def measuring(element, edge=None):
BMMuser.element = element
rkvs.set('BMM:pds:element', element)
if edge is not None:
BMMuser.edge = edge
rkvs.set('BMM:pds:edge', edge)
if use_4element:
xs.reset_rois()
if use_1element:
xs1.reset_rois()
show_edges()
def from_json(self, filename):
if os.path.isfile(filename):
with open(filename, 'r') as jsonfile:
config = json.load(jsonfile)
for k in config.keys():
if k in ('cycle', ):
continue
setattr(self, k, config[k])
#rois.trigger = True
from BMM.workspace import rkvs
try:
#rkvs.set('BMM:pds:edge', str(config['edge']))
#rkvs.set('BMM:pds:element', str(config['element']))
rkvs.set('BMM:pds:edge_energy',
edge_energy(config['element'], config['edge']))
BMMuser.element = rkvs.get('BMM:pds:element').decode('utf-8')
BMMuser.edge = rkvs.get('BMM:pds:edge').decode('utf-8')
except:
pass
def set_instrument(instrument=None):
if instrument.lower() == 'glancing angle':
print(bold_msg('Setting instrument as glancing angle stage'))
BMMuser.instrument = 'glancing angle stage'
elif instrument.lower() == 'double wheel':
print(bold_msg('Setting instrument as double sample wheel'))
BMMuser.instrument = 'double wheel'
elif instrument.lower() == 'linkam':
print(bold_msg('Setting instrument as Linkam stage'))
BMMuser.instrument = 'Linkam stage'
elif instrument.lower() == 'lakeshore':
print(bold_msg('Setting instrument as LakeShore 331'))
BMMuser.instrument = 'LakeShore'
elif instrument.lower() == 'grid':
print(bold_msg('Setting instrument as sample grid'))
BMMuser.instrument = 'motor grid'
else:
print(bold_msg('Default instrument choice: sample wheel'))
BMMuser.instrument = 'sample wheel'
rkvs.set('BMM:automation:type', instrument)
def main_plan(start, stop, nsteps, move, slp, force):
(ok, text) = BMM_clear_to_start()
if force is False and ok is False:
print(error_msg(text))
yield from null()
return
user_ns['RE'].msg_hook = None
BMMuser.motor = dm3_bct
func = lambda doc: (doc['data'][motor.name], doc['data']['I0'])
plot = DerivedPlot(func, xlabel=motor.name, ylabel='I0', title='I0 signal vs. slit height')
line1 = '%s, %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(motor.name, 'i0', start, stop, nsteps, motor.user_readback.get())
rkvs.set('BMM:scan:type', 'line')
rkvs.set('BMM:scan:starttime', str(datetime.datetime.timestamp(datetime.datetime.now())))
rkvs.set('BMM:scan:estimated', 0)
@subs_decorator(plot)
#@subs_decorator(src.callback)
def scan_slit(slp):
#if slit_height < 0.5:
# yield from mv(slits3.vsize, 0.5)
yield from mv(quadem1.averaging_time, 0.1)
yield from mv(motor.velocity, 0.4)
yield from mv(motor.kill_cmd, 1)
uid = yield from rel_scan([quadem1], motor, start, stop, nsteps, md={'plan_name' : f'rel_scan linescan {motor.name} I0'})
user_ns['RE'].msg_hook = BMM_msg_hook
BMM_log_info('slit height scan: %s\tuid = %s, scan_id = %d' %
(line1, uid, user_ns['db'][-1].start['scan_id']))
if move:
t = user_ns['db'][-1].table()
signal = t['I0']
#if get_mode() in ('A', 'B', 'C'):
# position = com(signal)
#else:
position = peak(signal)
top = t[motor.name][position]
