def export_mtz(self, filename=None, params=None):
if params is None:
params = export_phil_scope.extract()
if filename is not None:
params.mtz.hklout = filename
m = export_mtz(
self._reflections,
self._experiments,
params.mtz.hklout,
include_partials=params.mtz.include_partials,
keep_partials=params.mtz.keep_partials,
scale_partials=params.mtz.scale_partials,
min_isigi=params.mtz.min_isigi,
force_static_model=params.mtz.force_static_model,
filter_ice_rings=params.mtz.filter_ice_rings,
ignore_profile_fitting=params.mtz.ignore_profile_fitting,
apply_scales=params.mtz.apply_scales)
m.show_summary()
b1 = set(b.num() for b in m.batches())
b2 = set(m.get_column('BATCH').extract_values().as_double().iround())
assert len(b2.difference(b1)) == 0
return params.mtz.hklout
def export_mtz(params, experiments, reflections):
"""
Export reflections in MTZ format
:param params: The phil parameters
:param experiments: The experiment list
:param reflections: The reflection tables
"""
_check_input(experiments, reflections)
from dials.util.export_mtz import export_mtz
# Handle case where user has passed data before integration
if ("intensity.sum.value" not in reflections[0]
or "intensity.prf.value" not in reflections[0]):
sys.exit(
"Error: No intensity data in reflections; cannot export un-integrated data to MTZ"
)
try:
m = export_mtz(reflections[0], experiments, params)
except ValueError as e:
sys.exit(e)
from six.moves import cStringIO as StringIO
summary = StringIO()
m.show_summary(out=summary)
logger.info("")
logger.info(summary.getvalue())
def export_mtz(params, experiments, reflections):
"""
Export reflections in MTZ format
:param params: The phil parameters
:param experiments: The experiment list
:param reflections: The reflection tables
"""
_check_input(experiments, reflections)
from dials.util.export_mtz import export_mtz
# Handle case where user has passed data before integration
if (
"intensity.sum.value" not in reflections[0]
or "intensity.prf.value" not in reflections[0]
):
raise ValueError(
"Error: No intensity data in reflections; cannot export un-integrated data to MTZ"
)
reflection_table = reflections[0]
filename = params.mtz.hklout
# if mtz filename is auto, then choose scaled.mtz or integrated.mtz
if filename in (None, Auto, "auto"):
if ("intensity.scale.value" in reflection_table) and (
"intensity.scale.variance" in reflection_table
):
filename = "scaled.mtz"
logger.info("Data appears to be scaled, setting mtz.hklout = 'scaled.mtz'")
else:
filename = "integrated.mtz"
logger.info(
"Data appears to be unscaled, setting mtz.hklout = 'integrated.mtz'"
)
m = export_mtz(
reflection_table,
experiments,
intensity_choice=params.intensity,
filename=filename,
best_unit_cell=params.mtz.best_unit_cell,
partiality_threshold=params.mtz.partiality_threshold,
combine_partials=params.mtz.combine_partials,
min_isigi=params.mtz.min_isigi,
filter_ice_rings=params.mtz.filter_ice_rings,
d_min=params.mtz.d_min,
force_static_model=params.mtz.force_static_model,
crystal_name=params.mtz.crystal_name,
project_name=params.mtz.project_name,
)
summary = StringIO()
m.show_summary(out=summary)
logger.info("")
logger.info(summary.getvalue())
def run(args):
from dials.util.nexus import load
from dials.util.export_mtz import export_mtz
import libtbx.load_env
from dials.util.options import OptionParser
usage = "%s hklin=hklin.nxs hklout=hklout.mtz [options]" % (libtbx.env.dispatcher_name)
parser = OptionParser(usage=usage, phil=phil_scope, epilog=help_message)
params, options = parser.parse_args(show_diff_phil=True)
# Load the experiments and reflections from the NXmx file
experiments, reflections = load(params.hklin)
# Export the experiments and reflections to the MTZ file
m = export_mtz(reflections, experiments, params.hklout, params.ignore_panels, params.include_partials)
m.show_summary()
def export(self):
"""
Export the files
"""
from dials.util.export_mtz import export_mtz
try:
m = export_mtz(self.reflections, self.experiments, self.params)
except ValueError as e:
raise Sorry(e)
from six.moves import cStringIO as StringIO
summary = StringIO()
m.show_summary(out=summary)
logger.info("")
logger.info(summary.getvalue())
def export(self):
'''
Export the files
'''
from dials.util.export_mtz import export_mtz
m = export_mtz(self.reflections,
self.experiments,
self.params.mtz.hklout,
ignore_panels=params.mtz.ignore_panels,
include_partials=params.mtz.include_partials,
keep_partials=params.mtz.keep_partials,
min_isigi=params.mtz.min_isigi,
force_static_model=params.mtz.force_static_model)
from cStringIO import StringIO
summary = StringIO()
m.show_summary(out=summary)
logger.info(summary.getvalue())
def run(args):
from dials.util.nexus import load
from dials.util.export_mtz import export_mtz
import libtbx.load_env
from dials.util.options import OptionParser
usage = '%s hklin=hklin.nxs hklout=hklout.mtz [options]' % (
libtbx.env.dispatcher_name)
parser = OptionParser(usage=usage, phil=phil_scope, epilog=help_message)
params, options = parser.parse_args(show_diff_phil=True)
# Load the experiments and reflections from the NXmx file
experiments, reflections = load(params.hklin)
# Export the experiments and reflections to the MTZ file
m = export_mtz(reflections, experiments, params.hklout,
params.ignore_panels, params.include_partials)
m.show_summary()
def export(self):
'''
Export the files
'''
from dials.util.export_mtz import export_mtz
m = export_mtz(
self.reflections,
self.experiments,
self.params.mtz.hklout,
ignore_panels=params.mtz.ignore_panels,
include_partials=params.mtz.include_partials,
keep_partials=params.mtz.keep_partials,
min_isigi=params.mtz.min_isigi,
force_static_model=params.mtz.force_static_model)
from cStringIO import StringIO
summary = StringIO()
m.show_summary(out=summary)
info(summary.getvalue())
def export_mtz(params, experiments, reflections):
"""
Export reflections in MTZ format
:param params: The phil parameters
:param experiments: The experiment list
:param reflections: The reflection tables
"""
_check_input(experiments, reflections)
from dials.util.export_mtz import export_mtz
try:
m = export_mtz(reflections[0], experiments, params)
except ValueError as e:
sys.exit(e)
from six.moves import cStringIO as StringIO
summary = StringIO()
m.show_summary(out=summary)
logger.info("")
logger.info(summary.getvalue())
