def set(self, mode, config=None):
"""
(Re)-initialize all devices based on given mode
simulated devices <-- debug
actual devices <-- dryrun, production
"""
if mode.lower() not in ['debug', 'dryrun', 'production']:
raise ValueError(f"Unknown mode: {mode}")
else:
self._mode = mode
global A_shutter
global suspend_A_shutter
global tomostage
global preci, samX, ksamX, ksamZ, samY
global psofly
global det
# re-init all tomo related devices
A_shutter = get_shutter(self._mode)
tomostage = get_motors(self._mode)
preci = tomostage.preci
samX = tomostage.samX
ksamX = tomostage.ksamX
ksamZ = tomostage.ksamZ
samY = tomostage.samY
psofly = get_fly_motor(self._mode)
det = get_detector(self._mode)
# some quick sanity check production mode
import apstools.devices as APS_devices
aps = APS_devices.ApsMachineParametersDevice(name="APS")
suspend_A_shutter = SuspendFloor(A_shutter.pss_state, 1)
"""
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)
# monitor APS current
self.suspend_APS_current = SuspendFloor(self._aps.current,
2,
resume_thresh=10)
self.RE.install_suspender(self.suspend_APS_current)
def imprint_row(*args, events=1, min_mj=0.5):
"""
Run a single row of the imprint scan
Parameters
----------
args: passed to bluesky.plans.scan
events: int
The number of events to allow at each stopping point in the scan
min_mj, float, optional
The minimum energy the scan should continue to execute scans
Example
-------
.. code::
# Run a scan from -1, 1 in 10 steps with 40 shots at each step
RE(imprint_row(pi_x, -1, 1, 10, events=40))
# Run a scan with two motors from -1, 1 and 12, 20, in five steps with
# 10 shots at each step. Pause if we have less than 1 mJ in the GDET
RE(imprint_row(pi_x, -1, 1,
cxi.kb2.hl, 12, 20, 5,
events=10, min_mj=1))
"""
# Create a new suspender
suspender = SuspendFloor(beam_stats.mj_avg, min_mj)
# Install the new suspender
yield from bps.install_suspender(suspender)
# Execute a scan first configuring the Sequencer and DAQ
try:
yield from sequencer_mode(daq, sequencer, events, sequence_wait=.25)
yield from bp.scan([daq, sequencer], *args)
# Always ensure we remove the suspender
finally:
yield from bps.remove_suspender(suspender)
def get_shutter(mode='debug'):
"""
return
simulated shutter <-- dryrun, debug
acutal shutter <-- production
"""
import apstools.devices as APS_devices
aps = APS_devices.ApsMachineParametersDevice(name="APS")
if mode.lower() in ['debug', 'dryrun']:
A_shutter = APS_devices.SimulatedApsPssShutterWithStatus(name="A_shutter")
elif mode.lower() == 'production':
A_shutter = APS_devices.ApsPssShutterWithStatus(
_devices['A_shutter'][0],
_devices['A_shutter'][1],
name="A_shutter",
)
suspend_APS_current = SuspendFloor(aps.current, 2, resume_thresh=10)
RE.install_suspender(suspend_APS_current)
else:
raise ValueError(f"🙉: invalide mode, {mode}")
return A_shutter
# be placed in this file. You may instead wish to make a copy of this file in
# the user's data directory, and use that as a working copy.
################################################################################
from ophyd import EpicsSignal
from bluesky.suspenders import SuspendFloor, SuspendCeil
if True:
