# Set up the logbook. This configures bluesky's summaries of
# data acquisition (scan type, ID, etc.).
# Make ophyd listen to pyepics.
from ophyd import setup_ophyd
setup_ophyd()
from metadatastore.mds import MDS
# from metadataclient.mds import MDS
from databroker import Broker
from databroker.core import register_builtin_handlers
from filestore.fs import FileStore
# pull from /etc/metadatastore/connection.yaml or
# /home/BLUSER/.config/metdatastore/connection.yml
mds = MDS({'host': 'xf21id1-ca1',
'database': 'metadatastore',
'port': 27017,
'timezone': 'US/Eastern'}, auth=False)
# mds = MDS({'host': CA, 'port': 7770})
# pull configuration from /etc/filestore/connection.yaml or
# /home/BLUSER/.config/filestore/connection.yml
db = Broker(mds, FileStore({'host': 'xf21id1-ca1',
'port': 27017,
'database': 'filestore'}))
register_builtin_handlers(db.fs)
# Subscribe metadatastore to documents.
# If this is removed, data is not saved to metadatastore.
from bluesky.global_state import gs
gs.RE.subscribe('all', mds.insert)
import pytest
# some module level globals.
ophyd = None
reason = ''
try:
import ophyd
from ophyd import setup_ophyd
except ImportError as ie:
# pytestmark = pytest.mark.skip
ophyd = None
reason = str(ie)
else:
setup_ophyd()
# define the classes only if ophyd is available
# define a skip condition based on if ophyd is available or not
requires_ophyd = pytest.mark.skipif(ophyd is None, reason=reason)
def setUpModule():
ophyd.setup_ophyd()
logging.getLogger('ophyd.mixins').setLevel(logging.DEBUG)
def setup_module(module):
ophyd.setup_ophyd()
def configure_base(
user_ns,
broker_name,
*,
bec=True,
epics_context=False,
magics=True,
mpl=True,
configure_logging=True,
pbar=True,
ipython_exc_logging=True,
):
"""
Perform base setup and instantiation of important objects.
This factory function instantiates essential objects to data collection
environments at NSLS-II and adds them to the current namespace. In some
cases (documented below), it will check whether certain variables already
exist in the user name space, and will avoid creating them if so. The
following are added:
* ``RE`` -- a RunEngine
This is created only if an ``RE`` instance does not currently exist in
the namespace.
* ``db`` -- a Broker (from "databroker"), subscribe to ``RE``
* ``bec`` -- a BestEffortCallback, subscribed to ``RE``
* ``peaks`` -- an alias for ``bec.peaks``
* ``sd`` -- a SupplementalData preprocessor, added to ``RE.preprocessors``
* ``pbar_maanger`` -- a ProgressBarManager, set as the ``RE.waiting_hook``
And it performs some low-level configuration:
* creates a context in ophyd's control layer (``ophyd.setup_ophyd()``)
* turns on interactive plotting (``matplotlib.pyplot.ion()``)
* bridges the RunEngine and Qt event loops
(``bluesky.utils.install_kicker()``)
* logs ERROR-level log message from ophyd to the standard out
Parameters
----------
user_ns: dict
a namespace --- for example, ``get_ipython().user_ns``
broker_name : Union[str, Broker]
Name of databroker configuration or a Broker instance.
bec : boolean, optional
True by default. Set False to skip BestEffortCallback.
epics_context : boolean, optional
True by default. Set False to skip ``setup_ophyd()``.
magics : boolean, optional
True by default. Set False to skip registration of custom IPython
magics.
mpl : boolean, optional
True by default. Set False to skip matplotlib ``ion()`` at event-loop
bridging.
configure_logging : boolean, optional
True by default. Set False to skip INFO-level logging to
/var/logs/bluesky/bluesky.log.
pbar : boolean, optional
True by default. Set false to skip ProgressBarManager.
ipython_exc_logging : boolean, optional
True by default. Exception stack traces will be written to IPython
log file when IPython logging is enabled.
Returns
-------
names : list
list of names added to the namespace
Examples
--------
Configure IPython for CHX.
>>>> configure_base(get_ipython().user_ns, 'chx');
"""
ns = {} # We will update user_ns with this at the end.
