194 lines
7.6 KiB
Python
194 lines
7.6 KiB
Python
|
# -*- coding: iso-8859-1 -*-
|
|||
|
|
|
|||
|
|
TXEnableDelay = 0.5e-6
|
|||
|
|
TXEnableValue = 0b0001 # TTL line blanking RF amplifier (bit 0)
|
|||
|
|
TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1)
|
|||
|
|
ADCSensitivity = 1 # voltage span for ADC
|
|||
|
|
|
|||
|
|
def experiment(): # 2H Exchange Spectroscopy (2H EXSY) experiment [JMR 79, 269-290 (1988)]
|
|||
|
|
|
|||
|
|
# Cosine and sine modulated signals are acquired sequentially by switching
|
|||
|
|
# between Zeeman order and spin-alignment phase lists. The signals are
|
|||
|
|
# processed into a pure absorption mode 2D spectrum according to scheme by
|
|||
|
|
# [Bluemich, Schmidt, and Spiess, JMR 79, 269-290 (1988)]. Prior to writing
|
|||
|
|
# in a file (Tecmag), the sine-modulated signal is rotated by 90<39>, thus
|
|||
|
|
# enabling 2D processing via a regular States algorithm with NMRnotebook
|
|||
|
|
# or like NMR software.
|
|||
|
|
|
|||
|
|
# set up acquisition parameters:
|
|||
|
|
pars = {}
|
|||
|
|
pars['P90'] = 2.7e-6 # 90<39>-pulse length (s)
|
|||
|
|
pars['SF'] = 46.140e6 # spectrometer frequency (Hz)
|
|||
|
|
pars['O1'] = 1000 # offset from SF (Hz)
|
|||
|
|
pars['SW'] = 125e3 # spectral window (Hz)
|
|||
|
|
pars['SI1'] = 80 # number of (complex) data points in F1 (2nd dimension)
|
|||
|
|
pars['SI2'] = 1*256 # number of (complex) data points in F2
|
|||
|
|
pars['D3'] = 10e-6 # position of refocusing 90<39>-pulse, Delta (s)
|
|||
|
|
pars['D4'] = 2e-6 # pre-aquisition delay (s)
|
|||
|
|
pars['D8'] = 3e-3 # mixing time, tm (s)
|
|||
|
|
pars['NS'] = 512 # number of scans
|
|||
|
|
pars['DS'] = 0 # number of dummy scans
|
|||
|
|
pars['RD'] = 0.2 # delay between scans (s)
|
|||
|
|
pars['PHA'] = 65 # receiver reference phase (degree)
|
|||
|
|
pars['DATADIR'] = '/home/mathilda/Desktop/Oleg/temp/' # data directory
|
|||
|
|
pars['OUTFILE'] = 'dso_320K' # output file name
|
|||
|
|
|
|||
|
|
# specify a variable parameter (optional):
|
|||
|
|
pars['VAR_PAR'] = None # variable parameter's name (a string)
|
|||
|
|
start = 80 # starting value
|
|||
|
|
stop = 128 # end value
|
|||
|
|
steps = 2 # number of values
|
|||
|
|
log_scale = False # 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']%16 != 0:
|
|||
|
|
pars['NS'] = int(round(pars['NS'] / 32) + 1) * 32
|
|||
|
|
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 == 'D8':
|
|||
|
|
seconds = (sum(array) + (.5*pars['SI1']/pars['SW'] + pars['RD']) * steps) * (pars['NS'] + pars['DS']) * 2*pars['SI1']
|
|||
|
|
elif var_key == 'RD':
|
|||
|
|
seconds = (sum(array) + (.5*pars['SI1']/pars['SW'] + pars['D8']) * steps) * (pars['NS'] + pars['DS']) * 2*pars['SI1']
|
|||
|
|
else:
|
|||
|
|
seconds = (.5*pars['SI1']/pars['SW'] + pars['D8'] + pars['RD']) * steps * (pars['NS']+ pars['DS']) * 2*pars['SI1']
|
|||
|
|
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 and sampling the indirect dimension F1:
|
|||
|
|
for run in xrange((pars['NS']+pars['DS'])*2*pars['SI1']):
|
|||
|
|
yield exsy2h_experiment(pars, run)
|
|||
|
|
synchronize()
|
|||
|
|
|
|||
|
|
else:
|
|||
|
|
# estimate the experiment time:
|
|||
|
|
seconds = (.5*pars['SI1']/pars['SW'] + pars['D8'] + pars['RD']) * (pars['NS']+ pars['DS']) * 2*pars['SI1']
|
|||
|
|
print 'sec ', seconds
|
|||
|
|
