def run():
"""
# setup for simulated IOC
EPICS_CA_ADDR_LIST=127.0.0.1:5064
EPICS_CA_AUTO_ADDR_LIST=NO
Run mongo.
Run simulated IOC.
"""
# arg_parser = argparse.ArgumentParser()
# arg_parser.add_argument("--agent-name", required=True, type=str)
# arg_parser.add_argument("--episode-count", required=True, type=int)
# args = arg_parser.parse_args()
RE = RunEngine()
bec = BestEffortCallback()
RE.subscribe(bec)
db = catalog["mad"] # this is set up by entrypoint
RE.subscribe(db.v1.insert)
tiff_sim_detector = NewPerkinElmerDetector(prefix="Sim{{det1}}:",
name="tiff_sim_detector")
RE(count([tiff_sim_detector]))
def run(self):
"""
Overrides the `run()` function of the `multiprocessing.Process` class. Called
by the `start` method.
"""
self._exit_event.clear()
self._RE = RunEngine({})
bec = BestEffortCallback()
self._RE.subscribe(bec)
# db = Broker.named('temp')
self._RE.subscribe(self._db.insert)
self._execution_queue = queue.Queue()
self._thread_conn = threading.Thread(
target=self._receive_packet_thread, name="RE Worker Receive")
self._thread_conn.start()
# Now make the main thread busy
self._execute_in_main_thread()
self._thread_conn.join()
del self._RE
def test_serp_scan():
"""Note: run this standalone, not inside mfx hutch python."""
import numpy as np
from bluesky import RunEngine
from bluesky.callbacks.best_effort import BestEffortCallback
from ophyd.sim import motor1, motor2
from ophyd.status import StatusBase
from pcdsdaq.daq import Daq
from pcdsdaq.sim import set_sim_mode
class FakeSeq:
def trigger(self):
print('Triggered the sequencer!')
status = StatusBase()
status.set_finished()
return status
set_sim_mode(True)
RE = RunEngine({})
bec = BestEffortCallback()
RE.subscribe(bec)
seq = FakeSeq()
daq = Daq(RE=RE)
RE(serp_seq_scan(motor1, np.arange(100, 200, 10), motor2, [0, 100], seq))
def test_plans(RE, pln, args, kwargs, hw):
args = tuple(getattr(hw, v, v) if isinstance(v, str) else v for v in args)
det = hw.det
bec = BestEffortCallback()
RE.subscribe(bec)
RE.subscribe(checker)
RE(pln([det], *args, **kwargs))
def test_with_baseline(fresh_RE):
RE = fresh_RE
det = Detector()
bec = BestEffortCallback()
RE.subscribe(bec)
sd = SupplementalData(baseline=[det3])
RE.preprocessors.append(sd)
RE(scan([det], motor, 1, 5, 5))
def test_plans_motors_no_hints(RE, pln, args, kwargs, hw):
args = tuple(getattr(hw, v, v) if isinstance(v, str) else v for v in args)
det = hw.det
for v in args:
assert not hasattr(v, 'hints')
bec = BestEffortCallback()
RE.subscribe(bec)
RE(pln([det], *args, **kwargs))
def macro_sweep_test(target):
logging.info(
'macro_sweep_test initiated with target {:0.4f}'.format(target))
RE = RunEngine({})
bec = BestEffortCallback()
RE.subscribe(bec)
RE.waiting_hook = ProgressBarManager()
RE(run_wrapper(rel_smooth_sweep_test(tst_23, target)))
def test_multirun_nested_plan(capsys, caplog, RE, hw):
