def dark_current(self):
print(f'Measuring current offsets for {self.name}, this will take several seconds')
yield from mv(self.compute_current_offset1,1)
yield from mv(self.compute_current_offset2,1)
yield from mv(self.compute_current_offset3,1)
yield from mv(self.compute_current_offset4,1)
BMM_log_info('Measured dark current on quadem1')
def set_roi(self, i, el):
'''Configure an ROI channel i ∈ (1 .. 3) for element el'''
if Z_number(el) is None:
self.slots[i - 1] = None
else:
self.slots[i - 1] = element_symbol(el)
BMM_log_info('Set ROI channel %d to %s' % (i, str(self.slots[i - 1])))
def energystep(filename = None,
start = None,
end = None,
nsteps = None,
delay = 5,
dosteps = True):
'''A simple energy scan, just step forward in energy and don't measure
anything. This is a quick hack for use with a crude resonant
reflectivity experiment with IBM folks.
filename: name of file, will be appended to DATA for the full path (required)
start: starting energy value (required)
end: ending energy value (required)
nsteps: number of energy steps (required)
delay: pause between energy steps, in seconds [5]
dosteps: False to see energy values printed to screen without moving mono [True]
Writes a data file with columns of energy readback, energy
requested, time of epoch, and ISO 8601 timestamp
Example:
energystep(filename='blahblah', start=18936, end=19036, nsteps=101)
'''
BMMuser, dcm = user_ns['BMMuser'], user_ns['dcm']
BMM_log_info("energystep(filename=%s, start=%.1f, end=%.1f, nsteps=%d, delay=%.1f, dosteps=%s)" % (filename, start, end, nsteps, delay, str(dosteps)))
datafile = BMMuser.DATA + filename
handle = open(datafile, 'w')
handle.write('# energy steps from %.1f to %.1f in %d steps\n' % (start, end, nsteps))
handle.write('#----------------------------------------------------\n')
handle.write('# energy requested epoch iso8601\n')
handle.flush()
if dosteps:
yield from mv(dcm.energy, start)
print(' %.1f %.1f %.6f %s' % (dcm.energy.readback.get(), start, time.time(), now()))
handle.write(' %.1f %.1f %.6f %s\n' % (dcm.energy.readback.get(), start, time.time(), now()))
handle.flush()
yield from sleep(delay)
energy = start
estep = (end-start) / nsteps
while energy <= end:
if dosteps:
yield from mvr(dcm.energy, estep)
print(' %.1f %.1f %.6f %s' % (dcm.energy.readback.get(), energy, time.time(), now()))
handle.write(' %.1f %.1f %.6f %s\n' % (dcm.energy.readback.get(), energy, time.time(), now()))
handle.flush()
energy = energy + estep
yield from sleep(delay)
handle.flush()
handle.close()
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 abs_set(user_ns['_locked_dwell_time'], 0.1, wait=True)
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)
#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 = 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 sleep(3.0)
yield from abs_set(motor.kill_cmd, 1, wait=True)
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)
def cleanup_plan():
print('Cleaning up after an area scan')
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 dark_current():
shb = user_ns['shb']
reopen = shb.state.get() == shb.openval
if reopen:
print('\nClosing photon shutter')
yield from shb.close_plan()
print('Measuring current offsets, this will take several seconds')
EpicsSignal("XF:06BM-BI{EM:1}EM180:ComputeCurrentOffset1.PROC",
name='').put(1)
EpicsSignal("XF:06BM-BI{EM:1}EM180:ComputeCurrentOffset2.PROC",
name='').put(1)
EpicsSignal("XF:06BM-BI{EM:1}EM180:ComputeCurrentOffset3.PROC",
name='').put(1)
EpicsSignal("XF:06BM-BI{EM:1}EM180:ComputeCurrentOffset4.PROC",
name='').put(1)
yield from sleep(3)
BMM_log_info('Measured dark current on quadem1')
if reopen:
print('Opening photon shutter')
yield from shb.open_plan()
print('You are ready to measure!\n')
def dark_current(self):
reopen = shb.state.get() == shb.openval
if reopen:
print('\nClosing photon shutter')
yield from shb.close_plan()
print('Measuring current offsets, this will take several seconds')