# Protect against double-subscription.
SENTINEL = "__nslsii_configure_base_has_been_run"
if user_ns.get(SENTINEL):
raise RuntimeError(
"configure_base should only be called once per process.")
ns[SENTINEL] = True
# Set up a RunEngine and use metadata backed by files on disk.
from bluesky import RunEngine, __version__ as bluesky_version
if LooseVersion(bluesky_version) >= LooseVersion("1.6.0"):
# current approach using PersistentDict
from bluesky.utils import PersistentDict
directory = os.path.expanduser("~/.config/bluesky/md")
os.makedirs(directory, exist_ok=True)
md = PersistentDict(directory)
else:
# legacy approach using HistoryDict
from bluesky.utils import get_history
md = get_history()
# if RunEngine already defined grab it
# useful when users make their own custom RunEngine
if "RE" in user_ns:
RE = user_ns["RE"]
else:
RE = RunEngine(md)
ns["RE"] = RE
# Set up SupplementalData.
# (This is a no-op until devices are added to it,
# so there is no need to provide a 'skip_sd' switch.)
from bluesky import SupplementalData
sd = SupplementalData()
RE.preprocessors.append(sd)
ns["sd"] = sd
if isinstance(broker_name, str):
# Set up a Broker.
from databroker import Broker
db = Broker.named(broker_name)
ns["db"] = db
else:
db = broker_name
RE.subscribe(db.insert)
if pbar:
# Add a progress bar.
from bluesky.utils import ProgressBarManager
pbar_manager = ProgressBarManager()
RE.waiting_hook = pbar_manager
ns["pbar_manager"] = pbar_manager
if magics:
# Register bluesky IPython magics.
from bluesky.magics import BlueskyMagics
get_ipython().register_magics(BlueskyMagics)
if bec:
# Set up the BestEffortCallback.
from bluesky.callbacks.best_effort import BestEffortCallback
_bec = BestEffortCallback()
RE.subscribe(_bec)
ns["bec"] = _bec
ns["peaks"] = _bec.peaks # just as alias for less typing
if mpl:
# Import matplotlib and put it in interactive mode.
import matplotlib.pyplot as plt
ns["plt"] = plt
plt.ion()
# Make plots update live while scans run.
if LooseVersion(bluesky_version) < LooseVersion("1.6.0"):
from bluesky.utils import install_kicker
install_kicker()
if epics_context:
# Create a context in the underlying EPICS client.
from ophyd import setup_ophyd
setup_ophyd()
if configure_logging:
configure_bluesky_logging(ipython=get_ipython())
if ipython_exc_logging:
# IPython logging must be enabled separately
from nslsii.common.ipynb.logutils import log_exception
configure_ipython_exc_logging(exception_logger=log_exception,
ipython=get_ipython())
# always configure %xmode minimal
get_ipython().magic("xmode minimal")
# convenience imports
# some of the * imports are for 'back-compatibility' of a sort -- we have
# taught BL staff to expect LiveTable and LivePlot etc. to be in their
# namespace
import numpy as np
ns["np"] = np
import bluesky.callbacks
ns["bc"] = bluesky.callbacks
import_star(bluesky.callbacks, ns)
import bluesky.plans
ns["bp"] = bluesky.plans
import_star(bluesky.plans, ns)
import bluesky.plan_stubs
ns["bps"] = bluesky.plan_stubs
import_star(bluesky.plan_stubs, ns)
# special-case the commonly-used mv / mvr and its aliases mov / movr4
ns["mv"] = bluesky.plan_stubs.mv
ns["mvr"] = bluesky.plan_stubs.mvr
ns["mov"] = bluesky.plan_stubs.mov
ns["movr"] = bluesky.plan_stubs.movr
import bluesky.preprocessors
ns["bpp"] = bluesky.preprocessors
import bluesky.callbacks.broker
import_star(bluesky.callbacks.broker, ns)
import bluesky.simulators
import_star(bluesky.simulators, ns)
user_ns.update(ns)
return list(ns)
def configure_base(user_ns,
broker_name,
*,
bec=True,
epics_context=True,
magics=True,
mpl=True,
ophyd_logging=True,
pbar=True):
"""
Perform base setup and instantiation of important objects.
