179 lines
7.1 KiB
Python
179 lines
7.1 KiB
Python
# -*- 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 = 5 # voltage span for ADC
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def experiment(): # the diffusion editing sequence with stimulated echo and CPMG detection
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# set up acqusition parameters:
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pars = {}
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pars['P90'] = 0.8e-6 # 90-degree pulse length (s)
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pars['SF'] = 161.85e6 # spectrometer frequency (Hz)
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pars['O1'] = 0e3 # offset from SF (Hz)
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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'] = 6 # delay between scans (s)
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pars['D1'] = 20e-6 # delay after first STE pulse (s)
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pars['D2'] = 20e-6 # delay after second STE pulse (s)
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pars['D4'] = 2.5e-6 # pre-acquisition delay (s)
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pars['NECH'] = 128 # number of 180-degree pulses in the CPMG train
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pars['TAU'] = 50e-6 # half pulse period in the CPMG train (s)
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pars['PHA'] = -190 # receiver phase (degree)
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pars['DATADIR'] = '/home/fprak/Desktop/test/' # data directory
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pars['OUTFILE'] = None # 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 = 20e-6 # starting value
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stop = 3e-1 # end value
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steps = 24 # 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 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 ste2_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 ste2_experiment(pars, run)
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# the pulse program:
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def ste2_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'] = 'ste2_experiment'
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# phase lists [from J. Magn. Reson. 157, 31 (2002)]:
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pars['PH1'] = [0, 180, 0, 180, 0, 180, 0, 180, 90, 270, 90, 270, 90, 270, 90, 270] # 1st 90-degree pulse
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pars['PH3'] = [0, 0, 180, 180, 0, 0, 180, 180, 0, 0, 180, 180, 0, 0, 180, 180] # 2nd 90-degree pulse
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pars['PH4'] = [0, 0, 0, 0, 180, 180, 180, 180, 0, 0, 0, 0, 180, 180, 180, 180] # 3nd 90-degree pulse
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pars['PH5'] = [90, 90, 90, 90, 90, 90, 90, 90, 0, 0, 0, 0, 0, 0, 0, 0] # 180-degree pulses
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pars['PH2'] = [0, 180, 180, 0, 180, 0, 0, 180, 270, 90, 90, 270, 90, 270, 270, 90] # receiver
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# read in variables:
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P90 = pars['P90']
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P180 = pars['P90']*2
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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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D1 = pars['D1']
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D2 = pars['D2']
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D4 = pars['D4']
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TAU = pars['TAU']
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NECH = pars['NECH']
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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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# set sampling parameters:
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SI = 128 # number of echo samples
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SW = 20e6 # sample rate
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AQ = (SI+6)/SW # acquisition window
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if TAU < (P90+P180)/2+TXEnableDelay or TAU < (P180+TXEnableDelay+AQ)/2:
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raise Exception('pulse period is too short!')
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if 2*TAU < P180+TXEnableDelay+SI/SW:
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raise Exception('pulse period too short!')
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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) # 1st 90-degree pulse
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e.wait(D1-P90-TXEnableDelay) # short delay
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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) # 2nd 90-degree pulse
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e.wait(D2-P90-TXEnableDelay) # long delay
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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) # 3rd 90-degree pulse
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e.wait(D1+TAU-P90/2-P180/2-TXEnableDelay) # wait for first echo and tau
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e.set_phase(PH5)
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e.loop_start(NECH) # ----- loop for CPMG pulse train: -----
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
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e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply a 180-degree pulse
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e.set_phase(PHA) # set phase for receiver
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e.wait(TAU-(P180+TXEnableDelay+AQ)/2+D4) # pre-acquisition delay
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e.record(SI, SW, timelength=AQ, sensitivity=ADCSensitivity) # acquire echo samples
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e.wait(TAU-(P180+TXEnableDelay+AQ)/2-D4) # post-acquisition delay
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e.set_phase(PH5) # set phase for theta-degree pulse
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e.loop_end() # --------------------------------------
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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 |