initial check-in
This commit is contained in:
Markus Rosenstihl
156
Scripts/CPMG/op_cpmg_exp.py
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156
Scripts/CPMG/op_cpmg_exp.py
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# -*- coding: iso-8859-1 -*-
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TXEnableDelay = 2e-6
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TXEnableValue = 0b0001 # TTL line blanking RF amplifier (bit 0)
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TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1)
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ADCSensitivity = 2 # voltage span for ADC
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def experiment(): # Carr-Purcell-Meiboom-Gill (CPMG) experiment
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
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pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
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pars['O1'] = -60e3 # offset from SF (Hz)
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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'] = 3 # delay between scans (s)
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pars['NECH'] = 16 # number of 180-degree pulses
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pars['TAU'] = 40e-6 # half pulse period (s)
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pars['PHA'] = -127 # 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 = 40e-6 # starting value
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stop = 100e-6 # end value
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steps = 10 # 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']%4 != 0:
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pars['NS'] = int(round(pars['NS'] / 4) + 1) * 4
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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 experiment time:
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if var_key == 'TAU':
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seconds = (sum(array)* 2* pars['NECH'] + pars['RD'] * steps) * (pars['NS'] + pars['DS'])
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elif var_key == 'NECH':
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seconds = (pars['TAU']* 2* sum(array) + pars['RD'] * steps) * (pars['NS'] + pars['DS'])
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elif var_key == 'RD':
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seconds = (pars['TAU']* 2* pars['NECH'] + sum(array)) * (pars['NS'] + pars['DS'])
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else:
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seconds = (pars['TAU']* 2* pars['NECH'] + pars['RD']) * steps * (pars['NS']+ pars['DS'])
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m, s = divmod(seconds, 60)
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h, m = divmod(m, 60)
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print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
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# loop for a variable parameter:
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for index, pars[var_key] in enumerate(array):
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print 'Arrayed experiment for '+var_key+': run = '+str(index+1)+\
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' out of '+str(array.size)+': value = '+str(pars[var_key])
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# loop for accumulation:
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for run in xrange(pars['NS']+pars['DS']):
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yield cpmg_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['NECH'] + 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 cpmg_experiment(pars, run)
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# the pulse program:
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def cpmg_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'] = 'cpmg_experiment'
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# phase lists:
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pars['PH1'] = [0, 180, 90, 270] # 90-degree pulse
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pars['PH3'] = [90, 90, 180, 180] # 180-degree pulse
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pars['PH2'] = [0, 180, 90, 270] # receiver
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# read in variables:
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P90 = pars['P90']
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P180 = pars['P90']*2
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SF = pars['SF']
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O1 = pars['O1']
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RD = pars['RD']
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NECH = pars['NECH']
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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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PH2 = pars['PH2'][run%len(pars['PH2'])]
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PHA = pars['PHA']
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# set sampling parameters:
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SI = 128 # number of samples
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SW = 20e6 # sampling rate
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AQ = (SI+6)/SW # acquisition window
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if TAU < (P90+P180)/2+TXEnableDelay or TAU < (P180+TXEnableDelay+AQ)/2:
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raise Exception('pulse period is too short!')
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if 2*TAU < P180+TXEnableDelay+SI/SW:
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raise Exception('pulse period too short!')
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# run the pulse sequence:
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e.wait(RD) # delay between scans
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e.set_frequency(SF+O1, phase=PH1) # set frequency and phase for 90-degree pulse
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
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e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
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e.wait(TAU-P90/2-P180/2-TXEnableDelay) # wait for tau
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e.set_phase(PH3) # change phase for 180-degree pulse
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e.loop_start(NECH) # ----- loop for echoes: -----
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
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e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply 180-degree pulse
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e.set_phase(PHA) # set phase for receiver
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e.wait(TAU-(P180+TXEnableDelay+AQ)/2) # pre-acquisition delay
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e.record(SI, SW, timelength=AQ, sensitivity=ADCSensitivity) # acquire echo samples
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e.wait(TAU-(P180+TXEnableDelay+AQ)/2) # post-acquisition delay
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e.set_phase(PH3) # set phase for theta-degree pulse
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e.loop_end() # ----------------------------
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# write experiment parameters:
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for key in pars.keys():
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e.set_description(key, pars[key]) # acquisition parameters
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e.set_description('run', run) # current scan
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e.set_description('rec_phase', -PH2) # current data route
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return e
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176
Scripts/CPMG/op_cpmg_res.py
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176
Scripts/CPMG/op_cpmg_res.py
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# -*- coding: iso-8859-1 -*-
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from numpy import *
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from scipy.signal import *
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from scipy.optimize import *
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from os import path, rename
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def result():
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measurement = MeasurementResult('Magnetization')
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suffix = '' # output file name's suffix and...
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counter = 1 # counter for arrayed experiments
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# loop over the incoming results:
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for timesignal in results:
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if not isinstance(timesignal,ADC_Result):
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continue
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# read experiment parameters:
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pars = timesignal.get_description_dictionary()
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# rotate timesignal by current receiver's phase:
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timesignal.phase(pars['rec_phase'])
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# provide timesignal to the display tab:
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data['Current scan'] = timesignal
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# accumulate...
