def align_linear(self, force=False, drop=None):
'''Fit an error function to the linear scan against It. Plot the
result. Move to the centroid of the error function.'''
if self.orientation == 'parallel':
motor = user_ns['xafs_liny']
else:
motor = user_ns['xafs_linx']
yield from linescan(motor, 'it', -2.3, 2.3, 51, pluck=False)
close_last_plot()
table = user_ns['db'][-1].table()
yy = table[motor.name]
signal = table['It']/table['I0']
if drop is not None:
yy = yy[:-drop]
signal = signal[:-drop]
if float(signal[2]) > list(signal)[-2] :
ss = -(signal - signal[2])
self.inverted = 'inverted '
else:
ss = signal - signal[2]
self.inverted = ''
mod = StepModel(form='erf')
pars = mod.guess(ss, x=numpy.array(yy))
out = mod.fit(ss, pars, x=numpy.array(yy))
print(whisper(out.fit_report(min_correl=0)))
target = out.params['center'].value
yield from mv(motor, target)
self.y_plot(yy, out)
def align_y(self, force=False, drop=None):
'''Fit an error function to the xafs_y scan against It. Plot the
result. Move to the centroid of the error function.'''
xafs_y = user_ns['xafs_y']
db = user_ns['db']
yield from linescan(xafs_y, 'it', -1, 1, 31, pluck=False)
close_last_plot()
table = db[-1].table()
yy = table['xafs_y']
signal = table['It'] / table['I0']
if drop is not None:
yy = yy[:-drop]
signal = signal[:-drop]
if float(signal[2]) > list(signal)[-2]:
ss = -(signal - signal[2])
self.inverted = 'inverted '
else:
ss = signal - signal[2]
self.inverted = ''
mod = StepModel(form='erf')
pars = mod.guess(ss, x=numpy.array(yy))
out = mod.fit(ss, pars, x=numpy.array(yy))
print(whisper(out.fit_report(min_correl=0)))
self.y_plot(yy, out)
target = out.params['center'].value
yield from mv(xafs_y, target)
def wafer_edge(motor='x'):
'''Fit an error function to the linear scan against It. Plot the
result. Move to the centroid of the error function.'''
if motor == 'x':
motor = user_ns['xafs_linx']
else:
motor = user_ns['xafs_liny']
yield from linescan(motor, 'it', -2, 2, 41, pluck=False)
close_last_plot()
table = user_ns['db'][-1].table()
yy = table[motor.name]
signal = table['It'] / table['I0']
if float(signal[2]) > list(signal)[-2]:
ss = -(signal - signal[2])
else:
ss = signal - signal[2]
mod = StepModel(form='erf')
pars = mod.guess(ss, x=numpy.array(yy))
out = mod.fit(ss, pars, x=numpy.array(yy))
print(whisper(out.fit_report(min_correl=0)))
out.plot()
target = out.params['center'].value
yield from mv(motor, target)
yield from resting_state_plan()
print(
f'Edge found at X={user_ns["xafs_x"].position} and Y={user_ns["xafs_y"].position}'
)
def align_pitch(self, force=False):
'''Find the peak of xafs_pitch scan against It. Plot the
result. Move to the peak.'''
xafs_pitch = user_ns['xafs_pitch']
yield from linescan(xafs_pitch, 'it', -2.5, 2.5, 51, pluck=False, force=force)
close_last_plot()
table = user_ns['db'][-1].table()
pitch = table['xafs_pitch']
signal = table['It']/table['I0']
target = signal.idxmax()
yield from mv(xafs_pitch, pitch[target])
self.pitch_plot(pitch, signal)
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
'''
BMMuser, RE, dcm, dm3_bct = user_ns['BMMuser'], user_ns['RE'], user_ns[
'dcm'], user_ns['dm3_bct']
dcm_pitch, dcm_bragg = user_ns['dcm_pitch'], user_ns['dcm_bragg']
rkvs = user_ns['rkvs']
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())
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)
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())
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() the re-run the change_mode() command.')
print('If that doesn\'t work, call for help')
return (yield from null())
yield from user_ns['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 abs_set(dcm_pitch.kill_cmd, 1, wait=True)
yield from mv(dcm_pitch, approximate_pitch(energy + target))
yield from sleep(1)
yield from abs_set(dcm_pitch.kill_cmd, 1, wait=True)
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
rois = user_ns['rois']
print('Moving reference foil...')
yield from rois.select_plan(el)
## 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())')
self.to_json(os.path.join(self.DATA, '.BMMuser'))
yield from dcm.kill_plan()
end = time.time()
print('\n\nThat took %.1f min' % ((end - start) / 60))
return ()
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()
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()
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))
