def Refine(self):
refine = _Refine()
params = PhilIndex.params.dials.refine
refine.set_phil_file(params.phil_file)
refine.set_working_directory(self.get_working_directory())
if PhilIndex.params.dials.fast_mode:
# scan-static refinement in fast mode
refine.set_scan_varying(False)
else:
refine.set_scan_varying(params.scan_varying)
refine.set_reflections_per_degree(params.reflections_per_degree)
refine.set_interval_width_degrees(params.interval_width_degrees)
refine.set_outlier_algorithm(PhilIndex.params.dials.outlier.algorithm)
if PhilIndex.params.dials.fix_geometry:
refine.set_detector_fix("all")
refine.set_beam_fix("all")
elif PhilIndex.params.dials.fix_distance:
refine.set_detector_fix("distance")
refine.set_close_to_spindle_cutoff(
PhilIndex.params.dials.close_to_spindle_cutoff)
# For multiple-sweep joint refinement, use the user's preferred restraints or
# default to restraining using `tie_to_group` with some reasonably tight sigmas.
if (PhilIndex.params.xia2.settings.multi_sweep_refinement
and not params.restraints.tie_to_group):
params.restraints.tie_to_group = (
restraints_scope.extract().restraints.tie_to_group)
# If the user hasn't specified otherwise, use default sigmas of 0.01.
params.restraints.tie_to_group[0].sigmas = 6 * (0.01, )
# Set any specified restraints for joint refinement of multiple sweeps.
refine.tie_to_target = params.restraints.tie_to_target
refine.tie_to_group = params.restraints.tie_to_group
auto_logfiler(refine, "REFINE")
return refine
def Refine(self):
refine = _Refine()
params = PhilIndex.params.dials
refine.set_working_directory(self.get_working_directory())
refine.set_scan_varying(False)
refine.set_outlier_algorithm(params.outlier.algorithm)
refine.set_close_to_spindle_cutoff(params.close_to_spindle_cutoff)
if params.fix_geometry:
refine.set_detector_fix("all")
refine.set_beam_fix("all")
auto_logfiler(refine)
return refine
def Refine(self):
refine = _Refine()
params = PhilIndex.params.dials.refine
refine.set_working_directory(self.get_working_directory())
refine.set_scan_varying(False)
refine.set_outlier_algorithm(PhilIndex.params.dials.outlier.algorithm)
refine.set_close_to_spindle_cutoff(
PhilIndex.params.dials.close_to_spindle_cutoff)
if PhilIndex.params.dials.fix_geometry:
refine.set_detector_fix('all')
refine.set_beam_fix('all')
auto_logfiler(refine)
return refine
def Refine(self):
refine = _Refine()
params = PhilIndex.params.dials.refine
refine.set_phil_file(params.phil_file)
refine.set_working_directory(self.get_working_directory())
if PhilIndex.params.dials.fast_mode:
# scan-static refinement in fast mode
refine.set_scan_varying(False)
else:
refine.set_scan_varying(params.scan_varying)
refine.set_reflections_per_degree(params.reflections_per_degree)
refine.set_interval_width_degrees(params.interval_width_degrees)
refine.set_outlier_algorithm(PhilIndex.params.dials.outlier.algorithm)
if PhilIndex.params.dials.fix_geometry:
refine.set_detector_fix('all')
refine.set_beam_fix('all')
refine.set_close_to_spindle_cutoff(
PhilIndex.params.dials.close_to_spindle_cutoff)
auto_logfiler(refine, 'REFINE')
return refine
def Refine(self):
refine = _Refine()
params = PhilIndex.params.dials.refine
refine.set_phil_file(params.phil_file)
refine.set_working_directory(self.get_working_directory())
if PhilIndex.params.dials.fast_mode:
# scan-static refinement in fast mode
refine.set_scan_varying(False)
else:
refine.set_scan_varying(params.scan_varying)
refine.set_reflections_per_degree(params.reflections_per_degree)
refine.set_interval_width_degrees(params.interval_width_degrees)
refine.set_outlier_algorithm(PhilIndex.params.dials.outlier.algorithm)
if PhilIndex.params.dials.fix_geometry:
refine.set_detector_fix('all')
refine.set_beam_fix('all')
refine.set_close_to_spindle_cutoff(
PhilIndex.params.dials.close_to_spindle_cutoff)
auto_logfiler(refine, 'REFINE')
return refine