# This test only checks if the plan runs without crashing. If BEC crashes,
# the plan will still run, but data will not be displayed.
@bpp.set_run_key_decorator(run="inner_run")
def plan_inner():
yield from grid_scan([hw.det4], hw.motor1, 0, 1, 1, hw.motor2, 0, 1, 2,
True)
def sequence():
for n in range(5):
yield from bps.mov(hw.motor, n * 0.1 + 1)
yield from bps.trigger_and_read([hw.det1])
@bpp.set_run_key_decorator(run="outer_run")
@bpp.stage_decorator([hw.det1, hw.motor])
@bpp.run_decorator(md={})
def plan_outer():
yield from sequence()
# Call inner plan from within the plan
yield from plan_inner()
# Run another set of commands
yield from sequence()
# The first test should fail. We check if expected error message is printed in case
# of failure.
bec = BestEffortCallback()
bec_token = RE.subscribe(bec)
RE(plan_outer())
captured = capsys.readouterr()
# Check for the number of runs (the number of times UID is printed in the output)
scan_uid_substr = "Persistent Unique Scan ID"
n_runs = captured.out.count(scan_uid_substr)
assert n_runs == 2, "scan output contains incorrect number of runs"
# Check if the expected error message is printed once the callback fails. The same
# substring will be used in the second part of the test to check if BEC did not fail.
err_msg_substr = "is being suppressed to not interrupt plan execution"
assert err_msg_substr in str(caplog.text), \
"Best Effort Callback failed, but expected error message was not printed"
RE.unsubscribe(bec_token)
caplog.clear()
# The second test should succeed, i.e. the error message should not be printed
def factory(name, doc):
bec = BestEffortCallback()
return [bec], []
rr = RunRouter([factory])
RE.subscribe(rr)
RE(plan_outer())
captured = capsys.readouterr()
n_runs = captured.out.count(scan_uid_substr)
assert n_runs == 2, "scan output contains incorrect number of runs"
assert err_msg_substr not in caplog.text, \
"Best Effort Callback failed while executing nested plans"
def test_underhinted_plan(RE, hw):
bec = BestEffortCallback()
RE.subscribe(bec)
@bpp.run_decorator()
def broken_plan(dets):
yield from bps.trigger_and_read(dets)
RE(broken_plan([hw.det]))
def get_runengine(db=None):
"""
Return an instance of RunEngine. It is recommended to have only
one RunEngine per session.
"""
RE = RunEngine({})
db = metadata_db if db is None else db
RE.subscribe(db.insert)
RE.subscribe(BestEffortCallback())
return RE
def test_plans_motor_empty_hints(RE, pln, args, kwargs, hw):
args = tuple(getattr(hw, v, v) if isinstance(v, str) else v for v in args)
for v in args:
if hasattr(v, 'hints'):
v.hints = {}
assert v.hints == {}
det = hw.det
bec = BestEffortCallback()
RE.subscribe(bec)
RE(pln([det], *args, **kwargs))
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)
def replay(headers, callback=None, sort=True):
"""
replay the document stream from one (or more) scans (headers)
PARAMETERS
headers: scan or [scan]
Scan(s) to be replayed through callback.
A *scan* is an instance of a Bluesky `databroker.Header`.
see: https://nsls-ii.github.io/databroker/api.html?highlight=header#header-api
callback: scan or [scan]
The Bluesky callback to handle the stream of documents from a scan.
If `None`, then use the `bec` (BestEffortCallback) from the IPython shell.
(default:``None``)
sort: bool
Sort the headers chronologically if True.
(default:``True``)
*new in apstools release 1.1.11*
"""
callback = callback or ipython_shell_namespace().get(
"bec", # get from IPython shell
BestEffortCallback(), # make one, if we must
)
_headers = headers # do not mutate the input arg
if isinstance(_headers, databroker.Header):
_headers = [_headers]
def increasing_time_sorter(run):
return run.start["time"]
def decreasing_time_sorter(run):
"""Default for databroker v0 results."""
return -run.start["time"]
sorter = {
True: increasing_time_sorter,
False: decreasing_time_sorter
}[sort]
for h in sorted(_headers, key=sorter):
if not isinstance(h, databroker.Header):
raise TypeError(
f"Must be a databroker Header: received: {type(h)}: |{h}|")
cmd = _rebuild_scan_command(h.start)
logger.debug(f"{cmd}")
# at last, this is where the real action happens
for k, doc in h.documents(): # get the stream
callback(k, doc) # play it through the callback
def macro_RSXS_smooth_sweep(stroke_height,
stroke_spacing,
n_strokes,
both_directions=True):
"""
macro_RSXS_smooth_sweep
This method wraps up the bluesky/ophyd codeand allows users to drive
the LU20 experiment with minimal code overhead. It contains the following
bluesky plan.