This factory function instantiates the following and adds them to the
namespace:
* ``RE`` -- a RunEngine
* ``db`` -- a Broker (from "databroker"), subscribe to ``RE``
* ``bec`` -- a BestEffortCallback, subscribed to ``RE``
* ``peaks`` -- an alias for ``bec.peaks``
* ``sd`` -- a SupplementalData preprocessor, added to ``RE.preprocessors``
* ``pbar_maanger`` -- a ProgressBarManager, set as the ``RE.waiting_hook``
And it performs some low-level configuration:
* creates a context in ophyd's control layer (``ophyd.setup_ophyd()``)
* turns out interactive plotting (``matplotlib.pyplot.ion()``)
* bridges the RunEngine and Qt event loops
(``bluesky.utils.install_kicker()``)
* logs ERROR-level log message from ophyd to the standard out
Parameters
----------
user_ns: dict
a namespace --- for example, ``get_ipython().user_ns``
broker_name : string
Name of databroker configuration.
bec : boolean, optional
True by default. Set False to skip BestEffortCallback.
epics_context : boolean, optional
True by default. Set False to skip ``setup_ophyd()``.
magics : boolean, optional
True by default. Set False to skip registration of custom IPython
magics.
mpl : boolean, optional
True by default. Set False to skip matplotlib ``ion()`` at event-loop
bridging.
ophyd_logging : boolean, optional
True by default. Set False to skip ERROR-level log configuration for
ophyd.
pbar : boolean, optional
True by default. Set false to skip ProgressBarManager.
Returns
-------
names : list
list of names added to the namespace
Examples
--------
Configure IPython for CHX.
>>>> configure_base(get_ipython().user_ns, 'chx');
"""
ns = {} # We will update user_ns with this at the end.
# Set up a RunEngine and use metadata backed by a sqlite file.
from bluesky import RunEngine
from bluesky.utils import get_history
RE = RunEngine(get_history())
ns['RE'] = RE
# Set up SupplementalData.
# (This is a no-op until devices are added to it,
# so there is no need to provide a 'skip_sd' switch.)
from bluesky import SupplementalData
sd = SupplementalData()
RE.preprocessors.append(sd)
ns['sd'] = sd
if broker_name:
# Set up a Broker.
from databroker import Broker
db = Broker.named(broker_name)
ns['db'] = db
RE.subscribe(db.insert)
if pbar:
# Add a progress bar.
from bluesky.utils import ProgressBarManager
pbar_manager = ProgressBarManager()
RE.waiting_hook = pbar_manager
ns['pbar_manager'] = pbar_manager
if magics:
# Register bluesky IPython magics.
from bluesky.magics import BlueskyMagics
get_ipython().register_magics(BlueskyMagics)
if bec:
# Set up the BestEffortCallback.
from bluesky.callbacks.best_effort import BestEffortCallback
_bec = BestEffortCallback()
RE.subscribe(_bec)
ns['bec'] = _bec
ns['peaks'] = _bec.peaks # just as alias for less typing
if mpl:
# Import matplotlib and put it in interactive mode.
import matplotlib.pyplot as plt
ns['plt'] = plt
plt.ion()
# Make plots update live while scans run.
from bluesky.utils import install_kicker
install_kicker()
if epics_context:
# Create a context in the underlying EPICS client.
from ophyd import setup_ophyd
setup_ophyd()
if not ophyd_logging:
# Turn on error-level logging, particularly useful for knowing when
# pyepics callbacks fail.
import logging
import ophyd.ophydobj
ch = logging.StreamHandler()
ch.setLevel(logging.ERROR)
ophyd.ophydobj.logger.addHandler(ch)
# convenience imports
# some of the * imports are for 'back-compatibility' of a sort -- we have
# taught BL staff to expect LiveTable and LivePlot etc. to be in their
# namespace
import numpy as np
ns['np'] = np
import bluesky.callbacks
ns['bc'] = bluesky.callbacks
import_star(bluesky.callbacks, ns)
import bluesky.plans
ns['bp'] = bluesky.plans
import_star(bluesky.plans, ns)
import bluesky.plan_stubs
ns['bps'] = bluesky.plan_stubs
import_star(bluesky.plan_stubs, ns)
# special-case the commonly-used mv / mvr and its aliases mov / movr4
ns['mv'] = bluesky.plan_stubs.mv
ns['mvr'] = bluesky.plan_stubs.mvr
ns['mov'] = bluesky.plan_stubs.mov
ns['movr'] = bluesky.plan_stubs.movr
import bluesky.preprocessors
ns['bpp'] = bluesky.preprocessors
import bluesky.callbacks.broker
import_star(bluesky.callbacks.broker, ns)
import bluesky.simulators
import_star(bluesky.simulators, ns)
user_ns.update(ns)
return list(ns)
def setup_module(module):
ophyd.setup_ophyd()
def setUpModule():
ophyd.setup_ophyd()
