483 lines
19 KiB
Python
483 lines
19 KiB
Python
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# -*- coding: iso-8859-1 -*-
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TXEnableDelay = 2e-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(): # drives three experiments in a row: saturation-recovery, stimulated echo, and Hanh echo
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# experiments switches:
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satrec2_flag = True # saturation-recovery switch
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ste_flag = True # stimulated-echo switch
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hahn_flag = False # Hahn-echo switch
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# ------------------ Saturation-recovery experiment settings ----------------------
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if satrec2_flag == True:
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
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pars['SF'] = 62.92e6 # spectrometer frequency (Hz)
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pars['O1'] = 0e3 # offset from SF (Hz)
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pars['SW'] = 20e6 # spectral window (Hz)
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pars['SI'] = 1*512 # number of acquisition points
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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['TAU'] = 1 # delay for recovery (s)
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pars['D3'] = 20e-6 # echo delay (s)
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pars['D4'] = 0 # echo pre-aquisition delay (s)
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pars['PHA'] = 50 # receiver phase (degree)
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# -*- these ain't variable: -*-
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pars['NECH'] = 20 # number of saturation pulses
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pars['D1'] = 100e-3 # starting interval in saturation sequence (s)
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pars['D2'] = 1e-4 # end interval in saturation sequence (s)
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pars['DATADIR'] = '/home/fprak/Students/' # data directory
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pars['OUTFILE'] = '360K' # output file name
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# specify a variable parameter (optional):
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pars['VAR_PAR'] = 'TAU' # variable parameter name (a string)
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start = 1e-3 # starting value
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stop = 1e-0 # end value
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steps = 12 # 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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# 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']%8 != 0:
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pars['NS'] = int(round(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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if pars['D1'] < pars['D2']:
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raise Exception("D1 must be greater than D2!")
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sat_length = sum(log_range(pars['D1'],pars['D2'],pars['NECH']))
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if sat_length > 1.:
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raise Exception("saturation sequence too long!!!")
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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 == 'TAU':
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seconds = ((sat_length + pars['D3']*2) * steps + sum(array)) * (pars['NS'] + pars['DS'])
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elif var_key == 'D3':
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seconds = ((sat_length + pars['TAU']) * steps + sum(array)*2) * (pars['NS'] + pars['DS'])
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else:
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seconds = (sat_length + pars['TAU'] + pars['D3']*2) * steps * (pars['NS']+ pars['DS'])
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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 saturation-recovery 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:
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for run in xrange(pars['NS']+pars['DS']):
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yield satrec2_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 = (sat_length + pars['TAU'] + pars['D3']*2) * (pars['NS']+ pars['DS'])
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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:
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for run in xrange(pars['NS']+pars['DS']):
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yield satrec2_experiment(pars, run)
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# ---------------- Stimulated-echo experiment settings ------------------
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if ste_flag == True:
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 1.6e-6 # 90-degree pulse length (s)
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pars['SF'] = 62.92e6 # spectrometer frequency (Hz)
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pars['O1'] = 0e3 # offset from SF (Hz)
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pars['SW'] = 20e6 # spectral window (Hz)
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pars['SI'] = 1*512 # number of acquisition points
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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'] = 1 # delay between scans (s)
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pars['D1'] = 400e-6 # delay after first pulse (short tau) (s)
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pars['D2'] = 20e-6 # delay after second pulse (long tau) (s)
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pars['PHA'] = 240 # receiver phase (degree)
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pars['DATADIR'] = '/home/fprak/Students/' # data directory
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pars['OUTFILE'] = '210K' # output file name