This bluesky plan moves a 2-axis actuator across multiple traversals of a
sample. The plan traverses the entirety of the stroke_height (y-axis) and
after each traversal, steps in the x-axis by the stroke_spacing.It may be
configured to scan in only a single direction and shutter the beam for the
opposite direction. This removes the shutter at the beginning of the plan
and reinserts it at the end. At the end of the plan, the sample is moved to
its original y-axis position but with an x-axis posiiton ready for the next
run. For more details about the path, see the documentation of the
xy_sequencer, the method that generates the sample's path.
Parameters
----------
stroke_height : float
Vertical distance (y-axs) of each stroke.
stroke_spacing : float
Horizontal distance between individual strokes.
n_strokes : int
Number of strokes to complete.
both_directions : bool, optional
Defaults to True. If this value is true the beam will be scanned across
the sample while moving in both vertical directions. If false, the beam
is only scanned in a single direction.
"""
RE = RunEngine({})
bec = BestEffortCallback()
RE.subscribe(bec)
RE.waiting_hook = ProgressBarManager()
RE(
run_wrapper(
rel_smooth_sweep(mot_x=rsxs_sample_x,
mot_y=rsxs_sample_y,
shutter=shutter,
stroke_height=stroke_height,
stroke_spacing=stroke_spacing,
n_strokes=n_strokes,
both_directions=both_directions)))
def test_bec_peak_stats_derivative_and_stats(RE, hw):
bec = BestEffortCallback(calc_derivative_and_stats=True)
RE.subscribe(bec)
c = DocCollector()
RE.subscribe(c.insert)
res = RE(scan([hw.ab_det], hw.motor, 1, 5, 5))
if RE.call_returns_result:
uid = res.run_start_uids[0]
else:
uid = res[0]
desc_uid = c.descriptor[uid][0]["uid"]
ps = bec._peak_stats[desc_uid]["det_a"]
assert hasattr(ps, "derivative_stats")
fields = ["min", "max", "com", "cen", "fwhm", "crossings"]
der_fields = ["x", "y"] + fields
for field in der_fields:
assert hasattr(ps.derivative_stats,
field), f"{field} is not an attribute of ps.der"
assert isinstance(ps.__repr__(), str)
# These imports are needed by the `eval` below:
from numpy import array # noqa F401
from collections import OrderedDict # noqa F401
out = eval(str(ps))
assert isinstance(out, dict)
for key in ("stats", "derivative_stats"):
assert key in out
for field in fields:
stats_value = getattr(ps.stats, field)
out_value = out["stats"][field]
if stats_value is not None:
assert np.allclose(stats_value, out_value)
else:
stats_value == out_value
for field in der_fields:
stats_value = getattr(ps.derivative_stats, field)
out_value = out["derivative_stats"][field]
if stats_value is not None:
assert np.allclose(stats_value, out_value)
else:
stats_value == out_value
def __init__(self,
queue,
teleport,
*scan_widgets,
live_widget=None,
**kwargs):
super().__init__(**kwargs)
self.label = label = StartLabel()
self.queue = queue
self.teleport = teleport
self.md_parameters = MetaDataEntry(name='Metadata')
self.md_widget = ParameterTree()
self.md_widget.setParameters(self.md_parameters)
outmost_layout = QtWidgets.QHBoxLayout()
input_layout = QtWidgets.QVBoxLayout()
outmost_layout.addLayout(input_layout)
input_layout.addWidget(label)
self.tabs = TabScanSelector(*scan_widgets)
input_layout.addWidget(self.tabs)
for sw in scan_widgets:
sw.md_parameters = self.md_parameters
self.go_button = QtWidgets.QPushButton('SCAN!')
