initial check-in
This commit is contained in:
Markus Rosenstihl
commit
d994875c0f
635
AU_Programs/2H/op_2h_exp.py
Normal file
635
AU_Programs/2H/op_2h_exp.py
Normal file
@ -0,0 +1,635 @@
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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 four experiments in a row: saturation-recovery, solid echo, spin-alignment, and Zeeman-order
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# experiment toggles:
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satrec2_flag = True # saturation-recovery on/off
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solidecho_flag = True # solid-echo on/off
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spinal_flag = True # spin-alignment on/off
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zeeman_flag = False # Zeeman-order on/off
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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'] = 2.0e-6 # 90-degree pulse length (s)
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pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
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pars['O1'] = -60e3 # offset from SF (Hz)
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pars['SW'] = 10e6 # spectral window (Hz)
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pars['SI'] = 1*512 # number of acquisition points
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pars['NS'] = 8 # 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'] = 0 # receiver phase (degree)
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# -*- these ain't variable: -*-
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pars['NECH'] = 40 # 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'] = None # 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 = 1 # 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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# ------------------ Solid-echo experiment settings ----------------------
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if solidecho_flag == True:
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 2.0e-6 # 90-degree pulse length (s)
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pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
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pars['O1'] = -60e3 # offset from SF (Hz)
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pars['SW'] = 500e3 # spectral window (Hz)
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pars['SI'] = 1*1024 # number of acquisition points
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pars['NS'] = 8 # 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'] = 20e-6 # echo delay (s)
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pars['D4'] = 0e-6 # echo pre-acquisition delay (s)
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pars['PHA'] = 0 # receiver phase (degree)
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pars['DATADIR'] = '/home/fprak/Students/' # 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'] = None # variable parameter name (a string)
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start = 10e-6 # starting value
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stop = 30e-6 # end value
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steps = 5 # number of values
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log_scale = False # 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 solid-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 solidecho_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 solidecho_experiment(pars, run)
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# ---------------- Spin-alignment experiment settings ------------------
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if spinal_flag == True:
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 2.0e-6 # 90-degree pulse length (s)
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pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
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pars['O1'] = -60e3 # offset from SF (Hz)
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pars['SW'] = 10e6 # spectral window (Hz)
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pars['SI'] = 1*512 # number of acquisition points
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pars['NS'] = 8 # 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'] = 30e-6 # delay after first pulse, or tp (s)
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pars['D2'] = 100e-6 # delay after second pulse, or tm (s)
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pars['PHA'] = -36 # receiver phase (degree)
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pars['DATADIR'] = '/home/fprak/Students/' # 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 = 30e-6 # starting value
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stop = 1e-3 # 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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# 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 spin-alignment 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 spinal_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 spinal_experiment(pars, run)
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# ------------------ Zeeman-order experiment settings ----------------------
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if zeeman_flag == True:
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 2.0e-6 # 90-degree pulse length (s)
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pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
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pars['O1'] = -60e3 # offset from SF (Hz)
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pars['SW'] = 10e6 # spectral window (Hz)
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pars['SI'] = 1*512 # number of acquisition points
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pars['NS'] = 8 # 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'] = 30e-6 # delay after first pulse, or 'short tau' (s)
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pars['D2'] = 100e-6 # delay after second pulse, or 'long tau' (s)
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pars['PHA'] = 0 # receiver phase (degree)
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pars['DATADIR'] = '/home/fprak/Students/' # 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 = 30e-6 # starting value
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stop = 1e-3 # 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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# 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 Zeeman-order 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 zeeman_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 zeeman_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
|
||||
for delay in vdlist[::-1]:
|
||||
e.wait(delay-P90-TXEnableDelay) # wait for next saturation pulse
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
|
||||
# recovery:
|
||||
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 solidecho_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'solidecho_experiment'
|
||||
|
||||
# phase lists [from Tecmag's pulse sequence]:
|
||||
pars['PH1'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # 1st 90-degree pulse
|
||||
pars['PH3'] = [90, 90, 270, 270, 0, 0, 180, 180] # 2nd 90-degree pulse
|
||||
pars['PH2'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # receiver
|
||||
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
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(P90, value=TXEnableValue|TXPulseValue) # apply 2nd 90-degree pulse
|
||||
e.set_phase(PHA) # set phase for receiver
|
||||
e.wait(TAU-P90/2+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
|
||||
|
||||
def spinal_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'spinal_experiment'
|
||||
|
||||
# 8-step phase cycle (1-14 modifided to deal with T1-recovery and extended for Re/Im imbalance)
|
||||
pars['PH1'] = [0, 270, 0, 270, 90, 90, 180, 180 ] # 1st (90-degree) pulse
|
||||
pars['PH3'] = [90,180, 90, 180, 180, 180, 90, 90 ] # 2nd (45-degree) pulse
|
||||
pars['PH4'] = [90, 90, 270, 270, 180, 0, 0, 180 ] # 3rd (45-degree) pulse
|
||||
pars['PH2'] = [0, 180, 180, 0, 90, 270, 90, 270 ] # receiver
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
P45 = pars['P90']*0.5
|
||||
P1 = pars['P90']*0.5
|
||||
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'
|
||||
e.set_phase(PH3)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P45, value=TXEnableValue|TXPulseValue) # 45-degree pulse
|
||||
|
||||
e.wait(D2-P45/2-TXEnableDelay) # 'long tau'
|
||||
e.set_phase(PH4)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 45-degree pulse
|
||||
|
||||
e.wait(TXEnableDelay)
|
||||
e.set_phase(PHA)
|
||||
e.wait(5e-6)#D1-P45/2-TXEnableDelay) # 'short tau'
|
||||
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 zeeman_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'zeeman_experiment'
|
||||
|
||||
# 8-step phase cycle (1-21 modifided to deal with T1-recovery and extended for Re/Im imbalance)
|
||||
pars['PH1'] = [0, 270, 0, 270, 180, 90, 180, 90] # 1st (90-degree) pulse
|
||||
pars['PH3'] = [0, 90, 0, 90, 0, 90, 0, 90] # 2nd (90-degree) pulse
|
||||
pars['PH4'] = [0, 0, 180, 180, 270, 270, 90, 90] # 3rd (90-degree) pulse
|
||||
pars['PH2'] = [0, 180, 180, 0, 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'
|
||||
|
||||
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'
|
||||
|
||||
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'
|
||||
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
|
||||
282
AU_Programs/2H/op_2h_res.py
Normal file
282
AU_Programs/2H/op_2h_res.py
Normal file
@ -0,0 +1,282 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
the_experiment = None # current experiment's name
|
||||
|
||||
measurements = {'satrec2_experiment': MeasurementResult('Saturation Recovery'),
|
||||
'solidecho_experiment': MeasurementResult('Solid Echo'),
|
||||
'spinal_experiment': MeasurementResult('Spin Alignment'),
|
||||
'zeeman_experiment': MeasurementResult('Zeeman Order')}
|
||||
|
||||
measurement_ranges = {'satrec2_experiment': [0.5e-6, 4.5e-6],
|
||||
'solidecho_experiment': [0.5e-6, 4.5e-6],
|
||||
'spinal_experiment': [0.5e-6, 4.5e-6],
|
||||
'zeeman_experiment': [0.5e-6, 4.5e-6]}
|
||||
measurement_ranging = True
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# keep track of the actual experiment's name:
|
||||
if the_experiment != pars.get('PROG'):
|
||||
the_experiment = pars.get('PROG')
|
||||
suffix = '' # output file name's suffix
|
||||
counter = 1
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal according to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the signal's phase:
|
||||
#phi0 = arctan2(accu.y[1][0], accu.y[0][0]) * 180 / pi
|
||||
#if not locals().get('ref'): ref = phi0
|
||||
#print 'phi0 = ', phi0
|
||||
|
||||
# rotate the signal to maximize Re (optional):
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# estimate noise level:
|
||||
if not locals().get('noise'):
|
||||
n = int(0.1*accu.x.size)
|
||||
noise = 3*std(accu.y[0][-n-29:-30])
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if the_experiment in measurements.keys():
|
||||
|
||||
# option a: the sum of samples within the given range:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = echo.get_sampling_rate() * array(measurement_ranges[the_experiment])
|
||||
measurements[the_experiment][var_value] = sum(echo.y[0][int(start):int(stop)])
|
||||
|
||||
# option b: the sum of all samples above noise:
|
||||
else:
|
||||
measurements[the_experiment][var_value] = sum(echo.y[0][echo.y[0]>noise])
|
||||
|
||||
# store a measurement:
|
||||
data[measurements[the_experiment].get_title()] = measurements[the_experiment]
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
else:
|
||||
print "Cannot recognize experiment: continue without measuring"
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
if var_key == 'TAU' or var_key == 'D2':
|
||||
# mono-exponential saturation-recovery fit:
|
||||
try:
|
||||
xdata = measurements['satrec2_experiment'].get_xdata()
|
||||
ydata = measurements['satrec2_experiment'].get_ydata()
|
||||
[amplitude, rate, offset] = fitfunc_recovery(xdata, ydata)
|
||||
print 'Mono-exponential fit to saturation-recovery data:'
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T1 [s] = ', 1./rate)
|
||||
|
||||
# update display for fit:
|
||||
measurements['satrec2_experiment'].y = func_recovery([amplitude, rate, offset], xdata)
|
||||
data[measurements['satrec2_experiment'].get_title()] = measurements['satrec2_experiment']
|
||||
except:
|
||||
pass
|
||||
|
||||
# KWW fit to spin-alignment echoes:
|
||||
try:
|
||||
xdata = measurements['spinal_experiment'].get_xdata()
|
||||
ydata = measurements['spinal_experiment'].get_ydata()
|
||||
[amplitude, rate, beta] = fitfunc_kww(xdata, ydata)
|
||||
print 'KWW fit to spin-alignment echoes:'
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
print '%s%01g' % ('Beta = ', beta)
|
||||
|
||||
# update display for the fit:
|
||||
measurements['spinal_experiment'].y = func_kww([amplitude, rate, beta], xdata)
|
||||
data[measurements['spinal_experiment'].get_title()] = measurements['spinal_experiment']
|
||||
except:
|
||||
pass
|
||||
|
||||
# KWW fit to Zeeman-order echoes:
|
||||
try:
|
||||
xdata = measurements['zeeman_experiment'].get_xdata()
|
||||
ydata = measurements['zeeman_experiment'].get_ydata()
|
||||
[amplitude, rate, beta] = fitfunc_kww(xdata, ydata)
|
||||
print 'KWW fit to Zeeman-order echoes:'
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
print '%s%01g' % ('Beta = ', beta)
|
||||
|
||||
# update display for the fit:
|
||||
measurements['zeeman_experiment'].y = func_kww([amplitude, rate, beta], xdata)
|
||||
data[measurements['zeeman_experiment'].get_title()] = measurements['zeeman_experiment']
|
||||
except:
|
||||
pass
|
||||
|
||||
# the fitting procedure for satrec_experiment:
|
||||
def fitfunc_recovery(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(mean(ydata[-2:]) - ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[-1] - ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
offset = min(ydata)
|
||||
p0 = [amplitude, rate, offset]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals_recovery, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals_recovery(p, xdata, ydata):
|
||||
return ydata - func_recovery(p, xdata)
|
||||
|
||||
# here is the function to fit
|
||||
def func_recovery(p, xdata):
|
||||
return p[0]*(1-exp(-p[1]*xdata)) + p[2]
|
||||
|
||||
|
||||
# the fitting procedure for spinal_experiment and zeeman_experiment:
|
||||
def fitfunc_kww(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
beta = 1.
