def calibrate_high_end(mono='111'):
'''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)
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)
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)
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)
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)
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 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)
def timescan(detector, readings, dwell, delay, force=False, md={}):
'''
Generic timescan plan.
For example:
RE(timescan('it', 100, 0.5))
detector: detector to display -- if, it, ir, or i0
readings: number of measurements to make
dwell: dwell time in seconds for each measurement
delay: pause in seconds between measurements
outfile: data file name (relative to DATA), False to not write
force: flag for forcing a scan even if not clear to start
This does not write an ASCII data file, but it does make a log entry.
Use the ts2dat() function to extract the linescan from the
database and write it to a file.
'''
RE, BMMuser, quadem1, _locked_dwell_time = user_ns['RE'], user_ns['BMMuser'], user_ns['quadem1'], user_ns['_locked_dwell_time']
######################################################################
# 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 running a time scan.\n' %
BMMuser.macro_sleep))
countdown(BMMuser.macro_sleep)
return(yield from null())
######################################################################
(ok, text) = BMM_clear_to_start()
if force is False and ok is False:
print(error_msg(text))
yield from null()
return
RE.msg_hook = None
## sanitize and sanity checks on detector
detector = detector.capitalize()
if detector not in ('It', 'If', 'I0', 'Iy', 'Ir') and 'Dtc' not in detector:
print(error_msg('\n*** %s is not a timescan measurement (%s)\n' %
(detector, 'it, if, i0, iy, ir')))
yield from null()
return
yield from abs_set(_locked_dwell_time, dwell, wait=True)
dets = [quadem1,]
denominator = ''
epoch_offset = pandas.Timestamp.now(tz='UTC').value/10**9
## func is an anonymous function, built on the fly, for feeding to DerivedPlot
if detector == 'It':
denominator = ' / I0'
func = lambda doc: (doc['time']-epoch_offset, doc['data']['It']/doc['data']['I0'])
elif detector == 'Ir':
denominator = ' / It'
func = lambda doc: (doc['time']-epoch_offset, doc['data']['Ir']/doc['data']['It'])
elif detector == 'I0':
func = lambda doc: (doc['time']-epoch_offset, doc['data']['I0'])
elif detector == 'Iy':
denominator = ' / I0'
func = lambda doc: (doc['time']-epoch_offset, doc['data']['Iy']/doc['data']['I0'])
elif detector == 'Dtc':
dets.append(vor)
denominator = ' / I0'
func = lambda doc: (doc['time']-epoch_offset, doc['data'][BMMuser.dtc2]/doc['data']['I0'])
func3 = lambda doc: (doc['time']-epoch_offset, doc['data'][BMMuser.dtc3]/doc['data']['I0'])
elif detector == 'If':
dets.append(vor)
denominator = ' / I0'
func = lambda doc: (doc['time']-epoch_offset,
(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
if detector == 'Dtc':
plot = [DerivedPlot(func, xlabel='elapsed time (seconds)', ylabel='dtc2', title='time scan'),
DerivedPlot(func3, xlabel='elapsed time (seconds)', ylabel='dtc3', title='time scan')]
else:
plot = DerivedPlot(func,
xlabel='elapsed time (seconds)',
ylabel=detector+denominator,
title='time scan')
line1 = '%s, N=%s, dwell=%.3f, delay=%.3f\n' % (detector, readings, dwell, delay)
thismd = dict()
thismd['XDI'] = dict()
thismd['XDI']['Facility'] = dict()
thismd['XDI']['Facility']['GUP'] = BMMuser.gup
thismd['XDI']['Facility']['SAF'] = BMMuser.saf
thismd['XDI']['Beamline'] = dict()
thismd['XDI']['Beamline']['energy'] = dcm.energy.readback.get()
thismd['XDI']['Scan'] = dict()
thismd['XDI']['Scan']['dwell_time'] = dwell
thismd['XDI']['Scan']['delay'] = delay
@subs_decorator(plot)
#@subs_decorator(src.callback)
def count_scan(dets, readings, delay):
uid = yield from count(dets, num=readings, delay=delay, md={**thismd, **md})
return uid
dotfile = '/home/xf06bm/Data/.time.scan.running'
with open(dotfile, "w") as f:
f.write(str(datetime.datetime.timestamp(datetime.datetime.now())) + '\n')
uid = yield from count_scan(dets, readings, delay)
BMM_log_info('timescan: %s\tuid = %s, scan_id = %d' %
(line1, uid, db[-1].start['scan_id']))
if os.path.isfile(dotfile): os.remove(dotfile)
yield from abs_set(_locked_dwell_time, 0.5, wait=True)
RE.msg_hook = BMM_msg_hook
