# -*- coding: iso-8859-1 -*- TXEnableDelay = 2e-6 TXEnableValue = 0b0001 # TTL line enabling RF amplifier (bit 0) TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1) ADCSensitivity = 2 # voltage span for ADC def experiment(): # 2D NOESY experiment, using States-TPPI technique for quadrature detection in F1 # States-TPPI technique achieves two effects for an indirect dimension F1: # (1) signal frequency discrimination and (2) displacement of the unmodulated # artefact signal from an inconvenient location in the middle of spectrum to the edge. # (1) is achieved by recording two data sets at each t1 point - with orthogonal phases # of the preparation pulse and same receiver phase - and storing them in separate memory # locations. These two fid measurements yield one complex data point in F1. # (2) by inverting phase of the preparation pulse and the receiver each time when t1 is # incremented (that is for subsequent complex points). Therefore, the artefact signal # becomes modulated at the Nyquist frequency and appears in the spectrum at F1=ħSW/2 Hz # instead of 0 Hz, where SW is spectral width. [http://nmrwiki.org] # set up acqusition parameters: pars = {} pars['P90'] = 1.65e-6 # 90-degree pulse length (s) pars['SF'] = 338.7e6 # spectrometer frequency (Hz) pars['O1'] = -57.0e3 # offset from SF (Hz) pars['SW'] = 150e3 # spectral width (Hz) pars['SI1'] = 32 # number of (complex) data points in F1 (2D) pars['SI2'] = 128 # number of (complex) data points in F2 pars['D8'] = 100e-6 # mixing time, tm (s) pars['NS'] = 16 # number of scans pars['DS'] = 0 # number of dummy scans pars['RD'] = 2.5 # delay between scans (s) pars['DEAD1'] = 4e-6 # receiver dead time (s) pars['PHA'] = 150 # receiver reference phase (degree) pars['DATADIR'] = '/home/fprak/' # data directory pars['OUTFILE'] = 'test' # output file name # specify a variable parameter (optional): pars['VAR_PAR'] = 'D8' # variable parameter name (a string) start = 10.e-6 # starting value stop = 1000e-6 # end value steps = 3 # 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!!!") 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'] = (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 == '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 noesyst_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 noesyst_experiment(pars, run) # the pulse program: def noesyst_experiment(pars, run): e=Experiment() dummy_scans = pars.get('DS') if dummy_scans: run -= dummy_scans # phase lists (M.H.Levitt 'Spin Dynamics', 2nd edition, p.530): pars['PH1'] = [ 0, 180, 0, 180, 0, 180, 0, 180] pars['PH3'] = [180, 180, 180, 180, 180, 180, 180, 180] pars['PH4'] = [ 0, 0, 90, 90, 180, 180, 270, 270] pars['PH2'] = [ 0, 180, 90, 270, 180, 0, 270, 90] # receiver # read in variables: P90 = pars['P90'] SF = pars['SF'] O1 = pars['O1'] RD = pars['RD'] DEAD1 = pars['DEAD1'] D8 = pars['D8'] NS = pars['NS'] 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'] # F1 sampling parameters: IN0 = 1./pars['SW'] # t1 increment # the States-TPPI bit: PH1-= (run/(1*NS))%4*90 # PH1 changes by 90-deg. after every 1*NS scans D0 = (run/(2*NS)) *IN0 # t1 increases by IN0 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) # 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 e.wait(D0) # incremented delay t1 e.set_phase(PH3) e.ttl_pulse(TXEnableDelay, value=TXEnableValue) e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse e.wait(D8) # mixing time e.set_phase(PH4) e.ttl_pulse(TXEnableDelay, value=TXEnableValue) e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse e.set_phase(PHA) # set phase for receiver e.wait(DEAD1) # wait for coil ringdown e.record(SI2, SW2, sensitivity=ADCSensitivity) # acquire signal # 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