def show_reference_wheel():
xafs_ref = user_ns['xafs_ref']
wheel = xafs_ref.content.copy()
this = xafs_ref.current_slot() - 1
#wheel[this] = go_msg(wheel[this])
text = 'Foil wheel:\n'
text += bold_msg(
' 1 2 3 4 5 6 7 8 9 10 11 12\n'
)
text += ' '
for i in range(12):
if i == this:
text += go_msg('%4.4s' % str(wheel[i])) + ' '
else:
text += '%4.4s' % str(wheel[i]) + ' '
text += '\n'
text += bold_msg(
' 13 14 15 16 17 18 19 20 21 22 23 24\n'
)
text += ' '
for i in range(12, 24):
if i == this:
text += go_msg('%4.4s' % str(wheel[i])) + ' '
else:
text += '%4.4s' % str(wheel[i]) + ' '
text += '\n'
return (text)
def xlsx():
'''Prompt for a macro building spreadsheet for any instrument. Use the
content of cell B1 to direct this spreadsheet to the correct builder.
if cell B1 is "Glancing angle" --> build a glancing angle macro
if cell B1 is "Sample wheel" --> build a sample wheel macro
if cell B1 is empty --> build a sample wheel macro
'''
spreadsheet = present_options('xlsx')
if spreadsheet is None:
print(error_msg('No spreadsheet specified!'))
return None
#spreadsheet = os.path.join(BMMuser.folder, spreadsheet)
wb = load_workbook(os.path.join(BMMuser.folder, spreadsheet),
read_only=True)
ws = wb.active
instrument = str(ws['B1'].value).lower()
if instrument == 'glancing angle':
print(bold_msg('This is a glancing angle spreadsheet'))
pinwheel.spreadsheet(spreadsheet)
else:
print(bold_msg('This is a sample wheel spreadsheet'))
wmb.spreadsheet(spreadsheet)
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 finish_macro(self):
#######################################
# explain to the user what to do next #
#######################################
print(f'\nYour new {BMMuser.instrument} plan is called: ' + bold_msg('%s_macro' % self.basename))
print('\nVerify: ' + bold_msg('%s_macro??' % self.basename))
if 'glancing angle' in self.instrument:
print('Run: ' + bold_msg('RE(%s_macro())' % self.basename))
print('Add ref: ' + bold_msg('RE(%s_macro(ref=True))' % self.basename))
else:
print('Run: ' + bold_msg('RE(%s_macro())' % self.basename))
#print('Dryrun: ' + bold_msg('RE(%s_macro(dryrun=True))' % self.basename))
hours = int(self.totaltime/60)
minutes = int(self.totaltime - hours*60)
self.deltatime = numpy.sqrt(self.deltatime)
print(f'\nApproximate time: {hours} hours, {minutes} minutes +/- {self.deltatime:.1f} minutes')
def verify_roi(self, xs, el, edge, tab=''):
print(bold_msg(f'{tab}Attempting to set ROIs for {el} {edge} edge'))
try:
## if el is not one of the "standard" 12 ROI sets, insert it into xs.slots[12]/index 13
if xs.check_element(el, edge):
forceit = False
if el.capitalize() in ('Pb',
'Pt') and edge.capitalize() in ('L2',
'L1'):
forceit = True # Pb and Pt L3 edges are "standard" ROIs
if el not in xs.slots or forceit:
with open(os.path.join(startup_dir, 'rois.json'),
'r') as fl:
js = fl.read()
allrois = json.loads(js)
xs.slots[14] = el
for channel in xs.iterate_channels():
xs.set_roi_channel(
channel,
index=15,
name=f'{el.capitalize()}',
low=allrois[el.capitalize()][edge.lower()]['low'],
high=allrois[el.capitalize()][
edge.lower()]['high'])
xs.set_rois()
xs.measure_roi()
else:
report(
f'{tab}No tabulated ROIs for the {el.capitalize()} {edge.capitalize()} edge. Not setting ROIs for mesaurement.',
level='bold',
slack=True)
xs.reset_rois(tab=tab)
except Exception as E:
print(error_msg(E))
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 find_slot(close=False):
yield from rectangle_scan(motor=xafs_y, start=-3, stop=3, nsteps=31, detector='It')
yield from rectangle_scan(motor=xafs_x, start=-10, stop=10, nsteps=31, detector='It')
user_ns['xafs_wheel'].in_place()
print(bold_msg(f'Found slot at (X,Y) = ({xafs_x.position}, {xafs_y.position})'))
if close:
close_all_plots()
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 center_sample_y():
yield from linescan('it', xafs_liny, -1.5, 1.5, 61, pluck=False)
table = db[-1].table()
diff = -1 * table['It'].diff()
inflection = table['xafs_liny'][diff.idxmax()]
yield from mv(xafs_liny, inflection)
print(bold_msg('Optimal position in y at %.3f' % inflection))
def to_xdi(self, filename=None):
'''Write an XDI-style file with bin energy in the first column and the
waveform of each of the 4 channels in the other columns.