# Define suspenders to hold data collection if x-ray
# beam is not available.
ring_current = EpicsSignal('SR:OPS-BI{DCCT:1}I:Real-I')
sus = SuspendFloor(ring_current, 100, resume_thresh=101)
RE.install_suspender(sus)
#absorber_pos = EpicsSignal( 'XF:11BMB-ES{SM:1-Ax:ArmR}Mtr.RBV')
#sus_abs_low = SuspendFloor(absorber_pos, -56, resume_thresh=-55)
#sus_abs_hi = SuspendCeil(absorber_pos, -54, resume_thresh=-55)
#RE.install_suspender(sus_abs_low)
#RE.install_suspender(sus_abs_hi)
#RE.clear_suspenders()
if False:
# The following shortcuts can be used for unit conversions. For instance,
# for a motor operating in 'mm' units, one could instead do:
# sam.xr( 10*um )
print(__file__)
from bluesky.suspenders import (SuspendBoolHigh, SuspendBoolLow, SuspendFloor,
SuspendCeil, SuspendInBand, SuspendOutBand)
fe_shut_suspender = SuspendBoolHigh(EpicsSignalRO(shutter_fe.status.pvname),
sleep=10 * 60)
ph_shut_suspender = SuspendBoolHigh(EpicsSignalRO(shutter_ph.status.pvname),
sleep=10 * 60)
# suspender for beamline current is mA
beam_current_suspender = SuspendFloor(nsls_ii.beam_current,
suspend_thresh=300,
sleep=10 * 60)
suspenders = [
fe_shut_suspender,
ph_shut_suspender,
beam_current_suspender,
]
''' Some help on suspenders /bluesky
# how to add a suspender:
# Method 1:
# RE.install_suspender(fe_shut_suspender)
# Method 2 (in the plan):
# RE(bpp.suspend_wrapper(myplan(), [suspenders]))
# general bluesky info
# blue sky plans (mostly) reside here:
# general plans
import bluesky.plans as bp
from bluesky.suspenders import SuspendFloor, SuspendBoolLow, SuspendBoolHigh, SuspendCeil
print(f'Loading {__file__}')
# Count on XBPM2 suspender
susp_xbpm2_sum = SuspendFloor(xbpm2.sumY, 0.3, resume_thresh=0.8)
RE.install_suspender(susp_xbpm2_sum)
# Ring current suspender
susp_beam = SuspendFloor(ring.current, 100, resume_thresh=350)
RE.install_suspender(susp_beam)
# Front end shutter suspender
susp_smi_shutter = SuspendFloor(smi_shutter_enable, 0.1, resume_thresh=0.9)
RE.install_suspender(susp_smi_shutter)
# to clear suspenders RE.clear_suspenders()
def set_beamdump_suspender(xrun,
suspend_thres=None,
resume_thres=None,
wait_time=None,
clear=True):
"""helper function to set suspender based on ring_current
Parameters
----------
xrun : instance of RunEngine
the run engine instance suspender will be installed
suspend_thres : float, optional
suspend if ring current value falls below this threshold. ring
current value is read out from ring current signal when
set_beamdump_suspender function is executed. default is the
larger value between 50 mA or 50% of ring current
resume_thres : float, optional
resume if ring current value falls below this threshold. ring
current value is read out from ring current signal when
set_beamdump_suspender function is executed. default is the
larger value among 50 mA or 80% of current ring current
wait_time : float, optional
wait time in seconds after the resume condition is met. default
is 1200s (20 mins)
clear : bool, optional
option on whether to clear all the existing suspender(s).
default is True (only newly added suspender will be applied)
"""
signal = xpd_configuration.get("ring_current", None)
if signal is None:
# edge case, attribute is accidentally removed
raise RuntimeError("no ring current signal is found in "
"current configuration, please reach out to "
"local contact for more help.")
signal_val = signal.get()
default_suspend_thres = 50
default_resume_thres = 50
if suspend_thres is None:
suspend_thres = max(default_suspend_thres, 0.5 * signal_val)
if resume_thres is None:
resume_thres = max(default_resume_thres, 0.8 * signal_val)
if wait_time is None:
wait_time = 1200
if suspend_thres <= 50:
warnings.warn(
"suspender set when beam current is low.\n"
"For the best operation, run:\n"
">>> {}\n"
"when beam current is at its full value."