self.md_button = QtWidgets.QPushButton('edit metadata')
input_layout.addWidget(self.md_button)
input_layout.addWidget(self.go_button)
self.teleport.name_doc.connect(label.doc_consumer)
self.cbr = Dispatcher()
self.bec = BestEffortCallback()
self.teleport.name_doc.connect(
lambda name, doc: self.cbr.process(DocumentNames(name), doc))
self.cbr.subscribe(self.bec)
def runner():
self.queue.put(self.tabs.get_plan())
self.go_button.clicked.connect(runner)
self.md_button.clicked.connect(self.md_widget.show)
if live_widget is None:
live_widget = LivePlaceholder()
self.live_widget = live_widget
self.teleport.name_doc.connect(live_widget.doc_consumer)
outmost_layout.addWidget(live_widget)
self.setLayout(outmost_layout)
def test_plot_ints(RE):
from ophyd import Signal
from bluesky.callbacks.best_effort import BestEffortCallback
from bluesky.plans import count
import bluesky.plan_stubs as bps
bec = BestEffortCallback()
RE.subscribe(bec)
s = Signal(name='s')
RE(bps.mov(s, int(0)))
assert s.describe()['s']['dtype'] == 'integer'
s.kind = 'hinted'
with pytest.warns(None) as record:
RE(count([s], num=35))
assert len(record) == 0
def getRunEngine(db=None):
"""
Return an instance of RunEngine. It is recommended to have only
one RunEngine per session.
"""
RE = RunEngine({})
db = metadata_db if db is None else db
RE.subscribe(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['BLUESKY_VERSION'] = bluesky.__version__
RE.md['OPHYD_VERSION'] = ophyd.__version__
RE.md['apstools_VERSION'] = apstools.__version__
RE.md['SESSION_STARTED'] = datetime.isoformat(datetime.now(), " ")
return RE
def run(self):
"""
Overrides the `run()` function of the `multiprocessing.Process` class. Called
by the `start` method.
"""
self._exit_event = threading.Event()
# TODO: TC - Do you think that the following code may be included in RE.__init__()
# (for Python 3.8 and above)
# Setting the default event loop is needed to make the code work with Python 3.8.
loop = get_bluesky_event_loop()
asyncio.set_event_loop(loop)
self._RE = RunEngine({})
bec = BestEffortCallback()
self._RE.subscribe(bec)
# db = Broker.named('temp')
self._RE.subscribe(self._db.insert)
self._execution_queue = queue.Queue()
self._thread_conn = threading.Thread(
target=self._receive_packet_thread, name="RE Worker Receive")
self._thread_conn.start()
# Environment is initialized: send a report
msg = {"type": "report", "value": {"action": "environment_created"}}
self._conn.send(msg)
# Now make the main thread busy
self._execute_in_main_thread()
self._thread_conn.join()
del self._RE
# Finally send a report
msg = {"type": "report", "value": {"action": "environment_closed"}}
self._conn.send(msg)
def test_push_start_document(capsys):
""" Pass the start document to BEC and verify if the scan information is printed correctly"""
bec = BestEffortCallback()
uid = new_uid()
time = ttime.time()
scan_id = 113435 # Just some arbitrary number
# Include minimum information needed to print the header
bec("start", {"scan_id": scan_id, "time": time, "uid": uid})
captured = capsys.readouterr()
assert f"Transient Scan ID: {scan_id}" in captured.out, \
"BestEffortCallback: Scan ID is not printed correctly"
tt = datetime.fromtimestamp(time).utctimetuple()
assert f"Time: {ttime.strftime('%Y-%m-%d %H:%M:%S', tt)}" in captured.out, \
"BestEffortCallback: Scan time is not printed correctly"
assert f"Persistent Unique Scan ID: '{uid}'" in captured.out, \
"BestEffortCallback: Scan UID is not printed correctly"
def run():
arg_parser = argparse.ArgumentParser()
arg_parser.add_argument("--agent-name", required=True, type=str)
arg_parser.add_argument("--episode-count", required=True, type=int)
args = arg_parser.parse_args()
RE = RunEngine()
bec = BestEffortCallback()
RE.subscribe(bec)
db = Broker.named("bluesky-cartpole")
# insert bluesky documents into databroker
RE.subscribe(db.insert)
RE(
train_cartpole_agent(agent_name=args.agent_name,
episode_count=args.episode_count))
def getRunEngine(db=None):
"""
Return an instance of RunEngine. It is recommended to have only
one RunEngine per session.