|
||||
p0 = [amplitude, rate, beta]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals_kww, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals_kww(p, xdata, ydata):
|
||||
return ydata - func_kww(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func_kww(p, xdata):
|
||||
return p[0]*exp(-(p[1]*xdata)**p[2])
|
||||
|
||||
|
||||
pass
|
||||
483
AU_Programs/Diffusiometry/op_diff_exp.py
Normal file
483
AU_Programs/Diffusiometry/op_diff_exp.py
Normal file
@ -0,0 +1,483 @@
|
||||
# -*- 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 = 1 # voltage span for ADC
|
||||
|
||||
def experiment(): # drives three experiments in a row: saturation-recovery, stimulated echo, and Hanh echo
|
||||
|
||||
# experiments switches:
|
||||
satrec2_flag = True # saturation-recovery switch
|
||||
ste_flag = True # stimulated-echo switch
|
||||
hahn_flag = False # Hahn-echo switch
|
||||
|
||||
|
||||
# ------------------ Saturation-recovery experiment settings ----------------------
|
||||
|
||||
if satrec2_flag == True:
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 62.92e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = 0e3 # offset from SF (Hz)
|
||||
pars['SW'] = 20e6 # spectral window (Hz)
|
||||
pars['SI'] = 1*512 # number of acquisition points
|
||||
pars['NS'] = 512 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['TAU'] = 1 # delay for recovery (s)
|
||||
pars['D3'] = 20e-6 # echo delay (s)
|
||||
pars['D4'] = 0 # echo pre-aquisition delay (s)
|
||||
pars['PHA'] = 50 # receiver phase (degree)
|
||||
# -*- these ain't variable: -*-
|
||||
pars['NECH'] = 20 # number of saturation pulses
|
||||
pars['D1'] = 100e-3 # starting interval in saturation sequence (s)
|
||||
pars['D2'] = 1e-4 # end interval in saturation sequence (s)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = '360K' # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = 'TAU' # variable parameter name (a string)
|
||||
start = 1e-3 # starting value
|
||||
stop = 1e-0 # end value
|
||||
steps = 12 # 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']%8 != 0:
|
||||
pars['NS'] = int(round(pars['NS'] / 8) + 1) * 8
|
||||
print 'Number of scans changed to ',pars['NS'],' due to phase cycling'
|
||||
|
||||
if pars['D1'] < pars['D2']:
|
||||
raise Exception("D1 must be greater than D2!")
|
||||
|
||||
sat_length = sum(log_range(pars['D1'],pars['D2'],pars['NECH']))
|
||||
if sat_length > 1.:
|
||||
raise Exception("saturation sequence too long!!!")
|
||||
|
||||
# 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 == 'TAU':
|
||||
seconds = ((sat_length + pars['D3']*2) * steps + sum(array)) * (pars['NS'] + pars['DS'])
|
||||
elif var_key == 'D3':
|
||||
seconds = ((sat_length + pars['TAU']) * steps + sum(array)*2) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = (sat_length + pars['TAU'] + pars['D3']*2) * 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 saturation-recovery 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 satrec2_experiment(pars, run)
|
||||
synchronize()
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = (sat_length + pars['TAU'] + pars['D3']*2) * (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 satrec2_experiment(pars, run)
|
||||
|
||||
|
||||
# ---------------- Stimulated-echo experiment settings ------------------
|
||||
|
||||
if ste_flag == True:
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.6e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 62.92e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = 0e3 # offset from SF (Hz)
|
||||
pars['SW'] = 20e6 # spectral window (Hz)
|
||||
pars['SI'] = 1*512 # number of acquisition points
|
||||
pars['NS'] = 512 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 1 # delay between scans (s)
|
||||
pars['D1'] = 400e-6 # delay after first pulse (short tau) (s)
|
||||
pars['D2'] = 20e-6 # delay after second pulse (long tau) (s)
|
||||
pars['PHA'] = 240 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = '210K' # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = 'D2' # variable parameter name (a string)
|
||||
start = 350e-6 # starting value
|
||||
stop = 1e-0 # end value
|
||||
steps = 16 # 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 stimulated-echo 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 ste_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 ste_experiment(pars, run)
|
||||
|
||||
|
||||
# ------------------ Hahn-echo experiment settings ----------------------
|
||||
if hahn_flag == True:
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.6e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 62.92e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = 0e3 # offset from SF (Hz)
|
||||
pars['SW'] = 20e6 # spectral window (Hz)
|
||||
pars['SI'] = 1*512 # number of acquisition points
|
||||
pars['NS'] = 512 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 1 # delay between scans (s)
|
||||
pars['TAU'] = 10e-6 # echo delay (s)
|
||||
pars['D4'] = 0e-6 # echo pre-acquisition delay (s)
|
||||
pars['PHA'] = 170 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = 'test' # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = 'TAU' # variable parameter name (a string)
|
||||
start = 20e-6 # starting value
|
||||
stop = 1e-3 # end value
|
||||
steps = 16 # 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']%8 != 0:
|
||||
pars['NS'] = int(round(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 == 'TAU':
|
||||
seconds = (sum(array)*2 + pars['RD'] * steps) * (pars['NS'] + pars['DS'])
|
||||
elif var_key == 'RD':
|
||||
seconds = (sum(array) + pars['TAU']*2 * steps) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = (pars['TAU']*2 + 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 Hahn-echo 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 hahn_experiment(pars, run)
|
||||
synchronize()
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = (pars['TAU']*2 + 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 hahn_experiment(pars, run)
|
||||
|
||||
|
||||
|
||||
# the pulse programs:
|
||||
|
||||
def satrec2_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'satrec2_experiment'
|
||||
|
||||
# phase lists:
|
||||
pars['PH1'] = [ 0] # saturation pulses
|
||||
pars['PH3'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # 1st 90-degree pulse
|
||||
pars['PH4'] = [90, 90, 270, 270, 0, 0, 180, 180] # 2nd 90-degree pulse
|
||||
pars['PH2'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # receiver
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
SF = pars['SF']
|
||||
O1 = pars['O1']
|
||||
NECH = pars['NECH']
|
||||
D1 = pars['D1']
|
||||
D2 = pars['D2']
|
||||
D3 = pars['D3']
|
||||
D4 = pars['D4']
|
||||
TAU = pars['TAU']
|
||||
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 variable delay list for saturation pulses:
|
||||
vdlist = log_range(D2, D1, NECH-1)
|
||||
|
||||
# set sampling parameters:
|
||||
SI = pars['SI']
|
||||
SW = pars['SW']
|
||||
while SW <= 10e6 and SI < 256*1024:
|
||||
SI *= 2
|
||||
SW *= 2
|
||||
|
||||
# the pulse sequence:
|
||||
|
||||
# saturation:
|
||||
e.set_frequency(SF+O1, phase=PH1) # set frequency and phase for saturation pulses
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
for delay in vdlist[::-1]:
|
||||
e.wait(delay-P90-TXEnableDelay) # wait for next saturation pulse
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
|
||||
# recovery:
|
||||
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
|
||||
275
AU_Programs/Diffusiometry/op_diff_res.py
Normal file
275
AU_Programs/Diffusiometry/op_diff_res.py
Normal file
@ -0,0 +1,275 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
the_experiment = None # current experiment's name
|
||||
|
||||
measurements = {'satrec2_experiment': MeasurementResult('Saturation Recovery'),
|
||||
'ste_experiment': MeasurementResult('Stimulated Echo'),
|
||||
'hahn_experiment': MeasurementResult('Hahn Echo')}
|
||||
|
||||
measurement_ranges = {'satrec2_experiment': [0.5e-6, 4.5e-6],
|
||||
'ste_experiment': [1.5e-6, 4.5e-6],
|
||||
'hahn_experiment': [2.5e-6, 4.5e-6]}
|
||||
measurement_ranging = True
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# catch the actual experiment's name:
|
||||
if the_experiment != pars.get('PROG'):
|
||||
the_experiment = pars.get('PROG')
|
||||
suffix = '' # output file name's suffix
|
||||
counter = 1
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal according to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the signal's phase:
|
||||
#phi0 = arctan2(echo.y[1][0], echo.y[0][0]) * 180 / pi
|
||||
#if not locals().get('ref'): ref = phi0
|
||||
#print 'phi0 = ', phi0
|
||||
|
||||
# rotate the signal to maximize Re (optional):
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# store signals recorded for different var_values:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# estimate noise level:
|
||||
if not locals().get('noise'):
|
||||
n = int(0.1*echo.x.size)
|
||||
noise = 3*std(echo.y[0][-n-numtaps:-1-numtaps])
|
||||
|
||||
# measure echo intensity vs. var_value:
|
||||
if the_experiment in measurements.keys():
|
||||
|
||||
# option a: sum over the time interval specified:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = echo.get_sampling_rate() * array(measurement_ranges[the_experiment])
|
||||
measurements[the_experiment][var_value] = sum(echo.y[0][int(start):int(stop)])
|
||||
|
||||
# option b: sum of all samples above noise:
|
||||
else:
|
||||
measurements[the_experiment][var_value] = sum(echo.y[0][echo.y[0]>noise])
|
||||
|
||||
# store a measurement:
|
||||
data[measurements[the_experiment].get_title()] = measurements[the_experiment]
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
else:
|
||||
print "Cannot recognize experiment: continue without measuring"
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
if var_key == 'TAU' or var_key == 'D2':
|
||||
# mono-exponential recovery fit:
|
||||
try:
|
||||
xdata = measurements['satrec2_experiment'].get_xdata()
|
||||
ydata = measurements['satrec2_experiment'].get_ydata()
|
||||
[amplitude, rate, offset] = fitfunc_recovery(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T1 [s] = ', 1./rate)
|
||||
|
||||
# update display for fit:
|
||||
measurements['satrec2_experiment'].y = func_recovery([amplitude, rate, offset], xdata)
|
||||
data[measurements['satrec2_experiment'].get_title()] = measurements['satrec2_experiment']
|
||||
except:
|
||||
pass
|
||||
|
||||
# mono-exponential decay fit to Hahn echoes:
|
||||
try:
|
||||
xdata = measurements['hahn_experiment'].get_xdata()
|
||||
ydata = measurements['hahn_experiment'].get_ydata()
|
||||
[amplitude, rate] = fitfunc_decay(xdata, ydata)
|
||||
print 'Mono-exponential fit to Hahn echo decay:'
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
|
||||
# update display for the fit:
|
||||
measurements['hahn_experiment'].y = func_decay([amplitude, rate], xdata)
|
||||
data[measurements['hahn_experiment'].get_title()] = measurements['hahn_experiment']
