def cleanup_plan():
print(
'Cleaning up after single energy absorption detector measurement')
BMM_clear_suspenders()
#RE.clear_suspenders()
yield from resting_state_plan()
dcm.mode = 'fixed'
def cleanup_plan():
print('Cleaning up after an area scan')
BMM_clear_suspenders()
#RE.clear_suspenders()
if BMMuser.final_log_entry is True:
BMM_log_info('areascan finished\n\tuid = %s, scan_id = %d' %
(db[-1].start['uid'], db[-1].start['scan_id']))
yield from resting_state_plan()
RE.msg_hook = BMM_msg_hook
print('Disabling plot for re-plucking.')
try:
cid = BMMuser.fig.canvas.mpl_disconnect(cid)
except:
pass
BMMuser.x = None
BMMuser.y = None
BMMuser.motor = None
BMMuser.motor2 = None
BMMuser.fig = None
BMMuser.ax = None
def end_of_macro():
'''Plan for bringing controls into their resting state at the end of
a macro or when a macro is stopped or aborted:
- quadEM and Struck scaler enabled and measuring
- dwell time set to 1/2 second
- electron yield channel (quadEM channel 4) hinted as 'omitted'
- user prompt set to True. macro dry-run set to False, RE.msg_hook set to BMM_msg_hook
'''
BMMuser.prompt, BMMuser.macro_dryrun, BMMuser.instrument , quadem1.Iy.kind = True, False, '', 'omitted'
BMMuser.running_macro, BMMuser.lims = False, True
yield from quadem1.on_plan()
#yield from vor.on_plan()
yield from mv(_locked_dwell_time, 0.5)
#yield from mv(user_ns['dm3_bct'].kill_cmd, 1)
yield from sleep(0.2)
yield from dcm.kill_plan()
yield from xafs_wheel.recenter()
dcm.mode = 'fixed'
user_ns['RE'].msg_hook = BMM_msg_hook
resting_redis()
BMM_clear_suspenders()
def change_edge(el,
focus=False,
edge='K',
energy=None,
slits=True,
target=300.,
xrd=False,
bender=True):
'''Change edge energy by:
1. Moving the DCM above the edge energy
2. Moving the photon delivery system to the correct mode
3. Running a rocking curve scan
4. Running a slits_height scan
Parameters
----------
el : str
one- or two-letter symbol
focus : bool, optional
T=focused or F=unfocused beam [False, unfocused]
edge : str, optional
edge symbol ['K']
energy : float, optional
e0 value [None, determined from el/edge]
slits : bool, optional
perform slit_height() scan [False]
target : float, optional
energy where rocking curve is measured [300]
xrd : boolean, optional
force photon delivery system to XRD [False]
Examples
--------
Normal use, unfocused beam:
>>> RE(change_edge('Fe'))
Normal use, focused beam:
>>> RE(change_edge('Fe', focus=True))
L2 or L1 edge:
>>> RE(change_edge('Re', edge='L2'))
Measure rocking curve at edge energy:
>>> RE(change_edge('Fe', target=0))
XRD, new energy:
>>> RE(change_edge('Fe', xrd=True, energy=8600))
note that you must specify an element, but it doesn't matter which
one the energy will be moved to the specified energy xrd=True
implies focus=True and target=0
'''
# try:
# xs = user_ns['xs']
# except:
# pass
#BMMuser.prompt = True
el = el.capitalize()
######################################################################
# this is a tool for verifying a macro. this replaces an xafsmod scan #
# with a sleep, allowing the user to easily map out motor motions in #
# a macro #
if BMMuser.macro_dryrun:
print(
info_msg(
'\nBMMuser.macro_dryrun is True. Sleeping for %.1f seconds rather than changing to the %s edge.\n'
% (BMMuser.macro_sleep, el)))
countdown(BMMuser.macro_sleep)
return (yield from null())
######################################################################
if pds_motors_ready() is False:
print(
error_msg(
'\nOne or more motors are showing amplifier faults.\nToggle the correct kill switch, then re-enable the faulted motor.'