'''
dcm, BMMuser, ring = user_ns['dcm'], user_ns['BMMuser'], user_ns[
'ring']
column_list = ['MCA1', 'MCA2', 'MCA3', 'MCA4']
column_list = [
f'MCA{channel_number}' for channel_number in self.channel_numbers
]
m2state, m3state = mirror_state()
handle = open(filename, 'w')
handle.write('# XDI/1.0 BlueSky/%s\n' % bluesky_version)
#handle.write('# Scan.uid: %s\n' % dataframe['start']['uid'])
#handle.write('# Scan.transient_id: %d\n' % dataframe['start']['scan_id'])
handle.write(
'# Beamline.name: BMM (06BM) -- Beamline for Materials Measurement'
)
handle.write('# Beamline.xray_source: NSLS-II three-pole wiggler\n')
handle.write(
'# Beamline.collimation: paraboloid mirror, 5 nm Rh on 30 nm Pt\n')
handle.write('# Beamline.focusing: %s\n' % m2state)
handle.write('# Beamline.harmonic_rejection: %s\n' % m3state)
handle.write('# Beamline.energy: %.3f\n' % dcm.energy.position)
handle.write(
'# Detector.fluorescence: SII Vortex ME4 (4-element silicon drift)\n'
)
handle.write('# Scan.end_time: %s\n' % now())
handle.write('# Scan.dwell_time: %.2f\n' % self.cam.acquire_time.value)
handle.write('# Facility.name: NSLS-II\n')
handle.write('# Facility.current: %.1f mA\n' % ring.current.value)
handle.write('# Facility.mode: %s\n' % ring.mode.value)
handle.write('# Facility.cycle: %s\n' % BMMuser.cycle)
handle.write('# Facility.GUP: %d\n' % BMMuser.gup)
handle.write('# Facility.SAF: %d\n' % BMMuser.saf)
handle.write('# Column.1: energy (eV)\n')
for c, mca_number in enumerate(column_list):
handle.write(f'# Column.{c+2}: MCA{mca_number} (counts)\n')
handle.write(
'# ==========================================================\n')
handle.write('# energy ')
## data table
e = numpy.arange(0, len(
self.channels.channel01.mca.array_data.get())) * 10
mca_data_array_list = [
channel.mca.array_data.get()
for channel in self.iterate_channels()
]
a = numpy.vstack(mca_data_array_list)
b = pandas.DataFrame(a.transpose(), index=e, columns=column_list)
handle.write(b.to_csv(sep=' '))
handle.flush()
handle.close()
print(bold_msg('wrote XRF spectra to %s' % filename))
def ls2dat(datafile, key):
'''
Export a linescan database entry to a simple column data file.
ls2dat('/path/to/myfile.dat', '0783ac3a-658b-44b0-bba5-ed4e0c4e7216')
or
ls2dat('/path/to/myfile.dat', 1533)
The arguments are a data file name and the database key.