|
||||
except:
|
||||
pass
|
||||
|
||||
try:
|
||||
# mono-exponential decay fit to stimulated echoes:
|
||||
xdata = measurements['ste_experiment'].get_xdata()
|
||||
ydata = measurements['ste_experiment'].get_ydata()
|
||||
[amplitude, rate] = fitfunc_decay(xdata, ydata)
|
||||
print 'Mono-exponential fit to stimulated echo decay:'
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
|
||||
# update display for the fit:
|
||||
measurements['ste_experiment'].y = func_decay([amplitude, rate], xdata)
|
||||
data[measurements['ste_experiment'].get_title()] = measurements['ste_experiment']
|
||||
except:
|
||||
pass
|
||||
|
||||
# the fitting procedure for satrec:
|
||||
def fitfunc_recovery(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(mean(ydata[-2:]) - ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[-1] - ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
offset = min(ydata)
|
||||
p0 = [amplitude, rate, offset]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals_recovery, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals_recovery(p, xdata, ydata):
|
||||
return ydata - func_recovery(p, xdata)
|
||||
|
||||
# here is the function to fit
|
||||
def func_recovery(p, xdata):
|
||||
return p[0]*(1-exp(-p[1]*xdata)) + p[2]
|
||||
|
||||
|
||||
# the fitting procedure for hahn and ste:
|
||||
def fitfunc_decay(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
p0 = [amplitude, rate]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals_decay, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals_decay(p, xdata, ydata):
|
||||
return ydata - func_decay(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func_decay(p, xdata):
|
||||
return p[0]*exp(-p[1]*xdata)
|
||||
|
||||
pass
|
||||
156
Scripts/CPMG/op_cpmg_exp.py
Normal file
156
Scripts/CPMG/op_cpmg_exp.py
Normal file
@ -0,0 +1,156 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # Carr-Purcell-Meiboom-Gill (CPMG) experiment
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['NS'] = 8 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 3 # delay between scans (s)
|
||||
pars['NECH'] = 16 # number of 180-degree pulses
|
||||
pars['TAU'] = 40e-6 # half pulse period (s)
|
||||
pars['PHA'] = -127 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = None # variable parameter name (a string)
|
||||
start = 40e-6 # starting value
|
||||
stop = 100e-6 # end value
|
||||
steps = 10 # number of values
|
||||
log_scale = False # 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']%4 != 0:
|
||||
pars['NS'] = int(round(pars['NS'] / 4) + 1) * 4
|
||||
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 experiment time:
|
||||
if var_key == 'TAU':
|
||||
seconds = (sum(array)* 2* pars['NECH'] + pars['RD'] * steps) * (pars['NS'] + pars['DS'])
|
||||
elif var_key == 'NECH':
|
||||
seconds = (pars['TAU']* 2* sum(array) + pars['RD'] * steps) * (pars['NS'] + pars['DS'])
|
||||
elif var_key == 'RD':
|
||||
seconds = (pars['TAU']* 2* pars['NECH'] + sum(array)) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = (pars['TAU']* 2* pars['NECH'] + 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 cpmg_experiment(pars, run)
|
||||
synchronize()
|
||||
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = (pars['TAU']* 2* pars['NECH'] + 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 cpmg_experiment(pars, run)
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def cpmg_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'cpmg_experiment'
|
||||
|
||||
# phase lists:
|
||||
pars['PH1'] = [0, 180, 90, 270] # 90-degree pulse
|
||||
pars['PH3'] = [90, 90, 180, 180] # 180-degree pulse
|
||||
pars['PH2'] = [0, 180, 90, 270] # receiver
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
P180 = pars['P90']*2
|
||||
SF = pars['SF']
|
||||
O1 = pars['O1']
|
||||
RD = pars['RD']
|
||||
NECH = pars['NECH']
|
||||
TAU = pars['TAU']
|
||||
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 = 128 # number of samples
|
||||
SW = 20e6 # sampling 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) # set frequency and phase for 90-degree pulse
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
e.wait(TAU-P90/2-P180/2-TXEnableDelay) # wait for tau
|
||||
e.set_phase(PH3) # change phase for 180-degree pulse
|
||||
|
||||
e.loop_start(NECH) # ----- loop for echoes: -----
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply 180-degree pulse
|
||||
e.set_phase(PHA) # set phase for receiver
|
||||
e.wait(TAU-(P180+TXEnableDelay+AQ)/2) # pre-acquisition delay
|
||||
e.record(SI, SW, timelength=AQ, sensitivity=ADCSensitivity) # acquire echo samples
|
||||
e.wait(TAU-(P180+TXEnableDelay+AQ)/2) # post-acquisition delay
|
||||
e.set_phase(PH3) # set phase for theta-degree pulse
|
||||
e.loop_end() # ----------------------------
|
||||
|
||||
# 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 data route
|
||||
|
||||
return e
|
||||
176
Scripts/CPMG/op_cpmg_res.py
Normal file
176
Scripts/CPMG/op_cpmg_res.py
Normal file
@ -0,0 +1,176 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# rotate timesignal by current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# get number of echoes:
|
||||
num_echoes = pars['NECH']
|
||||
|
||||
# downsize accu to one point per echo:
|
||||
echodecay = accu + 0
|
||||
echodecay.x = resize(echodecay.x, int(num_echoes))
|
||||
echodecay.y[0] = resize(echodecay.y[0], int(num_echoes))
|
||||
echodecay.y[1] = resize(echodecay.y[1], int(num_echoes))
|
||||
|
||||
# specify noise level:
|
||||
if not locals().get('noise'):
|
||||
echo = accu.get_accu_by_index(0)
|
||||
noise = 0.1*max(abs(echo.y[0]))
|
||||
samples = abs(echo.y[0]) > noise
|
||||
|
||||
# set echo times and intensities:
|
||||
for i in range(num_echoes):
|
||||
# get ith echo:
|
||||
echo = accu.get_accu_by_index(i)
|
||||
# set echo timing:
|
||||
echodecay.x[i] = i*2*pars['TAU']
|
||||
# set echo value:
|
||||
echodecay.y[0][i] = sum(echo.y[0][samples]) # the sum of echo points that exeed noise
|
||||
echodecay.y[1][i] = sum(echo.y[1][samples])
|
||||
#echodecay.y[0][i] = sum(echo.y[0]) # the sum of all echo points
|
||||
#echodecay.y[1][i] = sum(echo.y[1])
|
||||
#echodecay.y[0][i] = echo.y[0][echo.x.size/2] # a middle echo point
|
||||
#echodecay.y[1][i] = echo.y[1][echo.x.size/2]
|
||||
|
||||
# compute a signal's phase:
|
||||
phi0 = arctan2(echodecay.y[1][0], echodecay.y[0][0]) * 180 / pi
|
||||
if not locals().get('ref'): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate signal to maximize Re (optional):
|
||||
#echodecay.phase(-phi0)
|
||||
|
||||
# provide echo decay to the display tab:
|
||||
data['Echo Decay'] = echodecay
|
||||
|
||||
# fit a mono-exponential function to the echo decay:
|
||||
[amplitude, rate] = fitfunc(echodecay.x, echodecay.y[0])
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
|
||||
# provide the fit to the display tab:
|
||||
fit = MeasurementResult('Mono-Exponential Fit')
|
||||
for i, key in enumerate(echodecay.x):
|
||||
fit[key] = echodecay.y[0][i]
|
||||
fit.y = func([amplitude, rate], echodecay.x)
|
||||
data[fit.get_title()] = fit
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide data recorded with different var_value's to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
data['Echo Decay'+"/"+var_key+"=%e"%(var_value)] = echodecay
|
||||
data[fit.get_title()+"/"+var_key+"=%e"%(var_value)] = fit
|
||||
|
||||
# measure a signal parameter vs. var_value:
|
||||
measurement[var_value] = amplitude
|
||||
#measurement[var_value] = sum(echodecay.y[0][:])
|
||||
#measurement[var_value] = 1./rate
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
p0 = [amplitude, rate]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*exp(-p[1]*xdata)
|
||||
|
||||
|
||||
pass
|
||||
137
Scripts/FID/op_fid_exp.py
Normal file
137
Scripts/FID/op_fid_exp.py
Normal file
@ -0,0 +1,137 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # the basic pulse-acquire experiment
|
||||
|
||||
# set up acqusition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['SW'] = 200e3 # spectral window (Hz)
|
||||
pars['SI'] = 1*256 # number of acquisition points
|
||||
pars['NS'] = 4 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 3 # delay between scans (s)
|
||||
pars['DEAD1'] = 5e-6 # receiver dead time (s)
|
||||
pars['PHA'] = 30 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = None # variable parameter name (a string)
|
||||
start = 1e-6 # starting value
|
||||
stop = 3e-6 # end value
|
||||
steps = 4 # number of values
|
||||
log_scale = False # 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']%4 != 0:
|
||||
pars['NS'] = int(round(pars['NS'] / 4) + 1) * 4
|
||||
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 == 'RD':
|
||||
seconds = sum(array) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = 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 fid_experiment(pars, run)
|
||||
synchronize()
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = 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 fid_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def fid_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'fid_experiment'
|
||||
|
||||
# phase lists:
|
||||
pars['PH1'] = [0, 180, 90, 270] # 90-degree pulse
|
||||
pars['PH2'] = [0, 180, 90, 270] # receiver
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
SF = pars['SF']
|
||||
O1 = pars['O1']
|
||||
RD = pars['RD']
|
||||
DEAD1 = pars['DEAD1']
|
||||
PH1 = pars['PH1'][run%len(pars['PH1'])]
|
||||
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 RF pulse
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply RF pulse
|
||||
e.set_phase(PHA) # set phase for receiver
|
||||
e.wait(DEAD1) # wait for coil ringdown
|
||||
e.record(SI, SW, 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
|
||||
167
Scripts/FID/op_fid_res.py
Normal file
167
Scripts/FID/op_fid_res.py
Normal file
@ -0,0 +1,167 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# phase timesignal according to current rec_phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulatioin is complete
|
||||
|
||||
# make a copy:
|
||||
fid = accu + 0
|
||||
|
||||
# compute the signal's phase:
|
||||
phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
|
||||
if not 'ref' in locals(): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate the signal to maximize Re (optional):
|
||||
#fid.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
fid.exp_window(line_broadening=10)
|
||||
spectrum = fid.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
if abs(abs(phi0)-abs(ref)) > 90:
|
||||
spectrum.phase(180)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
fid_phased = (accu + 0).phase(-ref)
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(fid_phased.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(fid_phased.y[0][0:31])
|
||||
|
||||
# provide measurements to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
pass
|
||||
147