######################################################################
# from Pete (email Feb 7, 2020): #
# caput XF:06BM-BI{EM:3}EM180:CalibrationMode 1 #
# caput XF:06BM-BI{EM:3}EM180:CopyADCOffsets.PROC 1 #
# caput XF:06BM-BI{EM:3}EM180:CalibrationMode 0 #
# ADC offset values should be around 3800, might need to hit Compute #
# buttons to get lovely low dark current values #
######################################################################
## this almost works....
self.current_offsets.ch1.put(0.0)
self.current_offsets.ch2.put(0.0)
self.calibration_mode.put(1)
yield from sleep(0.5)
self.copy_adc_offsets.put(1)
yield from sleep(0.5)
self.calibration_mode.put(0)
yield from sleep(0.5)
self.compute_current_offset1.put(1)
self.compute_current_offset1.put(2)
# EpicsSignal("XF:06BM-BI{EM:3}EM180:CalibrationMode", name='').put(1)
# EpicsSignal("XF:06BM-BI{EM:3}EM180:CopyADCOffsets.PROC", name='').put(1)
# EpicsSignal("XF:06BM-BI{EM:3}EM180:CalibrationMode", name='').put(0)
# EpicsSignal("XF:06BM-BI{EM:1}EM180:ComputeCurrentOffset1.PROC", name='').put(1)
# EpicsSignal("XF:06BM-BI{EM:1}EM180:ComputeCurrentOffset2.PROC", name='').put(1)
yield from sleep(0.5)
print(self.sigma1.get(), self.sigma2.get())
BMM_log_info('Measured dark current on dualio ion chamber')
if reopen:
print('Opening photon shutter')
yield from shb.open_plan()
print('You are ready to measure!\n')
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)
def main_plan(detector, axis, start, stop, nsteps, pluck, force):
(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())
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 abs_set(user_ns['_locked_dwell_time'], inttime, wait=True)
if detector == 'Xs':
yield from mv(xs.settings.acquire_time, inttime)
yield from mv(xs.total_points, nsteps)
dets = [
user_ns['quadem1'],
]
if user_ns['with_dualem']:
dualio = user_ns['dualio']
denominator = ''
detname = ''
## 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(user_ns['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(user_ns['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(user_ns['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(user_ns['xs'])
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(user_ns['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
#abs_set(_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
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
})
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 clear_encoder_loss(self):
self.clear_enc_lss.put(1)
self.enable()
BMM_log_info('clearing encoder loss for %s' % self.name)
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 change_mode(mode=None,
prompt=True,
edge=None,
reference=None,
bender=True):
'''Move the photon delivery system to a new mode.
A: focused at XAS end station, energy > 8000
B: focused at XAS end station, energy < 6000
C: focused at XAS end station, 6000 < energy < 8000
D: unfocused, energy > 8000
E: unfocused, 6000 < energy < 8000
F: unfocused, energy < 8000
XRD: focused at XRD end station, energy > 8000
'''
BMMuser, RE, dcm, dm3_bct, slits3 = user_ns['BMMuser'], user_ns[
'RE'], user_ns['dcm'], user_ns['dm3_bct'], user_ns['slits3']
xafs_table, m3, m2, m2_bender, xafs_ref = user_ns['xafs_table'], user_ns[
'm3'], user_ns['m2'], user_ns['m2_bender'], user_ns['xafs_ref']
if mode is None:
print('No mode specified')
return (yield from null())
mode = mode.upper()
if mode not in ('A', 'B', 'C', 'D', 'E', 'F', 'XRD'):
print('%s is not a mode' % mode)
return (yield from null())
current_mode = get_mode()
# crude hack around a problem I don't understand
if dm3_bct.hlm.get() < 55 or dm3_bct.llm.get() > -55:
dm3_bct.llm.put(-60)
dm3_bct.hlm.put(60)
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())
######################################################################
# this is a tool for verifying a macro. this replaces an xafs 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 mode %s.\n'
% (BMMuser.macro_sleep, mode)))
