def warmup(self):
"""
A convenience method for 'priming' the plugin.
The plugin has to 'see' one acquisition before it is ready to capture.
This sets the array size, etc.
NOTE : this comes from:
https://github.com/NSLS-II/ophyd/blob/master/ophyd/areadetector/plugins.py
We had to replace "cam" with "settings" here.
Also modified the stage sigs.
"""
print(whisper(" warming up the hdf5 plugin..."))
set_and_wait(self.enable, 1)
sigs = OrderedDict([(self.parent.settings.array_callbacks, 1),
(self.parent.settings.trigger_mode, 'Internal'),
# just in case the acquisition time is set very long...
(self.parent.settings.acquire_time, 1),
# (self.capture, 1),
(self.parent.settings.acquire, 1)])
original_vals = {sig: sig.get() for sig in sigs}
# Remove the hdf5.capture item here to avoid an error as it should reset back to 0 itself
# del original_vals[self.capture]
for sig, val in sigs.items():
ttime.sleep(0.1) # abundance of caution
set_and_wait(sig, val)
ttime.sleep(2) # wait for acquisition
for sig, val in reversed(list(original_vals.items())):
ttime.sleep(0.1)
set_and_wait(sig, val)
print(whisper(" done"))
def cycle(self, mc=None):
'''Cycle power to the amplifiers on a motor controller, then reenable
the motors on that controller.
Identify the motor controller by these strings:
'dcm', 'slits2', 'm2', 'm3', 'dm3'
'''
if self.check(mc) is False:
return
print(bold_msg(f'Cycling amplifiers on {mc} motor controller'))
print(whisper('killing amplifiers'))
self.kill(mc)
countdown(5)
print(whisper('reactivating amplifiers'))
self.enable(mc)
print(whisper('enabling motors'))
if mc == 'm2':
user_ns['m2'].ena()
elif mc == 'm3':
user_ns['m3'].ena()
elif mc == 'slits2':
user_ns['slits2'].enable()
elif mc == 'dm3':
user_ns['slits3'].enable()
for axis in ('dm3_bct', 'dm3_bpm', 'dm3_foils', 'dm3_fs'):
user_ns[axis].enable()
time.sleep(0.5)
user_ns[axis].kill()
elif mc == 'dcm':
user_ns['dcm'].ena()
time.sleep(0.5)
user_ns['dcm'].kill()
def make_merged_triplot(self, uidlist, filename, mode):
'''Make a pretty, three panel plot of the data from the scan sequence
just finished.
'''
BMMuser = user_ns['BMMuser']
cnt = 0
try:
base = Pandrosus()
projname = os.path.join(BMMuser.folder, 'prj',
os.path.basename(filename)).replace(
'.png', '.prj')
proj = create_athena(projname)
base.fetch(uidlist[0], mode=mode)
ee = base.group.energy
mm = base.group.mu
save = base.group.args['label']
proj.add_group(base.group)
base.group.args['label'] = save
cnt = 1
if len(uidlist) > 1:
for uid in uidlist[1:]:
this = Pandrosus()
try:
this.fetch(uid, mode=mode)
mu = numpy.interp(ee, this.group.energy, this.group.mu)
mm = mm + mu
save = this.group.args['label']
proj.add_group(this.group)
this.group.args['label'] = save
cnt += 1
except:
pass # presumably this is noisy data for which a valid background was not found
except:
pass # presumably this is noisy data for which a valid background was not found
if cnt == 0:
print(whisper(f'Unable to make triplot'))
try:
self.simple_plot(uidlist, filename, mode)
except:
print(whisper(f'Also unable to make simple plot'))
return
mm = mm / cnt
merge = Pandrosus()
merge.put(ee, mm, 'merge')
thisagg = matplotlib.get_backend()
matplotlib.use('Agg') # produce a plot without screen display
merge.triplot()
plt.savefig(filename)
print(whisper(f'Wrote triplot to {filename}'))
matplotlib.use(thisagg) # return to screen display
proj.save()
print(whisper(f'Wrote Athena project to {projname}'))
def do_ChangeXtals(self):
if user_ns['dcm']._crystal == '111':
print(
go_msg('You would like to change from the ') +
whisper('Si(111)') + go_msg(' to the ') + bold_msg('Si(311)') +
go_msg(' crystals...\n'))
print(disconnected_msg('yield from change_xtals("311")'))
else:
print(
go_msg('You would like to change from the ') +
whisper('Si(311)') + go_msg(' to the ') + bold_msg('Si(111)') +
go_msg(' crystals...\n'))
print(disconnected_msg('yield from change_xtals("111")'))
yield from null()
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 all_connected(with_m2=False):
motors = [
dm3_bct,
xafs_yu,
xafs_ydo,
xafs_ydi,
m3_yu,
m3_ydo,
m3_ydi,
m3_xu,
m3_xd,
]
if with_m2 is True:
motors.extend([m2_yu, m2_ydo, m2_ydi])
ok = True
for m in motors:
if m.connected is False:
print(disconnected_msg(f'{m.name} is not connected'))
for walk in m.walk_signals(include_lazy=False):
if walk.item.connected is False:
print(
disconnected_msg(
f' {walk.item.name} is a disconnected PV'))
print(
whisper(
f'try: {m.name} = {m.__class__}("{m.prefix}", name={m.name})'
))
ok = False
return ok
def select(self, el):
'''Choose the ROI configured for element el'''
if type(el) is int:
if el < 1 or el > 3:
self.myprint(error_msg('\n%d is not a valid ROI channel\n' % el))
return
el = self.slots[el-1]
if el is None:
self.myprint(error_msg('\nThat ROI is not configured\n'))
return
if Z_number(el) is None:
self.myprint(error_msg('\n%s is not an element\n' % el))
return
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:
self.myprint(whisper('%s is not in a configured channel, not changing BMMuser.roi_channel' % el.capitalize()))
def doscan():
line1 = '%s, %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(motor.name, sgnl, start, stop, nsteps, motor.user_readback.get())
uid = yield from rel_scan(dets, motor, start, stop, nsteps, md={'plan_name' : f'rel_scan linescan {motor.name} I0'})
t = user_ns['db'][-1].table()
if detector.lower() == 'if':
signal = numpy.array((t[BMMuser.xs1]+t[BMMuser.xs2]+t[BMMuser.xs3]+t[BMMuser.xs4])/t['I0'])
elif detector.lower() == 'it':
signal = numpy.array(t['It']/t['I0'])
elif detector.lower() == 'ir':
signal = numpy.array(t['Ir']/t['It'])
signal = signal - signal[0]
if negate is True:
signal = -1 * signal
pos = numpy.array(t[motor.name])
mod = RectangleModel(form='erf')
pars = mod.guess(signal, x=pos)
out = mod.fit(signal, pars, x=pos)
print(whisper(out.fit_report(min_correl=0)))
out.plot()
if filename is not None:
plt.savefig(filename)
#middle = out.params['center1'].value + (out.params['center2'].value - out.params['center1'].value)/2
yield from mv(motor, out.params['midpoint'].value)
print(bold_msg(f'Found center at {motor.name} = {motor.position}'))
rkvs.set('BMM:lmfit:center1', out.params['center1'].value)
rkvs.set('BMM:lmfit:center2', out.params['center2'].value)
rkvs.set('BMM:lmfit:sigma1', out.params['sigma1'].value)
rkvs.set('BMM:lmfit:sigma2', out.params['sigma2'].value)
rkvs.set('BMM:lmfit:amplitude', out.params['amplitude'].value)
rkvs.set('BMM:lmfit:midpoint', out.params['midpoint'].value)
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 do_ChangeEdge(self):
print(go_msg('You would like to change to a different edge...\n'))
el = input(" What element? ")
el = el.capitalize()
if el == '':
print(whisper('doing nothing'))
return (yield from null())
if el not in ELEMENTS:
print(error_msg(f'{el} is not an element'))
return (yield from null())
if Z_number(el) < 46:
default_ed = 'K'
prompt = go_msg('K') + '/L3/L2/L1'
else:
default_ed = 'L3'
prompt = 'K/' + go_msg('L3') + '/L2/L1'
ed = input(f' What edge? [{prompt}] ')
ed = ed.capitalize()
if ed not in ('K', 'L3', 'L2', 'L1'):
ed = default_ed
focus = input(' Focused beam? [y/N] ')
if focus.lower() == 'y':
focus = True
else:
focus = False
print(
disconnected_msg(
f'yield from change_edge("{el}", focus={focus}, edge="{ed}")'))
yield from null()
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 calibrate_pitch(mono='111'):
