New experimetns added
This commit is contained in:
Oleg Petrov
parent
58f9ee63f6
commit
d9beb94422
176
Scripts/EXSY/op_noesy_exp.py
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176
Scripts/EXSY/op_noesy_exp.py
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# -*- coding: iso-8859-1 -*-
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TXEnableDelay = 2e-6
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TXEnableValue = 0b0001 # TTL line enabling RF amplifier (bit 0)
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TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1)
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ADCSensitivity = 2 # voltage span for ADC
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def experiment(): # 2D NOESY experiment, using States-TPPI technique for quadrature detection in F1
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# States-TPPI technique achieves two effects for an indirect dimension F1:
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# (1) signal frequency discrimination and (2) displacement of the unmodulated
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# artefact signal from an inconvenient location in the middle of spectrum to the edge.
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# (1) is achieved by recording two data sets at each t1 point - with orthogonal phases
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# of the preparation pulse and same receiver phase - and storing them in separate memory
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# locations. These two fid measurements yield one complex data point in F1.
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# (2) by inverting phase of the preparation pulse and the receiver each time when t1 is
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# incremented (that is for subsequent complex points). Therefore, the artefact signal
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# becomes modulated at the Nyquist frequency and appears in the spectrum at F1=±SW/2 Hz
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# instead of 0 Hz, where SW is spectral width. [http://nmrwiki.org]
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# set up acqusition parameters:
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pars = {}
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pars['P90'] = 1.65e-6 # 90-degree pulse length (s)
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pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
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pars['O1'] = -57.0e3 # offset from SF (Hz)
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pars['SW'] = 150e3 # spectral width (Hz)
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pars['SI1'] = 32 # number of (complex) data points in F1 (2D)
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pars['SI2'] = 128 # number of (complex) data points in F2
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pars['D8'] = 100e-6 # mixing time, tm (s)
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pars['NS'] = 16 # number of scans
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pars['DS'] = 0 # number of dummy scans
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pars['RD'] = 2.5 # delay between scans (s)
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pars['DEAD1'] = 4e-6 # receiver dead time (s)
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pars['PHA'] = 150 # receiver reference phase (degree)
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pars['DATADIR'] = '/home/fprak/' # data directory
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pars['OUTFILE'] = 'test' # output file name
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# specify a variable parameter (optional):
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pars['VAR_PAR'] = 'D8' # variable parameter name (a string)
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start = 10.e-6 # starting value
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stop = 1000e-6 # end value
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steps = 3 # number of values
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log_scale = True # log scale flag
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stag_range = False # staggered range flag
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# check parameters for safety:
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if pars['PHA'] < 0:
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pars['PHA'] = 360 + pars['PHA']
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if pars['P90'] > 20e-6:
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raise Exception("Pulse too long!!!")
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var_key = pars.get('VAR_PAR')
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if var_key == 'P90' and (start > 20e-6 or stop > 20e-6):
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raise Exception("Pulse too long!!!")