countdown(BMMuser.macro_sleep)
return (yield from null())
######################################################################
if mode == 'B':
action = input(
"You are entering Mode B -- focused beam below 6 keV is not properly configured at BMM. Continue? [y/N then Enter] "
)
if action.lower() != 'y':
return (yield from null())
if mode == 'A':
description = 'focused, >8 keV'
elif mode == 'B':
description = 'focused, <6 keV'
elif mode == 'C':
description = 'focused, 6 to 8 keV'
elif mode == 'D':
description = 'unfocused, >8 keV'
elif mode == 'E':
description = 'unfocused, 6 to 8 keV'
elif mode == 'F':
description = 'unfocused, <6 keV'
elif mode == 'XRD':
description = 'focused at goniometer, >8 keV'
print('Moving to mode %s (%s)' % (mode, description))
if prompt:
action = input("Begin moving motors? [Y/n then Enter] ")
if action.lower() == 'q' or action.lower() == 'n':
return (yield from null())
RE.msg_hook = None
BMM_log_info('Changing photon delivery system to mode %s' % mode)
base = [
dm3_bct,
float(MODEDATA['dm3_bct'][mode]),
xafs_table.yu,
float(MODEDATA['xafs_yu'][mode]),
xafs_table.ydo,
float(MODEDATA['xafs_ydo'][mode]),
xafs_table.ydi,
float(MODEDATA['xafs_ydi'][mode]),
m3.yu,
float(MODEDATA['m3_yu'][mode]),
m3.ydo,
float(MODEDATA['m3_ydo'][mode]),
m3.ydi,
float(MODEDATA['m3_ydi'][mode]),
m3.xu,
float(MODEDATA['m3_xu'][mode]),
m3.xd,
float(MODEDATA['m3_xd'][mode]),
]
if reference is not None:
#base.extend([xafs_linxs, foils.position(reference.capitalize())])
base.extend(
[xafs_ref,
xafs_ref.position_of_slot(reference.capitalize())])
if edge is not None:
#dcm_bragg.clear_encoder_loss()
base.extend([dcm.energy, edge])
# if mode in ('D', 'E', 'F'):
# base.extend([slits3.hcenter, 2])
# else:
# base.extend([slits3.hcenter, 0])
###################################################################
# check for amplifier faults on the motors, return without moving #
# anything if any are found #
###################################################################
motors_ready = True
problem_motors = list()
for m in base[::2]:
try: # skip non-FMBO motors, which do not have the amfe or amfae attributes
if m.amfe.get() == 1 or m.amfae.get() == 1:
motors_ready = False
problem_motors.append(m.name)
except:
continue
if motors_ready is False:
BMMuser.motor_fault = ', '.join(problem_motors)
return (yield from null())
##########################
# do the motor movements #
##########################
yield from dcm.kill_plan()
if dm3_bct.ampen.get() == 0:
yield from mv(dm3_bct.enable_cmd, 1)
#yield from mv(dm3_bct.kill_cmd, 1) # need to explicitly kill this before
# starting a move, it is one of the
# motors that reports MOVN=1 even when
# still
yield from sleep(0.2)
yield from mv(dm3_bct.kill_cmd, 1)
if mode in ('D', 'E', 'F') and current_mode in ('D', 'E', 'F'):
yield from mv(*base)
elif mode in ('A', 'B',
'C') and current_mode in ('A', 'B',
'C'): # no need to move M2
yield from mv(*base)
else:
if bender is True:
yield from mv(m2_bender.kill_cmd, 1)
if mode == 'XRD':
if abs(
m2_bender.user_readback.get() - BMMuser.bender_xrd
) > BMMuser.bender_margin: # give some wiggle room for having
base.extend([m2_bender, BMMuser.bender_xrd
]) # recently adjusted the bend
elif mode in ('A', 'B', 'C'):
if abs(m2_bender.user_readback.get() -
BMMuser.bender_xas) > BMMuser.bender_margin:
base.extend([m2_bender, BMMuser.bender_xas])
base.extend([m2.yu, float(MODEDATA['m2_yu'][mode])])
base.extend([m2.ydo, float(MODEDATA['m2_ydo'][mode])])
base.extend([m2.ydi, float(MODEDATA['m2_ydi'][mode])])
yield from mv(*base)
yield from sleep(2.0)
yield from mv(m2_bender.kill_cmd, 1)
yield from mv(dm3_bct.kill_cmd, 1)
yield from m2.kill_jacks()
yield from m3.kill_jacks()
BMMuser.pds_mode = mode
RE.msg_hook = BMM_msg_hook
BMM_log_info(motor_status())
def change_xtals(xtal=None):
'''Move between the Si(111) and Si(311) monochromators, also moving
2nd crystal pitch and roll to approximate positions. Then do a
rocking curve scan.