m, s = divmod(seconds, 60)
|
|||
|
|
h, m = divmod(m, 60)
|
|||
|
|
print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
|
|||
|
|
|
|||
|
|
# loop for accumulation and sampling the indirect dimension F1:
|
|||
|
|
for run in xrange((pars['NS']+pars['DS'])*2*pars['SI1']):
|
|||
|
|
yield exsy2h_experiment(pars, run)
|
|||
|
|
|
|||
|
|
|
|||
|
|
# the pulse program:
|
|||
|
|
|
|||
|
|
def exsy2h_experiment(pars, run):
|
|||
|
|
e=Experiment()
|
|||
|
|
|
|||
|
|
dummy_scans = pars.get('DS')
|
|||
|
|
if dummy_scans:
|
|||
|
|
run -= dummy_scans
|
|||
|
|
|
|||
|
|
pars['PROG'] = 'exsy2h_experiment'
|
|||
|
|
|
|||
|
|
# 8-step phase cycle (1-21) modifided to deal with T1-recovery and extended for Re/Im imbalance)
|
|||
|
|
pars['PH1'] = [0, 270, 0, 270, 180, 90, 180, 90] # 1st pulse (90<39>)
|
|||
|
|
pars['PH3'] = [0, 90, 0, 90, 0, 90, 0, 90] # 2nd pulse (57.4<EFBFBD>)
|
|||
|
|
pars['PH4'] = [0, 0, 180, 180, 270, 270, 90, 90] # 3rd pulse (57.4<EFBFBD>)
|
|||
|
|
pars['PH5'] = [90, 90, 90, 90, 180, 180, 180, 180] # 4th pulse (90<39>)
|
|||
|
|
pars['PH2'] = [0, 180, 180, 0, 90, 270, 270, 90] # receiver
|
|||
|
|
|
|||
|
|
# read in variables:
|
|||
|
|
P90 = pars['P90']
|
|||
|
|
P1 = pars['P90']*(54.7/90)
|
|||
|
|
SF = pars['SF']
|
|||
|
|
O1 = pars['O1']
|
|||
|
|
RD = pars['RD']
|
|||
|
|
D4 = pars['D4']
|
|||
|
|
D8 = pars['D8']
|
|||
|
|
D3 = pars['D3']
|
|||
|
|
NS = pars['NS']
|
|||
|
|
PH1 = pars['PH1'][run%len(pars['PH1'])]
|
|||
|
|
PH3 = pars['PH3'][run%len(pars['PH3'])]
|
|||
|
|
PH4 = pars['PH4'][run%len(pars['PH4'])]
|
|||
|
|
PH5 = pars['PH5'][run%len(pars['PH5'])]
|
|||
|
|
PH2 = pars['PH2'][run%len(pars['PH2'])]
|
|||
|
|
PHA = pars['PHA']
|
|||
|
|
|
|||
|
|
# this is a part of phase cycling:
|
|||
|
|
PH5 += (run/len(pars['PH5']))%2*180
|
|||
|
|
PH1 += (run/len(pars['PH5']))%2*180
|
|||
|
|
PH2 += (run/len(pars['PH5']))%2*180
|
|||
|
|
|
|||
|
|
# F1 sampling parameters:
|
|||
|
|
IN0 = 1./pars['SW'] # t1 increment
|
|||
|
|
|
|||
|
|
# F1 sampling scheme:
|
|||
|
|
PH3+= (run/(1*NS))%4*90 # phases are upgraded after every NS scans
|
|||
|
|
PH4+= (run/(1*NS))%4*90
|
|||
|
|
D0 = (run/(2*NS)) *IN0 # t1 is incremented after every 2*NS scans
|
|||
|
|
|
|||
|
|
# F2 sampling parameters:
|
|||
|
|
SI2 = pars['SI2']
|
|||
|
|
SW2 = pars['SW']
|
|||
|
|
while SW2 <= 10e6 and SI2 < 256*1024:
|
|||
|
|
SI2 *= 2
|
|||
|
|
SW2 *= 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<39>-pulse
|
|||
|
|
|
|||
|
|
e.wait(D0) # incremented delay, t1
|
|||
|
|
e.set_phase(PH3)
|
|||
|
|
|
|||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
|||
|
|
e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 54.7<EFBFBD>-pulse
|
|||
|
|
|
|||
|
|
e.wait(D8) # mixing time, tm
|
|||
|
|
e.set_phase(PH4)
|
|||
|
|
|
|||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
|||
|
|
e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 54.7<EFBFBD>-pulse
|
|||
|
|
|
|||
|
|
e.wait(D3) # refocusing delay, Delta
|
|||
|
|
|
|||
|
|
e.set_phase(PH5)
|
|||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
|||
|
|
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90<39>-pulse
|
|||
|
|
|
|||
|
|
e.wait(TXEnableDelay)
|
|||
|
|
e.set_phase(PHA)
|
|||
|
|
e.wait(D3+D4) # pre-aquisition delay
|
|||
|
|
e.record(SI2, SW2, 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
|