str(s))
sys.exit(1)
except Exception as e:
traceback.print_exc(file=open(os.path.join(wd, 'xia2.error'), 'w'))
Chatter.write('Error: %s' % str(e))
Chatter.write(
'Please send the contents of xia2.txt, xia2.error and xia2-debug.txt to:'
)
Chatter.write('*****@*****.**')
sys.exit(1)
