194 lines
7.6 KiB
Python
194 lines
7.6 KiB
Python
# -*- coding: iso-8859-1 -*-
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TXEnableDelay = 0.5e-6
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TXEnableValue = 0b0001 # TTL line blanking RF amplifier (bit 0)
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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(): # 2H Exchange Spectroscopy (2H EXSY) experiment [JMR 79, 269-290 (1988)]
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# Cosine and sine modulated signals are acquired sequentially by switching
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# between Zeeman order and spin-alignment phase lists. The signals are
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# processed into a pure absorption mode 2D spectrum according to scheme by
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# [Bluemich, Schmidt, and Spiess, JMR 79, 269-290 (1988)]. Prior to writing
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# in a file (Tecmag), the sine-modulated signal is rotated by 90°, thus
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# enabling 2D processing via a regular States algorithm with NMRnotebook
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# or like NMR software.
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 2.7e-6 # 90°-pulse length (s)
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pars['SF'] = 46.140e6 # spectrometer frequency (Hz)
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pars['O1'] = 1000 # offset from SF (Hz)
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pars['SW'] = 125e3 # spectral window (Hz)
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pars['SI1'] = 80 # number of (complex) data points in F1 (2nd dimension)
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pars['SI2'] = 1*256 # number of (complex) data points in F2
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pars['D3'] = 10e-6 # position of refocusing 90°-pulse, Delta (s)
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pars['D4'] = 2e-6 # pre-aquisition delay (s)
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pars['D8'] = 3e-3 # mixing time, tm (s)
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pars['NS'] = 512 # number of scans
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pars['DS'] = 0 # number of dummy scans
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pars['RD'] = 0.2 # delay between scans (s)
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pars['PHA'] = 65 # receiver reference phase (degree)
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pars['DATADIR'] = '/home/mathilda/Desktop/Oleg/temp/' # data directory
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pars['OUTFILE'] = 'dso_320K' # output file name
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# specify a variable parameter (optional):
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pars['VAR_PAR'] = None # variable parameter's name (a string)
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start = 80 # starting value
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stop = 128 # end value
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steps = 2 # number of values
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log_scale = False # log scale flag
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stag_range = False # staggered range flag
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# check parameters for safety:
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if pars['PHA'] < 0:
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pars['PHA'] = 360 + pars['PHA']
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if pars['P90'] > 20e-6:
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raise Exception("Pulse too long!!!")
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# check whether a variable parameter is named:
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var_key = pars.get('VAR_PAR')
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if var_key == 'P90' and (start > 20e-6 or stop > 20e-6):
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raise Exception("Pulse too long!!!")
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if pars['NS']%16 != 0:
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pars['NS'] = int(round(pars['NS'] / 32) + 1) * 32
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print 'Number of scans changed to ', pars['NS'], ' due to phase cycling'
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# start the experiment:
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if var_key:
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# this is an arrayed experiment:
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if log_scale:
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array = log_range(start,stop,steps)
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else:
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array = lin_range(start,stop,steps)
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if stag_range:
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array = staggered_range(array, size = 2)
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# estimate the experiment time:
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if var_key == 'D8':
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seconds = (sum(array) + (.5*pars['SI1']/pars['SW'] + pars['RD']) * steps) * (pars['NS'] + pars['DS']) * 2*pars['SI1']
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elif var_key == 'RD':
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seconds = (sum(array) + (.5*pars['SI1']/pars['SW'] + pars['D8']) * steps) * (pars['NS'] + pars['DS']) * 2*pars['SI1']
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else:
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seconds = (.5*pars['SI1']/pars['SW'] + pars['D8'] + pars['RD']) * steps * (pars['NS']+ pars['DS']) * 2*pars['SI1']
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m, s = divmod(seconds, 60)
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h, m = divmod(m, 60)
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print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
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# loop for a variable parameter:
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for index, pars[var_key] in enumerate(array):
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print 'Arrayed experiment for '+var_key+': run = '+str(index+1)+\
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' out of '+str(array.size)+': value = '+str(pars[var_key])
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# loop for accumulation and sampling the indirect dimension F1:
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for run in xrange((pars['NS']+pars['DS'])*2*pars['SI1']):
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yield exsy2h_experiment(pars, run)
