def __init__(self):
super(DialsIntegrater, self).__init__()
# check that the programs exist - this will raise an exception if
# they do not...
integrate = _Integrate()
# place to store working data
self._data_files = { }
# internal parameters to pass around
self._integrate_parameters = { }
self._intgr_integrated_filename = None
def Integrate(self, indexed_filename=None):
params = PhilIndex.params.dials.integrate
integrate = _Integrate()
integrate.set_phil_file(params.phil_file)
if PhilIndex.params.dials.fast_mode:
integrate.set_profile_fitting(False)
else:
profile_fitting = PhilIndex.params.xia2.settings.integration.profile_fitting
integrate.set_profile_fitting(profile_fitting)
integrate.set_background_outlier_algorithm(
params.background_outlier_algorithm)
integrate.set_background_algorithm(
params.background_algorithm)
integrate.set_working_directory(self.get_working_directory())
integrate.set_experiments_filename(self._intgr_experiments_filename)
integrate.set_reflections_filename(self._intgr_indexed_filename)
integrate.set_use_threading(params.use_threading)
auto_logfiler(integrate, 'INTEGRATE')
return integrate