yield from sleep(slp)
yield from mv(motor.kill_cmd, 1)
yield from sleep(slp)
yield from mv(motor, top)
else:
action = input('\n' + bold_msg('Pluck motor position from the plot? [Y/n then Enter] '))
if action.lower() == 'n' or action.lower() == 'q':
return(yield from null())
yield from sleep(slp)
yield from mv(motor.kill_cmd, 1)
#yield from mv(motor.inpos, 1)
yield from sleep(slp)
yield from move_after_scan(motor)
yield from mv(quadem1.averaging_time, 0.5)
yield from scan_slit(slp)
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 main_plan(detector, slow, startslow, stopslow, nslow, fast, startfast,
stopfast, nfast, pluck, force, dwell, md):
(ok, text) = BMM_clear_to_start()
if force is False and ok is False:
print(error_msg(text))
BMMuser.final_log_entry = False
yield from null()
return
user_ns['RE'].msg_hook = None
## sanity checks on slow axis
if type(slow) is str: slow = slow.lower()
if slow not in motor_nicknames.keys() and 'EpicsMotor' not in str(
type(slow)) and 'PseudoSingle' not in str(type(slow)):
print(
error_msg('\n*** %s is not an areascan motor (%s)\n' %
(slow, str.join(', ', motor_nicknames.keys()))))
BMMuser.final_log_entry = False
yield from null()
return
if slow in motor_nicknames.keys():
slow = motor_nicknames[slow]
## sanity checks on fast axis
if type(fast) is str: fast = fast.lower()
if fast not in motor_nicknames.keys() and 'EpicsMotor' not in str(
type(fast)) and 'PseudoSingle' not in str(type(fast)):
print(
error_msg('\n*** %s is not an areascan motor (%s)\n' %
(fast, str.join(', ', motor_nicknames.keys()))))
BMMuser.final_log_entry = False
yield from null()
return
if fast in motor_nicknames.keys():
fast = motor_nicknames[fast]
detector = detector.capitalize()
yield from mv(_locked_dwell_time, dwell)
dets = [
quadem1,
]
if with_xspress3 and detector == 'If':
detector = 'Xs'
if detector == 'If':
dets.append(vor)
detector = 'ROI1'
if detector.lower() == 'xs':
dets.append(xs)
detector = BMMuser.xs1
yield from mv(xs.total_points, nslow * nfast)
if 'PseudoSingle' in str(type(slow)):
valueslow = slow.readback.get()
else:
valueslow = slow.user_readback.get()
line1 = 'slow motor: %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(slow.name, startslow, stopslow, nslow, valueslow)
if 'PseudoSingle' in str(type(fast)):
valuefast = fast.readback.get()
else:
valuefast = fast.user_readback.get()
line2 = 'fast motor: %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(fast.name, startfast, stopfast, nfast, valuefast)
npoints = nfast * nslow
estimate = int(npoints * (dwell + 0.7))
# extent = (
# valuefast + startfast,
# valueslow + startslow,
# valuefast + stopfast,
# valueslow + stopslow,
# )
# extent = (
# 0,
# nfast-1,
# 0,
# nslow-1
# )
# print(extent)
# return(yield from null())
# areaplot = LiveScatter(fast.name, slow.name, detector,
# xlim=(startfast, stopfast), ylim=(startslow, stopslow))
close_all_plots()
areaplot = LiveGrid(
(nslow, nfast),
detector, #aspect='equal', #aspect=float(nslow/nfast), extent=extent,
xlabel='fast motor: %s' % fast.name,