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# specify a variable parameter (optional):
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pars['VAR_PAR'] = 'D2' # variable parameter name (a string)
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start = 350e-6 # starting value
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stop = 1e-0 # end value
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steps = 16 # 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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# 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'] / 16) + 1) * 16
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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 == 'D1':
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seconds = (sum(array)*2 + (pars['D2'] + pars['RD']) * steps) * (pars['NS'] + pars['DS'])
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elif var_key == 'D2':
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seconds = (sum(array) + (pars['D1']*2 + pars['RD']) * steps) * (pars['NS'] + pars['DS'])
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elif var_key == 'RD':
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seconds = (sum(array) + (pars['D1']*2 + pars['D2']) * steps) * (pars['NS'] + pars['DS'])
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else:
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seconds = (pars['D1']*2 + pars['D2'] + pars['RD']) * steps * (pars['NS']+ pars['DS'])
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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 stimulated-echo 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:
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for run in xrange(pars['NS']+pars['DS']):
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yield ste_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 = (pars['D1']*2 + pars['D2'] + pars['RD']) * (pars['NS']+ pars['DS'])
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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:
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for run in xrange(pars['NS']+pars['DS']):
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yield ste_experiment(pars, run)
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# ------------------ Hahn-echo experiment settings ----------------------
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if hahn_flag == True:
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 1.6e-6 # 90-degree pulse length (s)
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pars['SF'] = 62.92e6 # spectrometer frequency (Hz)
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pars['O1'] = 0e3 # offset from SF (Hz)
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pars['SW'] = 20e6 # spectral window (Hz)
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pars['SI'] = 1*512 # number of acquisition points
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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'] = 1 # delay between scans (s)
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pars['TAU'] = 10e-6 # echo delay (s)
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pars['D4'] = 0e-6 # echo pre-acquisition delay (s)
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pars['PHA'] = 170 # receiver phase (degree)
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pars['DATADIR'] = '/home/fprak/Students/' # 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'] = 'TAU' # variable parameter name (a string)
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start = 20e-6 # starting value
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stop = 1e-3 # end value
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steps = 16 # 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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# 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']%8 != 0:
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pars['NS'] = int(round(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 == 'TAU':
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seconds = (sum(array)*2 + pars['RD'] * steps) * (pars['NS'] + pars['DS'])
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elif var_key == 'RD':
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seconds = (sum(array) + pars['TAU']*2 * steps) * (pars['NS'] + pars['DS'])
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else:
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seconds = (pars['TAU']*2 + pars['RD']) * steps * (pars['NS']+ pars['DS'])
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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 Hahn-echo 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:
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for run in xrange(pars['NS']+pars['DS']):
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yield hahn_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 = (pars['TAU']*2 + pars['RD']) * (pars['NS']+ pars['DS'])
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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:
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for run in xrange(pars['NS']+pars['DS']):
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yield hahn_experiment(pars, run)
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# the pulse programs:
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def satrec2_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'] = 'satrec2_experiment'
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# phase lists:
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pars['PH1'] = [ 0] # saturation pulses
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pars['PH3'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # 1st 90-degree pulse
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pars['PH4'] = [90, 90, 270, 270, 0, 0, 180, 180] # 2nd 90-degree pulse
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pars['PH2'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # 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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NECH = pars['NECH']
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D1 = pars['D1']
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D2 = pars['D2']
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D3 = pars['D3']
