本文整理汇总了Python中xia2.Handlers.Streams.Chatter.smallbanner方法的典型用法代码示例。如果您正苦于以下问题：Python Chatter.smallbanner方法的具体用法？Python Chatter.smallbanner怎么用？Python Chatter.smallbanner使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类xia2.Handlers.Streams.Chatter的用法示例。
在下文中一共展示了Chatter.smallbanner方法的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Python代码示例。
示例1: load_sweeps_with_common_indexing
# 需要导入模块: from xia2.Handlers.Streams import Chatter [as 别名]
# 或者: from xia2.Handlers.Streams.Chatter import smallbanner [as 别名]
def load_sweeps_with_common_indexing():
assert os.path.exists('xia2.json')
from xia2.Schema.XProject import XProject
xinfo = XProject.from_json(filename='xia2.json')
import dials # required for gaussian_rs warning
from xia2.Wrappers.Dials.Reindex import Reindex
Citations.cite('dials')
from dxtbx.model.experiment.experiment_list import ExperimentListFactory
import cPickle as pickle
crystals = xinfo.get_crystals()
assert len(crystals) == 1
crystal = next(crystals.itervalues())
working_directory = Environment.generate_directory([crystal.get_name(), 'analysis'])
os.chdir(working_directory)
scaler = crystal._get_scaler()
epoch_to_batches = {}
epoch_to_integrated_intensities = {}
epoch_to_sweep_name = {}
# Aimless only
epochs = scaler._sweep_handler.get_epochs()
reference_cell = None
reference_lattice = None
reference_vectors = None
reference_wavelength = None
# Reindex each sweep to same setting
all_miller_indices = flex.miller_index()
all_two_thetas = flex.double()
for epoch in epochs:
si = scaler._sweep_handler.get_sweep_information(epoch)
Chatter.smallbanner(si.get_sweep_name(), True)
Debug.smallbanner(si.get_sweep_name(), True)
intgr = si.get_integrater()
experiments_filename = intgr.get_integrated_experiments()
reflections_filename = intgr.get_integrated_reflections()
refiner = intgr.get_integrater_refiner()
Debug.write('experiment: %s' % experiments_filename)
Debug.write('reflection: %s' % reflections_filename)
# Use setting of first sweep as reference
if reference_vectors is None:
reference_vectors = experiments_filename
# Assume that all sweeps have the same lattice system
if reference_lattice is None:
reference_lattice = refiner.get_refiner_lattice()
else:
assert reference_lattice == refiner.get_refiner_lattice()
Debug.write("lattice: %s" % refiner.get_refiner_lattice())
# Read .json file for sweep
db = ExperimentListFactory.from_json_file(experiments_filename)
# Assume that each file only contains a single experiment
assert (len(db) == 1)
db = db[0]
# Get beam vector
s0 = db.beam.get_unit_s0()
# Use the unit cell of the first sweep as reference
if reference_cell is None:
reference_cell = db.crystal.get_unit_cell()
Debug.write("Reference cell: %s" % str(reference_cell))
dials_reindex = Reindex()
dials_reindex.set_working_directory(working_directory)
dials_reindex.set_cb_op("auto")
dials_reindex.set_reference_filename(reference_vectors)
dials_reindex.set_experiments_filename(experiments_filename)
dials_reindex.set_indexed_filename(reflections_filename)
auto_logfiler(dials_reindex)
dials_reindex.run()
# Assume that all data are collected at same wavelength
if reference_wavelength is None:
reference_wavelength = intgr.get_wavelength()
else:
assert abs(reference_wavelength - intgr.get_wavelength()) < 0.01
Debug.write("wavelength: %f A" % intgr.get_wavelength())
Debug.write("distance: %f mm" % intgr.get_distance())
# Get integrated reflection data
import dials
with open(dials_reindex.get_reindexed_reflections_filename(), 'rb') as fh:
reflections = pickle.load(fh)
selection = reflections.get_flags(reflections.flags.used_in_refinement)
Chatter.write("Found %d reflections used in refinement (out of %d entries)" % (selection.count(True), len(reflections['miller_index'])))
reflections = reflections.select(selection)
# Filter bad reflections
#.........这里部分代码省略.........