ylabel='slow motor: %s' % slow.name)
#BMMuser.ax = areaplot.ax
#BMMuser.fig = areaplot.ax.figure
BMMuser.motor = fast
BMMuser.motor2 = slow
#BMMuser.fig.canvas.mpl_connect('close_event', handle_close)
thismd = dict()
thismd['XDI'] = dict()
thismd['XDI']['Facility'] = dict()
thismd['XDI']['Facility']['GUP'] = BMMuser.gup
thismd['XDI']['Facility']['SAF'] = BMMuser.saf
thismd['slow_motor'] = slow.name
thismd['fast_motor'] = fast.name
report(
f'Starting areascan at x,y = {fast.position:.3f}, {slow.position:.3f}',
level='bold',
slack=True)
## engage suspenders right before starting scan sequence
if force is False: BMM_suspenders()
@subs_decorator(areaplot)
#@subs_decorator(src.callback)
def make_areascan(dets,
slow,
startslow,
stopslow,
nslow,
fast,
startfast,
stopfast,
nfast,
snake=False):
BMMuser.final_log_entry = False
uid = yield from grid_scan(
dets,
slow,
startslow,
stopslow,
nslow,
fast,
startfast,
stopfast,
nfast,
snake,
md={
'plan_name':
f'grid_scan measurement {slow.name} {fast.name} {detector}'
})
BMMuser.final_log_entry = True
return uid
rkvs.set('BMM:scan:type', 'area')
rkvs.set('BMM:scan:starttime',
str(datetime.datetime.timestamp(datetime.datetime.now())))
rkvs.set('BMM:scan:estimated', estimate)
BMM_log_info('begin areascan observing: %s\n%s%s' %
(detector, line1, line2))
uid = yield from make_areascan(dets,
slow,
valueslow + startslow,
valueslow + stopslow,
nslow,
fast,
valuefast + startfast,
valuefast + stopfast,
nfast,
snake=False)
if pluck is True:
close_all_plots()
thismap = user_ns['db'].v2[uid]
x = numpy.array(thismap.primary.read()[fast.name])
y = numpy.array(thismap.primary.read()[slow.name])
z=numpy.array(thismap.primary.read()[BMMuser.xs1]) +\
numpy.array(thismap.primary.read()[BMMuser.xs2]) +\
numpy.array(thismap.primary.read()[BMMuser.xs3]) +\
numpy.array(thismap.primary.read()[BMMuser.xs4])
z = z.reshape(nfast, nslow)
# grabbing the first nfast elements of x and every
# nslow-th element of y is more reliable than
# numpy.unique due to float &/or motor precision issues
#plt.title(f'Energy = {energies["below"]}')
plt.xlabel(f'fast axis ({fast.name}) position (mm)')
plt.ylabel(f'slow axis ({slow.name}) position (mm)')
plt.gca().invert_yaxis() # plot an xafs_x/xafs_y plot upright
plt.contourf(x[:nfast], y[::nslow], z, cmap=plt.cm.viridis)
plt.colorbar()
plt.show()
fname = os.path.join(BMMuser.folder, 'map-' + now() + '.png')
plt.savefig(fname)
try:
img_to_slack(fname)
except:
post_to_slack('failed to post image: {fname}')
pass
BMMuser.x = None
figs = list(map(plt.figure, plt.get_fignums()))
canvas = figs[0].canvas
action = input('\n' + bold_msg(
'Pluck motor position from the plot? [Y/n then Enter] '))
if action.lower() == 'n' or action.lower() == 'q':
return (yield from null())
print(
'Single click the left mouse button on the plot to pluck a point...'
)
cid = canvas.mpl_connect(
'button_press_event',
interpret_click) # see 65-derivedplot.py and
while BMMuser.x is None: # https://matplotlib.org/users/event_handling.html
yield from sleep(0.5)