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if not locals().get('accu'):
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accu = Accumulation()
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# skip dummy scans, if any:
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if pars['run'] < 0: continue
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# add up:
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accu += timesignal
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# provide accumulation to the display tab:
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data['Accumulation'] = accu
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# check how many scans are done:
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if accu.n == pars['NS']: # accumulation is complete
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# get number of echoes:
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num_echoes = pars['NECH']
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# downsize accu to one point per echo:
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echodecay = accu + 0
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echodecay.x = resize(echodecay.x, int(num_echoes))
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echodecay.y[0] = resize(echodecay.y[0], int(num_echoes))
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echodecay.y[1] = resize(echodecay.y[1], int(num_echoes))
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# specify noise level:
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if not locals().get('noise'):
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echo = accu.get_accu_by_index(0)
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noise = 0.1*max(abs(echo.y[0]))
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samples = abs(echo.y[0]) > noise
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# set echo times and intensities:
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for i in range(num_echoes):
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# get ith echo:
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echo = accu.get_accu_by_index(i)
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# set echo timing:
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echodecay.x[i] = i*2*pars['TAU']
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# set echo value:
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echodecay.y[0][i] = sum(echo.y[0][samples]) # the sum of echo points that exeed noise
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echodecay.y[1][i] = sum(echo.y[1][samples])
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#echodecay.y[0][i] = sum(echo.y[0]) # the sum of all echo points
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#echodecay.y[1][i] = sum(echo.y[1])
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#echodecay.y[0][i] = echo.y[0][echo.x.size/2] # a middle echo point
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#echodecay.y[1][i] = echo.y[1][echo.x.size/2]
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# compute a signal's phase:
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phi0 = arctan2(echodecay.y[1][0], echodecay.y[0][0]) * 180 / pi
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if not locals().get('ref'): ref = phi0
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print 'phi0 = ', phi0
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# rotate signal to maximize Re (optional):
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#echodecay.phase(-phi0)
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# provide echo decay to the display tab:
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data['Echo Decay'] = echodecay
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# fit a mono-exponential function to the echo decay:
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[amplitude, rate] = fitfunc(echodecay.x, echodecay.y[0])
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print '%s%02g' % ('Amplitude = ', amplitude)
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print '%s%02g' % ('T2 [s] = ', 1./rate)
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# provide the fit to the display tab:
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fit = MeasurementResult('Mono-Exponential Fit')
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for i, key in enumerate(echodecay.x):
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fit[key] = echodecay.y[0][i]
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fit.y = func([amplitude, rate], echodecay.x)
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data[fit.get_title()] = fit
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# check whether it is an arrayed experiment:
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var_key = pars.get('VAR_PAR')
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if var_key:
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# get variable parameter's value:
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var_value = pars.get(var_key)
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# provide data recorded with different var_value's to the display tab:
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data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
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data['Echo Decay'+"/"+var_key+"=%e"%(var_value)] = echodecay
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data[fit.get_title()+"/"+var_key+"=%e"%(var_value)] = fit
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# measure a signal parameter vs. var_value:
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measurement[var_value] = amplitude
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#measurement[var_value] = sum(echodecay.y[0][:])
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#measurement[var_value] = 1./rate
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# provide measurement to the display tab:
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data[measurement.get_title()] = measurement
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# save accu if required:
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outfile = pars.get('OUTFILE')
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if outfile:
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datadir = pars.get('DATADIR')
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# write data in Simpson format:
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filename = datadir+outfile+suffix+'.dat'
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if path.exists(filename):
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rename(filename, datadir+'~'+outfile+suffix+'.dat')
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accu.write_to_simpson(filename)
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# write data in Tecmag format:
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# filename = datadir+outfile+'.tnt'
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# accu.write_to_tecmag(filename, nrecords=20)
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# write parameters in a text file:
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filename = datadir+outfile+suffix+'.par'
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if path.exists(filename):
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rename(filename, datadir+'~'+outfile+suffix+'.par')
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fileobject = open(filename, 'w')
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for key in sorted(pars.iterkeys()):
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if key=='run': continue
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if key=='rec_phase': continue
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fileobject.write('%s%s%s'%(key,'=', pars[key]))
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fileobject.write('\n')
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fileobject.close()
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# reset accumulation:
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del accu
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# the fitting procedure:
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def fitfunc(xdata, ydata):
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# initialize variable parameters:
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try:
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# solve Az = b:
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A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
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b = log(abs(ydata[0:xdata.size/2]))
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z = linalg.lstsq(transpose(A), b)
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amplitude = exp(z[0][0])
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rate = -z[0][1]
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except:
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amplitude = abs(ydata[0])
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rate = 1./(xdata[-1] - xdata[0])
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p0 = [amplitude, rate]
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# run least-squares optimization:
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plsq = leastsq(residuals, p0, args=(xdata, ydata))
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return plsq[0] # best-fit parameters
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def residuals(p, xdata, ydata):
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return ydata - func(p, xdata)
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# here is the function to fit:
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def func(p, xdata):
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return p[0]*exp(-p[1]*xdata)
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pass
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