def __init__(self, params = None): super(XDSInitWrapper, self).__init__() # phil parameters if not params: from xia2.Handlers.Phil import master_phil params = master_phil.extract().xds.init self._params = params # now set myself up... self.set_executable('xds') # generic bits self._data_range = (0, 0) self._spot_range = [] self._background_range = (0, 0) self._resolution_range = (0, 0) self._input_data_files = { } self._output_data_files = { } self._input_data_files_list = ['X-CORRECTIONS.cbf', 'Y-CORRECTIONS.cbf'] self._output_data_files_list = ['BKGINIT.cbf', 'BLANK.cbf', 'GAIN.cbf'] return
def __init__(self, params=None): super(XDSIntegrateWrapper, self).__init__() # phil parameters if not params: from xia2.Handlers.Phil import master_phil params = master_phil.extract().xds.integrate self._params = params # now set myself up... self._parallel = PhilIndex.params.xia2.settings.multiprocessing.nproc self.set_cpu_threads(self._parallel) if self._parallel <= 1: self.set_executable('xds') else: self.set_executable('xds_par') # generic bits self._data_range = (0, 0) self._input_data_files = { } self._output_data_files = { } self._input_data_files_list = ['X-CORRECTIONS.cbf', 'Y-CORRECTIONS.cbf', 'BLANK.cbf', 'BKGPIX.cbf', 'GAIN.cbf', 'XPARM.XDS'] self._output_data_files_list = ['FRAME.cbf'] self._refined_xparm = False self._updates = { } # note well - INTEGRATE.HKL is not included in this list # because it is likely to be very large - this is treated # separately... self._integrate_hkl = None # FIXME these will also be wanted by the full integrater # interface I guess? self._mean_mosaic = None self._min_mosaic = None self._max_mosaic = None return
def __init__(self, params=None): super(XDSColspotWrapper, self).__init__() # phil parameters if not params: from xia2.Handlers.Phil import master_phil params = master_phil.extract().xds.colspot self._params = params # now set myself up... self._parallel = Flags.get_parallel() self.set_cpu_threads(self._parallel) if self._parallel <= 1: self.set_executable('xds') else: self.set_executable('xds_par') # generic bits self._data_range = (0, 0) self._spot_range = [] self._background_range = (0, 0) self._resolution_range = (0, 0) self._input_data_files = { } self._output_data_files = { } self._input_data_files_list = ['X-CORRECTIONS.cbf', 'Y-CORRECTIONS.cbf', 'BLANK.cbf', 'BKGINIT.cbf', 'GAIN.cbf'] self._output_data_files_list = ['SPOT.XDS'] return
def __init__(self, params=None): super(Merge2cbfWrapper, self).__init__() # phil parameters if not params: from xia2.Handlers.Phil import master_phil params = master_phil.extract().xds.merge2cbf self._params = params # now set myself up... # I don't think there is a parallel version self.set_executable('merge2cbf') self._input_data_files = { } self._output_data_files = { } self._input_data_files_list = [] self._output_data_files_list = [] return
def __init__(self, params=None): super(XDSIdxrefWrapper, self).__init__() # phil parameters if not params: from xia2.Handlers.Phil import master_phil params = master_phil.extract().xds.index self._params = params # now set myself up... self._parallel = PhilIndex.params.xia2.settings.multiprocessing.nproc self.set_cpu_threads(self._parallel) if self._parallel <= 1: self.set_executable('xds') else: self.set_executable('xds_par') # generic bits self._data_range = (0, 0) self._spot_range = [] self._background_range = (0, 0) self._resolution_range = (0, 0) self._org = [0.0, 0.0] self._refined_origin = None self._refined_beam_vector = None self._refined_rotation_axis = None self._starting_angle = 0.0 self._starting_frame = 0 self._cell = None self._symm = 0 self._a_axis = None self._b_axis = None self._c_axis = None # results self._refined_beam = (0, 0) self._refined_distance = 0 self._indexing_solutions = { } self._indxr_input_lattice = None self._indxr_input_cell = None self._indxr_user_input_lattice = False self._indxr_lattice = None self._indxr_cell = None self._indxr_mosaic = None self._input_data_files = { } self._output_data_files = { } self._input_data_files_list = ['SPOT.XDS'] self._output_data_files_list = ['SPOT.XDS', 'XPARM.XDS'] self._index_tree_problem = False self._fraction_rmsd_rmsphi = None return
def __init__(self, params=None): super(XDSCorrectWrapper, self).__init__() # phil parameters if not params: from xia2.Handlers.Phil import master_phil params = master_phil.extract().xds.correct self._params = params # now set myself up... self._parallel = Flags.get_parallel() self.set_cpu_threads(self._parallel) if self._parallel <= 1: self.set_executable('xds') else: self.set_executable('xds_par') # generic bits self._data_range = (0, 0) self._spot_range = [] self._background_range = (0, 0) self._resolution_range = (0, 0) self._resolution_high = 0.0 self._resolution_low = 40.0 # specific information self._cell = None self._spacegroup_number = None self._anomalous = False self._polarization = 0.0 self._reindex_matrix = None self._reindex_used = None self._input_data_files = { } self._output_data_files = { } self._input_data_files_list = [] self._output_data_files_list = ['GXPARM.XDS'] self._ice = 0 self._excluded_regions = [] # the following input files are also required: # # INTEGRATE.HKL # REMOVE.HKL # # and XDS_ASCII.HKL is produced. # in self._integrate_hkl = None self._remove_hkl = None # out self._xds_ascii_hkl = None self._results = None self._remove = [] return
def __init__(self, params=None): super(XDSIdxrefWrapper, self).__init__() # phil parameters if not params: from xia2.Handlers.Phil import master_phil params = master_phil.extract().xds.index self._params = params # now set myself up... self._parallel = PhilIndex.params.xia2.settings.multiprocessing.nproc self.set_cpu_threads(self._parallel) if self._parallel <= 1: self.set_executable("xds") else: self.set_executable("xds_par") # generic bits self._data_range = (0, 0) self._spot_range = [] self._background_range = (0, 0) self._resolution_range = (0, 0) self._org = [0.0, 0.0] self._refined_origin = None self._refined_beam_vector = None self._refined_rotation_axis = None self._starting_angle = 0.0 self._starting_frame = 0 self._cell = None self._symm = 0 self._a_axis = None self._b_axis = None self._c_axis = None # results self._refined_beam = (0, 0) self._refined_distance = 0 self._indexing_solutions = {} self._indxr_input_lattice = None self._indxr_input_cell = None self._indxr_user_input_lattice = False self._indxr_lattice = None self._indxr_cell = None self._indxr_mosaic = None self._input_data_files = {} self._output_data_files = {} self._input_data_files_list = ["SPOT.XDS"] self._output_data_files_list = ["SPOT.XDS", "XPARM.XDS"] self._index_tree_problem = False self._fraction_rmsd_rmsphi = None