# print('Converting plot coordinates to real coordinates...')
# begin = valuefast + startfast
# stepsize = (stopfast - startfast) / (nfast - 1)
# pointfast = begin + stepsize * BMMuser.x
# #print(BMMuser.x, pointfast)
# begin = valueslow + startslow
# stepsize = (stopslow - startslow) / (nslow - 1)
# pointslow = begin + stepsize * BMMuser.y
# #print(BMMuser.y, pointslow)
# print('That translates to x=%.3f, y=%.3f' % (pointfast, pointslow))
yield from mv(fast, BMMuser.x, slow, BMMuser.y)
report(
f'Moved to position x,y = {fast.position:.3f}, {slow.position:.3f}',
level='bold',
slack=True)
def main_plan(detector, axis, start, stop, nsteps, pluck, force, md):
(ok, text) = BMM_clear_to_start()
if force is False and ok is False:
print(error_msg(text))
yield from null()
return
detector, axis = ls_backwards_compatibility(detector, axis)
# print('detector is: ' + str(detector))
# print('axis is: ' + str(axis))
# return(yield from null())
user_ns['RE'].msg_hook = None
## sanitize input and set thismotor to an actual motor
if type(axis) is str: axis = axis.lower()
detector = detector.capitalize()
## sanity checks on axis
if axis not in motor_nicknames.keys() and 'EpicsMotor' not in str(type(axis)) \
and 'PseudoSingle' not in str(type(axis)) and 'WheelMotor' not in str(type(axis)):
print(error_msg('\n*** %s is not a linescan motor (%s)\n' %
(axis, str.join(', ', motor_nicknames.keys()))))
yield from null()
return
if 'EpicsMotor' in str(type(axis)):
thismotor = axis
elif 'PseudoSingle' in str(type(axis)):
thismotor = axis
elif 'WheelMotor' in str(type(axis)):
thismotor = axis
else: # presume it's an xafs_XXXX motor
thismotor = motor_nicknames[axis]
current = thismotor.position
if current+start < thismotor.limits[0]:
print(error_msg(f'These scan parameters will take {thismotor.name} outside it\'s lower limit of {thismotor.limits[0]}'))
print(whisper(f'(starting position = {thismotor.position})'))
return(yield from null())
if current+stop > thismotor.limits[1]:
print(error_msg(f'These scan parameters will take {thismotor.name} outside it\'s upper limit of {thismotor.limits[1]}'))
print(whisper(f'(starting position = {thismotor.position})'))
return(yield from null())
BMMuser.motor = thismotor
# sanity checks on detector
if detector not in ('It', 'If', 'I0', 'Iy', 'Ir', 'Both', 'Bicron', 'Ia', 'Ib', 'Dualio', 'Xs', 'Xs1'):
print(error_msg('\n*** %s is not a linescan measurement (%s)\n' %
(detector, 'it, if, i0, iy, ir, both, bicron, dualio, xs, xs1')))
yield from null()
return
yield from mv(_locked_dwell_time, inttime)
if detector == 'Xs':
yield from mv(xs.cam.acquire_time, inttime)
yield from mv(xs.total_points, nsteps)
dets = [quadem1, ]
denominator = ''
detname = ''
# If should be xs when using Xspress3
if with_xspress3 and detector == 'If':
detector = 'Xs'
# func is an anonymous function, built on the fly, for feeding to DerivedPlot
if detector == 'It':
denominator = ' / I0'
detname = 'transmission'
func = lambda doc: (doc['data'][thismotor.name], doc['data']['It']/doc['data']['I0'])
elif detector == 'Ia' and dualio is not None:
dets.append(dualio)
detname = 'Ia'
func = lambda doc: (doc['data'][thismotor.name], doc['data']['Ia'])
elif detector == 'Ib' and dualio is not None:
dets.append(dualio)
detname = 'Ib'
func = lambda doc: (doc['data'][thismotor.name], doc['data']['Ib'])
elif detector == 'Ir':
#denominator = ' / It'
detname = 'reference'
#func = lambda doc: (doc['data'][thismotor.name], doc['data']['Ir']/doc['data']['It'])