'''
if xtal is None:
print('No crystal set specified')
return (yield from null())
(ok, text) = BMM_clear_to_start()
if ok == 0:
print(error_msg(text))
yield from null()
return
BMMuser, RE, dcm, dm3_bct = user_ns['BMMuser'], user_ns['RE'], user_ns[
'dcm'], user_ns['dm3_bct']
dcm_pitch, dcm_roll, dcm_x = user_ns['dcm_pitch'], user_ns[
'dcm_roll'], user_ns['dcm_x']
if '111' in xtal:
xtal = 'Si(111)'
if '311' in xtal:
xtal = 'Si(311)'
if xtal not in ('Si(111)', 'Si(311)'):
print('%s is not a crytsal set' % xtal)
return (yield from null())
######################################################################
# this is a tool for verifying a macro. this replaces an xafs 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 crystal.\n'
% (BMMuser.macro_sleep, xtal)))
countdown(BMMuser.macro_sleep)
return (yield from null())
######################################################################
print('Moving to %s crystals' % xtal)
action = input('Begin moving motors? [Y/n then Enter] ')
if action.lower() == 'q' or action.lower() == 'n':
yield from null()
return
current_energy = dcm.energy.readback.get()
start = time.time()
RE.msg_hook = None
BMM_log_info('Moving to the %s crystals' % xtal)
yield from mv(dcm_pitch.kill_cmd, 1)
yield from mv(dcm_roll.kill_cmd, 1)
if xtal is 'Si(111)':
yield from mv(dcm_pitch, 4.1, dcm_roll, -6.26, dcm_x, 0.5)
#dcm._crystal = '111'
dcm.set_crystal('111') # set d-spacing and bragg offset
elif xtal is 'Si(311)':
yield from mv(dcm_pitch, 2.28, dcm_roll, -23.86, dcm_x, 65.3)
#dcm._crystal = '311'
dcm.set_crystal('311') # set d-spacing and bragg offset
yield from sleep(2.0)
yield from mv(dcm_roll.kill_cmd, 1)
print('Returning to %.1f eV' % current_energy)
yield from mv(dcm.energy, current_energy)
print('Performing a rocking curve scan')
yield from mv(dcm_pitch.kill_cmd, 1)
yield from mv(dcm_pitch, approximate_pitch(current_energy))
yield from sleep(1)
yield from mv(dcm_pitch.kill_cmd, 1)
yield from rocking_curve()
yield from sleep(2.0)
yield from mv(dcm_pitch.kill_cmd, 1)
RE.msg_hook = BMM_msg_hook
BMM_log_info(motor_status())
close_last_plot()
end = time.time()
print('\n\nTime elapsed: %.1f min' % ((end - start) / 60))
def main_plan(inifile, force, **kwargs):
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## read and check INI content
orig = inifile
if not os.path.isfile(inifile):
inifile = DATA + inifile
if not os.path.isfile(inifile):
print(
warning_msg('\n%s does not exist! Bailing out....\n' %
orig))
return (orig, -1)
print(bold_msg('reading ini file: %s' % inifile))
(p, f) = scan_metadata(inifile=inifile, **kwargs)
if not any(
p): # scan_metadata returned having printed an error message
return (yield from null())
#if not os.path.isdir(p['folder']):
# print(error_msg('\n%s is not a folder\n' % p['folder']))
# return(yield from null())
detector = 'It'
if 'trans' in p['mode']:
detector = 'It'
elif 'fluo' in p['mode']:
detector = 'If'
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## verify output file name won't be overwritten
outfile = '%s.%3.3d' % (os.path.join(p['folder'],
p['filename']), p['start'])
if os.path.isfile(outfile):
print(error_msg('%s already exists! Bailing out....' % outfile))
return (yield from null())
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## prompt user and verify that we are clear to start
text = '\n'
for k in ('folder', 'filename', 'experimenters', 'e0', 'npoints',
'dwell', 'delay', 'sample', 'prep', 'comment', 'mode',
'snapshots'):
text = text + ' %-13s : %-50s\n' % (k, p[k])