BMMuser = user_ns['BMMuser']
# read content from INI file
datafile = os.path.join(BMMuser.DATA, 'edges%s.ini' % mono)
print(f'reading {datafile}')
config.read_file(open(datafile))
edges = dict()
for i in config.items('edges'):
el = i[0]
vals = [float(j) for j in i[1].split(',')
] # convert CSV string -> list of strings -> list of floats
edges[el] = vals
# organize the data from the INI file
ordered = [y[1] for y in sorted([(edges[x][1], x) for x in edges.keys()])]
ee = list()
tt = list()
for el in ordered:
ee.append(edges[el][1])
tt.append(edges[el][3])
mod = LinearModel()
pars = mod.guess(tt, x=ee)
out = mod.fit(tt, pars, x=ee)
print(whisper(out.fit_report(min_correl=0)))
out.plot()
def show_shutters():
ena_text = ' Beamline: '
try:
if bl_enabled.get() == 1:
ena_text += 'enabled '
else:
ena_text += error_msg('disabled ')
except:
ena_text += whisper('unavailable ')
bmps_text = ' BMPS: '
try:
bmps_state = bool(bmps.state.get())
if bmps_state is True:
bmps_text += 'open'
else:
bmps_text += error_msg('closed')
except:
bmps_text += whisper('unavailable ')
idps_text = ' IDPS: '
try:
idps_state = bool(idps.state.get())
if idps_state is True:
idps_text += 'open'
else:
idps_text += error_msg('closed')
except:
idps_text += whisper('unavailable ')
# sha_state = bool(sha.enabled.get()) and bool(sha.state.get())
# sha_text = ' FOE Shutter: '
# if sha_state is True:
# sha_text += 'open'
# else:
# sha_text += error_msg('closed')
shb_state = bool(shb.state.get())
shb_text = ' Photon Shutter: '
if shb_state is False:
shb_text += 'open'
else:
shb_text += error_msg('closed')
return (ena_text + bmps_text + idps_text + shb_text)
def write_ini_and_plan(self):
#################################
# write out the master INI file #
#################################
config = configparser.ConfigParser()
default = self.measurements[0].copy()
# things in the spreadsheet but not in the INI file
for k in ('default', 'slot', 'measure', 'spin', 'focus', 'method', 'samplep', 'samplex', 'sampley', 'slitwidth', 'detectorx', 'settle', 'power', 'temperature', 'motor1', 'position1', 'motor2', 'position2'):
default.pop(k, None)
default['url'] = '...'
default['doi'] = '...'
default['cif'] = '...'
default['experimenters'] = self.ws['E1'].value # top line of xlsx file
default = self.ini_sanity(default)
if default is None:
print(error_msg(f'Could not interpret {self.source} as a wheel macro.'))
return
# print(default)
config.read_dict({'scan': default})
with open(self.ini, 'w') as configfile:
config.write(configfile)
print(whisper('Wrote default INI file: %s' % self.ini))
########################################################
# write the full macro to a file and %run -i that file #
########################################################
with open(self.tmpl) as f:
text = f.readlines()
fullmacro = ''.join(text).format(folder = self.folder,
base = self.basename,
content = self.content,
description = self.description,
instrument = self.instrument,
cleanup = self.cleanup,
initialize = self.initialize)
o = open(self.macro, 'w')
o.write(fullmacro)
o.close()
## I think this will never be called by queueserver
from IPython import get_ipython
ipython = get_ipython()
ipython.magic('run -i \'%s\'' % self.macro)
print(whisper('Wrote and read macro file: %s' % self.macro))
def reset_rois(self, el=None, tab=''):
BMMuser = user_ns['BMMuser']
if el is None:
el = BMMuser.element
if el in self.slots:
print(whisper(f'{tab}Resetting rois with {el} as the active ROI'))
BMMuser.element = el
self.set_rois()
self.measure_roi()
else:
print(
error_msg(
f'{tab}Cannot reset rois, {el} is not in {self.name}.slots'
))
def ocd(text, signal):
'''Indicated open/close/disconnected state with suitable text coloring.