"To interrogate suspenders have"
" been installed, please run :\n"
">>> {}\n".format("set_suspender(xrun)", "xrun.suspenders"),
UserWarning,
)
sus = SuspendFloor(signal,
suspend_thres,
resume_thresh=resume_thres,
sleep=wait_time)
if clear:
xrun.clear_suspenders()
xrun.install_suspender(sus)
print("INFO: suspender on signal {}, with suspend threshold {} and "
"resume threshold={}, wait time ={}s has been installed.\n".format(
signal.name, suspend_thres, resume_thres, wait_time))
# Shutter
from bluesky.suspenders import SuspendFloor
print("Setting up Shutter")
if in_production:
# define the real shutter used at 6BMA@APS
# NOTE:
# this requires connection to the hardware, otherwise a connection error will be raised
A_shutter = APS_devices.ApsPssShutterWithStatus(
"6bmb1:rShtrA:",
"PA:06BM:STA_A_FES_OPEN_PL",
name="A_shutter",
)
A_shutter.pss_state
# no scans until A_shutter is open
suspend_A_shutter = SuspendFloor(A_shutter.pss_state, 1)
# NOTE:
# since tomo scan take dark field images with shutter colosed, the
# suspender installation for A_shutter is located in the plan for
# granular control.
# no scans if aps.current is too low
suspend_APS_current = SuspendFloor(aps.current, 2, resume_thresh=10)
RE.install_suspender(suspend_APS_current)
else:
# for testing during dark time (no beam, shutter closed by APS)
A_shutter = APS_devices.SimulatedApsPssShutterWithStatus(name="A_shutter")
suspend_A_shutter = SuspendFloor(A_shutter.pss_state, 1)
print("---use simulated shutter---")
from bluesky.suspenders import SuspendFloor, SuspendBoolHigh
ring_suspender = SuspendFloor(ring_curr,
190,
resume_thresh=200,
sleep=120,
post_plan=beamline_align_v2)
#shutterb_suspender = SuspendBoolHigh(EpicsSignalRO(shutterb.status.pvname), sleep=5, post_plan=beamline_align_v2)
# Is this the right PV???
#fe_shut_suspender = SuspendBoolHigh(EpicsSignal('XF:02ID-PPS{Sh:FE}Enbl-Sts'), sleep=20*60)
## It needs:
## RE.install_suspender(test_shutsusp)
## RE.remove_suspender(test_shutsusp)
RE.install_suspender(ring_suspender)
#RE.install_suspender(shutterb_suspender)
print("")
print(
"You can safely ignore the 'SuspendOutBand' warning - this is a known issue that is fixed in a newer version."
)
from bluesky.suspenders import (SuspendFloor, SuspendCeil, SuspendBoolHigh,
SuspendBoolLow)
import bluesky.plans as bp
import bluesky.plan_stubs as bps
import bluesky.preprocessors as bpp
def shuttergenerator(shutter, value):
return (yield from bpp.rewindable_wrapper(bps.mv(shutter, value), False))
# Ring current suspender
susp_rc = SuspendFloor(ring_current,
140,
resume_thresh=160,
sleep=10 * 60,
pre_plan=list(shuttergenerator(shut_b, 'Close')),
post_plan=list(shuttergenerator(shut_b, 'Open')))
# Cryo cooler suspender
susp_cryo = SuspendCeil(cryo_v19,
0.8,
resume_thresh=0.2,
sleep=15 * 60,
pre_plan=list(shuttergenerator(shut_b, 'Close')),
post_plan=list(shuttergenerator(shut_b, 'Open')))