func = lambda doc: (doc['data'][thismotor.name], doc['data']['Ir'])
elif detector == 'I0':
detname = 'I0'
func = lambda doc: (doc['data'][thismotor.name], doc['data']['I0'])
elif detector == 'Bicron':
dets.append(vor)
detname = 'Bicron'
func = lambda doc: (doc['data'][thismotor.name], doc['data']['Bicron'])
elif detector == 'Iy':
denominator = ' / I0'
detname = 'electron yield'
func = lambda doc: (doc['data'][thismotor.name], doc['data']['Iy']/doc['data']['I0'])
elif detector == 'If':
dets.append(vor)
denominator = ' / I0'
detname = 'fluorescence'
func = lambda doc: (doc['data'][thismotor.name],
(doc['data'][BMMuser.dtc1] +
doc['data'][BMMuser.dtc2] +
doc['data'][BMMuser.dtc3] +
doc['data'][BMMuser.dtc4] ) / doc['data']['I0'])
elif detector == 'Xs':
dets.append(xs)
denominator = ' / I0'
detname = 'fluorescence'
func = lambda doc: (doc['data'][thismotor.name],
(doc['data'][BMMuser.xs1] +
doc['data'][BMMuser.xs2] +
doc['data'][BMMuser.xs3] +
doc['data'][BMMuser.xs4] ) / doc['data']['I0'])
yield from mv(xs.total_points, nsteps) # Xspress3 demands that this be set up front
elif detector == 'Xs1':
dets.append(xs1)
denominator = ' / I0'
detname = 'fluorescence'
func = lambda doc: (doc['data'][thismotor.name],
doc['data'][BMMuser.xs8] / doc['data']['I0'])
yield from mv(xs1.total_points, nsteps) # Xspress3 demands that this be set up front
elif detector == 'Dualio':
dets.append(dualio)
funcia = lambda doc: (doc['data'][thismotor.name], doc['data']['Ia'])
funcib = lambda doc: (doc['data'][thismotor.name], doc['data']['Ib'])
## need a "Both" for trans + xs !!!!!!!!!!
elif detector == 'Both':
dets.append(vor)
functr = lambda doc: (doc['data'][thismotor.name], doc['data']['It']/doc['data']['I0'])
funcfl = lambda doc: (doc['data'][thismotor.name],
(doc['data'][BMMuser.dtc1] +
doc['data'][BMMuser.dtc2] +
doc['data'][BMMuser.dtc3] +
doc['data'][BMMuser.dtc4] ) / doc['data']['I0'])
## and this is the appropriate way to plot this linescan
#mv(_locked_dwell_time, 0.5)
if detector == 'Both':
plot = [DerivedPlot(funcfl, xlabel=thismotor.name, ylabel='If/I0', title='fluorescence vs. %s' % thismotor.name),
DerivedPlot(functr, xlabel=thismotor.name, ylabel='It/I0', title='transmission vs. %s' % thismotor.name)]
elif detector == 'Dualio':
plot = [DerivedPlot(funcia, xlabel=thismotor.name, ylabel='Ia/I0', title='Ia vs. %s' % thismotor.name),
DerivedPlot(funcib, xlabel=thismotor.name, ylabel='Ib/I0', title='Ib vs. %s' % thismotor.name)]
else:
plot = DerivedPlot(func,
xlabel=thismotor.name,
ylabel=detector+denominator,
title='%s vs. %s' % (detname, thismotor.name))
if 'PseudoSingle' in str(type(axis)):
value = thismotor.readback.get()
else:
value = thismotor.user_readback.get()
line1 = '%s, %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(thismotor.name, detector, start, stop, nsteps, value)
##BMM_suspenders() # engage suspenders
thismd = dict()
thismd['XDI'] = dict()
thismd['XDI']['Facility'] = dict()
thismd['XDI']['Facility']['GUP'] = BMMuser.gup
thismd['XDI']['Facility']['SAF'] = BMMuser.saf
#if 'purpose' not in md:
# md['purpose'] = 'alignment'
rkvs.set('BMM:scan:type', 'line')
rkvs.set('BMM:scan:starttime', str(datetime.datetime.timestamp(datetime.datetime.now())))
rkvs.set('BMM:scan:estimated', 0)
@subs_decorator(plot)
#@subs_decorator(src.callback)
def scan_xafs_motor(dets, motor, start, stop, nsteps):
uid = yield from rel_scan(dets, motor, start, stop, nsteps, md={**thismd, **md, 'plan_name' : f'rel_scan linescan {motor.name} {detector}'})