'''
#BMMuser, db = user_ns['BMMuser'], user_ns['db']
if os.path.isfile(datafile):
print(error_msg('%s already exists! Bailing out....' % datafile))
return
handle = open(datafile, 'w')
dataframe = user_ns['db'][key]
devices = dataframe.devices() # note: this is a _set_ (this is helpful: https://snakify.org/en/lessons/sets/)
if 'vor' in devices:
abscissa = dataframe['start']['motors'][0]
column_list = [abscissa, 'I0', 'It', 'Ir',
BMMuser.dtc1, BMMuser.dtc2, BMMuser.dtc3, BMMuser.dtc4,
BMMuser.roi1, 'ICR1', 'OCR1',
BMMuser.roi2, 'ICR2', 'OCR2',
BMMuser.roi3, 'ICR3', 'OCR3',
BMMuser.roi4, 'ICR4', 'OCR4']
template = " %.3f %.6f %.6f %.6f %.6f %.6f %.6f %.6f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f\n"
elif 'DualI0' in devices:
abscissa = dataframe['start']['motors'][0]
column_list = [abscissa, 'Ia', 'Ib',]
template = " %.3f %.6f %.6f\n"
else:
abscissa = dataframe['start']['motors'][0]
template = " %.3f %.6f %.6f %.6f\n"
column_list = [abscissa, 'I0', 'It', 'Ir']
#print(column_list)
table = dataframe.table()
this = table.loc[:,column_list]
handle.write('# XDI/1.0 BlueSky/%s\n' % bluesky_version)
handle.write('# Scan.uid: %s\n' % dataframe['start']['uid'])
handle.write('# Scan.transient_id: %d\n' % dataframe['start']['scan_id'])
try:
handle.write('# Facility.GUP: %s\n' % dataframe['start']['XDI']['Facility']['GUP'])
except:
pass
try:
handle.write('# Facility.SAF: %s\n' % dataframe['start']['XDI']['Facility']['SAF'])
except:
pass
handle.write('# ==========================================================\n')
handle.write('# ' + ' '.join(column_list) + '\n')
for i in range(0,len(this)):
handle.write(template % tuple(this.iloc[i]))
handle.flush()
handle.close()
print(bold_msg('wrote linescan to %s' % datafile))
def to_xdi(self, filename=None):
'''Write an XDI-style file with bin energy in the first column and the
waveform of the measurement channel in the second column.
'''
dcm, BMMuser, ring = user_ns['dcm'], user_ns['BMMuser'], user_ns[
'ring']
column_list = ['MCA8']
#template = " %.3f %.6f %.6f %.6f %.6f\n"
m2state, m3state = mirror_state()
handle = open(filename, 'w')
handle.write('# XDI/1.0 BlueSky/%s\n' % bluesky_version)
#handle.write('# Scan.uid: %s\n' % dataframe['start']['uid'])
#handle.write('# Scan.transient_id: %d\n' % dataframe['start']['scan_id'])
handle.write(
'# Beamline.name: BMM (06BM) -- Beamline for Materials Measurement'
)
handle.write('# Beamline.xray_source: NSLS-II three-pole wiggler\n')
handle.write(
'# Beamline.collimation: paraboloid mirror, 5 nm Rh on 30 nm Pt\n')
handle.write('# Beamline.focusing: %s\n' % m2state)
handle.write('# Beamline.harmonic_rejection: %s\n' % m3state)
handle.write('# Beamline.energy: %.3f\n' % dcm.energy.position)
handle.write(
'# Detector.fluorescence: SII Vortex ME4 (4-element silicon drift)\n'
)
handle.write('# Scan.end_time: %s\n' % now())
handle.write('# Scan.dwell_time: %.2f\n' %
self.settings.acquire_time.value)
handle.write('# Facility.name: NSLS-II\n')
handle.write('# Facility.current: %.1f mA\n' % ring.current.value)
handle.write('# Facility.mode: %s\n' % ring.mode.value)
handle.write('# Facility.cycle: %s\n' % BMMuser.cycle)
handle.write('# Facility.GUP: %d\n' % BMMuser.gup)
handle.write('# Facility.SAF: %d\n' % BMMuser.saf)
handle.write('# Column.1: energy (eV)\n')
handle.write('# Column.2: MCA1 (counts)\n')
handle.write(
'# ==========================================================\n')
handle.write('# energy ')
## data table
e = numpy.arange(0, len(self.mca1.value)) * 10
a = numpy.vstack([
self.mca1.value, self.mca2.value, self.mca3.value, self.mca4.value
])
b = pd.DataFrame(a.transpose(), index=e, columns=column_list)
handle.write(b.to_csv(sep=' '))
handle.flush()
handle.close()
print(bold_msg('wrote XRF spectra to %s' % filename))
def show_rois(self):
BMMuser = user_ns['BMMuser']
text = 'Xspress3 ROIs:\n'
text += bold_msg(' 1 2 3 4 5 6 7 8\n')
text += ' '
for i in range(8):
if self.slots[i] == BMMuser.element:
text += go_msg('%4.4s' % self.slots[i]) + ' '
else:
text += '%4.4s' % self.slots[i] + ' '
text += '\n'
