def amfe():
print(bold_msg("%-12s : %s / %s" % ('motor', 'AMFE', 'AMFAE')))
for m in mcs8_motors:
if m.amfe.get():
fe = warning_msg(m.amfe.enum_strs[m.amfe.get()])
else:
fe = m.amfe.enum_strs[m.amfe.get()]
if m.amfae.get():
fae = warning_msg(m.amfae.enum_strs[m.amfae.get()])
else:
fae = m.amfae.enum_strs[m.amfae.get()]
print("%-12s : %s / %s" % (m.name, fe, fae))
def ampen():
for m in mcs8_motors:
if m.ampen.get():
print("%-12s : %s" %
(m.name, warning_msg(m.ampen.enum_strs[m.ampen.get()])))
else:
print("%-12s : %s" % (m.name, m.ampen.enum_strs[m.ampen.get()]))
def _pressure(self):
if self.pressure.get() == 'OFF':
return (disconnected_msg(-1.1e-15))
if float(self.pressure.get()) > 1e-1:
return warning_msg(self.pressure.get())
if float(self.pressure.get()) > 6e-3:
return error_msg(self.pressure.get())
return (self.pressure.get())
def _state(self, info=False):
t = "%.1f" % self.temperature.get()
if self.temperature.get() > self.alarm.get():
return(error_msg(t))
if self.temperature.get() > self.warning.get():
return(warning_msg(t))
if info is True and self.temperature.get() > (0.5 * self.warning.get()):
return(info_msg(t))
return(t)
def on(self, number):
'''Turn on the specified spinner'''
if self.spin is False:
print(warning_msg('The spinners are currently disabled. do "ga.spin = True" to re-enable.'))
return
if not self.valid(number):
print(error_msg('The fans are numbered from 1 to 8'))
return
this = getattr(self, f'spinner{number}')
this.put(1)
def _current(self):
curr = float(self.current.get())
if curr > 2e-3:
out = '%.1f' % (1e3 * curr)
return (error_msg(out))
if curr > 5e-4:
out = '%.1f' % (1e3 * curr)
return (warning_msg(out))
out = '%.1f' % (1e6 * curr)
return (out)
def _pressure(self):
#print(self.pressure.get())
#print(type(self.pressure.get()))
if self.pressure.get() == 'OFF':
return (disconnected_msg(-1.1E-15))
if float(self.pressure.get()) > 1e-6:
return error_msg(self.pressure.get())
if float(self.pressure.get()) > 1e-8:
return warning_msg(self.pressure.get())
return (self.pressure.get())
def _current(self):
if self.connected is False:
return(disconnected_msg('?????'))
curr = float(self.current.get())
if curr > 2e-3:
out = '%.1f' % (1e3*curr)
return(error_msg(out))
if curr > 5e-4:
out = '%.1f' % (1e3*curr)
return(warning_msg(out))
out = '%.1f' % (1e6*curr)
return(out)
def _pressure(self):
#print(self.pressure.get())
#print(type(self.pressure.get()))
if self.connected is False:
return(disconnected_msg('?????'))
if self.pressure.get() == 'OFF':
return(disconnected_msg(-1.1E-15))
if type(self.pressure.get()) is str and self.pressure.get() == 'LO<E-11':
return whisper('1.00e-11')
if float(self.pressure.get()) > 1e-6:
return error_msg(self.pressure.get())
if float(self.pressure.get()) > 1e-8:
return warning_msg(self.pressure.get())
return(self.pressure.get())
def report(text, level=None, slack=False):
'''Print a string to:
* the log file
* the screen
* the BMM beamtime slack channel
Report level decorations on screen:
* 'error' (red)
* 'warning' (yellow)
* 'info' (brown)
* 'url' (undecorated)
* 'bold' (bright white)
* 'verbosebold' (bright cyan)
* 'list' (cyan)
* 'disconnected' (purple)
* 'whisper' (gray)
not matching a report level will be undecorated
'''
BMMuser = user_ns['BMMuser']
BMM_log_info(text)
if color: # test that color is sensible...