# Shutter status suspender
susp_shut_fe = SuspendBoolHigh(EpicsSignalRO(shut_fe.status.pvname), sleep=10)
susp_shut_a = SuspendBoolHigh(EpicsSignalRO(shut_a.status.pvname), sleep=10)
susp_shut_b = SuspendBoolHigh(EpicsSignalRO(shut_b.status.pvname), sleep=10)
class glbl():
beamline_host_name = BEAMLINE_HOST_NAME
base = BASE_DIR
home = HOME_DIR
_export_tar_dir = _EXPORT_TAR_DIR
xpdconfig = BLCONFIG_DIR
import_dir = IMPORT_DIR
config_base = CONFIG_BASE
tiff_base = TIFF_BASE
usrScript_dir = USERSCRIPT_DIR
yaml_dir = YAML_DIR
allfolders = ALL_FOLDERS
archive_dir = USER_BACKUP_DIR
dk_yaml = DARK_YAML_NAME
dk_window = DARK_WINDOW
frame_acq_time = FRAME_ACQUIRE_TIME
auto_dark = True
owner = OWNER
beamline_id = BEAMLINE_ID
group = GROUP
_allowed_scanplan_type = ALLOWED_SCANPLAN_TYPE
# logic to assign correct objects depends on simulation or real experiment
if not simulation:
from bluesky.run_engine import RunEngine
from bluesky.register_mds import register_mds
# import real object as other names to avoid possible self-referencing later
from bluesky import Msg as msg
from bluesky.plans import Count as count
from bluesky.plans import AbsScanPlan as absScanPlan
from databroker import DataBroker
from databroker import get_images as getImages
from databroker import get_events as getEvents
from bluesky.callbacks import LiveTable as livetable
from bluesky.callbacks.broker import verify_files_saved as verifyFiles
from ophyd import EpicsSignalRO, EpicsSignal
from bluesky.suspenders import SuspendFloor
ring_current = EpicsSignalRO('SR:OPS-BI{DCCT:1}I:Real-I',
name='ring_current')
xpdRE = RunEngine()
xpdRE.md['owner'] = owner
xpdRE.md['beamline_id'] = beamline_id
xpdRE.md['group'] = group
register_mds(xpdRE)
beamdump_sus = SuspendFloor(ring_current,
ring_current.get() * 0.9,
resume_thresh=ring_current.get() * 0.9,
sleep=1200)
#xpdRE.install_suspender(beamdump_sus) # don't enable it untill beam is back
# real imports
Msg = msg
Count = count
db = DataBroker
LiveTable = livetable
get_events = getEvents
get_images = getImages
AbsScanPlan = absScanPlan
verify_files_saved = verifyFiles
# real collection objects
area_det = None
temp_controller = None
shutter = None
else:
simulation = True
ARCHIVE_BASE_DIR = os.path.join(BASE_DIR, 'userSimulationArchive')
# mock imports
Msg = MagicMock()
Count = MagicMock()
AbsScanPlan = MagicMock()
db = MagicMock()
get_events = MagicMock()
get_images = MagicMock()
LiveTable = mock_livetable
verify_files_saved = MagicMock()
# mock collection objects
xpdRE = MagicMock()
temp_controller = MagicMock()
shutter = mock_shutter()
area_det = MagicMock()
area_det.cam = MagicMock()
area_det.cam.acquire_time = MagicMock()
area_det.cam.acquire_time.put = MagicMock(return_value=0.1)
area_det.cam.acquire_time.get = MagicMock(return_value=0.1)
area_det.number_of_sets = MagicMock()
area_det.number_of_sets.put = MagicMock(return_value=1)
print('==== Simulation being created in current directory:{} ===='.