Scripts/FID_with_Background_Suppression/op_zgbs_exp.py
Normal file
147
Scripts/FID_with_Background_Suppression/op_zgbs_exp.py
Normal file
@ -0,0 +1,147 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # fid aquisition with background signal suppresion (the Bruker's zgbs)
|
||||
|
||||
# set up acqusition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 3.5e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 360.0e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -140e3 # offset from SF (Hz)
|
||||
pars['SW'] = 10e6 # spectrum width (Hz)
|
||||
pars['SI'] = 4*1024 # number of acquisition points
|
||||
pars['NS'] = 64 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 1 # delay between scans (s)
|
||||
pars['DEAD1'] = 5e-6 # receiver dead time (s)
|
||||
pars['PHA'] = 0 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = None # variable parameter name (a string)
|
||||
start = 1e-6 # starting value
|
||||
stop = 5e-6 # end value
|
||||
steps = 5 # number of values
|
||||
log_scale = False # 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 == 'RD':
|
||||
seconds = sum(array) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = 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 zgbs_experiment(pars, run)
|
||||
synchronize()
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = 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 zgbs_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def zgbs_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'zgbs_experiment'
|
||||
|
||||
# phase lists [from Bruker's zgbs]:
|
||||
pars['PH1'] = [0, 0, 0, 0, 90, 90, 90, 90, 180, 180, 180, 180, 270, 270, 270, 270] # 90-degree pulse
|
||||
pars['PH3'] = [0, 90, 180, 270] # 180-degree pulse
|
||||
pars['PH4'] = [0, 0, 0, 0, 180, 180, 180, 180, 270, 270, 270, 270, 90, 90, 90, 90] # 180-degree pulse
|
||||
pars['PH2'] = [0, 180, 0, 180, 90, 270, 90, 270] # receiver
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
P180 = 2*pars['P90']
|
||||
SF = pars['SF']
|
||||
O1 = pars['O1']
|
||||
RD = pars['RD']
|
||||
DEAD1 = pars['DEAD1']
|
||||
PH1 = pars['PH1'][run%len(pars['PH1'])]
|
||||
PH2 = pars['PH2'][run%len(pars['PH2'])]
|
||||
PH3 = pars['PH3'][run%len(pars['PH3'])]
|
||||
PH4 = pars['PH4'][run%len(pars['PH4'])]
|
||||
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 RF pulse
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
e.set_phase(PH3)
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply 180-degree pulse
|
||||
e.set_phase(PH4)
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply 180-degree pulse
|
||||
e.set_phase(PHA) # set phase for receiver
|
||||
e.wait(DEAD1) # wait for coil ringdown
|
||||
e.record(SI, SW, sensitivity=ADCSensitivity) # acquire signal
|
||||
|
||||
# write experiment parameters:
|
||||
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
|
||||
167
Scripts/FID_with_Background_Suppression/op_zgbs_res.py
Normal file
167
Scripts/FID_with_Background_Suppression/op_zgbs_res.py
Normal file
@ -0,0 +1,167 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# phase timesignal according to current rec_phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulatioin is complete
|
||||
|
||||
# make a copy:
|
||||
fid = accu + 0
|
||||
|
||||
# compute the signal's phase:
|
||||
phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
|
||||
if not 'ref' in locals(): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate the signal to maximize Re (optional):
|
||||
#fid.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
fid.exp_window(line_broadening=10)
|
||||
spectrum = fid.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
if abs(abs(phi0)-abs(ref)) > 90:
|
||||
spectrum.phase(180)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
fid_phased = (accu + 0).phase(-ref)
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(fid_phased.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(fid_phased.y[0][0:31])
|
||||
|
||||
# provide measurements to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
pass
|
||||
147
Scripts/Hahn_Echo/op_hahn_exp.py
Normal file
147
Scripts/Hahn_Echo/op_hahn_exp.py
Normal file
@ -0,0 +1,147 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # solid echo (quadrupolar echo) experiment
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['SW'] = 200e3 # spectral window (Hz)
|
||||
pars['SI'] = 1*256 # number of acquisition points
|
||||
pars['NS'] = 8 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 3 # delay between scans (s)
|
||||
pars['TAU'] = 13e-6 # echo delay (s)
|
||||
pars['D4'] = 2e-6 # echo pre-acquisition delay (s)
|
||||
pars['PHA'] = 0 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = None # variable parameter name (a string)
|
||||
start = 20e-6 # starting value
|
||||
stop = 100e-6 # end value
|
||||
steps = 12 # number of values
|
||||
log_scale = False # 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']%8 != 0:
|
||||
pars['NS'] = int(round(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 == 'TAU':
|
||||
seconds = (sum(array)*2 + pars['RD'] * steps) * (pars['NS'] + pars['DS'])
|
||||
elif var_key == 'RD':
|
||||
seconds = (sum(array) + pars['TAU']*2 * steps) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = (pars['TAU']*2 + 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 hahn_experiment(pars, run)
|
||||
synchronize()
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = (pars['TAU']*2 + 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 hahn_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
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
|
||||
167
Scripts/Hahn_Echo/op_hahn_res.py
Normal file
167
Scripts/Hahn_Echo/op_hahn_res.py
Normal file
@ -0,0 +1,167 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # no filter applied otherwise
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# replace the sampling_rate attribute of the signal:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal by current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy of signal:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the signal's phase:
|
||||
phi0 = arctan2(echo.y[1][0], echo.y[0][0]) * 180 / pi
|
||||
if not locals().get('ref'): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate to maximize Re (optional):
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
echo.exp_window(line_broadening=10)
|
||||
spectrum = echo.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# try baseline correction:
|
||||
spectrum.baseline()
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
pass
|
||||
39
Scripts/Miscellaneous/op_gs_exp.py
Normal file
39
Scripts/Miscellaneous/op_gs_exp.py
Normal file
@ -0,0 +1,39 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
def experiment(): # 'go setup' routine
|
||||
|
||||
pars = {}
|
||||
pars['P90'] = 2.5e-6 # 90-degree pulse length (s)
|
||||
pars['RD'] = 1 # delay between scans (s)
|
||||
pars['SW'] = 100e3 # spectrum window (Hz)
|
||||
pars['SI'] = 1*1024 # number of acquisition points
|
||||
pars['DEAD1'] = 10e-6 # receiver dead time (s)
|
||||
|
||||
while True:
|
||||
yield gs_experiment(pars)
|
||||
|
||||
|
||||
def gs_experiment(pars):
|
||||
e=Experiment()
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
RD = pars['RD']
|
||||
SI = pars['SI']
|
||||
SW = pars['SW']
|
||||
DEAD1 = pars['DEAD1']
|
||||
|
||||
if P90 > 20e-6:
|
||||
raise Exception("Pulse too long!!!")
|
||||
|
||||
e.ttl_pulse(2e-6, value=1) # unblank RF amplifier
|
||||
e.ttl_pulse(P90, value=3) # apply 90-degree pulse
|
||||
e.wait(DEAD1) # wait for receiver dead time
|
||||
e.record(SI, SW, sensitivity=2) # acquire signal
|
||||
e.wait(RD) # wait for next scan
|
||||
|
||||
# write experiment parameters:
|
||||
for key in pars.keys():
|
||||
e.set_description(key, pars[key])
|
||||
|
||||
return e
|
||||
54
Scripts/Miscellaneous/op_gs_res.py
Normal file
54
Scripts/Miscellaneous/op_gs_res.py
Normal file
@ -0,0 +1,54 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
|
||||
def result():
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# get list of parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# make a copy of timesignal:
|
||||
fid = timesignal + 0
|
||||
|
||||
# correct for the baseline offset:
|
||||
fid.baseline()
|
||||
|
||||
# compute the initial phase:
|
||||
phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
|
||||
|
||||
# do FFT:
|
||||
fid.exp_window(line_broadening=10)
|
||||
spectrum = fid.fft(samples=2*pars['SI'])
|
||||
spectrum.baseline()
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# provide timesignal and spectrum to the display tab:
|
||||
data['Timesignal'] = timesignal
|
||||
data["Spectrum"] = spectrum
|
||||
|
||||
# ------------- optional measurements: --------------
|
||||
|
||||
# measure signal intensity:
|
||||
signal = (timesignal +0).phase(-phi0)
|
||||
signal_intensity = sum(signal.y[0:10])
|
||||
|
||||
# measure spectrum integral:
|
||||
#spectrum_integral = cumsum(spectrum.y[0])
|
||||
spectrum_magnitude = (spectrum+0).magnitude()
|
||||
spectrum_integral = cumsum(spectrum_magnitude.y[0])
|
||||
|
||||
# find the centre of gravity of the spectrum:
|
||||
cg = argwhere(spectrum_integral > 0.5*spectrum_integral[-1])[0]
|
||||
|
||||
print ''
|
||||
print '%s%.3e'%('FID intensity = ', signal_intensity)
|
||||
print '%s%.3e'%('Spectrum integral = ', spectrum_integral[-1])
|
||||
print '%s%g%s'%("Spectrum middle frequency = ", spectrum.x[cg], ' Hz')
|
||||
print ''
|
||||
|
||||
pass
|
||||
169
Scripts/Saturation_Recovery/op_satrec_exp.py
Normal file
169
Scripts/Saturation_Recovery/op_satrec_exp.py
Normal file
@ -0,0 +1,169 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # saturation-recovery experiment
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['SW'] = 200e3 # spectral window (Hz)
|
||||
pars['SI'] = 1*256 # number of acquisition points
|
||||
pars['NS'] = 8 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['TAU'] = 1 # delay for recovery (s)
|
||||
pars['DEAD1'] = 5e-6 # receiver dead time (s)
|
||||
pars['PHA'] = 100 # receiver phase (degree)
|
||||
# -*- these aren't variable: -*-
|
||||
pars['NECH'] = 40 # number of saturation pulses
|
||||
pars['D1'] = 100e-3 # starting interval in saturation sequence (s)
|
||||
pars['D2'] = 1e-4 # end interval in saturation sequence (s)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = 'TAU' # variable parameter name (a string)
|
||||
start = 1e-3 # starting value
|
||||
stop = 5e-0 # end value
|
||||
steps = 10 # 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']%4 != 0:
|
||||
pars['NS'] = int(round(pars['NS'] / 4) + 1) * 4
|
||||
print 'Number of scans changed to ',pars['NS'],' due to phase cycling'
|
||||
|
||||
if pars['D1'] < pars['D2']:
|
||||
raise Exception("D1 must be greater than D2")
|
||||
|
||||
sat_length = sum(log_range(pars['D1'],pars['D2'],pars['NECH']))
|
||||
if sat_length > 1.:
|
||||
raise Exception("Saturation sequence too long!!!")
