# -*- coding: iso-8859-1 -*- TXEnableDelay = 2e-6 TXEnableValue = 0b0001 # TTL line blanking RF amplifier (bit 0) TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1) ADCSensitivity = 5 # voltage span for ADC def experiment(): # the diffusion editing sequence with stimulated echo and CPMG detection # set up acqusition parameters: pars = {} pars['P90'] = 0.8e-6 # 90-degree pulse length (s) pars['SF'] = 161.85e6 # spectrometer frequency (Hz) pars['O1'] = 0e3 # offset from SF (Hz) pars['NS'] = 16 # number of scans pars['DS'] = 0 # number of dummy scans pars['RD'] = 6 # delay between scans (s) pars['D1'] = 20e-6 # delay after first STE pulse (s) pars['D2'] = 20e-6 # delay after second STE pulse (s) pars['D4'] = 2.5e-6 # pre-acquisition delay (s) pars['NECH'] = 128 # number of 180-degree pulses in the CPMG train pars['TAU'] = 50e-6 # half pulse period in the CPMG train (s) pars['PHA'] = -190 # receiver phase (degree) pars['DATADIR'] = '/home/fprak/Desktop/test/' # data directory pars['OUTFILE'] = None # output file name # specify a variable parameter (optional): pars['VAR_PAR'] = 'D2' # variable parameter name (a string) start = 20e-6 # starting value stop = 3e-1 # 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']%16 != 0: pars['NS'] = int(round(pars['NS'] / 16) + 1) * 16 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 ste2_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 ste2_experiment(pars, run) # the pulse program: def ste2_experiment(pars, run): e=Experiment() dummy_scans = pars.get('DS') if dummy_scans: run -= dummy_scans pars['PROG'] = 'ste2_experiment' # phase lists [from J. Magn. Reson. 157, 31 (2002)]: pars['PH1'] = [0, 180, 0, 180, 0, 180, 0, 180, 90, 270, 90, 270, 90, 270, 90, 270] # 1st 90-degree pulse pars['PH3'] = [0, 0, 180, 180, 0, 0, 180, 180, 0, 0, 180, 180, 0, 0, 180, 180] # 2nd 90-degree pulse pars['PH4'] = [0, 0, 0, 0, 180, 180, 180, 180, 0, 0, 0, 0, 180, 180, 180, 180] # 3nd 90-degree pulse pars['PH5'] = [90, 90, 90, 90, 90, 90, 90, 90, 0, 0, 0, 0, 0, 0, 0, 0] # 180-degree pulses pars['PH2'] = [0, 180, 180, 0, 180, 0, 0, 180, 270, 90, 90, 270, 90, 270, 270, 90] # receiver # read in variables: P90 = pars['P90'] P180 = pars['P90']*2 SF = pars['SF'] O1 = pars['O1'] RD = pars['RD'] D1 = pars['D1'] D2 = pars['D2'] D4 = pars['D4'] TAU = pars['TAU'] NECH = pars['NECH'] 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'] # set sampling parameters: SI = 128 # number of echo samples SW = 20e6 # sample rate AQ = (SI+6)/SW # acquisition window if TAU < (P90+P180)/2+TXEnableDelay or TAU < (P180+TXEnableDelay+AQ)/2: raise Exception('pulse period is too short!') if 2*TAU < P180+TXEnableDelay+SI/SW: raise Exception('pulse period too short!') # run the pulse sequence: e.wait(RD) # delay between scans e.set_frequency(SF+O1, phase=PH1) e.ttl_pulse(TXEnableDelay, value=TXEnableValue) e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 1st 90-degree pulse e.wait(D1-P90-TXEnableDelay) # short delay e.set_phase(PH3) e.ttl_pulse(TXEnableDelay, value=TXEnableValue) e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 2nd 90-degree pulse e.wait(D2-P90-TXEnableDelay) # long delay e.set_phase(PH4) e.ttl_pulse(TXEnableDelay, value=TXEnableValue) e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 3rd 90-degree pulse e.wait(D1+TAU-P90/2-P180/2-TXEnableDelay) # wait for first echo and tau e.set_phase(PH5) e.loop_start(NECH) # ----- loop for CPMG pulse train: ----- e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply a 180-degree pulse e.set_phase(PHA) # set phase for receiver e.wait(TAU-(P180+TXEnableDelay+AQ)/2+D4) # pre-acquisition delay e.record(SI, SW, timelength=AQ, sensitivity=ADCSensitivity) # acquire echo samples e.wait(TAU-(P180+TXEnableDelay+AQ)/2-D4) # post-acquisition delay e.set_phase(PH5) # set phase for theta-degree pulse e.loop_end() # -------------------------------------- # write experiment attributes: for key in pars.keys(): e.set_description(key, pars[key]) # acqusition parameters e.set_description('run', run) # current scan e.set_description('rec_phase', -PH2) # current receiver phase return e