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if pars['NS']%8 != 0:
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pars['NS'] = (pars['NS'] / 8 + 1) * 8
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print 'Number of scans changed to', pars['NS'], 'due to phase cycling'
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# start the experiment:
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if var_key:
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# this is an arrayed experiment:
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if log_scale:
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array = log_range(start,stop,steps)
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else:
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array = lin_range(start,stop,steps)
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if stag_range:
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array = staggered_range(array, size=2)
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# estimate the experiment time:
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if var_key == 'D8':
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seconds = (sum(array) + (.5*pars['SI1']/pars['SW'] + pars['RD']) * steps) * (pars['NS'] + pars['DS']) * 2*pars['SI1']
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elif var_key == 'RD':
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seconds = (sum(array) + (.5*pars['SI1']/pars['SW'] + pars['D8']) * steps) * (pars['NS'] + pars['DS']) * 2*pars['SI1']
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else:
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seconds = (.5*pars['SI1']/pars['SW'] + pars['D8'] + pars['RD']) * steps * (pars['NS']+ pars['DS']) * 2*pars['SI1']
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m, s = divmod(seconds, 60)
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h, m = divmod(m, 60)
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print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
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# loop for a variable parameter:
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for index, pars[var_key] in enumerate(array):
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print 'Arrayed experiment for '+var_key+': run = '+str(index+1)+\
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' out of '+str(array.size)+': value = '+str(pars[var_key])
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# loop for accumulation and sampling the indirect dimension F1:
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for run in xrange((pars['NS']+pars['DS'])*2*pars['SI1']):
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yield noesyst_experiment(pars, run)
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synchronize()
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else:
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# estimate the experiment time:
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seconds = (.5*pars['SI1']/pars['SW'] + pars['D8'] + pars['RD']) * (pars['NS']+ pars['DS']) * 2*pars['SI1']
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print 'sec ', seconds
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m, s = divmod(seconds, 60)
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h, m = divmod(m, 60)
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print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
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# loop for accumulation and sampling the indirect dimension F1:
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for run in xrange((pars['NS']+pars['DS'])*2*pars['SI1']):
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yield noesyst_experiment(pars, run)
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# the pulse program:
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def noesyst_experiment(pars, run):
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e=Experiment()
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dummy_scans = pars.get('DS')
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if dummy_scans:
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run -= dummy_scans
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# phase lists (M.H.Levitt 'Spin Dynamics', 2nd edition, p.530):
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pars['PH1'] = [ 0, 180, 0, 180, 0, 180, 0, 180]
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pars['PH3'] = [180, 180, 180, 180, 180, 180, 180, 180]
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pars['PH4'] = [ 0, 0, 90, 90, 180, 180, 270, 270]
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pars['PH2'] = [ 0, 180, 90, 270, 180, 0, 270, 90] # receiver
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# read in variables:
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P90 = pars['P90']
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SF = pars['SF']
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O1 = pars['O1']
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RD = pars['RD']
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DEAD1 = pars['DEAD1']
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D8 = pars['D8']
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NS = pars['NS']
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PH1 = pars['PH1'][run%len(pars['PH1'])]
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PH3 = pars['PH3'][run%len(pars['PH3'])]
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PH4 = pars['PH4'][run%len(pars['PH4'])]
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PH2 = pars['PH2'][run%len(pars['PH2'])]
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PHA = pars['PHA']
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# F1 sampling parameters:
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IN0 = 1./pars['SW'] # t1 increment
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# the States-TPPI bit:
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PH1-= (run/(1*NS))%4*90 # PH1 changes by 90-deg. after every 1*NS scans
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D0 = (run/(2*NS)) *IN0 # t1 increases by IN0 after every 2*NS scans
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# F2 sampling parameters:
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SI2 = pars['SI2']
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SW2 = pars['SW']
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while SW2 <= 10e6 and SI2 < 256*1024:
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SI2 *= 2
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SW2 *= 2
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# run the pulse sequence:
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e.wait(RD) # delay between scans
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e.set_frequency(SF+O1, phase=PH1)
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
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e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
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e.wait(D0) # incremented delay t1
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e.set_phase(PH3)
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
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e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
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e.wait(D8) # mixing time
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e.set_phase(PH4)
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e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
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e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
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e.set_phase(PHA) # set phase for receiver
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e.wait(DEAD1) # wait for coil ringdown
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e.record(SI2, SW2, sensitivity=ADCSensitivity) # acquire signal
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# write experiment attributes:
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for key in pars.keys():
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e.set_description(key, pars[key]) # acqusition parameters
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e.set_description('run', run) # current scan
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e.set_description('rec_phase', -PH2) # current receiver phase
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return e
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157
Scripts/EXSY/op_noesy_res.py
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157
Scripts/EXSY/op_noesy_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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measurement_range = [0.0, 10e-6]
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measurement_ranging = False
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suffix = '' # output file name's suffix and...