|
||||
|
||||
# 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 == 'TAU':
|
||||
seconds = (sat_length * steps + sum(array)) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = (sat_length + pars['TAU']) * 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 satrec_experiment(pars, run)
|
||||
synchronize()
|
||||
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = (sat_length + pars['TAU']) * (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 satrec_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def satrec_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'satrec_experiment'
|
||||
|
||||
# phase lists:
|
||||
pars['PH1'] = [0] # saturation pulses
|
||||
pars['PH3'] = [0,180,90,270] # measuring pulse
|
||||
pars['PH2'] = [0,180,90,270] # receiver
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
SF = pars['SF']
|
||||
O1 = pars['O1']
|
||||
DEAD1 = pars['DEAD1']
|
||||
NECH = pars['NECH']
|
||||
D1 = pars['D1']
|
||||
D2 = pars['D2']
|
||||
TAU = pars['TAU']
|
||||
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
|
||||
|
||||
# set variable delay list for saturation pulses:
|
||||
vdlist = log_range(D2, D1, NECH-1)
|
||||
|
||||
# run the pulse sequence:
|
||||
|
||||
# saturation:
|
||||
e.set_frequency(SF+O1, phase=PH1) # set frequency and phase for saturation pulses
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
for delay in vdlist[::-1]:
|
||||
e.wait(delay-P90-TXEnableDelay) # wait for next pulse
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
|
||||
# recovery:
|
||||
e.wait(TAU) # recovery time
|
||||
e.set_phase(PH3) # set phase for measuring pulse
|
||||
|
||||
# detection:
|
||||
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(DEAD1) # wait for coil ringdown
|
||||
e.record(SI, SW, sensitivity=ADCSensitivity) # acquire signal
|
||||
|
||||
# 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
|
||||
208
Scripts/Saturation_Recovery/op_satrec_res.py
Normal file
208
Scripts/Saturation_Recovery/op_satrec_res.py
Normal file
@ -0,0 +1,208 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # no filter applied otherwise
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal according to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current Scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
fid = accu + 0
|
||||
|
||||
# compute the initial phase of FID:
|
||||
phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
|
||||
if not locals().get('ref'): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate FID to maximize Re (optional):
|
||||
#fid.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
fid.exp_window(line_broadening=10)
|
||||
spectrum = fid.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
if var_key == 'TAU':
|
||||
# mono-exponential recovery fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
[amplitude, rate, offset] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T1 [s] = ', 1./rate)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate, offset], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(mean(ydata[-2:]) - ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[-1] - ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
offset = min(ydata)
|
||||
p0 = [amplitude, rate, offset]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*(1-exp(-p[1]*xdata)) + p[2]
|
||||
|
||||
|
||||
pass
|
||||
@ -0,0 +1,178 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # saturation-recovery with soild-echo detection
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 2.3e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = 5.6e3 # offset from SF (Hz)
|
||||
pars['SW'] = 10e6 # spectral window (Hz)
|
||||
pars['SI'] = 1*1024 # number of acquisition points
|
||||
pars['NS'] = 16 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['TAU'] = 1 # delay for recovery (s)
|
||||
pars['D3'] = 20e-6 # echo delay (s)
|
||||
pars['D4'] = 0 # echo pre-aquisition delay (s)
|
||||
pars['PHA'] = -30 # receiver phase (degree)
|
||||
# -*- these ain't variable: -*-
|
||||
pars['NECH'] = 40 # number of saturation pulses
|
||||
pars['D1'] = 100e-3 # starting interval in saturation sequence (s)
|
||||
pars['D2'] = 1e-4 # end interval in saturation sequence (s)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = 'TAU' # variable parameter name (a string)
|
||||
start = 1e-4 # starting value
|
||||
stop = 1e-0 # end value
|
||||
steps = 10 # number of values
|
||||
log_scale = True # log scale flag
|
||||
stag_range = True # 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']%8 != 0:
|
||||
pars['NS'] = int(round(pars['NS'] / 8) + 1) * 8
|
||||
print 'Number of scans changed to ',pars['NS'],' due to phase cycling'
|
||||
|
||||
if pars['D1'] < pars['D2']:
|
||||
raise Exception("D1 must be greater than D2!")
|
||||
|
||||
sat_length = sum(log_range(pars['D1'],pars['D2'],pars['NECH']))
|
||||
if sat_length > 1.:
|
||||
raise Exception("saturation sequence too long!!!")
|
||||
|
||||
# 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 == 'TAU':
|
||||
seconds = ((sat_length + pars['D3']*2) * steps + sum(array)) * (pars['NS'] + pars['DS'])
|
||||
elif var_key == 'D3':
|
||||
seconds = ((sat_length + pars['TAU']) * steps + sum(array)*2) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = (sat_length + pars['TAU'] + pars['D3']*2) * 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 satrec2_experiment(pars, run)
|
||||
synchronize()
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = (sat_length + pars['TAU'] + pars['D3']*2) * (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 satrec2_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def satrec2_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'satrec2_experiment'
|
||||
|
||||
# phase lists:
|
||||
pars['PH1'] = [ 0] # saturation pulses
|
||||
pars['PH3'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # 1st 90-degree pulse
|
||||
pars['PH4'] = [90, 90, 270, 270, 0, 0, 180, 180] # 2nd 90-degree pulse
|
||||
pars['PH2'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # receiver
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
SF = pars['SF']
|
||||
O1 = pars['O1']
|
||||
NECH = pars['NECH']
|
||||
D1 = pars['D1']
|
||||
D2 = pars['D2']
|
||||
D3 = pars['D3']
|
||||
D4 = pars['D4']
|
||||
TAU = pars['TAU']
|
||||
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 variable delay list for saturation pulses:
|
||||
vdlist = log_range(D2, D1, NECH-1)
|
||||
|
||||
# set sampling parameters:
|
||||
SI = pars['SI']
|
||||
SW = pars['SW']
|
||||
while SW <= 10e6 and SI < 256*1024:
|
||||
SI *= 2
|
||||
SW *= 2
|
||||
|
||||
# the pulse sequence:
|
||||
|
||||
# saturation:
|
||||
e.set_frequency(SF+O1, phase=PH1) # set frequency and phase for saturation pulses
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
for delay in vdlist[::-1]:
|
||||
e.wait(delay-P90-TXEnableDelay) # wait for next saturation pulse
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
|
||||
|
||||
# recovery:
|
||||
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
|
||||
@ -0,0 +1,208 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # no filter applied otherwise
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal according to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current Scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
fid = accu + 0
|
||||
|
||||
# compute the initial phase of FID:
|
||||
phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
|
||||
if not locals().get('ref'): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate FID to maximize Re (optional):
|
||||
#fid.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
fid.exp_window(line_broadening=10)
|
||||
spectrum = fid.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
if var_key == 'TAU':
|
||||
# mono-exponential recovery fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
[amplitude, rate, offset] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T1 [s] = ', 1./rate)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate, offset], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(mean(ydata[-2:]) - ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[-1] - ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
offset = min(ydata)
|
||||
p0 = [amplitude, rate, offset]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*(1-exp(-p[1]*xdata)) + p[2]
|
||||
|
||||
|
||||
pass
|
||||
147
Scripts/Solid_Echo/op_solidecho_exp.py
Normal file
147
Scripts/Solid_Echo/op_solidecho_exp.py
Normal file
@ -0,0 +1,147 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # solid echo (quadrupolar echo) experiment
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['SW'] = 500e3 # spectral window (Hz)
|
||||
pars['SI'] = 1*1024 # number of acquisition points
|
||||
pars['NS'] = 8 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 3 # delay between scans (s)
|
||||
pars['TAU'] = 20e-6 # echo delay (s)
|
||||
pars['D4'] = 0e-6 # echo pre-acquisition delay (s)
|
||||
pars['PHA'] = -30 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = None # variable parameter name (a string)
|
||||
start = 1e-6 # starting value
|
||||
stop = 3e-6 # end value
|
||||
steps = 3 # number of values
|
||||
log_scale = False # 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']%8 != 0:
|
||||
pars['NS'] = int(round(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 == 'TAU':
|
||||
seconds = (sum(array)*2 + pars['RD'] * steps) * (pars['NS'] + pars['DS'])
|
||||
elif var_key == 'RD':
|
||||
seconds = (sum(array) + pars['TAU']*2 * steps) * (pars['NS'] + pars['DS'])
|
||||
else:
|
||||
seconds = (pars['TAU']*2 + 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 solidecho_experiment(pars, run)
|
||||
synchronize()
|
||||
else:
|
||||
# estimate the experiment time:
|
||||
seconds = (pars['TAU']*2 + 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 solidecho_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def solidecho_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'solidecho_experiment'
|
||||
|
||||
# phase lists [from Tecmag's pulse sequence]:
|
||||
pars['PH1'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # 1st 90-degree pulse
|
||||
pars['PH3'] = [90, 90, 270, 270, 0, 0, 180, 180] # 2nd 90-degree pulse
|
||||
pars['PH2'] = [ 0, 180, 0, 180, 90, 270, 90, 270] # receiver
|
||||
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
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(P90, value=TXEnableValue|TXPulseValue) # apply 2nd 90-degree pulse
|
||||
e.set_phase(PHA) # set phase for receiver
|
||||
e.wait(TAU-P90/2+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
|
||||
167
Scripts/Solid_Echo/op_solidecho_res.py
Normal file
167
Scripts/Solid_Echo/op_solidecho_res.py
Normal file
@ -0,0 +1,167 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # no filter applied otherwise
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# replace the sampling_rate attribute of the signal:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal by current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy of signal:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the signal's phase:
|
||||
phi0 = arctan2(echo.y[1][0], echo.y[0][0]) * 180 / pi
|
||||
if not locals().get('ref'): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate to maximize Re (optional):
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
echo.exp_window(line_broadening=10)
|
||||
spectrum = echo.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# try baseline correction:
|
||||
spectrum.baseline()
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
pass
|
||||
163
Scripts/Spin_Alignment/op_spinal_exp.py
Normal file
163
Scripts/Spin_Alignment/op_spinal_exp.py
Normal file
@ -0,0 +1,163 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # Jeener-Broekaert echo sequence (a.k.a. spin-alignment)
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 2.3e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -30e3 # offset from SF (Hz)
|
||||
pars['SW'] = 1e6 # spectral window (Hz)
|
||||
pars['SI'] = 1*512 # number of acquisition points
|
||||
pars['NS'] = 8 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 3 # delay between scans (s)
|
||||
pars['D1'] = 30e-6 # delay after first pulse, or tp (s)
