def overhead_per_point(self, element, edge=None):
a = json.load(open(self.json))
element = element_symbol(element)
if edge is not None and edge.lower() in ('l2', 'l1'):
return ([self.interpolate(edge_energy(element, edge)), 0])
if element in a and 'dpp' in a[element]:
return (a[element]['dpp'])
else:
if edge is None or edge.lower() not in ('l2', 'l1'):
edge = 'k'
if Z_number(element) > 45:
edge = 'l3'
return ([self.interpolate(edge_energy(element, edge)), 0])
def interpolate(self, energy):
a = json.load(open(self.json))
e, t = numpy.array([]), numpy.array([])
for z in self.all_elements:
if 'count' not in a[element_symbol(z)]:
continue
if a[element_symbol(z)]['count'] < self.reliability:
continue
t = numpy.append(t, a[element_symbol(z)]['dpp'][0])
if z < 46:
e = numpy.append(e, edge_energy(z, 'k'))
else:
e = numpy.append(e, edge_energy(z, 'l3'))
s = numpy.argsort(e)
return (numpy.interp(energy, e[s], t[s]))
def estimate_time(self, m, el, ed):
'''Approximate the time contribution from the current row'''
if type(m['bounds']) is str:
b = re.split('[ ,]+', m['bounds'].strip())
else:
b = re.split('[ ,]+', self.measurements[0]['bounds'].strip())
if type(m['steps']) is str:
s = re.split('[ ,]+', m['steps'].strip())
else:
s = re.split('[ ,]+', self.measurements[0]['steps'].strip())
if type(m['times']) is str:
t = re.split('[ ,]+', m['times'].strip())
else:
t = re.split('[ ,]+', self.measurements[0]['times'].strip())
b = [float(x) if isfloat(x) else x for x in b]
s = [float(x) if isfloat(x) else x for x in s]
t = [float(x) if isfloat(x) else x for x in t]
(e, t, at, delta) = conventional_grid(bounds=b,
steps=s,
times=t,
e0=edge_energy(el, ed),
element=el,
edge=ed,
ththth=False)
if type(m['nscans']) is int:
nsc = m['nscans']
else:
nsc = self.measurements[0]['nscans']
self.totaltime += at * nsc
self.deltatime += delta * delta
def from_json(self, filename):
rkvs = user_ns['rkvs']
if os.path.isfile(filename):
with open(filename, 'r') as jsonfile:
config = json.load(jsonfile)
for k in config.keys():
setattr(self, k, config[k])
user_ns['rois'].trigger = True
rkvs.set('BMM:pds:edge', str(config['edge']))
rkvs.set('BMM:pds:element', str(config['element']))
rkvs.set('BMM:pds:edge_energy', edge_energy(config['element'], config['edge']))
def from_json(self, filename):
if os.path.isfile(filename):
with open(filename, 'r') as jsonfile:
config = json.load(jsonfile)
for k in config.keys():
if k in ('cycle', ):
continue
setattr(self, k, config[k])
#rois.trigger = True
from BMM.workspace import rkvs
try:
#rkvs.set('BMM:pds:edge', str(config['edge']))
#rkvs.set('BMM:pds:element', str(config['element']))
rkvs.set('BMM:pds:edge_energy',
edge_energy(config['element'], config['edge']))
BMMuser.element = rkvs.get('BMM:pds:element').decode('utf-8')
BMMuser.edge = rkvs.get('BMM:pds:edge').decode('utf-8')
except:
pass
def 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 ()