'''
outtext = text
try:
if signal.connected is False:
outtext += disconnected_msg('disconnected ')
elif signal.get() == 1:
outtext += 'enabled '
else:
outtext += error_msg('disabled ')
except:
outtext += whisper('unavailable ')
return outtext
def status(self):
text = '\n %s is %s\n\n' % (self.name, self.prefix)
for signal in list(self.configuration_attrs):
if signal.upper() not in status_list.keys():
continue
suffix = getattr(self, signal).pvname.replace(self.prefix, '')
string = getattr(self, signal).enum_strs[getattr(self,
signal).get()]
if signal != 'asscs':
if getattr(self, signal).get() != status_list[signal.upper()]:
string = error_msg('%-19s' % string)
text += ' %-26s : %-19s %s %s \n' % (
getattr(self, signal + '_desc').get(), string,
bold_msg(getattr(self, signal).get()), whisper(suffix))
boxedtext('%s status signals' % self.name, text, 'green')
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 cycle(self, mc=None):
'''Cycle power to the amplifiers on a motor controller, then reenable
the motors on that controller.
Identify the motor controller by these strings:
'dcm', 'slits2', 'm2', 'm3', 'dm3'
'''
if self.check(mc) is False:
return
print(bold_msg(f'Cycling amplifiers on {mc} motor controller'))
print(whisper('killing amplifiers'))
self.kill(mc)
countdown(5)
print(whisper('reactivating amplifiers'))
self.enable(mc)
print(whisper('enabling motors'))
if mc == 'm2':
m2.ena()
elif mc == 'm3':
m3.ena()
elif mc == 'slits2':
slits2.enable()
elif mc == 'dm3':
slits3.enable()
for axis in (dm3_bct, dm3_bpm, dm3_foils, dm3_fs):
try:
axis.enable()
time.sleep(0.5)
axis.kill()
except:
pass
elif mc == dcm:
dcm.ena()
time.sleep(0.5)
dcm.kill()
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 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 status(self):
text = '\n %s is %s\n\n' % (self.name, self.prefix)
for signal in status_list.keys():
sig = signal.lower()
try:
suffix = getattr(self, sig).pvname.replace(self.prefix, '')
string = getattr(self, sig).enum_strs[getattr(self, sig).get()]
if signal != 'asscs':
if getattr(self, sig).get() != status_list[signal]:
string = verbosebold_msg('%-19s' % string)
#text += ' %-26s : %-19s %s %s \n' % (getattr(self, sig+'_desc').get(),
# string,
# bold_msg(getattr(self, sig).get()),
# whisper(suffix))
text += ' %-19s %s %s \n' % (
string, bold_msg(getattr(self,
sig).get()), whisper(suffix))
except:
pass
boxedtext('%s status signals' % self.name, text, 'green')
def simple_plot(self, uidlist, filename, mode):
'''If the triplot cannot be made for some reason, make a fallback,
much simpler plot so that something is available for Slack and
the dossier.
'''
BMMuser = user_ns['BMMuser']
this = db.v2[uidlist[0]].primary.read()
if mode == 'test':
title, ylab = 'XAS test scan', 'I0 (nA)'
signal = this['I0']
elif mode == 'transmission':
title, ylab = '', 'transmission'
signal = numpy.log(numpy.abs(this['I0'] / this['It']))
elif mode == 'reference':
title, ylab = '', 'reference'
signal = numpy.log(numpy.abs(this['It'] / this['Ir']))
elif mode == 'yield':
title, ylab = '', 'yield'
signal = this['Iy'] / this['I0']
elif mode == 'xs1':
title, ylab = '', 'fluorescence'
signal = (this[BMMuser.xs8] + 0.001) / (this['I0'] + 1)
else:
title, ylab = '', 'fluorescence'
signal = (this[BMMuser.xs1] + this[BMMuser.xs2] + this[BMMuser.xs3]
+ this[BMMuser.xs4] + 0.001) / (this['I0'] + 1)
thisagg = matplotlib.get_backend()
matplotlib.use('Agg') # produce a plot without screen display
plt.cla()
plt.title(title)
plt.xlabel('energy (eV)')
plt.ylabel(ylab)
plt.plot(this['dcm_energy'], signal)
plt.savefig(filename)
matplotlib.use(thisagg) # return to screen display
print(whisper(f'Wrote simple plot to {filename}'))
def check_for_synaxis():
'''A disconnected motor (due to IOC or controller not running) will be
defined as a SynAxis. This does a test for that situation and
reports about it at startup. It also sets BMMuser.syns to True so
things like motor_status() behave non-disastrously.