return(uid)
def main_plan(detector, slow, startslow, stopslow, nslow, fast, startfast,
stopfast, nfast, pluck, force, dwell, md):
(ok, text) = BMM_clear_to_start()
if force is False and ok is False:
print(error_msg(text))
BMMuser.final_log_entry = False
yield from null()
return
RE.msg_hook = None
## sanity checks on slow axis
if type(slow) is str: slow = slow.lower()
if slow not in motor_nicknames.keys() and 'EpicsMotor' not in str(
type(slow)) and 'PseudoSingle' not in str(type(slow)):
print(
error_msg('\n*** %s is not an areascan motor (%s)\n' %
(slow, str.join(', ', motor_nicknames.keys()))))
BMMuser.final_log_entry = False
yield from null()
return
if slow in motor_nicknames.keys():
slow = motor_nicknames[slow]
## sanity checks on fast axis
if type(fast) is str: fast = fast.lower()
if fast not in motor_nicknames.keys() and 'EpicsMotor' not in str(
type(fast)) and 'PseudoSingle' not in str(type(fast)):
print(
error_msg('\n*** %s is not an areascan motor (%s)\n' %
(fast, str.join(', ', motor_nicknames.keys()))))
BMMuser.final_log_entry = False
yield from null()
return
if fast in motor_nicknames.keys():
fast = motor_nicknames[fast]
detector = detector.capitalize()
yield from abs_set(_locked_dwell_time, dwell, wait=True)
dets = [
quadem1,
]
if detector == 'If':
dets.append(vor)
detector = 'ROI1'
if 'PseudoSingle' in str(type(slow)):
valueslow = slow.readback.get()
else:
valueslow = slow.user_readback.get()
line1 = 'slow motor: %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(slow.name, startslow, stopslow, nslow, valueslow)
if 'PseudoSingle' in str(type(fast)):
valuefast = fast.readback.get()
else:
valuefast = fast.user_readback.get()
line2 = 'fast motor: %s, %.3f, %.3f, %d -- starting at %.3f\n' % \
(fast.name, startfast, stopfast, nfast, valuefast)
npoints = nfast * nslow
estimate = int(npoints * (dwell + 0.7))
# extent = (
# valuefast + startfast,
# valueslow + startslow,
# valuefast + stopfast,
# valueslow + stopslow,
# )
# extent = (
# 0,
# nfast-1,
# 0,
# nslow-1
# )
# print(extent)
# return(yield from null())
# areaplot = LiveScatter(fast.name, slow.name, detector,
# xlim=(startfast, stopfast), ylim=(startslow, stopslow))
areaplot = LiveGrid(
(nslow, nfast),
detector, #aspect='equal', #aspect=float(nslow/nfast), extent=extent,
xlabel='fast motor: %s' % fast.name,
ylabel='slow motor: %s' % slow.name)
BMMuser.ax = areaplot.ax
BMMuser.fig = areaplot.ax.figure
BMMuser.motor = fast
BMMuser.motor2 = slow
BMMuser.fig.canvas.mpl_connect('close_event', handle_close)
thismd = dict()
thismd['XDI'] = dict()
thismd['XDI']['Facility'] = dict()
thismd['XDI']['Facility']['GUP'] = BMMuser.gup
thismd['XDI']['Facility']['SAF'] = BMMuser.saf
thismd['slow_motor'] = slow.name
thismd['fast_motor'] = fast.name
## engage suspenders right before starting scan sequence
if force is False: BMM_suspenders()
@subs_decorator(areaplot)
#@subs_decorator(src.callback)
def make_areascan(dets,
slow,
startslow,
stopslow,
nslow,
fast,
startfast,
stopfast,
nfast,
snake=False):
BMMuser.final_log_entry = False
uid = yield from grid_scan(dets, slow, startslow, stopslow, nslow,
fast, startfast, stopfast, nfast, snake)
BMMuser.final_log_entry = True
return uid
with open(dotfile, "w") as f:
f.write(
str(datetime.datetime.timestamp(datetime.datetime.now())) +
'\n')
f.write('%d\n' % estimate)
BMM_log_info('begin areascan observing: %s\n%s%s' %
(detector, line1, line2))
uid = yield from make_areascan(dets, slow, valueslow + startslow,
valueslow + stopslow, nslow, fast,
valuefast + startfast,
valuefast + stopfast, nfast, False)
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())
print(
'Single click the left mouse button on the plot to pluck a point...'
)
cid = BMMuser.fig.canvas.mpl_connect(
'button_press_event',
interpret_click) # see 65-derivedplot.py and
while BMMuser.x is None: # https://matplotlib.org/users/event_handling.html
yield from sleep(0.5)
print('Converting plot coordinates to real coordinates...')
begin = valuefast + startfast
stepsize = (stopfast - startfast) / (nfast - 1)
pointfast = begin + stepsize * BMMuser.x
#print(BMMuser.x, pointfast)
begin = valueslow + startslow
stepsize = (stopslow - startslow) / (nslow - 1)
pointslow = begin + stepsize * BMMuser.y
#print(BMMuser.y, pointslow)
print('That translates to x=%.3f, y=%.3f' % (pointfast, pointslow))
yield from mv(fast, pointfast, slow, pointslow)