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counter = 0 # counter for arrayed 2D 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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# ---------------- digital filter ------------------
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# get actual sampling rate of timesignal:
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sampling_rate = timesignal.get_sampling_rate()
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# get user-defined spectrum width:
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spec_width = pars['SW']
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# specify cutoff frequency, in relative units:
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cutoff = spec_width / sampling_rate
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if cutoff < 1: # otherwise no filter applied
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# number of filter's coefficients:
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numtaps = 29
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# use firwin to create a lowpass FIR filter:
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fir_coeff = firwin(numtaps, cutoff)
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# downsize x according to user-defined spectral window:
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skip = int(sampling_rate / spec_width)
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timesignal.x = timesignal.x[::skip]
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for i in range(2):
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# apply the filter to ith channel:
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timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
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# zeroize first N-1 "corrupted" samples:
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timesignal.y[i][:numtaps-1] = 0.0
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# circular left shift of y:
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timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
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# downsize y to user-defined number of samples (SI):
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timesignal.y[i] = timesignal.y[i][::skip]
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# update the sampling_rate attribute of the signal's:
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timesignal.set_sampling_rate(spec_width)
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# ----------------------------------------------------
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# rotate timesignal according to 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 whether accumulation is complete:
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# ----------------------------------------------------------------------------------------
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# Note that State-TPPI technique implies recording two data sets at each t1 point.
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# Cosine-modulated data are stored in record 1 as Re, and sine-modulated data are stored
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# in record 2 as Im, totally 2*SI1 records. Henceforth, accu represents one such a record.
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# -----------------------------------------------------------------------------------------
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if accu.n == pars['NS']:
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# make a copy:
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fid = accu + 0
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# compute the initial phase of FID:
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phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
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if not 'ref' in locals(): ref = phi0
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# print 'phi0 = ', phi0
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# rotate FID to maximize y[0][0]:
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#echo.phase(-phi0)
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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 signal recorded with this var_value to the display tab:
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data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
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# measure signal intensity vs. var_value:
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if measurement_ranging == True:
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[start, stop] = accu.get_sampling_rate() * array(measurement_range)
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measurement[var_value] = sum(accu.y[0][int(start):int(stop)])
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else:
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measurement[var_value] = sum(accu.y[0][0:31])
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# provide measurement to the display tab:
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data[measurement.get_title()] = measurement
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# update the file name suffix:
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counter2D = counter/(2*pars['SI1'])+1
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suffix = '_' + str(counter2D)
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counter += 1
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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 raw data in Tecmag format:
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filename = datadir+outfile+suffix+'.tnt'
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accu.write_to_tecmag(filename,\
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nrecords=2*pars['SI1'],\
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frequency=pars['SW']+pars['O1'])
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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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pass
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194
Scripts/EXSY_2H/op_exsy2h_exp.py
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194
Scripts/EXSY_2H/op_exsy2h_exp.py
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# -*- coding: iso-8859-1 -*-
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TXEnableDelay = 0.5e-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(): # 2H Exchange Spectroscopy (2H EXSY) experiment [JMR 79, 269-290 (1988)]
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# Cosine and sine modulated signals are acquired sequentially by switching
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# between Zeeman order and spin-alignment phase lists. The signals are
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# processed into a pure absorption mode 2D spectrum according to scheme by
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# [Bluemich, Schmidt, and Spiess, JMR 79, 269-290 (1988)]. Prior to writing
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# in a file (Tecmag), the sine-modulated signal is rotated by 90°, thus
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# enabling 2D processing via a regular States algorithm with NMRnotebook
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# or like NMR software.