'''
BMMuser.syns = False
syns = []
for m in mcs8_motors:
if 'SynAxis' in f'{m}':
syns.append(m.name)
if len(syns) > 0:
BMMuser.syns = True
text = 'The following are disconnected & defined as simulated motors:\n\n'
text += '\n'.join(
disconnected_msg(x)
for x in textwrap.wrap(', '.join(syns))) + '\n\n'
text += 'This allows bsui to operate normally, but do not expect anything\n'
text += 'involving those motors to work correctly.\n'
text += whisper(
'(This likely means that an IOC or a motor controller (or both) are off.)'
)
boxedtext('Disconnected motors', text, 'red', width=74)
def new_experiment(self,
folder,
gup=0,
saf=0,
name='Betty Cooper',
use_pilatus=False,
echem=False):
'''
Do the work of prepping for a new experiment. This will:
* Create a data folder and it's subfolders, if needed, and set the DATA variable
* Set up the experimental log, creating an experiment.log file, if needed
* Write templates for scan.ini and macro.py + xlsx templates, if needed
* Make folders for XRF, HDF5, Pilatus, and electrochemistry
* Set the GUP and SAF numbers as metadata
Parameters
----------
folder : str
data destination
gup : str
GUP number
saf : str
SAF number
name : str
name of PI
use_pilatus : bool
true if this experiment uses the Pilatus
echem : bool
true if this experiment uses the BioLogic potentiostat
'''
step = 1
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## Main folders, point BMMuser and wmb objects at data folder
data_folder = os.path.join(folder, self.date)
user_ns['DATA'] = self.DATA = self.folder = data_folder + '/'
try:
hdf5folder = os.path.join('/nsls2', 'data', 'bmm', 'assets',
'xspress3', *self.date.split('-'))
user_ns['xs'].hdf5.read_path_template = hdf5folder
user_ns['xs'].hdf5.write_path_template = hdf5folder
user_ns['xs'].hdf5.file_path.put(hdf5folder)
except:
# if we are starting up bsui, the xs folder will get set
# later. the try block is needed when running
# start_experiment from a running bsui instance.
pass
try:
user_ns['wmb'].folder = data_folder + '/'
except:
pass
imagefolder = os.path.join(data_folder, 'snapshots')
prjfolder = os.path.join(data_folder, 'prj')
htmlfolder = os.path.join(data_folder, 'dossier')
self.establish_folder(step, 'Lustre folder', folder)
self.establish_folder(0, 'data folder', data_folder)
self.establish_folder(0, 'snapshot folder', imagefolder)
self.establish_folder(0, 'Athena prj folder', prjfolder)
if self.establish_folder(0, 'dossier folder', htmlfolder) == 'Created':
# 'sample.tmpl', 'sample_xs.tmpl', 'sample_ga.tmpl'
for f in ('manifest.tmpl', 'logo.png', 'style.css', 'trac.css'):
shutil.copyfile(os.path.join(startup_dir, 'dossier', f),
os.path.join(htmlfolder, f))
manifest = open(os.path.join(self.DATA, 'dossier', 'MANIFEST'),
'a')
manifest.close()
print(' copied html generation files, touched MANIFEST')
step += 1
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## setup logger
BMM_user_log(os.path.join(data_folder, 'experiment.log'))
print('%2d. Set up experimental log file: %-75s' %
(step, os.path.join(data_folder, 'experiment.log')))
step += 1
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## scan.ini template, macro template & wheel/ga spreadsheets
initmpl = os.path.join(startup_dir, 'tmpl', 'scan.tmpl')
scanini = os.path.join(data_folder, 'scan.ini')
if not os.path.isfile(scanini):
with open(initmpl) as f:
content = f.readlines()
o = open(scanini, 'w')
o.write(''.join(content).format(folder=data_folder, name=name))
o.close()
verb, pad = 'Copied', ' '
else:
verb, pad = 'Found', ' '
self.print_verb_message(step, verb, 'INI file', pad, scanini)
macrotmpl = os.path.join(startup_dir, 'tmpl', 'macro.tmpl')
