def __init__(self, mode='debug'):
self.RE = bluesky.RunEngine({})
self.db = databroker.Broker.named("mongodb_config")
self.RE.subscribe(self.db.insert)
self.RE.subscribe(BestEffortCallback())
self._mode = mode
from apstools.devices import ApsMachineParametersDevice
self._aps = ApsMachineParametersDevice(name="APS")
self.shutter = Experiment.get_shutter(mode)
self.suspend_shutter = SuspendFloor(self.shutter.pss_state, 1)
from pygerm.handler import GeRMHandler, BinaryGeRMHandler
import numpy as np
import pandas as pd
from lmfit import Model
# generic configuration, is already on the beamline
reg = Registry({'dbpath': '/tmp/fs.sqlite'})
reg.register_handler('GeRM', GeRMHandler)
reg.register_handler('BinaryGeRM', BinaryGeRMHandler)
mds = MDS({'directory': '/tmp/mds.sqlite', 'timezone': 'US/Eastern'})
db = Broker(mds, reg=reg)
RE = bs.RunEngine()
RE.subscribe(db.insert)
# create the GeRM object
germ = GeRM('XF:28IDC-ES:1{Det:GeRM1}',
name='germ',
read_attrs=[
'filepath', 'last_file', 'chip', 'chan', 'td', 'pd', 'ts',
'count'
],
configuration_attrs=['frametime'])
# gaussian fit
def gaussian(x, area, center, sigma):
import bluesky.callbacks as bc
import csv
from ophyd.sim import motor, det
import matplotlib.pyplot as plt
# Do this if running the example interactively;
# skip it when building the documentation.
import os
if 'BUILDING_DOCS' not in os.environ:
from bluesky.utils import install_qt_kicker # for notebooks, qt -> nb
install_qt_kicker()
plt.ion()
det.exposure_time = .1 # simulate detector exposure time
RE = bs.RunEngine({})
###############################################################################
# Define a callback class which writes out a CSV file
class CSVWriter(bc.CallbackBase):
def __init__(self, fields, fname_format, fpath):
self._path = path.Path(fpath)
os.makedirs(self._path, exist_ok=True)
self._fname_fomat = fname_format
self._fields = fields
self._writer = None
self._fout = None
def close(self):
socket
yaml
for you, rejoice.
''')
# ----- Setup base bluesky RunEngine and MongoDB ----- #
# metadata streamed to MongoDB server over the network
import databroker
metadata_db = databroker.Broker.named("mongodb_config")
keywords_vars['metadata_db'] = 'Default metadata handler'
# setup RunEngine
from bluesky.callbacks.best_effort import BestEffortCallback
RE = bluesky.RunEngine({})
keywords_vars['RE'] = 'Default RunEngine instance'
RE.subscribe(metadata_db.insert)
RE.subscribe(BestEffortCallback())
RE.md['beamline_id'] = 'APS 6-BM-A'
RE.md['proposal_id'] = 'internal test'
RE.md['pid'] = os.getpid()
RE.md['login_id'] = USERNAME + '@' + HOSTNAME
RE.md['versions'] = {}
RE.md['versions']['apstools'] = apstools.__version__
RE.md['versions']['bluesky'] = bluesky.__version__
RE.md['versions']['databroker'] = databroker.__version__
RE.md['versions']['matplotlib'] = matplotlib.__version__
RE.md['versions']['numpy'] = np.__version__
RE.md['versions']['ophyd'] = ophyd.__version__