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 2.7e-6 # 90°-pulse length (s)
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pars['SF'] = 46.140e6 # spectrometer frequency (Hz)
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||||||
|
pars['O1'] = 1000 # offset from SF (Hz)
|
||||||
|
pars['SW'] = 125e3 # spectral window (Hz)
|
||||||
|
pars['SI1'] = 80 # number of (complex) data points in F1 (2nd dimension)
|
||||||
|
pars['SI2'] = 1*256 # number of (complex) data points in F2
|
||||||
|
pars['D3'] = 10e-6 # position of refocusing 90°-pulse, Delta (s)
|
||||||
|
pars['D4'] = 2e-6 # pre-aquisition delay (s)
|
||||||
|
pars['D8'] = 3e-3 # mixing time, tm (s)
|
||||||
|
pars['NS'] = 512 # number of scans
|
||||||
|
pars['DS'] = 0 # number of dummy scans
|
||||||
|
pars['RD'] = 0.2 # delay between scans (s)
|
||||||
|
pars['PHA'] = 65 # receiver reference phase (degree)
|
||||||
|
pars['DATADIR'] = '/home/mathilda/Desktop/Oleg/temp/' # data directory
|
||||||
|
pars['OUTFILE'] = 'dso_320K' # output file name
|
||||||
|
|
||||||
|
# specify a variable parameter (optional):
|
||||||
|
pars['VAR_PAR'] = None # variable parameter's name (a string)
|
||||||
|
start = 80 # starting value
|
||||||
|
stop = 128 # end value
|
||||||
|
steps = 2 # 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'] / 32) + 1) * 32
|
||||||
|
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 == 'D8':
|
||||||
|
seconds = (sum(array) + (.5*pars['SI1']/pars['SW'] + pars['RD']) * steps) * (pars['NS'] + pars['DS']) * 2*pars['SI1']
|
||||||
|
elif var_key == 'RD':
|
||||||
|
seconds = (sum(array) + (.5*pars['SI1']/pars['SW'] + pars['D8']) * steps) * (pars['NS'] + pars['DS']) * 2*pars['SI1']
|
||||||
|
else:
|
||||||
|
seconds = (.5*pars['SI1']/pars['SW'] + pars['D8'] + pars['RD']) * steps * (pars['NS']+ pars['DS']) * 2*pars['SI1']
|
||||||
|
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 and sampling the indirect dimension F1:
|
||||||
|
for run in xrange((pars['NS']+pars['DS'])*2*pars['SI1']):
|
||||||
|
yield exsy2h_experiment(pars, run)
|
||||||
|
synchronize()
|
||||||
|
|
||||||
|
else:
|
||||||
|
# estimate the experiment time:
|
||||||
|
seconds = (.5*pars['SI1']/pars['SW'] + pars['D8'] + pars['RD']) * (pars['NS']+ pars['DS']) * 2*pars['SI1']
|
||||||
|
print 'sec ', seconds
|
||||||
|
m, s = divmod(seconds, 60)
|
||||||
|
h, m = divmod(m, 60)
|
||||||
|
print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
|
||||||
|
|
||||||
|
# loop for accumulation and sampling the indirect dimension F1:
|
||||||
|
for run in xrange((pars['NS']+pars['DS'])*2*pars['SI1']):
|
||||||
|
yield exsy2h_experiment(pars, run)
|
||||||
|
|
||||||
|
|
||||||
|
# the pulse program:
|
||||||
|
|
||||||
|
def exsy2h_experiment(pars, run):
|
||||||
|
e=Experiment()
|
||||||
|
|
||||||
|
dummy_scans = pars.get('DS')
|
||||||
|
if dummy_scans:
|
||||||
|