text += bold_msg(' 9 10 11 12 13 14 15 16\n')
text += ' '
for i in range(8, 16):
if self.slots[i] == BMMuser.element:
text += go_msg('%4.4s' % self.slots[i]) + ' '
else:
text += '%4.4s' % self.slots[i] + ' '
text += '\n'
return(text)
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 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 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 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 read_spreadsheet(self):
'''Slurp up the content of the spreadsheet and write the default control file
'''
print('Reading spreadsheet: %s' % self.source)
count = 0
self.offset = 0
isok, explanation = True, ''
if self.has_e0_column: # deal with older xlsx that have e0 in column H
self.offset = 1
for row in self.ws.rows:
count += 1
if count < 6:
continue
defaultline = False
if count == 6:
defaultline = True
if count > 200:
break
self.measurements.append(self.get_keywords(row, defaultline))
# check that scan parameters make sense
if type(self.measurements[-1]['bounds']) is str:
b = re.split('[ ,]+', self.measurements[-1]['bounds'].strip())
else:
b = re.split('[ ,]+', self.measurements[0]['bounds'].strip())
if type(self.measurements[-1]['steps']) is str:
s = re.split('[ ,]+', self.measurements[-1]['steps'].strip())
else:
s = re.split('[ ,]+', self.measurements[0]['steps'].strip())
if type(self.measurements[-1]['times']) is str:
t = re.split('[ ,]+', self.measurements[-1]['times'].strip())
else:
t = re.split('[ ,]+', self.measurements[0]['times'].strip())
(problem, text, reference) = sanitize_step_scan_parameters(b, s, t)
if problem is True:
isok = False
explanation += bold_msg(f'\nrow {count}, sample {self.measurements[-1]["filename"]}:\n') + text
return(isok, explanation, reference)
def scan_slit(slp):
#if slit_height < 0.5:
# yield from mv(slits3.vsize, 0.5)
yield from mv(quadem1.averaging_time, 0.1)
yield from mv(motor.velocity, 0.4)
yield from mv(motor.kill_cmd, 1)
uid = yield from rel_scan([quadem1], motor, start, stop, nsteps, md={'plan_name' : f'rel_scan linescan {motor.name} I0'})
user_ns['RE'].msg_hook = BMM_msg_hook
BMM_log_info('slit height scan: %s\tuid = %s, scan_id = %d' %
(line1, uid, user_ns['db'][-1].start['scan_id']))
if move:
t = user_ns['db'][-1].table()
signal = t['I0']
#if get_mode() in ('A', 'B', 'C'):
# position = com(signal)
#else:
position = peak(signal)
top = t[motor.name][position]
yield from sleep(slp)
yield from mv(motor.kill_cmd, 1)
yield from sleep(slp)
yield from mv(motor, top)
else:
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 sleep(slp)
yield from mv(motor.kill_cmd, 1)
#yield from mv(motor.inpos, 1)
yield from sleep(slp)
yield from move_after_scan(motor)
yield from mv(quadem1.averaging_time, 0.5)
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 set_instrument(instrument=None):
if instrument.lower() == 'glancing angle':
print(bold_msg('Setting instrument as glancing angle stage'))
BMMuser.instrument = 'glancing angle stage'
elif instrument.lower() == 'double wheel':
print(bold_msg('Setting instrument as double sample wheel'))
BMMuser.instrument = 'double wheel'
elif instrument.lower() == 'linkam':
print(bold_msg('Setting instrument as Linkam stage'))
BMMuser.instrument = 'Linkam stage'
elif instrument.lower() == 'lakeshore':
print(bold_msg('Setting instrument as LakeShore 331'))
BMMuser.instrument = 'LakeShore'
elif instrument.lower() == 'grid':
print(bold_msg('Setting instrument as sample grid'))
BMMuser.instrument = 'motor grid'
else:
print(bold_msg('Default instrument choice: sample wheel'))
BMMuser.instrument = 'sample wheel'
rkvs.set('BMM:automation:type', instrument)
def find_slot(xmargin=0.5, ymargin=2, force=False):
'''Thin wrapper around repeated calls to linescan in order to align a
sample wheel slot in the beam. This will perform a linescan in
xafs_x over the range of -10 to 10 or in xafs_y from -3 to 3
(which are suitable ranges for the size of the slot). User is
prompted to scan in X or Y, or to quit the loop. The loop will
return after 6 scans -- 3 iterations is certainly enough for this
task.
