IPKM/damaris-script-library
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incorprated changes since August

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This commit is contained in:
Oleg Petrov
2015-09-30 11:23:17 +00:00
parent d9beb94422
commit 4ec93a212b
12 changed files with 65 additions and 55 deletions
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34
Scripts/Steady_Gradient_Spin_Echo_with_CPMG_Detection/op_sgse2_exp.py
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@ -3,31 +3,32 @@
TXEnableDelay = 2e-6
TXEnableValue = 0b0001 # TTL line blanking RF amplifier (bit 0)
TXPulseValue = 0b0010 # TTL line triggering RF pulses (bit 1)
ADCSensitivity = 2 # voltage span for ADC
ADCSensitivity = 5 # voltage span for ADC
def experiment(): # the diffusion editing sequence with stimulated echo and CPMG detection
# set up acqusition parameters:
pars = {}
pars['P90'] = 1.7e-6 # 90-degree pulse length (s)
pars['SF'] = 338.7e6 # spectrometer frequency (Hz)
pars['O1'] = -60e3 # offset from SF (Hz)
pars['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'] = 3 # delay between scans (s)
pars['RD'] = 6 # delay between scans (s)
pars['D1'] = 20e-6 # delay after first STE pulse (s)
pars['D2'] = 100e-6 # delay after second STE pulse (s)
pars['NECH'] = 16 # number of 180-degree pulses in the CPMG train
pars['TAU'] = 40e-6 # half pulse period in the CPMG train (s)
pars['PHA'] = -127 # receiver phase (degree)
pars['D2'] = 20e-6 # delay after second STE pulse (s)
pars['D4'] = 2.5e-6 # pre-acquisition delay (s)
pars['NECH'] = 128 # number of 180-degree pulses in the CPMG train
pars['TAU'] = 50e-6 # half pulse period in the CPMG train (s)
pars['PHA'] = -190 # receiver phase (degree)
pars['DATADIR'] = '/home/fprak/Desktop/test/' # data directory
pars['OUTFILE'] = None # output file name
# specify a variable parameter (optional):
pars['VAR_PAR'] = 'D2' # variable parameter name (a string)
start = 20e-6 # starting value
stop = 4e-3 # end value
steps = 3 # number of values
stop = 3e-1 # end value
steps = 24 # number of values
log_scale = True # log scale flag
stag_range = False # staggered range flag
@ -117,6 +118,7 @@ def ste2_experiment(pars, run):
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'])]
@ -143,28 +145,28 @@ def ste2_experiment(pars, run):
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.wait(D1-P90-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.wait(D2-P90-TXEnableDelay) # long delay
e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 3rd 90-degree pulse
e.wait(D1+TAU-P90/2-TXEnableDelay) # wait for first echo and tau
e.wait(D1+TAU-P90/2-P180/2-TXEnableDelay) # wait for first echo and tau
e.set_phase(PH5)
e.loop_start(NECH) # ----- loop for CPMG pulse train: -----
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply a 180-degree pulse
e.set_phase(PHA) # set phase for receiver
e.wait(TAU-(P180+TXEnableDelay+AQ)/2) # pre-acquisition delay
e.wait(TAU-(P180+TXEnableDelay+AQ)/2+D4) # pre-acquisition delay
e.record(SI, SW, timelength=AQ, sensitivity=ADCSensitivity) # acquire echo samples
e.wait(TAU-(P180+TXEnableDelay+AQ)/2) # post-acquisition delay
e.wait(TAU-(P180+TXEnableDelay+AQ)/2-D4) # post-acquisition delay
e.set_phase(PH5) # set phase for theta-degree pulse
e.loop_end() # --------------------------------------

4
Scripts/Steady_Gradient_Spin_Echo_with_CPMG_Detection/op_sgse2_res.py
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@ -77,6 +77,8 @@ def result():
#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]
#echodecay.y[0][i] = max(echo.y[0]) # or maximum echo point
#echodecay.y[1][i] = max(echo.y[1])
# compute a signal's phase:
phi0 = arctan2(echodecay.y[1][0], echodecay.y[0][0]) * 180 / pi
@ -105,7 +107,7 @@ def result():
# print '%s%02g' % ('T2 [s] = ', 1./rate)
# measurand[var_value] = amplitude
measurement[var_value] = sum(echodecay.y[0][:])
measurement[var_value] = sum(echodecay.y[0])
# provide measurement to the display tab:
data[measurement.get_title()] = measurement