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 cleanup_plan():
print(
'Cleaning up after single energy absorption detector measurement')
BMM_clear_suspenders()
#RE.clear_suspenders()
yield from resting_state_plan()
dcm.mode = 'fixed'
def cleanup_plan():
print('Cleaning up after single energy absorption detector measurement')
RE.clear_suspenders()
yield from resting_state_plan()
dotfile = '/home/xf06bm/Data/.time.scan.running'
if os.path.isfile(dotfile): os.remove(dotfile)
dcm.mode = 'fixed'
def cleanup_plan():
yield from mv(user_ns['slits3'].vsize, slit_height)
yield from abs_set(user_ns['_locked_dwell_time'], 0.5, wait=True)
yield from sleep(1.0)
yield from abs_set(motor.kill_cmd, 1, wait=True)
yield from sleep(1.0)
yield from user_ns['dcm'].kill_plan()
yield from resting_state_plan()
def cleanup_plan():
yield from mv(slits3.vsize, slit_height)
yield from mv(_locked_dwell_time, 0.5)
yield from sleep(1.0)
yield from mv(motor.kill_cmd, 1)
yield from sleep(1.0)
yield from dcm.kill_plan()
yield from resting_state_plan()
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 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 cleanup_plan():
yield from resting_state_plan()
def main_plan():
dcm = user_ns['dcm']
report(f'Calibrating the {dcm._crystal} monochrmoator', 'bold')
yield from calibrate_low_end(mono=dcm._crystal, focus=focus)
yield from calibrate_high_end(mono=dcm._crystal, focus=focus)
yield from resting_state_plan()
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 cleanup_plan():
## BMM_clear_suspenders()
##RE.clear_suspenders() # disable suspenders
yield from resting_state_plan()
def cleanup_plan():
## BMM_clear_suspenders()
##user_ns['RE'].clear_suspenders() # disable suspenders
yield from resting_state_plan()
