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New experimetns added

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Oleg Petrov
2015-09-30 11:09:36 +00:00
parent 58f9ee63f6
commit d9beb94422
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176
Scripts/EXSY/op_noesy_exp.py Normal file
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# -*- coding: iso-8859-1 -*-
TXEnableDelay = 2e-6
TXEnableValue = 0b0001 # TTL line enabling RF amplifier (bit 0)
TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1)
ADCSensitivity = 2 # voltage span for ADC
def experiment(): # 2D NOESY experiment, using States-TPPI technique for quadrature detection in F1
# States-TPPI technique achieves two effects for an indirect dimension F1:
# (1) signal frequency discrimination and (2) displacement of the unmodulated
# artefact signal from an inconvenient location in the middle of spectrum to the edge.
# (1) is achieved by recording two data sets at each t1 point - with orthogonal phases
# of the preparation pulse and same receiver phase - and storing them in separate memory
# locations. These two fid measurements yield one complex data point in F1.
# (2) by inverting phase of the preparation pulse and the receiver each time when t1 is
# incremented (that is for subsequent complex points). Therefore, the artefact signal
# becomes modulated at the Nyquist frequency and appears in the spectrum at F1=<3D>SW/2 Hz
# instead of 0 Hz, where SW is spectral width. [http://nmrwiki.org]
# set up acqusition parameters:
pars = {}
pars['P90'] = 1.65e-6 # 90-degree pulse length (s)
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
pars['O1'] = -57.0e3 # offset from SF (Hz)
pars['SW'] = 150e3 # spectral width (Hz)
pars['SI1'] = 32 # number of (complex) data points in F1 (2D)
pars['SI2'] = 128 # number of (complex) data points in F2
pars['D8'] = 100e-6 # mixing time, tm (s)
pars['NS'] = 16 # number of scans
pars['DS'] = 0 # number of dummy scans
pars['RD'] = 2.5 # delay between scans (s)
pars['DEAD1'] = 4e-6 # receiver dead time (s)
pars['PHA'] = 150 # receiver reference phase (degree)
pars['DATADIR'] = '/home/fprak/' # data directory
pars['OUTFILE'] = 'test' # output file name
# specify a variable parameter (optional):
pars['VAR_PAR'] = 'D8' # variable parameter name (a string)
start = 10.e-6 # starting value
stop = 1000e-6 # end value
steps = 3 # number of values
log_scale = True # log scale flag
stag_range = False # staggered range flag
# check parameters for safety:
if pars['PHA'] < 0:
pars['PHA'] = 360 + pars['PHA']
if pars['P90'] > 20e-6:
raise Exception("Pulse too long!!!")
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'] = (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 == '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 noesyst_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 noesyst_experiment(pars, run)
# the pulse program:
def noesyst_experiment(pars, run):
e=Experiment()
dummy_scans = pars.get('DS')
if dummy_scans:
run -= dummy_scans
# phase lists (M.H.Levitt 'Spin Dynamics', 2nd edition, p.530):
pars['PH1'] = [ 0, 180, 0, 180, 0, 180, 0, 180]
pars['PH3'] = [180, 180, 180, 180, 180, 180, 180, 180]
pars['PH4'] = [ 0, 0, 90, 90, 180, 180, 270, 270]
pars['PH2'] = [ 0, 180, 90, 270, 180, 0, 270, 90] # receiver
# read in variables:
P90 = pars['P90']
SF = pars['SF']
O1 = pars['O1']
RD = pars['RD']
DEAD1 = pars['DEAD1']
D8 = pars['D8']
NS = pars['NS']
PH1 = pars['PH1'][run%len(pars['PH1'])]
PH3 = pars['PH3'][run%len(pars['PH3'])]
PH4 = pars['PH4'][run%len(pars['PH4'])]
PH2 = pars['PH2'][run%len(pars['PH2'])]
PHA = pars['PHA']
# F1 sampling parameters:
IN0 = 1./pars['SW'] # t1 increment
# the States-TPPI bit:
PH1-= (run/(1*NS))%4*90 # PH1 changes by 90-deg. after every 1*NS scans
D0 = (run/(2*NS)) *IN0 # t1 increases by IN0 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) # 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(D0) # incremented delay t1
e.set_phase(PH3)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
e.wait(D8) # mixing time
e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
e.set_phase(PHA) # set phase for receiver
e.wait(DEAD1) # wait for coil ringdown
e.record(SI2, SW2, sensitivity=ADCSensitivity) # acquire signal
# write experiment attributes:
for key in pars.keys():
e.set_description(key, pars[key]) # acqusition parameters
e.set_description('run', run) # current scan
e.set_description('rec_phase', -PH2) # current receiver phase
return e

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Scripts/EXSY/op_noesy_res.py Normal file
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# -*- 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 = 0 # counter for arrayed 2D experiments
# loop over the incoming results:
for timesignal in results:
if not isinstance(timesignal,ADC_Result):
continue
# read experiment parameters:
pars = timesignal.get_description_dictionary()
# ---------------- digital filter ------------------
# get actual sampling rate of timesignal:
sampling_rate = timesignal.get_sampling_rate()
# get user-defined spectrum width:
spec_width = pars['SW']
# specify cutoff frequency, in relative units:
cutoff = spec_width / sampling_rate
if cutoff < 1: # otherwise no filter applied
# number of filter's coefficients:
numtaps = 29
# use firwin to create a lowpass FIR filter:
fir_coeff = firwin(numtaps, cutoff)
# downsize x according to user-defined spectral window:
skip = int(sampling_rate / spec_width)
timesignal.x = timesignal.x[::skip]
for i in range(2):
# apply the filter to ith channel:
timesignal.y[i] = lfilter(fir_coeff, 1.0, timesignal.y[i])
# zeroize first N-1 "corrupted" samples:
timesignal.y[i][:numtaps-1] = 0.0
# circular left shift of y:
timesignal.y[i] = roll(timesignal.y[i], -(numtaps-1))
# downsize y to user-defined number of samples (SI):
timesignal.y[i] = timesignal.y[i][::skip]
# update the sampling_rate attribute of the signal's:
timesignal.set_sampling_rate(spec_width)
# ----------------------------------------------------
# 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:
# ----------------------------------------------------------------------------------------
# Note that State-TPPI technique implies recording two data sets at each t1 point.
# Cosine-modulated data are stored in record 1 as Re, and sine-modulated data are stored
# in record 2 as Im, totally 2*SI1 records. Henceforth, accu represents one such a record.
# -----------------------------------------------------------------------------------------
if accu.n == pars['NS']:
# make a copy:
fid = accu + 0
# compute the initial phase of FID:
phi0 = arctan2(fid.y[1][0], fid.y[0][0]) * 180 / pi
if not 'ref' in locals(): ref = phi0
# print 'phi0 = ', phi0
# rotate FID to maximize y[0][0]:
#echo.phase(-phi0)
# check whether it is an arrayed experiment:
var_key = pars.get('VAR_PAR')
if var_key:
# get variable parameter's value:
var_value = pars.get(var_key)
# provide signal recorded with this var_value to the display tab:
data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu
# 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:
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