def _get_integrater(self):
'''Get my integrater, and if it is not set, create one.'''
if self._integrater == None:
# set the working directory for this, based on the hierarchy
# defined herein...
# that would be CRYSTAL_ID/WAVELENGTH/SWEEP/index &c.
if not self.get_wavelength():
wavelength_id = "default"
crystal_id = "default"
project_id = "default"
else:
wavelength_id = self.get_wavelength().get_name()
crystal_id = self.get_wavelength().get_crystal().get_name()
project_id = self.get_wavelength().get_crystal().get_project().get_name()
working_directory = Environment.generate_directory(
[crystal_id, wavelength_id, self.get_name(), 'integrate'])
json_file = os.path.join(working_directory, 'xia2.json')
if (Flags.get_serialize_state() and
os.path.isdir(working_directory) and
os.path.isfile(json_file)):
self._integrater = IntegraterFactory.IntegraterForXSweep(
self, json_file=json_file)
else:
self._integrater = IntegraterFactory.IntegraterForXSweep(self)
# configure the integrater with the indexer - unless
# we don't want to...
self._integrater.set_integrater_refiner(self._get_refiner())
Debug.write('Integrater / refiner / indexer for sweep %s: %s/%s/%s' % \
(self._name, self._integrater.__class__.__name__,
self._get_refiner().__class__.__name__,
self._get_indexer().__class__.__name__))
# or if we have been told this on the command-line -
# N.B. should really add a mechanism to specify the ice
# rings we want removing, #1317.
if Flags.get_ice():
self._integrater.set_integrater_ice(Flags.get_ice())
# or if we were told about ice or specific excluded resolution
# ranges via the xinfo file
if self._ice:
self._integrater.set_integrater_ice(self._ice)
if len(self._excluded_regions) > 0:
self._integrater.set_integrater_excluded_regions(
self._excluded_regions)
self._integrater.set_integrater_project_info(
project_id, crystal_id, wavelength_id)
self._integrater.set_integrater_sweep_name(self._name)
# copy across anomalous flags in case it's useful - #871
self._integrater.set_integrater_anomalous(
self.get_wavelength().get_crystal().get_anomalous())
# see if we have any useful detector parameters to pass on
if self.get_gain():
self._integrater.set_gain(self.get_gain())
if self.get_polarization():
self._integrater.set_polarization(self.get_polarization())
# look to see if there are any global integration parameters
# we can set...
if global_integration_parameters.get_parameters(crystal_id):
Debug.write('Using integration parameters for crystal %s' \
% crystal_id)
self._integrater.set_integrater_parameters(
global_integration_parameters.get_parameters(crystal_id))
# frames to process...
if self._frames_to_process:
frames = self._frames_to_process
self._integrater.set_integrater_wedge(frames[0],
frames[1])
self._integrater.set_frame_wedge(frames[0],
frames[1])
self._integrater.set_integrater_epoch(
self.get_epoch(self._frames_to_process[0]))
self._integrater.set_working_directory(working_directory)
return self._integrater
def _get_refiner(self):
if self._refiner == None:
# set the working directory for this, based on the hierarchy
# defined herein...
# that would be CRYSTAL_ID/WAVELENGTH/SWEEP/index &c.
if not self.get_wavelength():
wavelength_id = "default"
crystal_id = "default"
else:
wavelength_id = self.get_wavelength().get_name()
crystal_id = self.get_wavelength().get_crystal().get_name()
working_directory = Environment.generate_directory(
[crystal_id, wavelength_id, self.get_name(), 'refine'])
json_file = None
if Flags.get_serialize_state() and os.path.isdir(working_directory):
json_file = os.path.join(working_directory, 'xia2.json')
if not os.path.isfile(json_file):
json_file = None
# FIXME the indexer factory should probably be able to
# take self [this object] as input, to help with deciding
# the most appropriate indexer to use... this will certainly
# be the case for the integrater. Maintaining this link
# will also help the system cope with updates (which
# was going to be one of the big problems...)
# 06/SEP/06 no keep these interfaces separate - want to
# keep "pure" interfaces to the programs for reuse, then
# wrap in XStyle.
self._refiner = RefinerFactory.RefinerForXSweep(
self, json_file=json_file)
## set the user supplied lattice if there is one
#if self._user_lattice:
#self._indexer.set_indexer_input_lattice(self._user_lattice)
#self._indexer.set_indexer_user_input_lattice(True)
## and also the cell constants - but only if lattice is
## assigned
#if self._user_cell:
#self._indexer.set_indexer_input_cell(self._user_cell)
#else:
#if self._user_cell:
#raise RuntimeError, 'cannot assign cell without lattice'
self._refiner.set_working_directory(working_directory)
#if self._frames_to_process:
#frames = self._frames_to_process
#self._refiner.set_frame_wedge(frames[0], frames[1])
#self._refiner.set_indexer_sweep_name(self._name)
self._refiner.add_refiner_indexer(
self.get_epoch(self._frames_to_process[0]), self._get_indexer())
return self._refiner