if BMMuser.prompt:
boxedtext('How does this look?',
text + '\n %-13s : %-50s\n' %
('output file', outfile),
'green',
width=len(outfile) + 25) # see 05-functions
action = input("\nBegin time scan? [Y/n then Enter] ")
if action.lower() == 'q' or action.lower() == 'n':
return (yield from null())
(ok, ctstext) = BMM_clear_to_start()
if force is False and ok is False:
print(error_msg(ctstext))
yield from null()
return
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
# organize metadata for injection into database and XDI output
print(bold_msg('gathering metadata'))
md = bmm_metadata(
measurement=p['mode'],
experimenters=p['experimenters'],
edge=p['edge'],
element=p['element'],
edge_energy=p['e0'],
direction=0,
scantype='fixed',
channelcut=p['channelcut'],
mono='Si(%s)' % dcm._crystal,
i0_gas='N2', #\
it_gas='N2', # > these three need to go into INI file
ir_gas='N2', #/
sample=p['sample'],
prep=p['prep'],
stoichiometry=None,
mode=p['mode'],
comment=p['comment'],
)
del (md['XDI']['Element']['edge'])
del (md['XDI']['Element']['symbol'])
md['XDI']['Column']['01'] = 'time seconds'
md['XDI']['Column']['02'] = md.copy()['XDI']['Column']['03']
md['XDI']['Column']['03'] = md.copy()['XDI']['Column']['04']
md['XDI']['Column']['04'] = md['XDI']['Column']['05']
del (md['XDI']['Column']['05'])
md['_kind'] = 'sead'
rightnow = metadata_at_this_moment() # see 62-metadata.py
for family in rightnow.keys(): # transfer rightnow to md
if type(rightnow[family]) is dict:
if family not in md:
md[family] = dict()
for k in rightnow[family].keys():
md[family][k] = rightnow[family][k]
xdi = {'XDI': md}
BMM_log_info(
'Starting single-energy absorption detection time scan using\n%s:\n%s\nCommand line arguments = %s\nMoving to measurement energy: %.1f eV'
% (inifile, text, str(kwargs), p['e0']))
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## move to the energy specified in the INI file
print(bold_msg('Moving to measurement energy: %.1f eV' % p['e0']))
dcm.mode = 'fixed'
yield from mv(dcm.energy, p['e0'])
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## snap photos
if p['snapshots']:
image = os.path.join(
p['folder'], 'snapshots',
"%s_XASwebcam_%s.jpg" % (p['filename'], now()))
snap('XAS', filename=image)
image = os.path.join(p['folder'], 'snapshots',
"%s_analog_%s.jpg" % (p['filename'], now()))
snap('analog', filename=image)
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## engage suspenders right before starting measurement
if not force: BMM_suspenders()
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## perform the actual time scan
uid = yield from timescan(detector,
p['npoints'],
p['dwell'],
p['delay'],
force=force,
md={**xdi})
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## write the output file
header = db[uid]
write_XDI(outfile, header) # yield from ?
report('wrote time scan to %s' % outfile)
def timescan(detector, readings, dwell, delay, force=False, md={}):
'''
Generic timescan plan.
Parameters
----------
detector : str
detector to display -- if, it, ir, or i0
readings : int
number of measurements to make
dwell : float
dwell time in seconds for each measurement
delay : float
pause in seconds between measurements
outfile : str
data file name (relative to DATA), False to not write
force : bool
flag for forcing a scan even if not clear to start
This does not write an ASCII data file, but it does make a log entry.
Use the ts2dat() function to extract the linescan from the
database and write it to a file.