"""
RE = RunEngine({})
db = db or metadata_db
RE.subscribe(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__
RE.md['SESSION_STARTED'] = datetime.isoformat(datetime.now(), " ")
return RE
def test_plot_prune_fifo(RE, hw):
bec = BestEffortCallback()
RE.subscribe(bec)
num_pruned = 2
# create the LivePlot
RE(bps.repeater(num_pruned, scan, [hw.ab_det], hw.motor, 1, 5, 5))
# test it
assert len(bec._live_plots) == 1
# get the reference key for our LivePlot dict
uuid = next(iter(bec._live_plots))
assert len(bec._live_plots[uuid]) == 1
# get reference key for our detector
det_name = next(iter(bec._live_plots[uuid]))
# should be same as hw.ab_det.a.name (`.a` comes from .read_attrs[0]), prove it now
assert det_name == hw.ab_det.a.name
# get the LivePlot object
lp = bec._live_plots[uuid][det_name]
assert lp is not None
assert len(lp.ax.lines) == num_pruned
# prune the LivePlot (has no effect since we have exact number to keep)
bec.plot_prune_fifo(num_pruned, hw.motor, hw.ab_det.a)
assert len(lp.ax.lines) == num_pruned
# add more lines to the LivePlot
RE(bps.repeater(num_pruned, scan, [hw.ab_det], hw.motor, 1, 5, 5))
# get the LivePlot object, again, in case the UUID was changed
assert len(bec._live_plots) == 1
uuid = next(iter(bec._live_plots))
lp = bec._live_plots[uuid][det_name]
assert lp is not None
assert len(lp.ax.lines) == num_pruned * 2
# prune again, this time reduces number of lines
bec.plot_prune_fifo(num_pruned, hw.motor, hw.ab_det.a)
assert len(lp.ax.lines) == num_pruned
from bluesky import RunEngine
from bluesky.plans import scan
from bluesky.callbacks.best_effort import BestEffortCallback
from ophyd.sim import SynGauss
from status import StatusAxis
# Create simulated devices
motor = StatusAxis(name='motor')
det = SynGauss('det', motor, 'motor', center=0, Imax=1, sigma=1)
det.kind = 'hinted'
motor.prefix = 'fake:Prefix'
# Create our RunEngine
RE = RunEngine()
RE.subscribe(BestEffortCallback())
from bluesky import RunEngine from bluesky.callbacks.best_effort import BestEffortCallback from bluesky.utils import install_kicker bec = BestEffortCallback() RE = RunEngine(bec) install_kicker()
for motor, pos in step.items():
if pos == pos_cache[motor]:
# This step does not move this motor.
continue
yield from abs_set(motor, pos, group=grp)
pos_cache[motor] = pos
yield from wait(group=grp)
motors = step.keys()
yield from move()
plt.pause(.001)
yield from trigger_and_read(list(detectors) + list(motors))
install_kicker()
bec = BestEffortCallback()
bec.enable_plots()
hw = hw()
RE = RunEngine()
# build the pipeline
raw_source = Stream()
raw_output = SimpleFromEventStream('event', ('data', 'det_a'),
raw_source,
principle=True)
raw_output2 = SimpleFromEventStream('event', ('data', 'noisy_det'), raw_source)
pipeline = raw_output.union(raw_output2).map(lambda x: 1).accumulate(
lambda x, y: x + y)
res = SimpleToEventStream(pipeline, ('result', ))