|
||||
pars['D2'] = 100e-6 # delay after second pulse, or tm (s)
|
||||
pars['PHA'] = -36 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = 'D2' # variable parameter name (a string)
|
||||
start = 30e-6 # starting value
|
||||
stop = 2e-0 # 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']%8 != 0:
|
||||
pars['NS'] = int(round(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 == '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 spinal_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 spinal_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def spinal_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'spinal_experiment'
|
||||
|
||||
# 8-step phase cycle (1-14 modifided to deal with T1-recovery and extended for Re/Im imbalance)
|
||||
pars['PH1'] = [0, 270, 0, 270, 90, 90, 180, 180 ] # 1st (90-degree) pulse
|
||||
pars['PH3'] = [90,180, 90, 180, 180, 180, 90, 90 ] # 2nd (45-degree) pulse
|
||||
pars['PH4'] = [90, 90, 270, 270, 180, 0, 0, 180 ] # 3rd (45-degree) pulse
|
||||
pars['PH2'] = [0, 180, 180, 0, 90, 270, 90, 270 ] # receiver
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
P45 = pars['P90']*0.5
|
||||
P1 = pars['P90']*0.5
|
||||
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'
|
||||
e.set_phase(PH3)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P45, value=TXEnableValue|TXPulseValue) # 45-degree pulse
|
||||
|
||||
e.wait(D2-P45/2-TXEnableDelay) # 'long tau'
|
||||
e.set_phase(PH4)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 45-degree pulse
|
||||
|
||||
e.wait(TXEnableDelay)
|
||||
e.set_phase(PHA)
|
||||
e.wait(5e-6)#D1-P45/2-TXEnableDelay) # 'short tau'
|
||||
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
|
||||
210
Scripts/Spin_Alignment/op_spinal_res.py
Normal file
210
Scripts/Spin_Alignment/op_spinal_res.py
Normal file
@ -0,0 +1,210 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # no filter applied otherwise
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal according to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the initial phase of FID:
|
||||
phi0 = arctan2(echo.y[1][0], echo.y[0][0]) * 180 / pi
|
||||
if not 'ref' in locals(): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate FID to maximize y[0][0]:
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
echo.exp_window(line_broadening=10)
|
||||
spectrum = echo.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
|
||||
if var_key == 'D2':
|
||||
# KWW fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
[amplitude, rate, beta] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
print '%s%02g' % ('Beta = ', beta)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate, beta], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
beta = 1
|
||||
p0 = [amplitude, rate, beta]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*exp(-(p[1]*xdata)**p[2])
|
||||
|
||||
|
||||
pass
|
||||
163
Scripts/Spin_Alignment_Spin32/op_spinal32_exp.py
Normal file
163
Scripts/Spin_Alignment_Spin32/op_spinal32_exp.py
Normal file
@ -0,0 +1,163 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # Jeener-Broekaert echoes (a.k.a. spin-alignment) for spins-3/2
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 2.0e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 139.9e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -31e3 # offset from SF (Hz)
|
||||
pars['SW'] = 10e6 # spectral window (Hz)
|
||||
pars['SI'] = 4*1024 # number of acquisition points
|
||||
pars['NS'] = 32 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 25 # delay between scans (s)
|
||||
pars['D1'] = 30e-6 # delay after first pulse, or short tau (s)
|
||||
pars['D2'] = 10e-6 # delay after second pulse, or long tau (s)
|
||||
pars['PHA'] = 65 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Desktop/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = 'D2' # variable parameter name (a string)
|
||||
start = 10e-6 # starting value
|
||||
stop = 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']%8 != 0:
|
||||
pars['NS'] = int(round(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 == '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 spinal32_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 spinal32_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def spinal32_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'spinal32_experiment'
|
||||
|
||||
# phase cycle by F. Qi et al. [JMR 169 (2004) 225-239] with 3rd-phase invertion
|
||||
pars['PH1'] = [0, 180, 0, 180, 90, 270, 90, 270, 90, 270, 90, 270, 180, 0, 180, 0]
|
||||
pars['PH3'] = [90, 90, 270, 270, 0, 0, 180, 180, 180, 180, 0, 0, 90, 90, 270, 270]
|
||||
pars['PH4'] = [0, 0, 0, 0, 180, 180, 180, 180, 90, 90, 90, 90, 270, 270, 270, 270]
|
||||
pars['PH2'] = [180, 0, 0, 180, 180, 0, 0, 180, 270, 90, 90, 270, 270, 90, 90, 270]
|
||||
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
P45 = pars['P90']*0.5
|
||||
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 program:
|
||||
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'
|
||||
e.set_phase(PH3)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P45, value=TXEnableValue|TXPulseValue) # 45-degree pulse
|
||||
|
||||
e.wait(D2-P45/2-TXEnableDelay) # 'long tau'
|
||||
e.set_phase(PH4)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P45, value=TXEnableValue|TXPulseValue) # 45-degree pulse
|
||||
|
||||
e.wait(TXEnableDelay)
|
||||
e.set_phase(PHA)
|
||||
e.wait(D1-P45/2-TXEnableDelay) # 'short tau'
|
||||
e.record(SI, SW, sensitivity=ADCSensitivity) # acquisition
|
||||
|
||||
# write experiment parameters:
|
||||
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
|
||||
210
Scripts/Spin_Alignment_Spin32/op_spinal32_res.py
Normal file
210
Scripts/Spin_Alignment_Spin32/op_spinal32_res.py
Normal file
@ -0,0 +1,210 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # no filter applied otherwise
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal according to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the initial phase of FID:
|
||||
phi0 = arctan2(echo.y[1][0], echo.y[0][0]) * 180 / pi
|
||||
if not 'ref' in locals(): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate FID to maximize y[0][0]:
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
echo.exp_window(line_broadening=10)
|
||||
spectrum = echo.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
|
||||
if var_key == 'D2':
|
||||
# KWW fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
[amplitude, rate, beta] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
print '%s%02g' % ('Beta = ', beta)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate, beta], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
beta = 1
|
||||
p0 = [amplitude, rate, beta]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*exp(-(p[1]*xdata)**p[2])
|
||||
|
||||
|
||||
pass
|
||||
160
Scripts/Steady_Gradient_Spin_Echo/op_sgse_exp.py
Normal file
160
Scripts/Steady_Gradient_Spin_Echo/op_sgse_exp.py
Normal file
@ -0,0 +1,160 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # the diffusion editing sequence with stimulated echo
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['SW'] = 10e6 # spectral window (Hz)
|
||||
pars['SI'] = 1*1024 # number of acquisition points
|
||||
pars['NS'] = 8 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 3 # delay between scans (s)
|
||||
pars['D1'] = 20e-6 # delay after first pulse (short tau) (s)
|
||||
pars['D2'] = 100e-6 # delay after second pulse (long tau) (s)
|
||||
pars['PHA'] = -150 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # 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 = 4e-0 # 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 ste_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 ste_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
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) # 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'
|
||||
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'
|
||||
e.set_phase(PH4)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
|
||||
|
||||
e.set_phase(PHA)
|
||||
e.wait(D1-P90/2-TXEnableDelay) # 'short tau'
|
||||
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
|
||||
201
Scripts/Steady_Gradient_Spin_Echo/op_sgse_res.py
Normal file
201
Scripts/Steady_Gradient_Spin_Echo/op_sgse_res.py
Normal file
@ -0,0 +1,201 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = True
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal according to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the signal's phase:
|
||||
phi0 = arctan2(echo.y[1][0], echo.y[0][0]) * 180 / pi
|
||||
if not locals().get('ref'): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate the signal to maximize Re (optional):
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# specify noise level:
|
||||
if not locals().get('noise'):
|
||||
noise = 0.1*max(abs(echo.y[0]))
|
||||
samples = echo.y[0] > noise
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = echo.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(echo.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(echo.y[0][samples])
|
||||
|
||||
# provide the measurement result to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
if var_key == 'D2':
|
||||
# mono-exponential decay fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
[amplitude, rate] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T1 [s] = ', 1./rate)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
p0 = [amplitude, rate]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*exp(-p[1]*xdata)
|
||||
|
||||
pass
|
||||
@ -0,0 +1,177 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # the diffusion editing sequence with stimulated echo and CPMG detection
|
||||
|
||||
# set up acqusition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['NS'] = 16 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 3 # delay between scans (s)
|
||||
pars['D1'] = 20e-6 # delay after first STE pulse (s)
|
||||
pars['D2'] = 100e-6 # delay after second STE pulse (s)
|
||||
pars['NECH'] = 16 # number of 180-degree pulses in the CPMG train
|
||||
pars['TAU'] = 40e-6 # half pulse period in the CPMG train (s)
|
||||
pars['PHA'] = -127 # 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 = 4e-3 # 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!!!")
|
||||
|
||||
# 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']
|
||||
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-P90/2-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-P90/2-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-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) # pre-acquisition delay
|
||||
e.record(SI, SW, timelength=AQ, sensitivity=ADCSensitivity) # acquire echo samples
|
||||
e.wait(TAU-(P180+TXEnableDelay+AQ)/2) # 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
|
||||
@ -0,0 +1,185 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# rotate timesignal acording to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# get number of echoes:
|
||||
num_echoes = pars['NECH']
|
||||
|
||||
# downsize accu to one point per echo:
|
||||
echodecay = accu + 0
|
||||
echodecay.x = resize(echodecay.x, int(num_echoes))
|
||||
echodecay.y[0] = resize(echodecay.y[0], int(num_echoes))
|
||||
echodecay.y[1] = resize(echodecay.y[1], int(num_echoes))
|
||||
|
||||
# find where first echo exceeds noise:
|
||||
# if not locals().get('noise'):
|
||||
# last_echo = accu.get_accu_by_index(num_echoes-1)
|
||||
# first_echo = accu.get_accu_by_index(0)
|
||||
# noise = 3*std(last_echo.y[1][:])
|
||||
# samples = first_echo.y[0] > noise
|
||||
|
||||
if not locals().get('noise'):
|
||||
echo = accu.get_accu_by_index(0)
|
||||
noise = 0.1*max(abs(echo.y[0]))
|
||||
samples = abs(echo.y[0]) > noise
|
||||
|
||||
# set echo times and intensities:
|
||||
for i in range(num_echoes):
|
||||
# get ith echo:
|
||||
echo = accu.get_accu_by_index(i)
|
||||
# set echo time:
|
||||
echodecay.x[i] = i*2*pars['TAU']
|
||||
# set echo value:
|
||||
echodecay.y[0][i] = sum(echo.y[0][samples]) # the sum of echo points that exceed noise...
|
||||
echodecay.y[1][i] = sum(echo.y[1][samples])
|
||||
#echodecay.y[0][i] = sum(echo.y[0]) # or the sum of all echo points...