return uid
uid = yield from scan_xafs_motor(dets, thismotor, start, stop, nsteps)
#global mytable
#run = src.retrieve()
#mytable = run.primary.read().to_dataframe()
BMM_log_info('linescan: %s\tuid = %s, scan_id = %d' %
(line1, uid, user_ns['db'][-1].start['scan_id']))
if pluck is True:
action = input('\n' + bold_msg('Pluck motor position from the plot? [Y/n then Enter] '))
if action.lower() == 'n' or action.lower() == 'q':
return(yield from null())
yield from move_after_scan(thismotor)
def doscan():
line1 = '%s, %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(motor.name, sgnl, start, stop, nsteps, motor.user_readback.get())
uid = yield from rel_scan(dets, motor, start, stop, nsteps, md={'plan_name' : f'rel_scan linescan {motor.name} I0'})
t = user_ns['db'][-1].table()
if detector.lower() == 'if':
signal = numpy.array((t[BMMuser.xs1]+t[BMMuser.xs2]+t[BMMuser.xs3]+t[BMMuser.xs4])/t['I0'])
elif detector.lower() == 'it':
signal = numpy.array(t['It']/t['I0'])
elif detector.lower() == 'ir':
signal = numpy.array(t['Ir']/t['It'])
signal = signal - signal[0]
if negate is True:
signal = -1 * signal
pos = numpy.array(t[motor.name])
mod = RectangleModel(form='erf')
pars = mod.guess(signal, x=pos)
out = mod.fit(signal, pars, x=pos)
print(whisper(out.fit_report(min_correl=0)))
out.plot()
if filename is not None:
plt.savefig(filename)
#middle = out.params['center1'].value + (out.params['center2'].value - out.params['center1'].value)/2
yield from mv(motor, out.params['midpoint'].value)
print(bold_msg(f'Found center at {motor.name} = {motor.position}'))
rkvs.set('BMM:lmfit:center1', out.params['center1'].value)
rkvs.set('BMM:lmfit:center2', out.params['center2'].value)
rkvs.set('BMM:lmfit:sigma1', out.params['sigma1'].value)
rkvs.set('BMM:lmfit:sigma2', out.params['sigma2'].value)
rkvs.set('BMM:lmfit:amplitude', out.params['amplitude'].value)
rkvs.set('BMM:lmfit:midpoint', out.params['midpoint'].value)
def main_plan(motor, start, stop, nsteps, detector, negate):
(ok, text) = BMM_clear_to_start()
if ok is False:
print(error_msg(text))
yield from null()
return
user_ns['RE'].msg_hook = None
BMMuser.motor = motor
dets = [user_ns['quadem1'],]
sgnl = 'fluorescence (Xspress3)'
if detector.lower() == 'if':
dets.append(user_ns['xs'])
denominator = ' / I0'
sgnl = 'fluorescence (Xspress3)'
func = lambda doc: (doc['data'][motor.name],
(doc['data'][BMMuser.xs1] +
doc['data'][BMMuser.xs2] +
doc['data'][BMMuser.xs3] +
doc['data'][BMMuser.xs4] ) / doc['data']['I0'])
yield from mv(xs.total_points, nsteps)
elif detector.lower() == 'it':
sgnl = 'transmission'
func = lambda doc: (doc['data'][motor.name], doc['data']['It']/ doc['data']['I0'])
elif detector.lower() == 'ir':
sgnl = 'reference'
func = lambda doc: (doc['data'][motor.name], doc['data']['Ir']/ doc['data']['It'])
titl = f'{sgnl} vs. {motor.name}'
plot = DerivedPlot(func, xlabel=motor.name, ylabel=sgnl, title=titl)
rkvs.set('BMM:scan:type', 'line')
rkvs.set('BMM:scan:starttime', str(datetime.datetime.timestamp(datetime.datetime.now())))
rkvs.set('BMM:scan:estimated', 0)
@subs_decorator(plot)
#@subs_decorator(src.callback)
def doscan():
line1 = '%s, %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(motor.name, sgnl, start, stop, nsteps, motor.user_readback.get())
uid = yield from rel_scan(dets, motor, start, stop, nsteps, md={'plan_name' : f'rel_scan linescan {motor.name} I0'})
t = user_ns['db'][-1].table()
