PFG STE added
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README.md
26
README.md
@ -7,4 +7,30 @@ You can get a clone of this repository via:
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Details of the pulse programs can be found [[https://chaos3.fkp.physik.tu-darmstadt.de/diffusion/DSL/browse/master/The%20DAMARIS%20Script%20Library.pdf | here]].
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## For people working with this and thy want to revert the local changes:
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(This is from [[https://stackoverflow.com/questions/1146973/how-do-i-revert-all-local-changes-in-git-managed-project-to-previous-state|from StackOverflow]])
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If you want to revert changes made to your working copy, do this:
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git checkout .
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If you want to revert changes made to the index (i.e., that you have added), do this. Warning this will reset all of your unpushed commits to master!:
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git reset
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If you want to revert a change that you have committed, do this:
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git revert <commit 1> <commit 2>
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If you want to remove untracked files (e.g., new files, generated files):
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git clean -f
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Or untracked directories (e.g., new or automatically generated directories):
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git clean -fd
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Current maintainer of this library is @markusro.
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174
Scripts/PFG/Stimulated_Echo/pfg_ste_exp.py
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174
Scripts/PFG/Stimulated_Echo/pfg_ste_exp.py
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# -*- coding: iso-8859-1 -*-
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TXEnableDelay = 2e-6 # test
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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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DAC_conv = 6.32e-5 # T/dac_value
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def experiment(): # stimulated echo experiment
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# set up acquisition parameters:
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pars = {}
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pars['P90'] = 3.2e-6 # 90-degree pulse length (s)
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pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
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pars['O1'] = -87e3 # offset from SF (Hz)
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pars['SW'] = 500e3 # spectrum width (Hz)
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pars['SI'] = 8*1024 # number of acquisition points
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pars['NS'] = 16*2 # number of scans
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pars['DS'] = 0 # number of dummy scans
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pars['RD'] = 3*7.7 # delay between scans (s)
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pars['D1'] = 1e-3 # delay after first pulse (short tau) (s)
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pars['D2'] = 50e-3 # delay after second pulse (long tau) (s)
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pars['D4'] = 0e-6 # echo pre-acquisition delay (s)
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pars["DAC1"] = 1000 # DAC value (PFG)
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pars["D5"] = 0.9e-3 # PFG pulse length
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pars['PHA'] = 30+180 # receiver phase (degree)
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pars['DATADIR'] = '/home/markusro/STE' # data directory
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pars['OUTFILE'] = "" # output file name
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# specify a variable parameter (optional):
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pars['VAR_PAR'] = "DAC1" # variable parameter name (a string)
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start = 0 # starting value
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stop = int(5/DAC_conv) #1.5e5 # end value
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steps = 21 # 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']%16 != 0:
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pars['NS'] = int(round(pars['NS'] / 16) + 1) * 16
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print 'Number of scans changed to ',pars['NS'],' due to phase cycling'
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# start the experiment:
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# check if a variable parameter is named:
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var_key = pars.get('VAR_PAR')
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if var_key:
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# this is an arrayed experiment:
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if log_scale:
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array = log_range(start,stop,steps)
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else:
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array = lin_range(start,stop,steps)
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if stag_range:
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array = staggered_range(array, size = 2)
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# estimate the experiment time:
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if var_key == 'D1':
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seconds = (sum(array)*2 + (pars['D2'] + pars['RD']) * steps) * (pars['NS'] + pars['DS'])
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elif var_key == 'D2':
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seconds = (sum(array) + (pars['D1']*2 + pars['RD']) * steps) * (pars['NS'] + pars['DS'])
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elif var_key == 'RD':
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seconds = (sum(array) + (pars['D1']*2 + pars['D2']) * steps) * (pars['NS'] + pars['DS'])
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else:
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seconds = (pars['D1']*2 + pars['D2'] + pars['RD']) * steps * (pars['NS']+ pars['DS'])
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m, s = divmod(seconds, 60)
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h, m = divmod(m, 60)
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print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
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# loop for a variable parameter:
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for index, pars[var_key] in enumerate(array):
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print 'Arrayed experiment for '+var_key+': run = '+str(index+1)+\
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' out of '+str(array.size)+': value = '+str(pars[var_key])
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# loop for accumulation:
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for run in xrange(pars['NS']+pars['DS']):
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yield ste_experiment(pars, run)
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synchronize()
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else:
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# estimate the experiment time:
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seconds = (pars['D1']*2 + pars['D2'] + pars['RD']) * (pars['NS']+ pars['DS'])
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m, s = divmod(seconds, 60)
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h, m = divmod(m, 60)
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print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
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# loop for accumulation:
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for run in xrange(pars['NS']+pars['DS']):
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yield ste_experiment(pars, run)
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# the pulse program:
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def ste_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'] = 'ste_experiment'
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# phase lists [16-phase cycle from JMR 157, 31 (2002)]:
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pars['PH1'] = [0, 180, 0, 180, 0, 180, 0, 180, 90, 270, 90, 270, 90, 270, 90, 270] # 1st 90-degree pulse
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pars['PH3'] = [0, 0, 180, 180, 0, 0, 180, 180, 0, 0, 180, 180, 0, 0, 180, 180] # 2nd 90-degree pulse
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pars['PH4'] = [0, 0, 0, 0, 180, 180, 180, 180, 0, 0, 0, 0, 180, 180, 180, 180] # 3nd 90-degree pulse
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pars['PH2'] = [0, 180, 180, 0, 180, 0, 0, 180, 270, 90, 90, 270, 90, 270, 270, 90] # receiver
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# read in variables:
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P90 = pars['P90']
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SF = pars['SF']
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O1 = pars['O1']
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RD = pars['RD']
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D1 = pars['D1']
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D2 = pars['D2']
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D4 = pars['D4']
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D5 = pars['D5']
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DAC1 = pars['DAC1']
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PH1 = pars['PH1'][run%len(pars['PH1'])]
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PH3 = pars['PH3'][run%len(pars['PH3'])]
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PH4 = pars['PH4'][run%len(pars['PH4'])]
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PH2 = pars['PH2'][run%len(pars['PH2'])]
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PHA = pars['PHA']
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# set sampling parameters:
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SI = pars['SI']
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SW = pars['SW']
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while SW <= 10e6 and SI < 256*1024:
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SI *= 2
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SW *= 2
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# 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.set_phase(PH3)
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e.set_pfg(dac_value=DAC1, length=D5, shape=("rec",100e-6))
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e.wait(D1-P90/2-TXEnableDelay - D5) # 'short tau'
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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(D2-P90/2-TXEnableDelay) # 'long tau'
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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)
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e.set_pfg(dac_value=DAC1, length=D5, shape=("rec",100e-6))
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e.wait(D1-P90/2-TXEnableDelay+D4-D5) # 'short tau'
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e.record(SI, SW, sensitivity=ADCSensitivity) # acquisition
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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 receiver phase
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return e
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209
Scripts/PFG/Stimulated_Echo/pfg_ste_res.py
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209
Scripts/PFG/Stimulated_Echo/pfg_ste_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 = 1 # counter for arrayed experiments
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var_key = '' # variable parameter name
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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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# phase timesignal according to current rec_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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# make a copy:
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echo = accu + 0
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# compute the initial phase of the signal:
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phi0 = arctan2(accu.y[1][0], accu.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 the signal to maximize Re (optional):
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#echo.phase(-phi0)
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# do FFT:
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echo.exp_window(line_broadening=10)
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spectrum = echo.fft(samples=2*pars['SI'])
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# try zero-order phase correction:
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spectrum.phase(-phi0)
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# provide spectrum to the display tab:
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data['Spectrum'] = spectrum
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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 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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suffix = '_' + str(counter)
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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 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 raw 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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if var_key == 'D2':
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# mono-exponential decay fit:
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xdata = measurement.get_xdata()
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ydata = measurement.get_ydata()
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[amplitude, rate, offset] = fitfunc(xdata, ydata)
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print '%s%02g' % ('Amplitude = ', amplitude)
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print '%s%02g' % ('T1 [s] = ', 1./rate)
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print '%s%02g' % ('Offset = ', offset)
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# update display for the fit:
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measurement.y = func([amplitude, rate, offset], xdata)
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data[measurement.get_title()] = measurement
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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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offset = min(ydata)
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p0 = [amplitude, rate, offset]
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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) + p[2]
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pass
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