))
return (yield from null())
(ok, text) = BMM_clear_to_start()
if ok is False:
print(
error_msg('\n' + text) +
bold_msg('Quitting change_edge() macro....\n'))
return (yield from null())
if energy is None:
energy = edge_energy(el, edge)
if energy is None:
print(
error_msg('\nEither %s or %s is not a valid symbol\n' %
(el, edge)))
return (yield from null())
if energy > 23500:
edge = 'L3'
energy = edge_energy(el, 'L3')
if energy < 4000:
print(warning_msg('The %s edge energy is below 4950 eV' % el))
print(warning_msg('You have to change energy by hand.'))
return (yield from null())
if energy > 23500:
print(
warning_msg(
'The %s edge energy is outside the range of this beamline!' %
el))
return (yield from null())
BMM_suspenders()
if energy > 8000:
mode = 'A' if focus else 'D'
elif energy < 6000:
#mode = 'B' if focus else 'F' ## mode B currently is inaccessible :(
mode = 'C' if focus else 'F'
else:
mode = 'C' if focus else 'E'
if xrd:
mode = 'XRD'
focus = True
target = 0.0
current_mode = get_mode()
if mode in ('D', 'E', 'F') and current_mode in ('D', 'E', 'F'):
with_m2 = False
elif mode in ('A', 'B',
'C') and current_mode in ('A', 'B',
'C'): # no need to move M2
with_m2 = False
else:
with_m2 = True
if all_connected(with_m2) is False:
print(warning_msg('Ophyd connection failure' % el))
return (yield from null())
################################
# confirm configuration change #
################################
print(bold_msg('\nEnergy change:'))
print(' %s: %s %s' %
(list_msg('edge'), el.capitalize(), edge.capitalize()))
print(' %s: %.1f' % (list_msg('edge energy'), energy))
print(' %s: %.1f' % (list_msg('target energy'), energy + target))
print(' %s: %s' % (list_msg('focus'), str(focus)))
print(' %s: %s' % (list_msg('photon delivery mode'), mode))
print(' %s: %s' % (list_msg('optimizing slits height'), str(slits)))
if BMMuser.prompt:
action = input("\nBegin energy change? [Y/n then Enter] ")
if action.lower() == 'q' or action.lower() == 'n':
return (yield from null())
if mode == 'C' and energy < 6000:
print(
warning_msg(
'\nMoving to mode C for focused beam and an edge energy below 6 keV.'
))
action = input(
"You will not get optimal harmonic rejection. Continue anyway? [Y/n then Enter] "
)
if action.lower() == 'q' or action.lower() == 'n':
return (yield from null())
BMMuser.edge = edge
BMMuser.element = el
BMMuser.edge_energy = energy
rkvs.set('BMM:pds:edge', edge)
rkvs.set('BMM:pds:element', el)
rkvs.set('BMM:pds:edge_energy', energy)
start = time.time()
if mode == 'XRD':
report('Configuring beamline for XRD', level='bold', slack=True)
else:
report(
f'Configuring beamline for {el.capitalize()} {edge.capitalize()} edge',
level='bold',
slack=True)
yield from dcm.kill_plan()
################################################
# change to the correct photon delivery mode #
# + move mono to correct energy #
# + move reference holder to correct slot #
################################################
# if not calibrating and mode != current_mode:
# print('Moving to photon delivery mode %s...' % mode)
yield from mv(dcm_bragg.acceleration, BMMuser.acc_slow)
yield from change_mode(mode=mode,
prompt=False,
edge=energy + target,
reference=el,
bender=bender)
yield from mv(dcm_bragg.acceleration, BMMuser.acc_fast)
if arrived_in_mode(mode=mode) is False:
print(error_msg(f'\nFailed to arrive in Mode {mode}'))
print(
'Fixing this is often as simple as re-running the change_mode() command.'
)
print(
'Or try dm3_bct.kill_cmd() then dm3_bct.enable_cmd() then re-run the change_mode() command.'
)
print('If that doesn\'t work, call for help')
return (yield from null())
yield from kill_mirror_jacks()
yield from sleep(1)
if BMMuser.motor_fault is not None:
print(
error_msg('\nSome motors are reporting amplifier faults: %s' %
BMMuser.motor_fault))
print(
'Clear the faults and try running the same change_edge() command again.'