In bsui terms, this is a wrapper around these command:
linescan(xafs_x, 'it', -10, 10, 31)
and
linescan(xafs_y, 'it', -3, 3, 31)
which are suitable linescans for aligning the sample wheel once it
has been aligned roughly by hand.
The high limit in xafs_x will be set to 500 microns (the default)
above the selected position. The margin cannot be less than 50
microns. The low limit in xafs_x is presumed not to be important.
The high limit in xafs_y will be set to 2 mm (the default) above
the selected position. The low limit in xafs_y will be set to 2
mm (the default) below the selected position. The margin cannot
be less than 50 microns.
Parameters
==========
xmargin : float
margin for setting the high limit of the xafs_x axis,
default=0.5, minimum=0.05
ymargin : float
margin for setting the high limit of the xafs_y axis,
default=2, minimum=0.05
force : bool
passed along to linescan(), flag for forcing a scan even if
not clear to start
'''
xafs_x, xafs_y = user_ns['xafs_x'], user_ns['xafs_y']
count = 1
if xmargin < 0.05:
xmargin = 0.05
if ymargin < 0.05:
ymargin = 0.05
while True:
action = input(
bold_msg(
"\nScan axis? [x=xafs_x / y=xafs_y / q=quit] (then Enter) "))
if action[:1].lower() == 'x':
yield from mv(xafs_x.hlm, xafs_x.default_hlm)
yield from linescan(xafs_x, 'it', -10, 10, 31, force=force)
yield from mv(xafs_x.hlm, xafs_x.position + xmargin)
elif action[:1].lower() == 'y':
yield from mv(xafs_y.hlm, xafs_y.default_hlm, xafs_y.llm,
xafs_y.default_llm)
yield from linescan(xafs_y, 'it', -3, 3, 31, force=force)
yield from mv(xafs_y.hlm, xafs_y.position + ymargin, xafs_y.llm,
xafs_y.position - ymargin)
elif action[:1].lower() in ('q', 'n', 'c'): # quit/no/cancel
yield from null()
close_all_plots()
return
else:
continue
count += 1
if count > 6:
print('Three iterations is plenty....')
close_all_plots()
return
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 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 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 as2dat(datafile, key):
'''
Export an areascan database entry to a simple column data file.
as2dat('/path/to/myfile.dat', '42447313-46a5-42ef-bf8a-46fedc2c2bd1')
or
as2dat('/path/to/myfile.dat', 2948)
The arguments are a data file name and the database key.