if detector.lower() == 'if':
signal = numpy.array((t[BMMuser.xs1]+t[BMMuser.xs2]+t[BMMuser.xs3]+t[BMMuser.xs4])/t['I0'])
elif detector.lower() == 'it':
signal = numpy.array(t['It']/t['I0'])
elif detector.lower() == 'ir':
signal = numpy.array(t['Ir']/t['It'])
signal = signal - signal[0]
if negate is True:
signal = -1 * signal
pos = numpy.array(t[motor.name])
mod = RectangleModel(form='erf')
pars = mod.guess(signal, x=pos)
out = mod.fit(signal, pars, x=pos)
print(whisper(out.fit_report(min_correl=0)))
out.plot()
if filename is not None:
plt.savefig(filename)
#middle = out.params['center1'].value + (out.params['center2'].value - out.params['center1'].value)/2
yield from mv(motor, out.params['midpoint'].value)
print(bold_msg(f'Found center at {motor.name} = {motor.position}'))
rkvs.set('BMM:lmfit:center1', out.params['center1'].value)
rkvs.set('BMM:lmfit:center2', out.params['center2'].value)
rkvs.set('BMM:lmfit:sigma1', out.params['sigma1'].value)
rkvs.set('BMM:lmfit:sigma2', out.params['sigma2'].value)
rkvs.set('BMM:lmfit:amplitude', out.params['amplitude'].value)
rkvs.set('BMM:lmfit:midpoint', out.params['midpoint'].value)
yield from doscan()
def main_plan(start, stop, nsteps, detector):
(ok, text) = BMM_clear_to_start()
if ok is False:
print(error_msg(text))
yield from null()
return
user_ns['RE'].msg_hook = None
BMMuser.motor = motor
if detector.lower() == 'bicron':
func = lambda doc: (doc['data'][motor.name], doc['data']['Bicron'])
dets = [bicron,]
sgnl = 'Bicron'
titl = 'Bicron signal vs. DCM 2nd crystal pitch'
else:
func = lambda doc: (doc['data'][motor.name], doc['data']['I0'])
dets = [quadem1,]
sgnl = 'I0'
titl = 'I0 signal vs. DCM 2nd crystal pitch'
plot = DerivedPlot(func, xlabel=motor.name, ylabel=sgnl, title=titl)
rkvs.set('BMM:scan:type', 'line')
rkvs.set('BMM:scan:starttime', str(datetime.datetime.timestamp(datetime.datetime.now())))
rkvs.set('BMM:scan:estimated', 0)
@subs_decorator(plot)
#@subs_decorator(src.callback)
def scan_dcmpitch(sgnl):
line1 = '%s, %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(motor.name, sgnl, start, stop, nsteps, motor.user_readback.get())
yield from mv(_locked_dwell_time, 0.1)
yield from dcm.kill_plan()
yield from mv(slits3.vsize, 3)
if sgnl == 'Bicron':
yield from mv(slitsg.vsize, 5)
uid = yield from rel_scan(dets, motor, start, stop, nsteps, md={'plan_name' : f'rel_scan linescan {motor.name} I0'})
#yield from rel_adaptive_scan(dets, 'I0', motor,
# start=start,
# stop=stop,
# min_step=0.002,
# max_step=0.03,
# target_delta=.15,
# backstep=True)
t = user_ns['db'][-1].table()
signal = t[sgnl]
if choice.lower() == 'com':
position = com(signal)
top = t[motor.name][position]
elif choice.lower() == 'fit':
pitch = t['dcm_pitch']
mod = SkewedGaussianModel()
pars = mod.guess(signal, x=pitch)
out = mod.fit(signal, pars, x=pitch)
print(whisper(out.fit_report(min_correl=0)))
out.plot()
top = out.params['center'].value
else:
position = peak(signal)
top = t[motor.name][position]
yield from mv(motor.kill_cmd, 1)
yield from sleep(1.0)
user_ns['RE'].msg_hook = BMM_msg_hook
BMM_log_info('rocking curve scan: %s\tuid = %s, scan_id = %d' %
(line1, uid, user_ns['db'][-1].start['scan_id']))
yield from mv(motor, top)
if sgnl == 'Bicron':
yield from mv(slitsg.vsize, gonio_slit_height)
yield from scan_dcmpitch(sgnl)
def xlsx():
'''Prompt for a macro building spreadsheet for any instrument. Use the
content of cell B1 to direct this spreadsheet to the correct builder.