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synchronize()
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else:
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# estimate the experiment time:
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seconds = (.5*pars['SI1']/pars['SW'] + pars['D8'] + pars['RD']) * (pars['NS']+ pars['DS']) * 2*pars['SI1']
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print 'sec ', seconds
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m, s = divmod(seconds, 60)
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h, m = divmod(m, 60)
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print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
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# loop for accumulation and sampling the indirect dimension F1:
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for run in xrange((pars['NS']+pars['DS'])*2*pars['SI1']):
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yield exsy2h_experiment(pars, run)
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# the pulse program:
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def exsy2h_experiment(pars, run):
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e=Experiment()
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dummy_scans = pars.get('DS')
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if dummy_scans:
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run -= dummy_scans
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pars['PROG'] = 'exsy2h_experiment'
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# 8-step phase cycle (1-21) 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 pulse (90°)
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pars['PH3'] = [0, 90, 0, 90, 0, 90, 0, 90] # 2nd pulse (57.4°)
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pars['PH4'] = [0, 0, 180, 180, 270, 270, 90, 90] # 3rd pulse (57.4°)
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pars['PH5'] = [90, 90, 90, 90, 180, 180, 180, 180] # 4th pulse (90°)
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pars['PH2'] = [0, 180, 180, 0, 90, 270, 270, 90] # receiver
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# read in variables:
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P90 = pars['P90']
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P1 = pars['P90']*(54.7/90)
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SF = pars['SF']
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O1 = pars['O1']
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RD = pars['RD']
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D4 = pars['D4']
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D8 = pars['D8']
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D3 = pars['D3']
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NS = pars['NS']
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PH1 = pars['PH1'][run%len(pars['PH1'])]
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PH3 = pars['PH3'][run%len(pars['PH3'])]
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PH4 = pars['PH4'][run%len(pars['PH4'])]
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PH5 = pars['PH5'][run%len(pars['PH5'])]
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PH2 = pars['PH2'][run%len(pars['PH2'])]
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PHA = pars['PHA']
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# this is a part of phase cycling:
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PH5 += (run/len(pars['PH5']))%2*180
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PH1 += (run/len(pars['PH5']))%2*180
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PH2 += (run/len(pars['PH5']))%2*180
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# F1 sampling parameters:
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IN0 = 1./pars['SW'] # t1 increment
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# F1 sampling scheme:
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PH3+= (run/(1*NS))%4*90 # phases are upgraded after every NS scans
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PH4+= (run/(1*NS))%4*90
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D0 = (run/(2*NS)) *IN0 # t1 is incremented after every 2*NS scans
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# F2 sampling parameters:
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SI2 = pars['SI2']
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SW2 = pars['SW']
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while SW2 <= 10e6 and SI2 < 256*1024:
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SI2 *= 2
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SW2 *= 2
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# run the pulse sequence:
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e.wait(RD) # relaxation delay between scans
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e.set_frequency(SF+O1, phase=PH1)
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
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e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90°-pulse
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e.wait(D0) # incremented delay, t1
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e.set_phase(PH3)
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
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e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 54.7°-pulse
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e.wait(D8) # mixing time, tm
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e.set_phase(PH4)
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
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e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 54.7°-pulse
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e.wait(D3) # refocusing delay, Delta
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e.set_phase(PH5)
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
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e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90°-pulse
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e.wait(TXEnableDelay)
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e.set_phase(PHA)
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e.wait(D3+D4) # pre-aquisition delay
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e.record(SI2, SW2, sensitivity=ADCSensitivity) # acquisition
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# write experiment parameters:
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for key in pars.keys():
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e.set_description(key, pars[key]) # acquisition parameters
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e.set_description('run', run) # current scan
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e.set_description('rec_phase', -PH2) # current receiver phase
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return e |