removed op_ from all experiments
This commit is contained in:
Markus Rosenstihl
176
Scripts/EXSY/noesy_exp.py
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176
Scripts/EXSY/noesy_exp.py
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# -*- coding: iso-8859-1 -*-
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TXEnableDelay = 2e-6
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TXEnableValue = 0b0001 # TTL line enabling RF amplifier (bit 0)
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TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1)
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ADCSensitivity = 2 # voltage span for ADC
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def experiment(): # 2D NOESY experiment, using States-TPPI technique for quadrature detection in F1
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# States-TPPI technique achieves two effects for an indirect dimension F1:
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# (1) signal frequency discrimination and (2) displacement of the unmodulated
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# artefact signal from an inconvenient location in the middle of spectrum to the edge.
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# (1) is achieved by recording two data sets at each t1 point - with orthogonal phases
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# of the preparation pulse and same receiver phase - and storing them in separate memory
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# locations. These two fid measurements yield one complex data point in F1.
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# (2) by inverting phase of the preparation pulse and the receiver each time when t1 is
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# incremented (that is for subsequent complex points). Therefore, the artefact signal
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# becomes modulated at the Nyquist frequency and appears in the spectrum at F1=<3D>SW/2 Hz
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# instead of 0 Hz, where SW is spectral width. [http://nmrwiki.org]
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# set up acqusition parameters:
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pars = {}
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pars['P90'] = 1.65e-6 # 90-degree pulse length (s)
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pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
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pars['O1'] = -57.0e3 # offset from SF (Hz)
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pars['SW'] = 150e3 # spectral width (Hz)
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pars['SI1'] = 32 # number of (complex) data points in F1 (2D)
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pars['SI2'] = 128 # number of (complex) data points in F2
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pars['D8'] = 100e-6 # mixing time, tm (s)
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pars['NS'] = 16 # number of scans
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pars['DS'] = 0 # number of dummy scans
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pars['RD'] = 2.5 # delay between scans (s)
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pars['DEAD1'] = 4e-6 # receiver dead time (s)
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pars['PHA'] = 150 # receiver reference phase (degree)
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pars['DATADIR'] = '/home/fprak/' # data directory
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pars['OUTFILE'] = 'test' # output file name
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# specify a variable parameter (optional):
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pars['VAR_PAR'] = 'D8' # variable parameter name (a string)
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start = 10.e-6 # starting value
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stop = 1000e-6 # end value
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steps = 3 # number of values
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log_scale = True # 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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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']%8 != 0:
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pars['NS'] = (pars['NS'] / 8 + 1) * 8
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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 noesyst_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 noesyst_experiment(pars, run)
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# the pulse program:
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def noesyst_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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# phase lists (M.H.Levitt 'Spin Dynamics', 2nd edition, p.530):
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pars['PH1'] = [ 0, 180, 0, 180, 0, 180, 0, 180]
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pars['PH3'] = [180, 180, 180, 180, 180, 180, 180, 180]
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pars['PH4'] = [ 0, 0, 90, 90, 180, 180, 270, 270]
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pars['PH2'] = [ 0, 180, 90, 270, 180, 0, 270, 90] # receiver
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# read in variables:
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P90 = pars['P90']
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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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DEAD1 = pars['DEAD1']
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D8 = pars['D8']
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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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PH2 = pars['PH2'][run%len(pars['PH2'])]
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PHA = pars['PHA']
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# F1 sampling parameters:
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IN0 = 1./pars['SW'] # t1 increment
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# the States-TPPI bit:
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PH1-= (run/(1*NS))%4*90 # PH1 changes by 90-deg. after every 1*NS scans
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D0 = (run/(2*NS)) *IN0 # t1 increases by IN0 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) # 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-degree 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(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
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e.wait(D8) # mixing time
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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(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
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e.set_phase(PHA) # set phase for receiver
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e.wait(DEAD1) # wait for coil ringdown
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e.record(SI2, SW2, sensitivity=ADCSensitivity) # acquire signal
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# write experiment attributes:
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for key in pars.keys():
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e.set_description(key, pars[key]) # acqusition 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
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