if cell B1 is "Glancing angle" --> build a glancing angle macro
if cell B1 is "Sample wheel" --> build a sample wheel macro
if cell B1 is empty --> build a sample wheel macro
Then prompt for the sheet, if there are more than 1 sheet in the
spreadsheet file.
'''
spreadsheet = present_options('xlsx')
if spreadsheet is None:
print(error_msg('No spreadsheet specified!'))
return None
wb = load_workbook(os.path.join(BMMuser.folder, spreadsheet),
read_only=True)
#ws = wb.active
sheets = wb.sheetnames
if len(sheets) == 1:
sheet = sheets[0]
elif len(sheets) == 2 and 'Version history' in sheets:
sheet = sheets[0]
else:
print(f'Select a sheet from {spreadsheet}:\n')
actual = []
for i, x in enumerate(sheets):
if x == 'Version history':
continue
print(f' {i+1:2}: {x}')
actual.append(x)
print('\n r: return')
choice = input("\nSelect a sheet > ")
try:
if int(choice) > 0 and int(choice) <= len(actual):
sheet = actual[int(choice) - 1]
else:
print('No sheet specified')
return
except Exception as E:
print(E)
print('No sheet specified')
return
instrument = str(wb[sheet]['B1'].value).lower()
if instrument.lower() == 'glancing angle':
print(bold_msg('This is a glancing angle spreadsheet'))
gawheel.spreadsheet(spreadsheet, sheet)
BMMuser.instrument = 'glancing angle stage'
elif instrument.lower() == 'double wheel':
print(bold_msg('This is a double sample wheel spreadsheet'))
wmb.spreadsheet(spreadsheet, sheet, double=True)
BMMuser.instrument = 'double wheel'
elif instrument.lower() == 'linkam':
print(bold_msg('This is a Linkam spreadsheet'))
lmb.spreadsheet(spreadsheet, sheet)
BMMuser.instrument = 'Linkam stage'
elif instrument.lower() == 'lakeshore':
print(bold_msg('This is a LakeShore spreadsheet'))
lsmb.spreadsheet(spreadsheet, sheet)
BMMuser.instrument = 'LakeShore 331'
elif instrument.lower() == 'grid':
print(bold_msg('This is a motor grid spreadsheet'))
gmb.spreadsheet(spreadsheet, sheet)
BMMuser.instrument = 'motor grid'
else:
print(bold_msg('This is a sample wheel spreadsheet'))
wmb.spreadsheet(spreadsheet, sheet, double=False)
BMMuser.instrument = 'sample wheel'
rkvs.set('BMM:automation:type', instrument)
def in_place(self):
#user_ns['wmb'].outer_position = user_ns['xafs_x'].position
#user_ns['wmb'].inner_position = user_ns['wmb'].outer_position + 26
self.outer_position = user_ns['xafs_x'].position
self.inner_position = self.outer_position + 26
rkvs.set('BMM:wheel:outer', self.outer_position)