run -= dummy_scans
|
||||||
|
|
||||||
|
pars['PROG'] = 'exsy2h_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 pulse (90°)
|
||||||
|
pars['PH3'] = [0, 90, 0, 90, 0, 90, 0, 90] # 2nd pulse (57.4°)
|
||||||
|
pars['PH4'] = [0, 0, 180, 180, 270, 270, 90, 90] # 3rd pulse (57.4°)
|
||||||
|
pars['PH5'] = [90, 90, 90, 90, 180, 180, 180, 180] # 4th pulse (90°)
|
||||||
|
pars['PH2'] = [0, 180, 180, 0, 90, 270, 270, 90] # receiver
|
||||||
|
|
||||||
|
# read in variables:
|
||||||
|
P90 = pars['P90']
|
||||||
|
P1 = pars['P90']*(54.7/90)
|
||||||
|
SF = pars['SF']
|
||||||
|
O1 = pars['O1']
|
||||||
|
RD = pars['RD']
|
||||||
|
D4 = pars['D4']
|
||||||
|
D8 = pars['D8']
|
||||||
|
D3 = pars['D3']
|
||||||
|
NS = pars['NS']
|
||||||
|
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']
|
||||||
|
|
||||||
|
# this is a part of phase cycling:
|
||||||
|
PH5 += (run/len(pars['PH5']))%2*180
|
||||||
|
PH1 += (run/len(pars['PH5']))%2*180
|
||||||
|
PH2 += (run/len(pars['PH5']))%2*180
|
||||||
|
|
||||||
|
# F1 sampling parameters:
|
||||||
|
IN0 = 1./pars['SW'] # t1 increment
|
||||||
|
|
||||||
|
# F1 sampling scheme:
|
||||||
|
PH3+= (run/(1*NS))%4*90 # phases are upgraded after every NS scans
|
||||||
|
PH4+= (run/(1*NS))%4*90
|
||||||
|
D0 = (run/(2*NS)) *IN0 # t1 is incremented after every 2*NS scans
|
||||||
|
|
||||||
|
# F2 sampling parameters:
|
||||||
|
SI2 = pars['SI2']
|
||||||
|
SW2 = pars['SW']
|
||||||
|
while SW2 <= 10e6 and SI2 < 256*1024:
|
||||||
|
SI2 *= 2
|
||||||
|
SW2 *= 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°-pulse
|
||||||
|
|
||||||
|
e.wait(D0) # incremented delay, t1
|
||||||
|
e.set_phase(PH3)
|
||||||
|
|
||||||
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||||
|
e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 54.7°-pulse
|
||||||
|
|
||||||
|
e.wait(D8) # mixing time, tm
|
||||||
|
e.set_phase(PH4)
|
||||||
|
|
||||||
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||||
|
e.ttl_pulse(P1, value=TXEnableValue|TXPulseValue) # 54.7°-pulse
|
||||||
|
|
||||||
|
e.wait(D3) # refocusing delay, Delta
|
||||||
|
|
||||||
|
e.set_phase(PH5)
|
||||||
|
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
|
||||||
|
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90°-pulse
|
||||||
|
|
||||||
|
e.wait(TXEnableDelay)
|
||||||
|
e.set_phase(PHA)
|
||||||
|
e.wait(D3+D4) # pre-aquisition delay
|
||||||
|
e.record(SI2, SW2, 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
|
||||||
170
Scripts/EXSY_2H/op_exsy2h_res.py
Normal file
170
Scripts/EXSY_2H/op_exsy2h_res.py
Normal file
@ -0,0 +1,170 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
from numpy import *
|
||||||
|
from scipy.signal import *
|
||||||
|
from scipy.optimize import *
|
||||||
|
from scipy.fftpack import fft, ifft
|
||||||
|
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 = 0 # counter for arrayed 2D experiments