|
||||
#echodecay.y[1][i] = sum(echo.y[1])
|
||||
#echodecay.y[0][i] = echo.y[0][echo.x.size/2] # or a middle echo point
|
||||
#echodecay.y[1][i] = echo.y[1][echo.x.size/2]
|
||||
|
||||
# compute a signal's phase:
|
||||
phi0 = arctan2(echodecay.y[1][0], echodecay.y[0][0]) * 180 / pi
|
||||
if not locals().get('ref'): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate signal to maximize Re (optional):
|
||||
#echodecay.phase(-phi0)
|
||||
|
||||
# provide echo decay to the display tab:
|
||||
data['Echo Decay'] = echodecay
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with different var_value's to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
data['Echo Decay'+"/"+var_key+"=%e"%(var_value)] = echodecay
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
# [amplitude, rate] = fitfunc(echodecay.x, echodecay.y[0])
|
||||
# print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
# print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
|
||||
# measurand[var_value] = amplitude
|
||||
measurement[var_value] = sum(echodecay.y[0][:])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
if var_key == 'D2':
|
||||
# mono-exponential decay fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
[amplitude, rate] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
print amplitude, 1./rate
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
p0 = [amplitude, rate]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*exp(-p[1]*xdata)
|
||||
|
||||
pass
|
||||
165
Scripts/Stimulated_Echo/op_ste_exp.py
Normal file
165
Scripts/Stimulated_Echo/op_ste_exp.py
Normal file
@ -0,0 +1,165 @@
|
||||
# -*- 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(): # stimulated echo experiment
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -87e3 # offset from SF (Hz)
|
||||
pars['SW'] = 500e3 # spectrum width (Hz)
|
||||
pars['SI'] = 1*1024 # number of acquisition points
|
||||
pars['NS'] = 16 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 1 # delay between scans (s)
|
||||
pars['D1'] = 100e-6 # delay after first pulse (short tau) (s)
|
||||
pars['D2'] = 100e-6 # delay after second pulse (long tau) (s)
|
||||
pars['D4'] = 0e-6 # echo pre-acquisition delay (s)
|
||||
pars['PHA'] = 30 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = None # variable parameter name (a string)
|
||||
start = 50e-6 # starting value
|
||||
stop = 3e-3 # end value
|
||||
steps = 10 # number of values
|
||||
log_scale = False # 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:
|
||||
|
||||
# check if a variable parameter is named:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
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 ste_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 ste_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
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']
|
||||
D4 = pars['D4']
|
||||
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) # 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'
|
||||
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'
|
||||
e.set_phase(PH4)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
|
||||
|
||||
e.set_phase(PHA)
|
||||
e.wait(D1-P90/2-TXEnableDelay+D4) # 'short tau'
|
||||
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
|
||||
209
Scripts/Stimulated_Echo/op_ste_res.py
Normal file
209
Scripts/Stimulated_Echo/op_ste_res.py
Normal file
@ -0,0 +1,209 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# phase timesignal according to current rec_phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the initial phase of the signal:
|
||||
phi0 = arctan2(accu.y[1][0], accu.y[0][0]) * 180 / pi
|
||||
if not locals().get('ref'): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate the signal to maximize Re (optional):
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
echo.exp_window(line_broadening=10)
|
||||
spectrum = echo.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
if var_key == 'D2':
|
||||
# mono-exponential decay fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
[amplitude, rate, offset] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T1 [s] = ', 1./rate)
|
||||
print '%s%02g' % ('Offset = ', offset)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate, offset], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
offset = min(ydata)
|
||||
p0 = [amplitude, rate, offset]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*exp(-p[1]*xdata) + p[2]
|
||||
|
||||
|
||||
pass
|
||||
169
Scripts/T1Q/op_t1q_exp.py
Normal file
169
Scripts/T1Q/op_t1q_exp.py
Normal file
@ -0,0 +1,169 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # Jeener-Broekaert sequence with solid-echo detection to measure T1Q [JMR 43, 213 (1981)].
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 2.3e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = 5.6e3 # offset from SF (Hz)
|
||||
pars['SW'] = 200e3 # spectrum width (Hz)
|
||||
pars['SI'] = 1*256 # number of acquisition points
|
||||
pars['NS'] = 32 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = .5 # delay between scans (s)
|
||||
pars['D1'] = 30e-6 # delay after first pulse or 'short tau' (s)
|
||||
pars['D2'] = 30e-6 # delay after second pulse or 'long tau' (s)
|
||||
pars['PHA'] = -27 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter (optional):
|
||||
pars['VAR_PAR'] = 'D2' # variable parameter name (a string)
|
||||
start = 30e-6 # starting value
|
||||
stop = 2e-0 # end value
|
||||
steps = 16 # 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']%8 != 0:
|
||||
pars['NS'] = int(round(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 == '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 t1q_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 t1q_experiment(pars, run)
|
||||
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def t1q_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 't1q_experiment'
|
||||
|
||||
# phase cycle from J. Magn. Reson. 43, 213-223 (1981) extended for 90-deg refocusing pulse which also eliminates echo(es) after 3rd 45-deg pulse:
|
||||
pars['PH1'] = [0, 0, 90, 90, 180, 180, 270, 270] # 90-deg pulse
|
||||
pars['PH3'] = [90, 90, 180, 180, 270, 270, 0, 0] # 1st 45-deg pulse
|
||||
pars['PH4'] = [0, 180, 0, 180, 180, 0, 180, 0] # 2nd 45-deg pulse
|
||||
pars['PH5'] = [0, 0, 180, 180, 270, 90, 90, 270] # refocucing 90-deg pulse
|
||||
pars['PH2'] = [0, 180, 0, 180, 180, 0, 180, 0] # receiver
|
||||
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
P45 = pars['P90']*0.5
|
||||
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'])]
|
||||
PH5 = pars['PH5'][run%len(pars['PH5'])]
|
||||
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)
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
|
||||
|
||||
e.wait(D1-P90/2-TXEnableDelay) # 'short tau'
|
||||
e.set_phase(PH3)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P45, value=TXEnableValue|TXPulseValue) # 45-degree pulse
|
||||
|
||||
e.wait(D2-P45/2-TXEnableDelay) # 'long tau'
|
||||
e.set_phase(PH4)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P45, value=TXEnableValue|TXPulseValue) # 45-degree pulse
|
||||
|
||||
e.wait(10e-6-TXEnableDelay)
|
||||
e.set_phase(PH5)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
|
||||
|
||||
e.set_phase(PHA)
|
||||
e.wait(13e-6)
|
||||
e.record(SI, SW, sensitivity=ADCSensitivity) # acquisition
|
||||
|
||||
# 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
|
||||
209
Scripts/T1Q/op_t1q_res.py
Normal file
209
Scripts/T1Q/op_t1q_res.py
Normal file
@ -0,0 +1,209 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from scipy.fftpack import rfft
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# phase timesignal according to current rec_phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
fid = accu + 0
|
||||
|
||||
# compute the signal's phase:
|
||||
phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
|
||||
if not 'ref' in locals(): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# do FFT:
|
||||
fid.exp_window(line_broadening=10)
|
||||
spectrum = fid.fft(samples=2*pars['SI'])
|
||||
spectrum.baseline()
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get ('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with the var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
signal = (accu + 0).y[1]
|
||||
|
||||
# -*- discrete cosine transform of Im -*-
|
||||
N = len(signal)
|
||||
y = empty(2*N, float)
|
||||
y[:N] = signal[:]
|
||||
y[N:] = signal[::-1]
|
||||
c = rfft(y)
|
||||
phi = exp(-1j*pi*arange(N)/(2*N))
|
||||
dct = real(phi*c[:N])
|
||||
# ---------------------------------------
|
||||
measurement[var_value] = sum(dct[0:9])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
if var_key == 'D2':
|
||||
# mono-exponential decay fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
|
||||
[amplitude, rate, offset] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T1Q [s] = ', 1./rate)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate, offset], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
offset = min(ydata)
|
||||
p0 = [amplitude, rate, offset]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*exp(-p[1]*xdata)+p[2]
|
||||
|
||||
|
||||
pass
|
||||
172
Scripts/ZZ_Exchange_with_T2_Selection/op_t2zz_exp.py
Normal file
172
Scripts/ZZ_Exchange_with_T2_Selection/op_t2zz_exp.py
Normal file
@ -0,0 +1,172 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # ZZ-exchange with T2-selection
|
||||
|
||||
# set up acqusition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['SW'] = 200e3 # spectral width (Hz)
|
||||
pars['SI'] = 128 # acquisition points
|
||||
pars['D1'] = 10e-6 # echo delay (s)
|
||||
pars['D2'] = 100e-6 # z-storage duration (s)
|
||||
pars['NS'] = 16 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = 3 # delay between scans (s)
|
||||
pars['DEAD1'] = 5e-6 # receiver dead time (s)
|
||||
pars['PHA'] = 0 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # data directory
|
||||
pars['OUTFILE'] = None # output file name
|
||||
|
||||
# specify a variable parameter:
|
||||
pars['VAR_PAR'] = 'D2' # variable parameter name
|
||||
start = 20e-6 # first value
|
||||
stop = 1e-3 # last value
|
||||
steps = 20 # 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!!!")