macropy = os.path.join(data_folder, 'sample_macro.py')
commands = '''
## sample 1
yield from slot(1)
yield from xafs('scan.ini', filename='samp1', sample='first sample')
close_last_plot()
## sample 2
yield from slot(2)
## yield from mvr(xafs_x, 0.5)
yield from xafs('scan.ini', filename='samp2', sample='another sample', comment='my comment')
close_last_plot()
## sample 3
yield from slot(3)
yield from xafs('scan.ini', filename='samp3', sample='a different sample', prep='this sample prep', nscans=4)
close_last_plot()'''
if not os.path.isfile(macropy):
with open(macrotmpl) as f:
content = f.readlines()
o = open(macropy, 'w')
o.write(''.join(content).format(folder=data_folder,
base='sample',
content=commands,
description='(example...)',
instrument='',
cleanup='',
initialize=''))
o.close()
verb, pad = 'Copied', ' '
else:
verb, pad = 'Found', ' '
self.print_verb_message(0, verb, 'macro template', pad, macropy)
self.find_or_copy_file(0, 'wheel macro spreadsheet', 'wheel.xlsx')
self.find_or_copy_file(0, 'glancing angle spreadsheet',
'glancing_angle.xlsx')
self.find_or_copy_file(0, 'double wheel spreadsheet',
'doublewheel.xlsx')
self.find_or_copy_file(0, 'Linkam stage spreadsheet', 'linkam.xlsx')
self.find_or_copy_file(0, 'motor grid spreadsheet', 'grid.xlsx')
step += 1
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## XRF & HDF5folders
xrffolder = os.path.join(data_folder, 'XRF')
self.establish_folder(step, 'XRF spectra folder', xrffolder)
#hdf5folder = os.path.join(data_folder, 'raw', 'HDF5')
#hdf5folder = os.path.join('/nsls2', 'data', 'bmm', 'assets', 'xspress3', *self.date.split('-'))
#self.establish_folder(0, 'Xspress3 HDF5 folder', hdf5folder)
#xs.hdf5.file_path.put(hdf5folder)
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## Pilatus folder
if use_pilatus:
pilfolder = os.path.join(data_folder, 'raw', 'Pilatus')
self.establish_folder(0, 'Pilatus folder', pilfolder)
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## echem folder
if echem:
self.echem = True
ecfolder = os.path.join(data_folder, 'raw', 'electrochemistry')
self.establish_folder(0, 'electrochemistry folder', ecfolder)
#self.echem_remote = os.path.join('/mnt/nfs/ws3', name, self.date)
#if not os.path.isdir(self.echem_remote):
# os.makedirs(self.echem_remote)
# print(' Created remote echem folder: %-75s' % (self.echem_remote))
#else:
# print(' Found remote echem folder: %-75s' % (self.echem_remote))
step += 1
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## GDrive folder
user_folder = make_gdrive_folder(prefix=' ', update=False)
for f in ('logo.png', 'style.css', 'trac.css'):
shutil.copyfile(os.path.join(startup_dir, 'dossier', f),
os.path.join(user_folder, 'dossier', f))
print('%2d. Established Google Drive folder: %-75s' %
(step, user_folder))
print(
whisper(
f' Don\'t foget to share Google Drive folder and Slack channel with {name}'
))
step += 1
## --*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--*--
## SAF and GUP
self.gup = gup
self.saf = saf
print(
f'{step:2d}. Set GUP and SAF numbers as metadata GUP: {gup} SAF: {saf}'
)
shipping_folder = os.path.join(os.getenv('HOME'), 'SDS', self.cycle,
f'{saf}')
self.establish_folder(0, 'shipping docs folder', shipping_folder)
step += 1
self.user_is_defined = True
return None
def _write_macro(self):
'''Write a macro paragraph for each sample described in the
spreadsheet. A paragraph consists of lines to change the
temperature, lines to move sample and detector to the correct
positions (if needed), a line to change the edge energy (if
needed), a line to measure the XAFS using the correct set of
control parameters, and a line to close plot windows after the
scan.