|
||||||
|
# npts = 0
|
||||||
|
|
||||||
|
# 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 whether accumulation is complete:
|
||||||
|
# ------------------------------------------------------------------------------------
|
||||||
|
# The hypercomplex technique implies recording two data sets for each t1 value.
|
||||||
|
# One dataset (a cosine-modulated signal) is stored in odd records as Re, while
|
||||||
|
# the other dataset (a sine-modulated signal) in even records as Im, totally 2*SI1
|
||||||
|
# records. Henceforth, accu represents one such a record.
|
||||||
|
# ------------------------------------------------------------------------------------
|
||||||
|
if accu.n == pars['NS']:
|
||||||
|
# compute the initial phase of FID:
|
||||||
|
phi0 = arctan2(accu.y[1][0], accu.y[0][0]) * 180 / pi
|
||||||
|
if not 'ref' in locals(): ref = phi0
|
||||||
|
print 'phi0 = ', phi0
|
||||||
|
|
||||||
|
# rotate every other record by 90° so that States algorithm is applicable:
|
||||||
|
rec = (accu.job_id/accu.n)%(2*pars['SI1']) + 1
|
||||||
|
if rec%2 == 0:
|
||||||
|
accu.phase(90)
|
||||||
|
coeff = 1.5
|
||||||
|
accu.y[0] *= coeff # XY-balancing
|
||||||
|
accu.y[1] *= coeff
|
||||||
|
|
||||||
|
else: # baseline correction )))))
|
||||||
|
tmp = fft(accu.y[0]+1j*accu.y[1])
|
||||||
|
[start, stop] = len(accu.y[0])*array([0.4, 0.6])
|
||||||
|
tmp -= mean(tmp.real[start:stop])
|
||||||
|
tmp = ifft(tmp)
|
||||||
|
accu.y[0] = tmp.real
|
||||||
|
accu.y[1] = tmp.imag
|
||||||
|
|
||||||
|
# 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])
|
||||||
|
measurement[var_value+counter*1e-6] = sum(accu.y[0][0:31])
|
||||||
|
|
||||||
|
# provide measurement to the display tab:
|
||||||
|
data[measurement.get_title()] = measurement
|
||||||
|
|
||||||
|
# update the file name suffix:
|
||||||
|
counter2D = counter/(2*pars['SI1'])+1
|
||||||
|
suffix = '_' + str(counter2D)
|
||||||
|
counter += 1
|
||||||
|
|
||||||
|
# save accu if required:
|
||||||
|
outfile = pars.get('OUTFILE')
|
||||||
|
if outfile:
|
||||||
|
datadir = pars.get('DATADIR')
|
||||||
|
|
||||||
|
# write raw data in Tecmag format:
|
||||||
|
filename = datadir+outfile+suffix+'.tnt'
|
||||||
|
accu.write_to_tecmag(filename,\
|
||||||
|
nrecords=2*pars['SI1'],\
|
||||||
|
frequency=pars['SW']+pars['O1'])
|
||||||
|
|
||||||
|
# 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
|
||||||
176
Scripts/Spin_Alignment_Four_Pulses/op_spinal4pulses_exp.py
Normal file
176
Scripts/Spin_Alignment_Four_Pulses/op_spinal4pulses_exp.py
Normal file
@ -0,0 +1,176 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
TXEnableDelay = 1e-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(): # Jeener-Broekaert echo sequence (a.k.a. spin-alignment)
|
||||||
|
|
||||||
|
# set up acquisition parameters:
|
||||||
|
pars = {}
|
||||||
|
pars['P90'] = 4.2e-6 # 90-degree pulse length (s)
|
||||||
|
pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
|
||||||
|
pars['O1'] = -30e3 # 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['RD'] = 0.5 # 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['D3'] = 20e-6 # refocusing pulse delay (s)
|
||||||
|
pars['PHA'] = 30 # receiver reference 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']%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 spinal4pulses_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 spinal4pulses_experiment(pars, run)
|
||||||
|
|
||||||
|
|
||||||
|
# the pulse program:
|
||||||
|
|
||||||
|
def spinal4pulses_experiment(pars, run):
|
||||||
|
e=Experiment()
|
||||||
|
|
||||||
|
dummy_scans = pars.get('DS')
|
||||||
|
if dummy_scans:
|
||||||