|
||||
|
||||
if pars['NS']%16 != 0:
|
||||
pars['NS'] = (pars['NS'] / 16 + 1) * 16
|
||||
print 'Number of scans changed to', pars['NS'], 'due to phase cycling'
|
||||
|
||||
# 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']%8 != 0:
|
||||
pars['NS'] = int(round(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 == '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 t2zz_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 t2zz_experiment(pars, run)
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def t2zz_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 't2zz_experiment'
|
||||
|
||||
# eliminates T1 recovery and contaminating echo signals:
|
||||
pars['PH1'] = [0, 180, 90, 270, 180, 0, 270, 90, 180, 0, 270, 90, 0, 180, 90, 270]
|
||||
pars['PH3'] = [90, 90, 180, 180, 270, 270, 0, 0, 270, 270, 0, 0, 90, 90, 180, 180]
|
||||
pars['PH4'] = [0, 0, 90, 90, 180, 180, 270, 270, 180, 180, 270, 270, 0, 0, 90, 90]
|
||||
pars['PH5'] = [0, 0, 90, 90, 180, 180, 270, 270, 0, 0, 90, 90, 180, 180, 270, 270]
|
||||
pars['PH2'] = [0, 180, 90, 270, 180, 0, 270, 90, 0, 180, 90, 270, 180, 0, 270, 90] # data routing
|
||||
|
||||
# read in variables:
|
||||
P90 = pars['P90']
|
||||
SF = pars['SF']
|
||||
O1 = pars['O1']
|
||||
RD = pars['RD']
|
||||
DEAD1 = pars['DEAD1']
|
||||
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'])]
|
||||
PH5 = pars['PH5'][run%len(pars['PH5'])]
|
||||
PH2 = pars['PH2'][run%len(pars['PH2'])]
|
||||
PHA = pars['PHA']
|
||||
|
||||
# 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)
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 1st pulse
|
||||
|
||||
e.wait(D1-P90/2-TXEnableDelay) # echo delay
|
||||
e.set_phase(PH3)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 2nd pulse (90- or 180-degree)
|
||||
|
||||
e.wait(D1-P90/2-TXEnableDelay) # echo delay
|
||||
e.set_phase(PH4)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 3rd pulse (z-storage pulse)
|
||||
|
||||
e.wait(D2-P90/2-TXEnableDelay) # mixing time
|
||||
e.set_phase(PH5)
|
||||
|
||||
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 4th pulse (readout pulse)
|
||||
|
||||
e.set_phase(PHA) # set phase for receiver
|
||||
e.wait(DEAD1) # wait for coil ringdown
|
||||
e.record(SI, SW, 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
|
||||
173
Scripts/ZZ_Exchange_with_T2_Selection/op_t2zz_res.py
Normal file
173
Scripts/ZZ_Exchange_with_T2_Selection/op_t2zz_res.py
Normal file
@ -0,0 +1,173 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# sort timesignal data (data routing):
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
# print 'job id: ', accu.get_job_id()
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu#(accu+0).magnitude()
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == 1 and pars.has_key('COMMENT'):
|
||||
print pars['COMMENT']
|
||||
|
||||
if accu.n == pars['NS']: # accumulatioin is complete
|
||||
|
||||
# correct accu's baselines:
|
||||
accu.baseline(last_part=0.2)
|
||||
|
||||
# make a copy to process:
|
||||
fid = accu + 0
|
||||
|
||||
# compute the initial phase of FID:
|
||||
phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
|
||||
if not 'ref' in locals(): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate FID to maximize y[0][0]:
|
||||
#fid.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
fid.exp_window(line_broadening=10)
|
||||
spectrum = fid.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
pass
|
||||
159
Scripts/Zeeman_Order/op_zeeman_exp.py
Normal file
159
Scripts/Zeeman_Order/op_zeeman_exp.py
Normal file
@ -0,0 +1,159 @@
|
||||
# -*- 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 = 2 # voltage span for ADC
|
||||
|
||||
def experiment(): # Three-pulse STE sequence (Zeeman order)
|
||||
|
||||
# set up acquisition parameters:
|
||||
pars = {}
|
||||
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
|
||||
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
|
||||
pars['O1'] = -60e3 # offset from SF (Hz)
|
||||
pars['SW'] = 1e6 # spectral window (Hz)
|
||||
pars['SI'] = 1*1024 # number of acquisition points
|
||||
pars['NS'] = 8 # number of scans
|
||||
pars['DS'] = 0 # number of dummy scans
|
||||
pars['RD'] = .5 # delay between scans (s)
|
||||
pars['D1'] = 20e-6 # delay after first pulse, or 'short tau' (s)
|
||||
pars['D2'] = 100e-6 # delay after second pulse, or 'long tau' (s)
|
||||
pars['PHA'] = 30 # receiver phase (degree)
|
||||
pars['DATADIR'] = '/home/fprak/Students/' # 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 = 5e-0 # 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']%8 != 0:
|
||||
pars['NS'] = int(round(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 == '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 zeeman_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 zeeman_experiment(pars, run)
|
||||
|
||||
# the pulse program:
|
||||
|
||||
def zeeman_experiment(pars, run):
|
||||
e=Experiment()
|
||||
|
||||
dummy_scans = pars.get('DS')
|
||||
if dummy_scans:
|
||||
run -= dummy_scans
|
||||
|
||||
pars['PROG'] = 'zeeman_experiment'
|
||||
|
||||
# 8-step phase cycle (1-21 modifided to deal with T1-recovery and extended for Re/Im imbalance)
|
||||
pars['PH1'] = [0, 270, 0, 270, 180, 90, 180, 90] # 1st (90-degree) pulse
|
||||
pars['PH3'] = [0, 90, 0, 90, 0, 90, 0, 90] # 2nd (90-degree) pulse
|
||||
pars['PH4'] = [0, 0, 180, 180, 270, 270, 90, 90] # 3rd (90-degree) pulse
|
||||
pars['PH2'] = [0, 180, 180, 0, 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'
|
||||
|
||||
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'
|
||||
|
||||
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'
|
||||
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
|
||||
210
Scripts/Zeeman_Order/op_zeeman_res.py
Normal file
210
Scripts/Zeeman_Order/op_zeeman_res.py
Normal file
@ -0,0 +1,210 @@
|
||||
# -*- coding: iso-8859-1 -*-
|
||||
|
||||
from numpy import *
|
||||
from scipy.signal import *
|
||||
from scipy.optimize import *
|
||||
from os import path, rename
|
||||
|
||||
def result():
|
||||
|
||||
measurement = MeasurementResult('Magnetization')
|
||||
|
||||
measurement_range = [0.0, 10e-6]
|
||||
measurement_ranging = False
|
||||
|
||||
suffix = '' # output file name's suffix and...
|
||||
counter = 1 # counter for arrayed experiments
|
||||
var_key = '' # variable parameter name
|
||||
|
||||
# loop over the incoming results:
|
||||
for timesignal in results:
|
||||
if not isinstance(timesignal,ADC_Result):
|
||||
continue
|
||||
|
||||
# read experiment parameters:
|
||||
pars = timesignal.get_description_dictionary()
|
||||
|
||||
# ---------------- digital filter ------------------
|
||||
|
||||
# get actual sampling rate of timesignal:
|
||||
sampling_rate = timesignal.get_sampling_rate()
|
||||
|
||||
# get user-defined spectrum width:
|
||||
spec_width = pars['SW']
|
||||
|
||||
# specify cutoff frequency, in relative units:
|
||||
cutoff = spec_width / sampling_rate
|
||||
|
||||
if cutoff < 1: # otherwise no filter applied
|
||||
|
||||
# number of filter's coefficients:
|
||||
numtaps = 29
|
||||
|
||||
# use firwin to create a lowpass FIR filter:
|
||||
fir_coeff = firwin(numtaps, cutoff)
|
||||
|
||||
# downsize x according to user-defined spectral window:
|
||||
skip = int(sampling_rate / spec_width)
|
||||
timesignal.x = timesignal.x[::skip]
|
||||
|
||||
for i in range(2):
|
||||
# apply the filter to ith channel:
|
||||
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
|
||||
|
||||
# zeroize first N-1 "corrupted" samples:
|
||||
timesignal.y[i][:numtaps-1] = 0.0
|
||||
|
||||
# circular left shift of y:
|
||||
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
|
||||
|
||||
# downsize y to user-defined number of samples (SI):
|
||||
timesignal.y[i] = timesignal.y[i][::skip]
|
||||
|
||||
# update the sampling_rate attribute of the signal's:
|
||||
timesignal.set_sampling_rate(spec_width)
|
||||
|
||||
# ----------------------------------------------------
|
||||
|
||||
# rotate timesignal according to current receiver's phase:
|
||||
timesignal.phase(pars['rec_phase'])
|
||||
|
||||
# provide timesignal to the display tab:
|
||||
data['Current scan'] = timesignal
|
||||
|
||||
# accumulate...
|
||||
if not locals().get('accu'):
|
||||
accu = Accumulation()
|
||||
|
||||
# skip dummy scans, if any:
|
||||
if pars['run'] < 0: continue
|
||||
|
||||
# add up:
|
||||
accu += timesignal
|
||||
|
||||
# provide accumulation to the display tab:
|
||||
data['Accumulation'] = accu
|
||||
|
||||
# check how many scans are done:
|
||||
if accu.n == pars['NS']: # accumulation is complete
|
||||
|
||||
# make a copy:
|
||||
echo = accu + 0
|
||||
|
||||
# compute the initial phase of FID:
|
||||
phi0 = arctan2(echo.y[1][0], echo.y[0][0]) * 180 / pi
|
||||
if not 'ref' in locals(): ref = phi0
|
||||
print 'phi0 = ', phi0
|
||||
|
||||
# rotate FID to maximize y[0][0]:
|
||||
#echo.phase(-phi0)
|
||||
|
||||
# do FFT:
|
||||
echo.exp_window(line_broadening=10)
|
||||
spectrum = echo.fft(samples=2*pars['SI'])
|
||||
|
||||
# try zero-order phase correction:
|
||||
spectrum.phase(-phi0)
|
||||
|
||||
# provide spectrum to the display tab:
|
||||
data['Spectrum'] = spectrum
|
||||
|
||||
# check whether it is an arrayed experiment:
|
||||
var_key = pars.get('VAR_PAR')
|
||||
if var_key:
|
||||
# get variable parameter's value:
|
||||
var_value = pars.get(var_key)
|
||||
|
||||
# provide signal recorded with this var_value to the display tab:
|
||||
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
|
||||
|
||||
# measure signal intensity vs. var_value:
|
||||
if measurement_ranging == True:
|
||||
[start, stop] = accu.get_sampling_rate() * array(measurement_range)
|
||||
measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
|
||||
|
||||
else:
|
||||
measurement[var_value] = sum(accu.y[0][0:31])
|
||||
|
||||
# provide measurement to the display tab:
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# update the file name suffix:
|
||||
suffix = '_' + str(counter)
|
||||
counter += 1
|
||||
|
||||
# save accu if required:
|
||||
outfile = pars.get('OUTFILE')
|
||||
if outfile:
|
||||
datadir = pars.get('DATADIR')
|
||||
|
||||
# write raw data in Simpson format:
|
||||
filename = datadir+outfile+suffix+'.dat'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.dat')
|
||||
accu.write_to_simpson(filename)
|
||||
|
||||
# write raw data in Tecmag format:
|
||||
# filename = datadir+outfile+'.tnt'
|
||||
# accu.write_to_tecmag(filename, nrecords=20)
|
||||
|
||||
# write parameters in a text file:
|
||||
filename = datadir+outfile+suffix+'.par'
|
||||
if path.exists(filename):
|
||||
rename(filename, datadir+'~'+outfile+suffix+'.par')
|
||||
|
||||
fileobject = open(filename, 'w')
|
||||
for key in sorted(pars.iterkeys()):
|
||||
if key=='run': continue
|
||||
if key=='rec_phase': continue
|
||||
fileobject.write('%s%s%s'%(key,'=', pars[key]))
|
||||
fileobject.write('\n')
|
||||
fileobject.close()
|
||||
|
||||
# reset accumulation:
|
||||
del accu
|
||||
|
||||
|
||||
if var_key == 'D2':
|
||||
# KWW fit:
|
||||
xdata = measurement.get_xdata()
|
||||
ydata = measurement.get_ydata()
|
||||
[amplitude, rate, beta] = fitfunc(xdata, ydata)
|
||||
print '%s%02g' % ('Amplitude = ', amplitude)
|
||||
print '%s%02g' % ('T2 [s] = ', 1./rate)
|
||||
print '%s%02g' % ('Beta = ', beta)
|
||||
|
||||
# update display for the fit:
|
||||
measurement.y = func([amplitude, rate, beta], xdata)
|
||||
data[measurement.get_title()] = measurement
|
||||
|
||||
# the fitting procedure:
|
||||
def fitfunc(xdata, ydata):
|
||||
|
||||
# initialize variable parameters:
|
||||
try:
|
||||
# solve Az = b:
|
||||
A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
|
||||
b = log(abs(ydata[0:xdata.size/2]))
|
||||
z = linalg.lstsq(transpose(A), b)
|
||||
amplitude = exp(z[0][0])
|
||||
rate = -z[0][1]
|
||||
except:
|
||||
amplitude = abs(ydata[0])
|
||||
rate = 1./(xdata[-1] - xdata[0])
|
||||
beta = 1
|
||||
p0 = [amplitude, rate, beta]
|
||||
|
||||
# run least-squares optimization:
|
||||
plsq = leastsq(residuals, p0, args=(xdata, ydata))
|
||||
|
||||
return plsq[0] # best-fit parameters
|
||||
|
||||
def residuals(p, xdata, ydata):
|
||||
return ydata - func(p, xdata)
|
||||
|
||||
# here is the function to fit:
|
||||
def func(p, xdata):
|
||||
return p[0]*exp(-(p[1]*xdata)**p[2])
|
||||
|
||||
|
||||
pass
|
||||
BIN
The DAMARIS Script Library.pdf
Normal file
BIN
The DAMARIS Script Library.pdf
Normal file
Binary file not shown.
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Reference in New Issue
Block a user