if level == 'error':
print(error_msg(text))
elif level == 'warning':
print(warning_msg(text))
elif level == 'info':
print(info_msg(text))
elif level == 'url':
print(url_msg(text))
elif level == 'bold':
print(bold_msg(text))
elif level == 'verbosebold':
print(verbosebold_msg(text))
elif level == 'disconnected':
print(disconnected_msg(text))
elif level == 'list':
print(list_msg(text))
elif level == 'whisper':
print(whisper(text))
else:
print(text)
else:
print(text)
if BMMuser.use_slack and slack:
post_to_slack(text)
def select(self, el):
'''Choose the ROI configured for element el'''
if type(el) is int:
if el < 1 or el > 3:
print(error_msg('\n%d is not a valid ROI channel\n' % el))
return (yield from null())
el = self.slots[el - 1]
if el is None:
print(error_msg('\nThat ROI is not configured\n'))
return (yield from null())
if Z_number(el) is None:
print(error_msg('\n%s is not an element\n' % el))
return (yield from null())
selected = False
vor = user_ns['vor']
BMMuser = user_ns['BMMuser']
for i in range(3):
if element_symbol(el) == self.slots[i]:
BMMuser.roi_channel = i + 1
if i == 0: # help out the best effort callback
(BMMuser.roi1, BMMuser.roi2, BMMuser.roi3,
BMMuser.roi4) = ('ROI1', 'ROI2', 'ROI3', 'ROI4')
(BMMuser.dtc1, BMMuser.dtc2, BMMuser.dtc3,
BMMuser.dtc4) = ('DTC1', 'DTC2', 'DTC3', 'DTC4')
vor.set_hints(1)
elif i == 1:
(BMMuser.roi1, BMMuser.roi2, BMMuser.roi3,
BMMuser.roi4) = ('ROI2_1', 'ROI2_2', 'ROI2_3', 'ROI2_4')
(BMMuser.dtc1, BMMuser.dtc2, BMMuser.dtc3,
BMMuser.dtc4) = ('DTC2_1', 'DTC2_2', 'DTC2_3', 'DTC2_4')
vor.set_hints(2)
elif i == 2:
(BMMuser.roi1, BMMuser.roi2, BMMuser.roi3,
BMMuser.roi4) = ('ROI3_1', 'ROI3_2', 'ROI3_3', 'ROI3_4')
(BMMuser.dtc1, BMMuser.dtc2, BMMuser.dtc3,
BMMuser.dtc4) = ('DTC3_1', 'DTC3_2', 'DTC3_3', 'DTC3_4')
vor.set_hints(3)
report('Set ROI channel to %s at channel %d' %
(el.capitalize(), i + 1))
selected = True
if not selected:
print(
warning_msg(
'%s is not in a configured channel, not changing BMMuser.roi_channel'
% el.capitalize()))
yield from null()
def _current(self, num=None):
if num is None:
num = 1
if num < 1:
num = 1
if num > 6:
num = 6
sgnl = getattr(self, 'c' + str(num))
curr = float(sgnl.get())
if curr > 2e-3:
out = '%.1f' % (1e3 * curr)
return (error_msg(out))
if curr > 5e-4:
out = '%.1f' % (1e3 * curr)
return (warning_msg(out))
out = '%.1f' % (1e6 * curr)
return (out)
def _pressure(self, num=None):
if num is None:
num = 1
if num < 1:
num = 1
if num > 6:
num = 6
sgnl = getattr(self, 'p' + str(num))
#print(self.pressure.get())
#print(type(self.pressure.get()))
if sgnl.get() == 'OFF':
return (disconnected_msg(-1.1E-15))
if float(sgnl.get()) > 1e-6:
return error_msg(self.pressure.get())
if float(sgnl.get()) > 1e-8:
return warning_msg(self.pressure.get())
return (sgnl.get())
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 sanitize_step_scan_parameters(bounds, steps, times):
'''Attempt to identify and flag/correct some common scan parameter mistakes.'''
problem = False
text = ''
############################################################################
# bounds is one longer than steps/times, length of steps = length of times #
############################################################################
if (len(bounds) - len(steps)) != 1:
text += error_msg('\nbounds must have one more item than steps\n')
text += error_msg('\tbounds = %s\n' % ' '.join(map(str, bounds)))
text += error_msg('\tsteps = %s\n' % ' '.join(map(str, steps)))
problem = True
if (len(bounds) - len(times)) != 1:
text += error_msg('\nbounds must have one more item than times\n')
text += error_msg('\tbounds = %s\n' % ' '.join(map(str, bounds)))
text += error_msg('\ttimes = %s\n' % ' '.join(map(str, times)))
problem = True
############################
# tests of boundary values #
############################
for b in bounds:
if not isfloat(b) and b[-1:].lower() == 'k':
if not isfloat(b[:-1]):
text += error_msg('\n%s is not a valid scan boundary value\n' % b)
problem = True
elif not isfloat(b):
text += error_msg('\n%s is not a valid scan boundary value\n' % b)
problem = True
if not isfloat(b) and b[:1] == '-' and b[-1:].lower() == 'k':
text += error_msg('\nNegative bounds must be energy-valued, not k-valued (%s)\n' % b)
problem = True
#############################
# tests of step size values #
#############################
for s in steps:
if not isfloat(s) and s[-1:].lower() == 'k':
if not isfloat(s[:-1]):
text += error_msg('\n%s is not a valid scan step size value\n' % s)
problem = True
elif float(s[:-1]) < 0:
text += error_msg('\nStep sizes cannot be negative (%s)\n' % s)
problem = True
elif not isfloat(s):
text += error_msg('\n%s is not a valid scan step size value\n' % s)
problem = True
if isfloat(s) and float(s) < 0:
text += error_msg('\nStep sizes cannot be negative (%s)\n' % s)
problem = True
elif isfloat(s) and float(s) <= 0.09:
text += warning_msg('\n%s is a very small step size!\n' % s)
elif not isfloat(s) and s[-1:].lower() == 'k' and isfloat(s[-1:]) and float(s[:-1]) < 0.01:
text += warning_msg('\n%s is a very small step size!\n' % s)
####################################
# tests of integration time values #
####################################
for t in times:
if not isfloat(t) and t[-1:].lower() == 'k':
if not isfloat(t[:-1]):
text += error_msg('\n%s is not a valid integration time value\n' % t)
problem = True
elif float(t[:-1]) < 0:
text += error_msg('\nIntegration times cannot be negative (%s)\n' % t)
problem = True
elif not isfloat(t):
text += error_msg('\n%s is not a valid integration time value\n' % t)
problem = True
if isfloat(t) and float(t) < 0:
text += error_msg('\nIntegration times cannot be negative (%s)\n' % t)
problem = True
elif isfloat(t) and float(t) <= 0.1:
text += warning_msg('\n%s is a very short integration time!\n' % t)
elif not isfloat(t) and t[-1:].lower() == 'k' and isfloat(t[-1:]) and float(t[:-1]) < 0.05:
text += warning_msg('\n%s is a very short integration time!\n' % t)
reference = 'https://nsls-ii-bmm.github.io/BeamlineManual/xafs.html#scan-regions\n'
return problem, text, reference
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)