format(BASE_DIR))
from bluesky.suspenders import SuspendFloor, SuspendBoolHigh, SuspendBoolLow
from BMM import user_ns as user_ns_module
user_ns = vars(user_ns_module)
from BMM.user_ns.detectors import quadem1
from BMM.user_ns.metadata import ring
from BMM.user_ns.instruments import bmps, idps
#RE.clear_suspenders()
all_BMM_suspenders = list()
## ----------------------------------------------------------------------------------
## suspend when I0 drops below 0.1 nA (not in use)
suspender_I0 = SuspendFloor(quadem1.I0, 0.1, resume_thresh=1, sleep=5)
#all_BMM_suspenders.append(suspender_I0)
## ----------------------------------------------------------------------------------
## suspend upon beam dump, resume 30 seconds after hitting 90% of fill target
try:
if ring.filltarget.connected is True and ring.filltarget.get() > 20:
suspender_ring_current = SuspendFloor(ring.current,
10,
resume_thresh=0.9 *
ring.filltarget.get(),
sleep=60)
all_BMM_suspenders.append(suspender_ring_current)
except Exception as e:
print(f'failed to create ring current suspender: {e}')
pass
"""
suspender.py
callbacks that suspend operation (beam low, )
"""
from ..framework import RE
from ..devices.misc_devices import I1
from ..plans import tablev_scan
from bluesky.suspenders import SuspendFloor
susp_tablev = SuspendFloor(I1,
suspend_thresh=0.1,
resume_thresh=0.5,
sleep=20
tripped_message='I1 dropped below threshold',
pre_plan=tablev_scan)
RE.install_suspender(tablev_suspender)
from bluesky.suspenders import (SuspendBoolHigh, SuspendBoolLow, SuspendFloor,
SuspendCeil, SuspendInBand, SuspendOutBand)
from ophyd import EpicsSignal
from .startup import RE
ring_suspender = SuspendFloor(EpicsSignal('XF:23ID-SR{}I-I'),
250,
sleep=3 * 60)
#ring_suspender = SuspendFloor(EpicsSignal('XF:23ID-SR{}I-I'), 250, sleep=3)
fe_shut_suspender = SuspendBoolHigh(EpicsSignal('XF:23ID-PPS{Sh:FE}Pos-Sts'),
sleep=10 * 60)
#fe_shut_suspender = SuspendBoolHigh(EpicsSignal('XF:23ID-PPS{Sh:FE}Pos-Sts'), sleep=3)
ps1_shut_suspender = SuspendBoolHigh(EpicsSignal('XF:23IDA-PPS:1{PSh}Pos-Sts'),
sleep=5 * 60)
#ps1_shut_suspender = SuspendBoolHigh(EpicsSignal('XF:23IDA-PPS:1{PSh}Pos-Sts'),sleep=3)
RE.install_suspender(ring_suspender)
RE.install_suspender(fe_shut_suspender)
RE.install_suspender(ps1_shut_suspender)
from bluesky.suspenders import (SuspendFloor, SuspendBoolHigh, SuspendBoolLow)
# Here are some conditions that will cause scans to pause automatically:
# - when the beam current goes below a certain threshold
susp_current = SuspendFloor(beamline_status.beam_current,
suspend_thresh=150.0,
resume_thresh=240.0,
tripped_message='beam current too low',
)
# - when the shutter is closed
susp_shutter = SuspendBoolLow(beamline_status.shutter_status,
tripped_message='shutter not open',
)
# - if the beamline isn't enabled
susp_enabled = SuspendBoolLow(beamline_status.beamline_enabled,
tripped_message='beamline is not enabled',
)
susp_cryo_cooler = SuspendBoolHigh(beamline_status.cryo_filling,
sleep=60*10,
tripped_message='Cyrocooler is refilling')
# NOTE: to enable or disable the suspenders, (un)comment the following:
# Install all suspenders:
#RE.install_suspender(susp_current)
#RE.install_suspender(susp_shutter)
#RE.install_suspender(susp_enabled)
#RE.install_suspender(susp_cryo_cooler)
from bluesky.suspenders import SuspendFloor
ring_suspender = SuspendFloor(ring_curr, 290, resume_thresh=300, sleep=120)
# Is this the right PV???
#fe_shut_suspender = SuspendBoolHigh(EpicsSignal('XF:02ID-PPS{Sh:FE}Enbl-Sts'), sleep=20*60)
## It needs:
## RE.install_suspender(test_shutsusp)
## RE.remove_suspender(test_shutsusp)
RE.install_suspender(ring_suspender)
#RE.install_suspender(fe_shut_suspender)
print("")
print(
"You can safely ignore the 'SuspendOutBand' warning - this is a known issue that is fixed in a newer version."