|
run -= dummy_scans
|
||||||
|
|
||||||
|
pars['PROG'] = 'spinal4pulses_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, 180, 90, 180, 90] # 1st (90-degree) pulse
|
||||||
|
pars['PH3'] = [90, 180, 90, 180, 90, 180, 90, 180] # 2nd (90-degree) pulse
|
||||||
|
pars['PH4'] = [90, 90, 270, 270, 0, 0, 180, 180] # 3rd (90-degree) pulse
|
||||||
|
pars['PH5'] = [90, 90, 90, 90, 180, 180, 180, 180] # 3rd (90-degree) pulse
|
||||||
|
pars['PH2'] = [0, 180, 180, 0, 90, 270, 270, 90] # 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']
|
||||||
|
D3 = pars['D3']
|
||||||
|
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']
|
||||||
|
|
||||||
|
if (run/8)%2 != 0:
|
||||||
|
PH5 += 180
|
||||||
|
|
||||||
|
# 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-P45/2-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-P1/2-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(D3-P1/2-P90/2-TXEnableDelay) # 'delta'
|
||||||
|
|
||||||
|
e.set_phase(PH5)
|
||||||
|
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(D3+D1-P90/2-TXEnableDelay) # wait for echo
|
||||||
|
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_Four_Pulses/op_spinal4pulses_res.py
Normal file
210
Scripts/Spin_Alignment_Four_Pulses/op_spinal4pulses_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
|
||||||
@ -0,0 +1,183 @@
|
|||||||
|
# -*- 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 = 5 # voltage span for ADC
|
||||||
|
|
||||||
|
def experiment(): # a diffusion editing sequence with stimulated echo and XY-16 detection
|
||||||
|
|
||||||
|
# set up acqusition parameters:
|
||||||
|
pars = {}
|
||||||
|
pars['P90'] = 0.8e-6 # 90-degree pulse length (s)
|
||||||
|
pars['SF'] = 161.85e6 # spectrometer frequency (Hz)
|
||||||
|
pars['O1'] = 0e3 # offset from SF (Hz)
|
||||||
|
pars['NS'] = 16 # number of scans
|
||||||
|
pars['DS'] = 0 # number of dummy scans
|
||||||
|
pars['RD'] = 6 # delay between scans (s)
|
||||||
|
pars['D1'] = 20e-6 # delay after first STE pulse (s)
|
||||||
|
pars['D2'] = 30e-6 # delay after second STE pulse (s)
|
||||||
|
pars['D4'] = 2.5e-6 # pre-acquisition offset
|
||||||
|
pars['NECH'] = 128 # number of 180-degree pulses
|
||||||
|
pars['TAU'] = 50e-6 # half pulse period (s)
|
||||||
|
pars['PHA'] = -95 # 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 = 3e-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']%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 ste16_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 ste16_experiment(pars, run)
|
||||||
|
|
||||||
|
|
||||||
|
# the pulse program:
|
||||||
|
|
||||||
|
def ste16_experiment(pars, run):
|
||||||
|
e=Experiment()
|
||||||
|
|
||||||
|
dummy_scans = pars.get('DS')
|
||||||
|
if dummy_scans:
|
||||||
|
run -= dummy_scans
|
||||||
|
|
||||||
|
pars['PROG'] = 'ste16_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'] = [0, 0, 0, 0, 0, 0, 0, 0, 270, 270, 270, 270, 270, 270, 270, 270] # 180-degree pulses
|
||||||
|
pars['PH2'] = [0, 180, 180, 0, 180, 0, 0, 180, 270, 90, 90, 270, 90, 270, 270, 90] # receiver
|
||||||
|
|
||||||
|
# XY-16 phase cycle
|
||||||
|
pars['PH5_XY16'] = [0, 90, 0, 90, 90, 0, 90, 0, 180, 270, 180, 270, 270, 180, 270, 180] # XY-16: 180-degree pulses
|
||||||
|
pars['PH2_XY16'] = [90, 270, 270, 90, 270, 270, 90, 90, 90, 270, 270, 90, 270, 270, 90, 90] # XY_16: 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']
|
||||||
|
D4 = pars['D4']
|
||||||
|
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'])]
|
||||||
|
PH5_XY16 = [x+PH5 for x in pars['PH5_XY16']*(NECH/16)]
|
||||||
|
PH2_XY16 = [x+PH2 for x in pars['PH2_XY16']*(NECH/16)]
|
||||||
|