'''
BMMuser, db = user_ns['BMMuser'], user_ns['db']
if os.path.isfile(datafile):
print(error_msg('%s already exists! Bailing out....' % datafile))
return
dataframe = db[key]
if 'slow_motor' not in dataframe['start']:
print(
error_msg(
'That database entry does not seem to be a an areascan (missing slow_motor)'
))
return
if 'fast_motor' not in dataframe['start']:
print(
error_msg(
'That database entry does not seem to be a an areascan (missing fast_motor)'
))
return
devices = dataframe.devices(
) # note: this is a _set_ (this is helpful: https://snakify.org/en/lessons/sets/)
if 'vor' in devices:
column_list = [
dataframe['start']['slow_motor'], dataframe['start']['fast_motor'],
'I0', 'It', 'Ir', BMMuser.dtc1, BMMuser.dtc2, BMMuser.dtc3,
BMMuser.dtc4, BMMuser.roi1, 'ICR1', 'OCR1', BMMuser.roi2, 'ICR2',
'OCR2', BMMuser.roi3, 'ICR3', 'OCR3', BMMuser.roi4, 'ICR4', 'OCR4'
]
template = " %.3f %.3f %.6f %.6f %.6f %.6f %.6f %.6f %.6f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f %.1f\n"
else:
column_list = [
dataframe['start']['slow_motor'], dataframe['start']['fast_motor'],
'I0', 'It', 'Ir'
]
template = " %.3f %.3f %.6f %.6f %.6f\n"
table = dataframe.table()
this = table.loc[:, column_list]
handle = open(datafile, 'w')
handle.write('# Scan.uid: %s\n' % dataframe['start']['uid'])
handle.write('# Scan.transient_id: %d\n' % dataframe['start']['scan_id'])
try:
handle.write('# Facility.GUP: %d\n' %
dataframe['start']['XDI']['Facility']['GUP'])
except:
pass
try:
handle.write('# Facility.SAF: %d\n' %
dataframe['start']['XDI']['Facility']['SAF'])
except:
pass
handle.write(
'# ==========================================================\n')
handle.write('# ' + ' '.join(column_list) + '\n')
slowval = None
for i in range(0, len(this)):
if i > 0 and this.iloc[i, 0] != slowval:
handle.write('\n')
handle.write(template % tuple(this.iloc[i]))
slowval = this.iloc[i, 0]
handle.flush()
handle.close()
print(bold_msg('wrote areascan to %s' % datafile))
def center_sample_roll():
yield from linescan('it', xafs_roll, -3, 3, 61, pluck=False)
table = db[-1].table()
peak = table['xafs_roll'][table['It'].idxmax()]
yield from mv(xafs_roll, peak)
print(bold_msg('Optimal position in roll at %.3f' % peak))
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 detector.lower() == 'xs':
dets.append(xs)
detector = BMMuser.xs1
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
rkvs.set('BMM:scan:type', 'area')
rkvs.set('BMM:scan:starttime',
str(datetime.datetime.timestamp(datetime.datetime.now())))
rkvs.set('BMM:scan:estimated', 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)
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 align_ga(ymargin=0.5, force=False):
'''Thin wrapper around repeated calls to linescan in order to align
the glancing angle stage in the beam. This will perform a linescan in
xafs_pitch over the range of -2 to 2 or in xafs_y from -1 to 1
(which are suitable ranges for the size of the slot). User is
prompted to scan in pitch or Y, or to quit the loop. The loop will
return after 6 scans -- 3 iterations is certainly enough for this
task.
In bsui terms, this is a wrapper around these command:
linescan(xafs_y, 'it', -1, 1, 31)
and
linescan(xafs_pitch, 'it', -2, 2, 31)
which are suitable linescans for aligning the glancing angle stage
once it has been aligned roughly by hand.
The high limit in xafs_y will be set to 0.5 mm (the default) above
the selected position. The low limit in xafs_y will be set to 0.5
mm (the default) below the selected position. The margin cannot
be less than 50 microns.
Parameters
==========
ymargin : float
margin for setting the high limit of the xafs_y axis,
default=2, minimum=0.05
force : bool
passed along to linescan(), flag for forcing a scan even if
not clear to start
'''
xafs_pitch, xafs_y = user_ns['xafs_pitch'], user_ns['xafs_y']
db = user_ns['db']
count = 1
if ymargin < 0.05:
ymargin = 0.05
while True:
action = input(
bold_msg(
"\nScan axis? [p=xafs_pitch / y=xafs_y / q=quit] (then Enter) "
))
if action[:1].lower() == 'p':
yield from linescan(xafs_pitch, 'it', -3, 3, 31, force=force)
elif action[:1].lower() == 'y':
yield from mv(xafs_y.hlm, xafs_y.default_hlm, xafs_y.llm,
xafs_y.default_llm)
yield from linescan(xafs_y, 'it', -2, 2, 31, force=force)
#yield from mv(xafs_y.hlm, xafs_y.position+ymargin, xafs_y.llm, xafs_y.position-ymargin)
elif action[:1].lower() in ('q', 'n', 'c'): # quit/no/cancel
yield from null()
close_all_plots()
return
else:
continue
count += 1
if count > 6:
print('Three iterations is plenty....')
close_all_plots()
return