)
def test_suspenders_stress(RE):
"""
Run scan with tons of inconvenient suspenders
"""
sig = Signal(name="dull signal")
def pre_plan(*args, **kwargs):
yield from null()
logger.debug("starting suspender")
def post_plan(*args, **kwargs):
yield from null()
logger.debug("releasing suspender")
suspenders = [
SuspendFloor(sig, i, sleep=10, pre_plan=pre_plan, post_plan=post_plan)
for i in range(10)
]
for s in suspenders:
RE.install_suspender(s)
mot = SlowSoftPositioner(n_steps=1000,
delay=0.001,
position=0,
name='test_mot')
def sig_sequence(sig):
sig.put(15)
time.sleep(1)
sig.put(9)
logger.debug('expect suspend soon')
time.sleep(1)
sig.put(8)
logger.debug('expect second suspend layer')
time.sleep(1)
sig.put(14)
logger.debug('expect resume after 1 second')
time.sleep(2)
sig.put(2)
logger.debug('expect many layered suspend')
time.sleep(1)
sig.put(15)
logger.debug('expect resume after 1 second')
time.sleep(2)
sig.put(-10)
logger.debug('expect to confuse the scan now')
sig.put(10)
sig.put(3)
sig.put(5)
sig.put(456)
sig.put(0)
sig.put(23)
sig.put(0)
sig.put(15)
logger.debug('hopefully it suspended and is now waiting to resume')
# 3 suspends and 3 resumes should add 6s to the scan
@run_decorator()
def dull_scan(mot, count, sig=None, sleep_time=0):
if sig:
thread = threading.Thread(target=sig_sequence, args=(sig, ))
thread.start()
for i in range(count):
yield from checkpoint()
try:
yield from mv(mot, i)
except:
pass
# make every step take 1s extra
yield from sleep(sleep_time)
yield from checkpoint()
yield from create()
yield from read(mot)
yield from save()
yield from checkpoint()
out = []
coll = collector("test_mot", out)
RE.subscribe('event', coll)
base_start = time.time()
RE(dull_scan(mot, 10, sleep_time=1))
base_elapsed = time.time() - base_start
susp_start = time.time()
RE(dull_scan(mot, 10, sig=sig, sleep_time=1))
susp_elapsed = time.time() - susp_start
assert susp_elapsed - base_elapsed > 6
from ophyd import EpicsSignal
from bluesky.suspenders import SuspendFloor
from bluesky.suspenders import SuspendCeil
#from bluesky.suspenders import SuspendBoolLow
BEAM_RECOVER_TIME = 30 #Time in seconds
BEAM_THRES = 300
beam_current = EpicsSignal('SR:OPS-BI{DCCT:1}I:Real-I')
beam_current_sus = SuspendFloor(beam_current,
BEAM_THRES,
sleep=BEAM_RECOVER_TIME)
def install_beam_suspender():
RE.install_suspender(beam_current_sus)
def uninstall_beam_suspender():
RE.remove_suspender(beam_current_sus)
bpm_xpos = EpicsSignal('XF:16IDB-CT{Best}:BPM0:PosX_Mean')
BPM_X_THRES_HIGH = 20
BPM_X_THRES_LOW = -20
BPM_RECOVER_TIME = 5
bpm_ypos = EpicsSignal('XF:16IDB-CT{Best}:BPM0:PosY_Mean')
BPM_Y_THRES_HIGH = 20
BPM_Y_THRES_LOW = -20
from bluesky.suspenders import SuspendFloor, SuspendBoolHigh, SuspendBoolLow
from IPython import get_ipython
user_ns = get_ipython().user_ns
#RE.clear_suspenders()
all_BMM_suspenders = list()
## ----------------------------------------------------------------------------------
## suspend when I0 drops below 0.1 nA (not in use)
suspender_I0 = SuspendFloor(user_ns['quadem1'].I0,
0.1,
resume_thresh=1,
sleep=5)
#all_BMM_suspenders.append(suspender_I0)
## ----------------------------------------------------------------------------------
## suspend upon beam dump, resume 30 seconds after hitting 90% of fill target
try:
if user_ns['ring'].filltarget.get() > 20:
suspender_ring_current = SuspendFloor(user_ns['ring'].current,
10,
resume_thresh=0.9 *
user_ns['ring'].filltarget.get(),
sleep=60)
all_BMM_suspenders.append(suspender_ring_current)
except:
pass
## ----------------------------------------------------------------------------------
## suspend if the BM photon shutter closes, resume 5 seconds after opening