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
|
||||||
|
|
||||||
|
for i in range(NECH):
|
||||||
|
e.set_phase(PH5_XY16[i]) # set phase for 180-degree pulse
|
||||||
|
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+D4) # pre-acquisition delay
|
||||||
|
e.record(SI, SW, timelength=AQ, sensitivity=ADCSensitivity) # echo acquisition
|
||||||
|
e.wait(TAU-(P180+TXEnableDelay+AQ)/2-D4) # post-acquisition delay
|
||||||
|
|
||||||
|
# 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', [-1*x for x in PH2_XY16]) # current phase list for data routing
|
||||||
|
|
||||||
|
return e
|
||||||
@ -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')
|
||||||
|
|
||||||
|
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()
|
||||||
|
|
||||||
|
# get number of echoes:
|
||||||
|
num_echoes = pars['NECH']
|
||||||
|
|
||||||
|
# get phase list for data routung:
|
||||||
|
rec_phase = eval(pars['rec_phase'])
|
||||||
|
|
||||||
|
# phase individual echoes in timesignal:
|
||||||
|
for i in range(num_echoes):
|
||||||
|
echo = timesignal.get_result_by_index(i)
|
||||||
|
echo.phase(rec_phase[i])
|
||||||
|
|
||||||
|
start = timesignal.index[i][0]
|
||||||
|
end = timesignal.index[i][1]
|
||||||
|
for k in range(timesignal.get_number_of_channels()):
|
||||||
|
if i%2 == 0:
|
||||||
|
timesignal.y[k][start:end+1] = echo.y[k]
|
||||||
|
else:
|
||||||
|
timesignal.y[k][start:end+1] = -echo.y[k]
|
||||||
|
|
||||||
|
# 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
|
||||||
173
Scripts/Zeeman_Order_Four_Pulses/op_zeeman4pulses_exp.py
Normal file
173
Scripts/Zeeman_Order_Four_Pulses/op_zeeman4pulses_exp.py
Normal file
@ -0,0 +1,173 @@
|
|||||||
|
# -*- coding: iso-8859-1 -*-
|
||||||
|
|
||||||
|
TXEnableDelay = 1e-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(): # Four-pulse STE sequence (Zeeman order)
|
||||||
|
|
||||||
|
# set up acquisition parameters:
|
||||||
|
pars = {}
|
||||||
|
pars['P90'] = 4.2e-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'] = 16 # 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'] = 100e-6 # delay after second pulse, or 'long tau' (s)
|
||||||
|
pars['D3'] = 20e-6 # refocusing pusle delay (s)
|
||||||
|
pars['PHA'] = 124 # 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 zeeman4pulses_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 zeeman4pulses_experiment(pars, run)
|
||||||
|
|
||||||
|
# the pulse program:
|
||||||
|
|
||||||
|
def zeeman4pulses_experiment(pars, run):
|
||||||
|
e=Experiment()
|
||||||
|
|
||||||
|
dummy_scans = pars.get('DS')
|
||||||
|
if dummy_scans:
|
||||||
|
run -= dummy_scans
|
||||||
|
|
||||||
|
pars['PROG'] = 'zeeman4pulses_experiment'
|
||||||
|
|
||||||
|
# ok 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['PH5'] = [90, 90, 90, 90, 180, 180, 180, 180] # 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']
|
||||||
|
D3 = pars['D3']
|
||||||
|
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']
|
||||||
|
|
||||||
|
if (run/8)%2 != 0:
|
||||||
|
PH5 += 180
|
||||||
|
|
||||||
|
# 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-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-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(D3-P90-TXEnableDelay) # echo delay
|
||||||
|
|
||||||
|
e.set_phase(PH5)
|
||||||
|
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(D3+D1-P90/2-TXEnableDelay) # echo delay
|
||||||
|
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_Four_Pulses/op_zeeman4pulses_res.py
Normal file
210
Scripts/Zeeman_Order_Four_Pulses/op_zeeman4pulses_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
|
||||||
Loading…
Reference in New Issue
Block a user