def _integrate_finish(self):
'''Finish off the integration by running dials.export.'''
# FIXME - do we want to export every time we call this method
# (the file will not have changed) and also (more important) do
# we want a different exported MTZ file every time (I do not think
# that we do; these can be very large) - was exporter.get_xpid() ->
# now dials
exporter = self.ExportMtz()
exporter.set_reflections_filename(self._intgr_integrated_pickle)
mtz_filename = os.path.join(self.get_working_directory(),
'%s_integrated.mtz' % 'dials')
exporter.set_mtz_filename(mtz_filename)
exporter.run()
self._intgr_integrated_filename = mtz_filename
# record integrated MTZ file for e.g. BLEND.
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
'%s %s %s %s INTEGRATE' % (pname, xname, dname, sweep),
mtz_filename)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(
self._intgr_integrated_filename).as_miller_arrays()
# look for profile-fitted intensities
intensities = [
ma for ma in miller_arrays
if ma.info().labels == ['IPR', 'SIGIPR']
]
if len(intensities) == 0:
# look instead for summation-integrated intensities
intensities = [
ma for ma in miller_arrays
if ma.info().labels == ['I', 'SIGI']
]
assert len(intensities)
self._intgr_n_ref = intensities[0].size()
if not os.path.isfile(self._intgr_integrated_filename):
raise RuntimeError("dials.export failed: %s does not exist." %
self._intgr_integrated_filename)
if self._intgr_reindex_operator is None and \
self._intgr_spacegroup_number == lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice()):
Debug.write('Not reindexing to spacegroup %d (%s)' % \
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return mtz_filename
if self._intgr_reindex_operator is None and \
self._intgr_spacegroup_number == 0:
Debug.write('Not reindexing to spacegroup %d (%s)' % \
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return mtz_filename
Debug.write('Reindexing to spacegroup %d (%s)' % \
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
hklin = mtz_filename
reindex = Reindex()
reindex.set_working_directory(self.get_working_directory())
auto_logfiler(reindex)
reindex.set_operator(self._intgr_reindex_operator)
if self._intgr_spacegroup_number:
reindex.set_spacegroup(self._intgr_spacegroup_number)
else:
reindex.set_spacegroup(
lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice()))
hklout = '%s_reindex.mtz' % hklin[:-4]
reindex.set_hklin(hklin)
reindex.set_hklout(hklout)
reindex.reindex()
self._intgr_integrated_filename = hklout
self._intgr_cell = reindex.get_cell()
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
'%s %s %s %s experiments' % (pname, xname, dname, sweep),
self.get_integrated_experiments())
return hklout
def _integrate_finish(self):
'''Finish off the integration by running dials.export.'''
# FIXME - do we want to export every time we call this method
# (the file will not have changed) and also (more important) do
# we want a different exported MTZ file every time (I do not think
# that we do; these can be very large) - was exporter.get_xpid() ->
# now dials
exporter = self.ExportMtz()
exporter.set_reflections_filename(self._intgr_integrated_pickle)
mtz_filename = os.path.join(
self.get_working_directory(), '%s_integrated.mtz' % 'dials')
exporter.set_mtz_filename(mtz_filename)
exporter.run()
self._intgr_integrated_filename = mtz_filename
# record integrated MTZ file for e.g. BLEND.
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
'%s %s %s %s INTEGRATE' % (pname, xname, dname, sweep), mtz_filename)
if not os.path.isfile(self._intgr_integrated_filename):
raise RuntimeError("dials.export failed: %s does not exist."
% self._intgr_integrated_filename)
if self._intgr_reindex_operator is None and \
self._intgr_spacegroup_number == lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice()):
Debug.write('Not reindexing to spacegroup %d (%s)' % \
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return mtz_filename
if self._intgr_reindex_operator is None and \
self._intgr_spacegroup_number == 0:
Debug.write('Not reindexing to spacegroup %d (%s)' % \
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return mtz_filename
Debug.write('Reindexing to spacegroup %d (%s)' % \
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
hklin = mtz_filename
reindex = Reindex()
reindex.set_working_directory(self.get_working_directory())
auto_logfiler(reindex)
reindex.set_operator(self._intgr_reindex_operator)
if self._intgr_spacegroup_number:
reindex.set_spacegroup(self._intgr_spacegroup_number)
else:
reindex.set_spacegroup(lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice()))
hklout = '%s_reindex.mtz' % hklin[:-4]
reindex.set_hklin(hklin)
reindex.set_hklout(hklout)
reindex.reindex()
self._intgr_integrated_filename = hklout
self._intgr_cell = reindex.get_cell()
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
'%s %s %s %s experiments' % (pname, xname, dname, sweep),
self.get_integrated_experiments())
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(hklout).as_miller_arrays()
# look for profile-fitted intensities
intensities = [ma for ma in miller_arrays
if ma.info().labels == ['IPR', 'SIGIPR']]
if len(intensities) == 0:
# look instead for summation-integrated intensities
intensities = [ma for ma in miller_arrays
if ma.info().labels == ['I', 'SIGI']]
assert len(intensities)
self._intgr_n_ref = intensities[0].size()
return hklout
def _integrate_finish(self):
"""Finish off the integration by running dials.export."""