# Add a progress bar.
from timeit import default_timer as timer
from bluesky.utils import ProgressBarManager
pbar_manager = ProgressBarManager()
#RE.waiting_hook = pbar_manager
# Register bluesky IPython magics.
from bluesky.magics import BlueskyMagics
get_ipython().register_magics(BlueskyMagics)
# Set up the BestEffortCallback.
from bluesky.callbacks.best_effort import BestEffortCallback
bec = BestEffortCallback()
bec.disable_plots()
bec.disable_table()
RE.subscribe(bec)
peaks = bec.peaks # just as alias for less typing
# Make plots update live while scans run.
from bluesky.utils import install_qt_kicker
install_qt_kicker()
from pathlib import Path
from historydict import HistoryDict
try:
RE.md = HistoryDict('/nsls2/xf08id/metadata/bluesky_history.db')
def test_with_baseline(RE, hw):
bec = BestEffortCallback()
RE.subscribe(bec)
sd = SupplementalData(baseline=[hw.det])
RE.preprocessors.append(sd)
RE(scan([hw.ab_det], hw.motor, 1, 5, 5))
def test_blank_hints(RE, hw):
bec = BestEffortCallback()
RE.subscribe(bec)
RE(scan([hw.ab_det], hw.motor, 1, 5, 5, md={'hints': {}}))
def test_disable(RE, hw):
det, motor = hw.ab_det, hw.motor
bec = BestEffortCallback()
RE.subscribe(bec)
bec.disable_table()
RE(scan([det], motor, 1, 5, 5))
assert bec._table is None
bec.enable_table()
RE(scan([det], motor, 1, 5, 5))
assert bec._table is not None
bec.peaks.com
bec.peaks['com']
assert ast.literal_eval(repr(bec.peaks)) == vars(bec.peaks)
bec.clear()
assert bec._table is None
# smoke test
bec.disable_plots()
bec.enable_plots()
bec.disable_baseline()
bec.enable_baseline()
bec.disable_heading()
bec.enable_heading()
def test_simple(RE, hw):
bec = BestEffortCallback()
RE.subscribe(bec)
RE(scan([hw.ab_det], hw.motor, 1, 5, 5))
def test_disable(RE, hw):
det, motor = hw.ab_det, hw.motor
bec = BestEffortCallback()
RE.subscribe(bec)
bec.disable_table()
RE(scan([det], motor, 1, 5, 5))
assert bec._table is None
bec.enable_table()
RE(scan([det], motor, 1, 5, 5))
assert bec._table is not None
bec.peaks.com
bec.peaks['com']
assert ast.literal_eval(repr(bec.peaks)) == vars(bec.peaks)
bec.clear()
assert bec._table is None
# smoke test
bec.disable_plots()
bec.enable_plots()
bec.disable_baseline()
bec.enable_baseline()
bec.disable_heading()
bec.enable_heading()
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 bluesky.magics import BlueskyMagics get_ipython().register_magics(BlueskyMagics) # Set up the BestEffortCallback. from bluesky.callbacks.best_effort import BestEffortCallback bec = BestEffortCallback() RE.subscribe(bec) peaks = bec.peaks # just as alias for less typing bec.disable_baseline() # At the end of every run, verify that files were saved and # print a confirmation message. from bluesky.callbacks.broker import verify_files_saved # RE.subscribe(post_run(verify_files_saved), 'stop') # Import matplotlib and put it in interactive mode. import matplotlib.pyplot as plt plt.ion() # Make plots update live while scans run. from bluesky.utils import install_qt_kicker