Examples
>>> RE(timescan('it', 100, 0.5))
'''
RE, BMMuser, quadem1, _locked_dwell_time = user_ns['RE'], user_ns[
'BMMuser'], user_ns['quadem1'], user_ns['_locked_dwell_time']
rkvs = user_ns['rkvs']
######################################################################
# this is a tool for verifying a macro. this replaces an xafs 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 running a time scan.\n'
% BMMuser.macro_sleep))
countdown(BMMuser.macro_sleep)
return (yield from null())
######################################################################
(ok, text) = BMM_clear_to_start()
if force is False and ok is False:
print(error_msg(text))
yield from null()
return
RE.msg_hook = None
## sanitize and sanity checks on detector
detector = detector.capitalize()
if detector not in ('It', 'If', 'I0', 'Iy',
'Ir') and 'Dtc' not in detector:
print(
error_msg('\n*** %s is not a timescan measurement (%s)\n' %
(detector, 'it, if, i0, iy, ir')))
yield from null()
return
yield from mv(_locked_dwell_time, dwell)
dets = [
quadem1,
]
denominator = ''
epoch_offset = pandas.Timestamp.now(tz='UTC').value / 10**9
## func is an anonymous function, built on the fly, for feeding to DerivedPlot
if detector == 'It':
denominator = ' / I0'
func = lambda doc: (doc['time'] - epoch_offset, doc['data']['It'] /
doc['data']['I0'])
elif detector == 'Ir':
denominator = ' / It'
func = lambda doc: (doc['time'] - epoch_offset, doc['data']['Ir'] /
doc['data']['It'])
elif detector == 'I0':
func = lambda doc: (doc['time'] - epoch_offset, doc['data']['I0'])
elif detector == 'Iy':
denominator = ' / I0'
func = lambda doc: (doc['time'] - epoch_offset, doc['data']['Iy'] /
doc['data']['I0'])
elif detector == 'Dtc':
dets.append(vor)
denominator = ' / I0'
func = lambda doc: (doc['time'] - epoch_offset, doc['data'][
BMMuser.dtc2] / doc['data']['I0'])
func3 = lambda doc: (doc['time'] - epoch_offset, doc['data'][
BMMuser.dtc3] / doc['data']['I0'])
elif detector == 'If':
dets.append(vor)
denominator = ' / I0'
func = lambda doc: (doc['time'] - epoch_offset, (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
if detector == 'Dtc':
plot = [
DerivedPlot(func,
xlabel='elapsed time (seconds)',
ylabel='dtc2',
title='time scan'),
DerivedPlot(func3,
xlabel='elapsed time (seconds)',
ylabel='dtc3',
title='time scan')
]
else:
plot = DerivedPlot(func,
xlabel='elapsed time (seconds)',
ylabel=detector + denominator,
title='time scan')
line1 = '%s, N=%s, dwell=%.3f, delay=%.3f\n' % (detector, readings, dwell,
delay)
thismd = dict()
thismd['XDI'] = dict()
thismd['XDI']['Facility'] = dict()
thismd['XDI']['Facility']['GUP'] = BMMuser.gup
thismd['XDI']['Facility']['SAF'] = BMMuser.saf
thismd['XDI']['Beamline'] = dict()
thismd['XDI']['Beamline']['energy'] = dcm.energy.readback.get()
thismd['XDI']['Scan'] = dict()
thismd['XDI']['Scan']['dwell_time'] = dwell
thismd['XDI']['Scan']['delay'] = delay
@subs_decorator(plot)
#@subs_decorator(src.callback)
def count_scan(dets, readings, delay):
#if 'purpose' not in md:
# md['purpose'] = 'measurement'
uid = yield from count(dets,
num=readings,
delay=delay,
md={
**thismd,
**md, 'plan_name':
f'count measurement {detector}'
})
return uid
rkvs.set('BMM:scan:type', 'time')
rkvs.set('BMM:scan:starttime',
str(datetime.datetime.timestamp(datetime.datetime.now())))
rkvs.set('BMM:scan:estimated', 0)
uid = yield from count_scan(dets, readings, delay, md)
BMM_log_info('timescan: %s\tuid = %s, scan_id = %d' %
(line1, uid, db[-1].start['scan_id']))
yield from mv(_locked_dwell_time, 0.5)
RE.msg_hook = BMM_msg_hook
return (uid)
def calibrate_high_end(mono='111', focus=False):
'''Step through the upper 5 elements of the mono calibration procedure.'''
BMMuser, shb, dcm_pitch = user_ns['BMMuser'], user_ns['shb'], user_ns[
'dcm_pitch']
(ok, text) = BMM_clear_to_start()
if ok is False:
print(error_msg('\n' + text) + bold_msg('Quitting macro....\n'))
return (yield from null())
BMM_log_info('Beginning high end calibration macro')
def main_plan():
BMMuser.prompt = False
datafile = os.path.join(BMMuser.DATA, 'edges%s.ini' % mono)
handle = open(datafile, 'a')
#yield from shb.open_plan()
yield from change_edge('Pt', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='ptcal',
edge='Pt',
e0=11563,
sample='Pt foil')
close_last_plot()
handle.write('pt = 11111.11, 11562.76, 22222.22, %.5f\n' %
pitch)
handle.flush()
yield from change_edge('Au', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='aucal',
edge='Au',
e0=11919,
sample='Au foil')
close_last_plot()
handle.write('au = 11111.11, 11919.70, 22222.22, %.5f\n' %
pitch)
handle.flush()
yield from change_edge('Pb', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='pbcal',
edge='Pb',
e0=13035,
sample='Pb foil')
close_last_plot()
handle.write('pb = 11111.11, 13035.07, 22222.22, %.5f\n' %
pitch)
handle.flush()
yield from change_edge('Nb', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='nbcal',
edge='Nb',
e0=18986,
sample='Nb foil')
close_last_plot()
handle.write('nb = 11111.11, 18982.97, 22222.22, %.5f\n' %
pitch)
handle.flush()
yield from change_edge('Mo', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='mocal',
edge='Mo',
e0=20000,
sample='Mo foil')
close_last_plot()
handle.write('mo = 11111.11, 20000.36, 22222.22, %.5f\n' %
pitch)
handle.flush()
handle.close()
#yield from shb.close_plan()
def cleanup_plan():
yield from resting_state_plan()
yield from finalize_wrapper(main_plan(), cleanup_plan())
yield from resting_state_plan()
BMM_log_info('High end calibration macro finished!')