)
print('Troubleshooting: ' + url_msg(
'https://nsls-ii-bmm.github.io/BeamlineManual/trouble.html#amplifier-fault'
))
BMMuser.motor_fault = None
return (yield from null())
BMMuser.motor_fault = None
############################
# run a rocking curve scan #
############################
print('Optimizing rocking curve...')
yield from mv(dcm_pitch.kill_cmd, 1)
yield from mv(dcm_pitch, approximate_pitch(energy + target))
yield from sleep(1)
yield from mv(dcm_pitch.kill_cmd, 1)
yield from sleep(1)
yield from rocking_curve()
close_last_plot()
##########################
# run a slit height scan #
##########################
if slits:
print('Optimizing slits height...')
yield from slit_height(move=True)
close_last_plot()
## redo rocking curve?
##################################
# set reference and roi channels #
##################################
if not xrd:
## reference channel
print('Moving reference foil...')
yield from rois.select_plan(el)
## Xspress3
if with_xspress3:
BMMuser.verify_roi(xs, el, edge)
## feedback
show_edges()
if mode == 'XRD':
report('Finished configuring for XRD', level='bold', slack=True)
else:
report(
f'Finished configuring for {el.capitalize()} {edge.capitalize()} edge',
level='bold',
slack=True)
if slits is False:
print(
' * You may need to verify the slit position: RE(slit_height())')
#xBMMuser.to_json(os.path.join(BMMuser.folder, '.BMMuser'))
BMM_clear_suspenders()
yield from dcm.kill_plan()
yield from mv(m2_bender.kill_cmd, 1)
end = time.time()
print('\n\nThat took %.1f min' % ((end - start) / 60))
return ()
def auto_align(self, pitch=2, drop=None):
'''Align a sample on a spinner automatically. This performs 5 scans.
The first four iterate twice between linear and pitch
against the signal in It. This find the flat position.
Then the sample is pitched to the requested angle and a fifth
scan is done to optimize the linear motor position against the
fluorescence signal.
The linear scans against It look like a step-down function.
The center of this step is found as the centroid of a fitted
error function.
The xafs_pitch scan should be peaked. Move to the max of the
signal.
The linear scan against fluorescence ideally looks like a
flat-topped peak. Move to the center of mass.
At the end, a three-panel figure is drawn showing the last
three scans. This is posted to Slack. It also finds its way
into the dossier as a record of the quality of the alignment.
Arguments
=========
pitch : int
The angle at which to make the glancing angle measurements.
drop : int or None
If not None, then this many points will be dropped from the
end of linear scan against transmission when fitting the error
function. This is an attempt to deal gracefully with leakage
through the adhesive at very high energy.
'''
BMMuser = user_ns['BMMuser']
if BMMuser.macro_dryrun:
report(f'Auto-aligning glancing angle stage, spinner {self.current()}', level='bold', slack=False)
print(info_msg(f'\nBMMuser.macro_dryrun is True. Sleeping for %.1f seconds at spinner %d.\n' %
(BMMuser.macro_sleep, self.current())))
countdown(BMMuser.macro_sleep)
return(yield from null())
report(f'Auto-aligning glancing angle stage, spinner {self.current()}', level='bold', slack=True)
BMM_suspenders()
## first pass in transmission
yield from self.align_linear(drop=drop)
yield from self.align_pitch()
## for realsies X or Y in transmission
yield from self.align_linear(drop=drop)
self.y_uid = user_ns['db'].v2[-1].metadata['start']['uid']
## for realsies Y in pitch
yield from self.align_pitch()
self.pitch_uid = user_ns['db'].v2[-1].metadata['start']['uid']
## record the flat position
if self.orientation == 'parallel':
motor = user_ns['xafs_y']
else:
motor = user_ns['xafs_x']
self.flat = [motor.position, user_ns['xafs_pitch'].position]
## move to measurement angle and align
yield from mvr(user_ns['xafs_pitch'], pitch)
yield from linescan(motor, 'xs', -2.3, 2.3, 51, pluck=False)
self.f_uid = user_ns['db'].v2[-1].metadata['start']['uid']
tf = user_ns['db'][-1].table()
yy = tf[motor.name]
signal = (tf[BMMuser.xs1] + tf[BMMuser.xs2] + tf[BMMuser.xs3] + tf[BMMuser.xs4]) / tf['I0']
if BMMuser.element == 'Zr':
centroid = yy[signal.idxmax()]
else:
com = int(center_of_mass(signal)[0])+1
centroid = yy[com]
yield from mv(motor, centroid)
## make a pretty picture, post it to slack
self.alignment_plot(self.y_uid, self.pitch_uid, self.f_uid)
self.alignment_filename = os.path.join(BMMuser.folder, 'snapshots', f'spinner{self.current()}-alignment-{now()}.png')
plt.savefig(self.alignment_filename)
try:
img_to_slack(self.alignment_filename)
except:
post_to_slack('failed to post image: {self.alignment_filename}')
pass
BMM_clear_suspenders()