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D4 = pars['D4']
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TAU = pars['TAU']
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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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# set variable delay list for saturation pulses:
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vdlist = log_range(D2, D1, NECH-1)
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# set sampling parameters:
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SI = pars['SI']
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SW = pars['SW']
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while SW <= 10e6 and SI < 256*1024:
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SI *= 2
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SW *= 2
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# the pulse sequence:
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# saturation:
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e.set_frequency(SF+O1, phase=PH1) # set frequency and phase for saturation pulses
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
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e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
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for delay in vdlist[::-1]:
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e.wait(delay-P90-TXEnableDelay) # wait for next saturation pulse
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
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e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
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# recovery:
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||
|
|
e.wait(TAU) # wait for tau
|
||
|
|
e.set_phase(PH3) # set phase for next pulse
|
||
|
|
|
||
|
|
# echo detection:
|
||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||
|
|
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||
|
|
e.wait(D3-P90/2-TXEnableDelay) # echo delay
|
||
|
|
e.set_phase(PH4) # set phase for next pulse
|
||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||
|
|
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||
|
|
e.set_phase(PHA) # set phase for receiver
|
||
|
|
e.wait(D3-P90/2+D4) # echo delay
|
||
|
|
e.record(SI, SW, sensitivity=ADCSensitivity) # acquisition
|
||
|
|
|
||
|
|
# write experiment attributes:
|
||
|
|
for key in pars.keys():
|
||
|
|
e.set_description(key, pars[key]) # pulse sequence parameters
|
||
|
|
e.set_description('run', run) # current scan
|
||
|
|
e.set_description('rec_phase', -PH2) # current receiver phase
|
||
|
|
|
||
|
|
return e
|
||
|
|
|
||
|
|
|
||
|
|
def ste_experiment(pars, run):
|
||
|
|
e=Experiment()
|
||
|
|
|
||
|
|
dummy_scans = pars.get('DS')
|
||
|
|
if dummy_scans:
|
||
|
|
run -= dummy_scans
|
||
|
|
|
||
|
|
pars['PROG'] = 'ste_experiment'
|
||
|
|
|
||
|
|
# phase lists [16-phase cycle from JMR 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['PH2'] = [0, 180, 180, 0, 180, 0, 0, 180, 270, 90, 90, 270, 90, 270, 270, 90] # receiver
|
||
|
|
|
||
|
|
|
||
|
|
# read in variables:
|
||
|
|
P90 = pars['P90']
|
||
|
|
SF = pars['SF']
|
||
|
|
O1 = pars['O1']
|
||
|
|
RD = pars['RD']
|
||
|
|
D1 = pars['D1']
|
||
|
|
D2 = pars['D2']
|
||
|
|
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']
|
||
|
|
|
||
|
|
# set sampling parameters:
|
||
|
|
SI = pars['SI']
|
||
|
|
SW = pars['SW']
|
||
|
|
while SW <= 10e6 and SI < 256*1024:
|
||
|
|
SI *= 2
|
||
|
|
SW *= 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-degree pulse
|
||
|
|
|
||
|
|
e.wait(D1-P90/2-TXEnableDelay) # 'short tau or tp'
|
||
|
|
|
||
|
|
e.set_phase(PH3)
|
||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||
|
|
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
|
||
|
|
|
||
|
|
e.wait(D2-P90/2-TXEnableDelay) # 'long tau or tm'
|
||
|
|
|
||
|
|
e.set_phase(PH4)
|
||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||
|
|
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
|
||
|
|
|
||
|
|
e.wait(TXEnableDelay)
|
||
|
|
e.set_phase(PHA)
|
||
|
|
e.wait(D1-P90/2-TXEnableDelay) # 'short tau or tp'
|
||
|
|
e.record(SI, SW, 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
|
||
|
|
|
||
|
|
|
||
|
|
def hahn_experiment(pars, run):
|
||
|
|
e=Experiment()
|
||
|
|
|
||
|
|
dummy_scans = pars.get('DS')
|
||
|
|
if dummy_scans:
|
||
|
|
run -= dummy_scans
|
||
|
|
|
||
|
|
pars['PROG'] = 'hahn_experiment'
|
||
|
|
|
||
|
|
# phase lists [from Tecmag's pulse sequence]:
|
||
|
|
pars['PH1'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # 90-degree pulse
|
||
|
|
pars['PH3'] = [ 0, 0, 180, 180, 270, 270, 90, 90] # 180-degree pulse
|
||
|
|
pars['PH2'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # receiver
|
||
|
|
|
||
|
|
# read in variables:
|
||
|
|
P90 = pars['P90']
|
||
|
|
P180 = pars['P90']*2
|
||
|
|
SF = pars['SF']
|
||
|
|
O1 = pars['O1']
|
||
|
|
RD = pars['RD']
|
||
|
|
TAU = pars['TAU']
|
||
|
|
D4 = pars['D4']
|
||
|
|
PH1 = pars['PH1'][run%len(pars['PH1'])]
|
||
|
|
PH3 = pars['PH3'][run%len(pars['PH3'])]
|
||
|
|
PH2 = pars['PH2'][run%len(pars['PH2'])]
|
||
|
|
PHA = pars['PHA']
|
||
|
|
|
||
|
|
# set sampling parameters:
|
||
|
|
SI = pars['SI']
|
||
|
|
SW = pars['SW']
|
||
|
|
while SW <= 10e6 and SI < 256*1024:
|
||
|
|
SI *= 2
|
||
|
|
SW *= 2
|
||
|
|
|
||
|
|
# run the pulse sequence:
|
||
|
|
e.wait(RD) # delay between scans
|
||
|
|
e.set_frequency(SF+O1, phase=PH1) # set frequency and phase for 1st RF pulse
|
||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||
|
|
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 1st 90-degree pulse
|
||
|
|
e.wait(TAU-P90/2-TXEnableDelay) # wait for TAU
|
||
|
|
e.set_phase(PH3) # set phase for 2nd 90-degree pulse
|
||
|
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enalble RF amplifier
|
||
|
|
e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply 2nd 90-degree pulse
|
||
|
|
e.set_phase(PHA) # set phase for receiver
|
||
|
|
e.wait(TAU-P180/2+D4) # wait for TAU
|
||
|
|
e.record(SI, SW, sensitivity=ADCSensitivity) # acquire echo points
|
||
|
|
|
||
|
|
# write the experiment parameters:
|
||
|
|
for key in pars.keys():
|
||
|
|
e.set_description(key, pars[key]) # pulse sequence parameters
|
||
|
|
e.set_description('run', run) # current scan
|
||
|
|
e.set_description('rec_phase', -PH2) # current receiver phase
|
||
|
|
|
||
|
|
return e
|