def calibrate_low_end(mono='111', focus=False):
'''Step through the lower 5 elements of the mono calibration procedure.'''
BMMuser, shb, dcm_pitch = user_ns['BMMuser'], user_ns['shb'], user_ns[
'dcm_pitch']
(ok, text) = BMM_clear_to_start()
if ok is False:
print(error_msg('\n' + text) + bold_msg('Quitting macro....\n'))
return (yield from null())
BMM_log_info('Beginning low end calibration macro')
def main_plan():
BMMuser.prompt = False
datafile = os.path.join(BMMuser.DATA, 'edges%s.ini' % mono)
handle = open(datafile, 'w')
handle.write('[config]\n')
handle.write("mono = %s\n" % mono)
if mono == '111':
handle.write('DSPACING = 3.13597211\n')
else:
handle.write('DSPACING = 1.63762644\n')
handle.write('thistitle = Si(%s) calibration curve\n' % mono)
handle.write(
'reference = Kraft et al, Review of Scientific Instruments 67, 681 (1996)\n'
)
handle.write('doi = https://doi.org/10.1063/1.1146657\n\n')
handle.write('## found, tabulated, found_angle, dcm_pitch\n')
handle.write('[edges]\n')
handle.flush()
yield from change_edge('Fe', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='fecal',
edge='Fe',
e0=7112,
sample='Fe foil')
close_last_plot()
handle.write('fe = 11111.11, 7110.75, 22222.22, %.5f\n' %
pitch)
handle.flush()
yield from change_edge('Co', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='cocal',
edge='Co',
e0=7709,
sample='Co foil')
close_last_plot()
handle.write('co = 11111.11, 7708.78, 22222.22, %.5f\n' %
pitch)
handle.flush()
yield from change_edge('Ni', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='nical',
edge='Ni',
e0=8333,
sample='Ni foil')
close_last_plot()
handle.write('ni = 11111.11, 8331.49, 22222.22, %.5f\n' %
pitch)
handle.flush()
yield from change_edge('Cu', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='cucal',
edge='Cu',
e0=8979,
sample='Cu foil')
close_last_plot()
handle.write('cu = 11111.11, 8980.48, 22222.22, %.5f\n' %
pitch)
handle.flush()
yield from change_edge('Zn', target=0, focus=focus)
pitch = dcm_pitch.user_readback.get()
yield from xafs('/home/xf06bm/Data/Staff/mono_calibration/cal.ini',
folder=BMMuser.DATA,
filename='zncal',
edge='Zn',
e0=9659,
sample='Zn foil')
close_last_plot()
handle.write('zn = 11111.11, 9660.76, 22222.22, %.5f\n' %
pitch)
handle.flush()
handle.close()
#yield from shb.close_plan()
def cleanup_plan():
yield from resting_state_plan()
yield from finalize_wrapper(main_plan(), cleanup_plan())
yield from resting_state_plan()
BMM_log_info('Low end calibration macro finished!')
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
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 abs_set(_locked_dwell_time, dwell, wait=True)
dets = [
quadem1,
]
if detector == 'If':
dets.append(vor)
detector = 'ROI1'
if detector.lower() == 'xs':
dets.append(xs)
detector = BMMuser.xs1
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))
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
## 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)
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, False)
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())
print(
'Single click the left mouse button on the plot to pluck a point...'
)
cid = BMMuser.fig.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, pointfast, slow, pointslow)
