def test_uid_passthrough(RE, hw):
# Test that none of the preprocessors in SupplementalData break plans
# returning uids (a bug that was caught on the floor).
RE.msg_hook = print
# preliminary sanity check
def mycount1():
uid = yield from count([])
assert uid is not None
assert isinstance(uid, str)
RE(mycount1())
# actual test
sd = SupplementalData()
sd.baseline = [hw.det]
sd.monitors = [hw.rand]
sd.flyers = [hw.flyer1]
hw.flyer1.loop = RE.loop
def mycount2():
uid = yield from sd(count([]))
assert uid is not None
assert isinstance(uid, str)
RE(mycount2())
def test_uid_passthrough(RE, hw):
# Test that none of the preprocessors in SupplementalData break plans
# returning uids (a bug that was caught on the floor).
RE.msg_hook = print
# preliminary sanity check
def mycount1():
uid = yield from count([])
assert uid is not None
assert isinstance(uid, str)
RE(mycount1())
# actual test
sd = SupplementalData()
sd.baseline = [hw.det]
sd.monitors = [hw.rand]
sd.flyers = [hw.flyer1]
hw.flyer1.loop = RE.loop
def mycount2():
uid = yield from sd(count([]))
assert uid is not None
assert isinstance(uid, str)
RE(mycount2())
def test_monitors(hw):
det = hw.det
rand = hw.rand
rand2 = hw.rand2
# no-op
D = SupplementalData()
original = list(count([det]))
processed = list(D(count([det])))
assert len(processed) == len(original)
# one monitor
D.monitors.append(rand)
original = list(count([det]))
processed = list(D(count([det])))
assert len(processed) == 2 + len(original)
# two monitors
D.monitors.append(rand2)
processed = list(D(count([det])))
assert len(processed) == 4 + len(original)
# two monitors applied a plan with consecutive runs
original = list(list(count([det])) + list(count([det])))
processed = list(D(pchain(count([det]), count([det]))))
assert len(processed) == 8 + len(original)
def test_mixture(hw):
D = SupplementalData(baseline=[hw.det2],
flyers=[hw.flyer1],
monitors=[hw.rand])
original = list(count([hw.det]))
processed = list(D(count([hw.det])))
assert len(processed) == 2 + 5 + 10 + len(original)
def test_pickle():
D = SupplementalData(baseline=['placeholder1'],
monitors=['placeholder2'],
flyers=['placeholder3'])
D2 = pickle.loads(pickle.dumps(D))
assert D2.baseline == D.baseline
assert D2.monitors == D.monitors
assert D2.flyers == D.flyers
def test_baseline(hw):
# one baseline detector
D = SupplementalData(baseline=[hw.det2])
original = list(count([hw.det]))
processed = list(D(count([hw.det])))
# should add 2X (trigger, wait, create, read, save)
assert len(processed) == 10 + len(original)
# two baseline detectors
D.baseline.append(hw.det3)
processed = list(D(count([hw.det])))
# should add 2X (trigger, triger, wait, create, read, read, save)
assert len(processed) == 14 + len(original)
# two baseline detectors applied to a plan with two consecutive runs
original = list(list(count([hw.det])) + list(count([hw.det])))
processed = list(D(pchain(count([hw.det]), count([hw.det]))))
assert len(processed) == 28 + len(original)
def test_flyers(hw):
# one flyer
D = SupplementalData(flyers=[hw.flyer1])
original = list(count([hw.det]))
processed = list(D(count([hw.det])))
# should add kickoff, wait, complete, wait, collect
assert len(processed) == 5 + len(original)
# two flyers
D.flyers.append(hw.flyer2)
processed = list(D(count([hw.det])))
# should add 2 * (kickoff, complete, collect) + 2 * (wait)
assert len(processed) == 8 + len(original)
# two flyers applied to a plan with two consecutive runs
original = list(list(count([hw.det])) + list(count([hw.det])))
processed = list(D(pchain(count([hw.det]), count([hw.det]))))
assert len(processed) == 16 + len(original)
def test_order(hw):
D = SupplementalData(baseline=[hw.det2],
flyers=[hw.flyer1],
monitors=[hw.rand])
def null_run():
yield Msg('open_run')
yield Msg('null')
yield Msg('close_run')
actual = [msg.command for msg in D(null_run())]
expected = [
'open_run',
# baseline
'trigger',
'wait',
'create',
'read',
'save',
# monitors
'monitor',
# flyers
'kickoff',
'wait',
# plan
'null',
# flyers
'complete',
'wait',
'collect',
# montiors
'unmonitor',
# baseline
'trigger',
'wait',
'create',
'read',
'save',
'close_run'
]
assert actual == expected
RE.md = PersistentDict(md_path)
if old_md is not None:
logger.info('migrating RE.md storage to PersistentDict')
RE.md.update(old_md)
# keep track of callback subscriptions
callback_db = {}
# set up databroker
import databroker
db = databroker.Broker.named('mongoCat')
callback_db['Broker'] = RE.subscribe(db.insert)
# Set up SupplementalData.
from bluesky import SupplementalData
sd = SupplementalData()
RE.preprocessors.append(sd)
# Add a progress bar.
from bluesky.utils import ProgressBarManager
pbar_manager = ProgressBarManager()
RE.waiting_hook = pbar_manager
# Register bluesky IPython magics.
from IPython import get_ipython
from bluesky.magics import BlueskyMagics
get_ipython().register_magics(BlueskyMagics)
get_ipython().magic("automagic 0") # Turn off automagic
# Set up the BestEffortCallback.
from bluesky.callbacks.best_effort import BestEffortCallback
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 : 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.
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.
# Test if we are in Jupyter or IPython:
in_jupyter = user_ns['get_ipython']().has_trait('kernel')
# Set up a RunEngine and use metadata backed by a sqlite file.
from bluesky import RunEngine
from bluesky.utils import 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(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 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 and not in_jupyter:
# 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()
bec = _bec
RE.subscribe(_bec)
if in_jupyter:
_bec.disable_plots()
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()
# Commented to allow more intelligent setting of kickers (for Jupyter and IPython):
## Make plots update live while scans run.
# from bluesky.utils import install_kicker
# install_kicker()
# Make plots update live while scans run.
if in_jupyter:
from bluesky.utils import install_nb_kicker
install_nb_kicker()
else:
from bluesky.utils import install_qt_kicker
install_qt_kicker()
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 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 test_repr():
expected = "SupplementalData(baseline=[], monitors=[], flyers=[])"
D = SupplementalData()
actual = repr(D)
assert actual == expected