# FIXME - do we want to export every time we call this method
# (the file will not have changed) and also (more important) do
# we want a different exported MTZ file every time (I do not think
# that we do; these can be very large) - was exporter.get_xpid() ->
# now dials
if self._output_format == "hkl":
exporter = self.ExportMtz()
exporter.set_reflections_filename(
self._intgr_integrated_reflections)
mtz_filename = os.path.join(self.get_working_directory(),
"%s_integrated.mtz" % "dials")
exporter.set_mtz_filename(mtz_filename)
exporter.run()
self._intgr_integrated_filename = mtz_filename
# record integrated MTZ file for e.g. BLEND.
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
"%s %s %s %s INTEGRATE" % (pname, xname, dname, sweep),
mtz_filename)
from iotbx.reflection_file_reader import any_reflection_file
miller_arrays = any_reflection_file(
self._intgr_integrated_filename).as_miller_arrays()
# look for profile-fitted intensities
intensities = [
ma for ma in miller_arrays
if ma.info().labels == ["IPR", "SIGIPR"]
]
if len(intensities) == 0:
# look instead for summation-integrated intensities
intensities = [
ma for ma in miller_arrays
if ma.info().labels == ["I", "SIGI"]
]
assert len(intensities)
self._intgr_n_ref = intensities[0].size()
if not os.path.isfile(self._intgr_integrated_filename):
raise RuntimeError("dials.export failed: %s does not exist." %
self._intgr_integrated_filename)
if (self._intgr_reindex_operator is None
and self._intgr_spacegroup_number == lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice())):
Debug.write("Not reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return mtz_filename
if (self._intgr_reindex_operator is None
and self._intgr_spacegroup_number == 0):
Debug.write("Not reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return mtz_filename
Debug.write(
"Reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number, self._intgr_reindex_operator))
hklin = mtz_filename
from xia2.Wrappers.CCP4.Reindex import Reindex
reindex = Reindex()
reindex.set_working_directory(self.get_working_directory())
auto_logfiler(reindex)
reindex.set_operator(self._intgr_reindex_operator)
if self._intgr_spacegroup_number:
reindex.set_spacegroup(self._intgr_spacegroup_number)
else:
reindex.set_spacegroup(
lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice()))
hklout = "%s_reindex.mtz" % hklin[:-4]
reindex.set_hklin(hklin)
reindex.set_hklout(hklout)
reindex.reindex()
self._intgr_integrated_filename = hklout
self._intgr_cell = reindex.get_cell()
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
"%s %s %s %s" % (pname, xname, dname, sweep),
self.get_integrated_experiments(),
)
FileHandler.record_more_data_file(
"%s %s %s %s" % (pname, xname, dname, sweep),
self.get_integrated_reflections(),
)
return hklout
elif self._output_format == "pickle":
if (self._intgr_reindex_operator is None
and self._intgr_spacegroup_number == lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice())):
Debug.write("Not reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return self._intgr_integrated_reflections
if (self._intgr_reindex_operator is None
and self._intgr_spacegroup_number == 0):
Debug.write("Not reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number,
self._intgr_reindex_operator))
return self._intgr_integrated_reflections
Debug.write(
"Reindexing to spacegroup %d (%s)" %
(self._intgr_spacegroup_number, self._intgr_reindex_operator))
from xia2.Wrappers.Dials.Reindex import Reindex
reindex = Reindex()
reindex.set_working_directory(self.get_working_directory())
auto_logfiler(reindex)
reindex.set_cb_op(self._intgr_reindex_operator)
if self._intgr_spacegroup_number:
reindex.set_space_group(self._intgr_spacegroup_number)
else:
reindex.set_space_group(
lattice_to_spacegroup(
self.get_integrater_refiner().get_refiner_lattice()))
reindex.set_experiments_filename(self.get_integrated_experiments())
reindex.set_indexed_filename(self.get_integrated_reflections())
reindex.run()
self._intgr_integrated_reflections = (
reindex.get_reindexed_reflections_filename())
self._intgr_integrated_filename = (
reindex.get_reindexed_reflections_filename())
self._intgr_experiments_filename = (
reindex.get_reindexed_experiments_filename())
pname, xname, dname = self.get_integrater_project_info()
sweep = self.get_integrater_sweep_name()
FileHandler.record_more_data_file(
"%s %s %s %s" % (pname, xname, dname, sweep),
self.get_integrated_experiments(),
)
FileHandler.record_more_data_file(
"%s %s %s %s" % (pname, xname, dname, sweep),
self.get_integrated_reflections(),
)
return None # this will be set to intgr_hklout - better to cause failure
