damaris-script-library/Scripts/Spin_Alignment/spinal_exp.py

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# -*- coding: iso-8859-1 -*-
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TXEnableDelay = 1e-6
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TXEnableValue = 0b0001 # TTL line blanking RF amplifier (bit 0)
TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1)
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ADCSensitivity = 1 # voltage span for ADC
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def experiment(): # Jeener-Broekaert echo sequence (a.k.a. spin-alignment)
# set up acquisition parameters:
pars = {}
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pars['P90'] = 4.2e-6 # 90-degree pulse length (s)
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pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
pars['O1'] = -30e3 # offset from SF (Hz)
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pars['SW'] = 10e6 # spectral window (Hz)
pars['SI'] = 1*1024 # number of acquisition points
pars['NS'] = 16 # number of scans
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pars['DS'] = 0 # number of dummy scans
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pars['RD'] = 0.5 # delay between scans (s)
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pars['D1'] = 30e-6 # delay after first pulse, or tp (s)
pars['D2'] = 100e-6 # delay after second pulse, or tm (s)
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pars['PHA'] = -52 # receiver phase (degree)
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pars['DATADIR'] = '/home/fprak/Students/' # data directory
pars['OUTFILE'] = None # output file name
# specify a variable parameter (optional):
pars['VAR_PAR'] = 'D2' # variable parameter name (a string)
start = 30e-6 # starting value
stop = 2e-0 # end value
steps = 24 # number of values
log_scale = True # log scale flag
stag_range = False # staggered range flag
# check parameters for safety:
if pars['PHA'] < 0:
pars['PHA'] = 360 + pars['PHA']
if pars['P90'] > 20e-6:
raise Exception("Pulse too long!!!")
# check whether a variable parameter is named:
var_key = pars.get('VAR_PAR')
if var_key == 'P90' and (start > 20e-6 or stop > 20e-6):
raise Exception("Pulse too long!!!")
if pars['NS']%8 != 0:
pars['NS'] = int(round(pars['NS'] / 8) + 1) * 8
print 'Number of scans changed to ', pars['NS'], ' due to phase cycling'
# start the experiment:
if var_key:
# this is an arrayed experiment:
if log_scale:
array = log_range(start,stop,steps)
else:
array = lin_range(start,stop,steps)
if stag_range:
array = staggered_range(array, size = 2)
# estimate the experiment time:
if var_key == 'D1':
seconds = (sum(array)*2 + (pars['D2'] + pars['RD']) * steps) * (pars['NS'] + pars['DS'])
elif var_key == 'D2':
seconds = (sum(array) + (pars['D1']*2 + pars['RD']) * steps) * (pars['NS'] + pars['DS'])
elif var_key == 'RD':
seconds = (sum(array) + (pars['D1']*2 + pars['D2']) * steps) * (pars['NS'] + pars['DS'])
else:
seconds = (pars['D1']*2 + pars['D2'] + pars['RD']) * steps * (pars['NS']+ pars['DS'])
m, s = divmod(seconds, 60)
h, m = divmod(m, 60)
print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
# loop for a variable parameter:
for index, pars[var_key] in enumerate(array):
print 'Arrayed experiment for '+var_key+': run = '+str(index+1)+\
' out of '+str(array.size)+': value = '+str(pars[var_key])
# loop for accumulation:
for run in xrange(pars['NS']+pars['DS']):
yield spinal_experiment(pars, run)
synchronize()
else:
# estimate the experiment time:
seconds = (pars['D1']*2 + pars['D2'] + pars['RD']) * (pars['NS']+ pars['DS'])
m, s = divmod(seconds, 60)
h, m = divmod(m, 60)
print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
# loop for accumulation:
for run in xrange(pars['NS']+pars['DS']):
yield spinal_experiment(pars, run)
# the pulse program:
def spinal_experiment(pars, run):
e=Experiment()
dummy_scans = pars.get('DS')
if dummy_scans:
run -= dummy_scans
pars['PROG'] = 'spinal_experiment'
# 8-step phase cycle (1-14 modifided to deal with T1-recovery and extended for Re/Im imbalance)
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pars['PH1'] = [0, 270, 0, 270, 180, 90, 180, 90] # 1st (90-degree) pulse
pars['PH3'] = [90, 180, 90, 180, 90, 180, 90, 180] # 2nd (90-degree) pulse
pars['PH4'] = [90, 90, 270, 270, 0, 0, 180, 180] # 3rd (90-degree) pulse
pars['PH2'] = [0, 180, 180, 0, 90, 270, 270, 90] # receiver
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# read in variables:
P90 = pars['P90']
P45 = pars['P90']*0.5
P1 = pars['P90']*0.5
SF = pars['SF']
O1 = pars['O1']
RD = pars['RD']
D1 = pars['D1']
D2 = pars['D2']
PH1 = pars['PH1'][run%len(pars['PH1'])]
PH3 = pars['PH3'][run%len(pars['PH3'])]
PH4 = pars['PH4'][run%len(pars['PH4'])]
PH2 = pars['PH2'][run%len(pars['PH2'])]
PHA = pars['PHA']
# set sampling parameters:
SI = pars['SI']
SW = pars['SW']
while SW <= 10e6 and SI < 256*1024:
SI *= 2
SW *= 2
# run the pulse sequence:
e.wait(RD) # relaxation delay between scans
e.set_frequency(SF+O1, phase=PH1)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
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e.wait(D1-P90/2-P45/2-TXEnableDelay) # 'short tau'
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e.set_phase(PH3)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P45, value=TXEnableValue|TXPulseValue) # 45-degree pulse
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e.wait(D2-P45-TXEnableDelay) # 'long tau'
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e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 45-degree pulse
e.wait(TXEnableDelay)
e.set_phase(PHA)
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e.wait(D1-P45/2-TXEnableDelay) # 'short tau'
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e.record(SI, SW, sensitivity=ADCSensitivity) # acquisition
# write experiment parameters:
for key in pars.keys():
e.set_description(key, pars[key]) # acquisition parameters
e.set_description('run', run) # current scan
e.set_description('rec_phase', -PH2) # current receiver phase
return e