def __init__(self,
iparams,
write_pickle=True,
write_logs=True,
last_stage='integrate'):
''' Constructor
:param iparams: IOTA params
:param write_pickle: Set to True to write out an integration pickle
'''
self.iparams = iparams
self.write_pickle = write_pickle
self.write_logs = write_logs
self.last_stage = last_stage
self.dlog_bookmark = 0
# Get Processor PHIL and initialize Processor
if self.iparams.cctbx_xfel.target:
with open(self.iparams.cctbx_xfel.target, 'r') as tf:
tphil_string = tf.read()
tparams = phil_scope.fetch(source=parse(tphil_string)).extract()
else:
tparams = phil_scope.extract()
Processor.__init__(self, params=tparams)
# IOTA-specific settings from here
# Turn off all peripheral output
self.params.output.experiments_filename = None
self.params.output.indexed_filename = None
self.params.output.strong_filename = None
self.params.output.refined_experiments_filename = None
self.params.output.integrated_experiments_filename = None
self.params.output.integrated_filename = None
self.params.output.profile_filename = None
# Set customized parameters
beamX = self.iparams.image_import.beam_center.x
beamY = self.iparams.image_import.beam_center.y
if beamX != 0 or beamY != 0:
self.params.geometry.detector.slow_fast_beam_centre = '{} {}'.format(
beamY, beamX)
if self.iparams.image_import.distance != 0:
self.params.geometry.detector.distance = self.iparams.image_import.distance
if self.iparams.image_import.mask is not None:
self.params.spotfinder.lookup.mask = self.iparams.image_import.mask
self.params.integration.lookup.mask = self.iparams.image_import.mask
if self.iparams.cctbx_xfel.target_space_group is not None:
sg = self.iparams.cctbx_xfel.target_space_group
self.params.indexing.known_symmetry.space_group = sg
if self.iparams.cctbx_xfel.target_unit_cell is not None:
uc = self.iparams.cctbx_xfel.target_unit_cell
self.params.indexing.known_symmetry.unit_cell = uc
if not self.params.indexing.stills.method_list:
self.params.indexing.stills.method_list = [
'fft1d', 'real_space_grid_search'
]
if self.iparams.cctbx_xfel.use_fft3d:
self.params.indexing.stills.method_list.insert(2, 'fft3d')
if self.iparams.cctbx_xfel.significance_filter.flag_on:
sigma = self.iparams.cctbx_xfel.significance_filter.sigma
sigma = sigma if sigma else 1
self.params.significance_filter.enable = True
self.params.significance_filter.isigi_cutoff = sigma
# Load reference geometry
self.reference_detector = None
if self.iparams.advanced.reference_geometry:
from dxtbx.model.experiment_list import ExperimentListFactory
try:
ref_experiments = ExperimentListFactory.from_json_file(
str(self.iparams.advanced.reference_geometry),
check_format=False)
except Exception as e:
print('DEBUG: Could not make exp. list because: ', e)
try:
import dxtbx
img = dxtbx.load(
str(self.iparams.advanced.reference_geometry))
except Exception:
print("DEBUG: Couldn't load geometry file {}"
"".format(self.iparams.advanced.reference_geometry))
else:
self.reference_detector = img.get_detector()
else:
assert len(ref_experiments.detectors()) == 1
self.reference_detector = ref_experiments.detectors()[0]
def __init__(self, params, write_pickle=True):
self.phil = params
self.write_pickle = write_pickle
Processor.__init__(self, params=params)