'''
element, edge, focus = (None, None, None)
settle_time, ramp_time = 0,0
previous = 25
self.content += self.tab + 'yield from mv(linkam.setpoint, linkam.readback.get())\n\n'
self.content += self.tab + 'yield from linkam.on_plan()\n'
self.content += self.tab + 'yield from sleep(15)\n'
for m in self.measurements:
if m['default'] is True:
element = m['element']
edge = m['edge']
temperature = m['temperature']
continue
if m['temperature'] is None:
continue
if self.skip_row(m) is True:
continue
#######################################
# default element/edge(/focus) values #
#######################################
for k in ('element', 'edge', 'focus'):
if m[k] is None:
m[k] = self.measurements[0][k]
if m['settle'] == 0:
m['settle'] = self.measurements[0]['settle']
################################
# change temperature is needed #
################################
if m['temperature'] != temperature:
self.content += self.tab + f"report('== Moving to temperature {m['temperature']:.1f}C', slack=True)\n"
self.content += self.tab + f'linkam.settle_time = {m["settle"]:.1f}\n'
self.content += self.tab + f'yield from mv(linkam, {m["temperature"]:.1f})\n'
temperature = m['temperature']
settle_time += m["settle"]
ramp_time += (temperature - previous) / user_ns['linkam'].RR.get()
previous = temperature
############################
# sample and slit movement #
############################
if m['samplex'] is not None:
self.content += self.tab + f'yield from mv(xafs_x, {m["samplex"]:.3f})\n'
if m['sampley'] is not None:
self.content += self.tab + f'yield from mv(xafs_y, {m["sampley"]:.3f})\n'
if m['detectorx'] is not None:
self.content += self.tab + f'yield from mv(xafs_det, {m["detectorx"]:.2f})\n'
##########################
# change edge, if needed #
##########################
focus = False
if m['focus'] == 'focused':
focus = True
if self.do_first_change is True:
self.content += self.tab + 'yield from change_edge(\'%s\', edge=\'%s\', focus=%r)\n' % (m['element'], m['edge'], focus)
self.do_first_change = False
self.totaltime += 4
elif m['element'] != element or m['edge'] != edge: # focus...
element = m['element']
edge = m['edge']
self.content += self.tab + 'yield from change_edge(\'%s\', edge=\'%s\', focus=%r)\n' % (m['element'], m['edge'], focus)
self.totaltime += 4
else:
if self.verbose:
self.content += self.tab + '## staying at %s %s\n' % (m['element'], m['edge'])
pass
######################################
# measure XAFS, then close all plots #
######################################
command = self.tab + 'yield from xafs(\'%s.ini\'' % self.basename
for k in m.keys():
## skip cells with macro-building parameters that are not INI parameters
if self.skip_keyword(k):
continue
## skip element & edge if they are same as default
elif k in ('element', 'edge'):
if m[k] == self.measurements[0][k]:
continue
## skip cells with only whitespace
if type(m[k]) is str and len(m[k].strip()) == 0:
m[k] = None
## if a cell has data, put it in the argument list for xafs()
if m[k] is not None:
if k == 'filename':
fname = self.make_filename(m)
command += f', filename=\'{fname}\''
elif type(m[k]) is int:
command += ', %s=%d' % (k, m[k])
elif type(m[k]) is float:
command += ', %s=%.3f' % (k, m[k])
else:
command += ', %s=\'%s\'' % (k, m[k])
command += ')\n'
self.content += command
self.content += self.tab + 'close_last_plot()\n\n'
#self.content += self.tab + 'yield from linkam.off_plan()\n\n'
########################################
# approximate time cost of this sample #
########################################
self.estimate_time(m, element, edge)
print(whisper(f'XAS time: about {self.totaltime/60:.1f} hours'))
print(whisper(f'ramp time: about {ramp_time:.1f} minutes'))
print(whisper(f'settling time: about {settle_time/60:.1f} minutes'))
self.totaltime = self.totaltime + (settle_time / 60) + ramp_time
if self.close_shutters:
self.content += self.tab + 'if not dryrun:\n'
self.content += self.tab + ' BMMuser.running_macro = False\n'
self.content += self.tab + ' BMM_clear_suspenders()\n'
self.content += self.tab + ' yield from shb.close_plan()\n'
def bailout():
print(whisper('doing nothing'))
yield from null()
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 recenter(self):
here = self.user_readback.get()
center = round(here / 15) * 15
yield from mv(self, center)
print(whisper('recentered %s to %.1f' % (self.name, center)))
def do_nothing(self):
print(whisper('doing nothing'))
yield from null()
