IPKM/damaris-script-library
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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6
Scripts/Hahn_Echo/op_hahn_exp.py
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@ -128,12 +128,16 @@ def hahn_experiment(pars, run):
# run the pulse sequence:
e.wait(RD) # delay between scans
e.set_frequency(SF+O1, phase=PH1) # set frequency and phase for 1st RF pulse
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 1st 90-degree pulse
e.wait(TAU-P90/2-TXEnableDelay) # wait for TAU
e.wait(TAU-P90/2-P180/2-TXEnableDelay) # wait for TAU
e.set_phase(PH3) # set phase for 2nd 90-degree pulse
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enalble RF amplifier
e.ttl_pulse(P180, value=TXEnableValue|TXPulseValue) # apply 2nd 90-degree pulse
e.set_phase(PHA) # set phase for receiver
e.wait(TAU-P180/2+D4) # wait for TAU
e.record(SI, SW, sensitivity=ADCSensitivity) # acquire echo points

2
Scripts/Saturation_Recovery_with_Solid_Echo_Detection/op_satrec2_exp.py
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@ -161,7 +161,7 @@ def satrec2_experiment(pars, run):
# echo detection:
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
e.wait(D3-P90/2-TXEnableDelay) # echo delay
e.wait(D3-P90-TXEnableDelay) # echo delay
e.set_phase(PH4) # set phase for next pulse
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse

2
Scripts/Solid_Echo/op_solidecho_exp.py
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@ -130,7 +130,7 @@ def solidecho_experiment(pars, run):
e.set_frequency(SF+O1, phase=PH1) # set frequency and phase for 1st RF pulse
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enable RF amplifier
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 1st 90-degree pulse
e.wait(TAU-P90/2-TXEnableDelay) # wait for TAU
e.wait(TAU-P90-TXEnableDelay) # wait for TAU
e.set_phase(PH3) # set phase for 2nd 90-degree pulse
e.ttl_pulse(TXEnableDelay, value=TXEnableValue) # enalble RF amplifier
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 2nd 90-degree pulse

30
Scripts/Spin_Alignment/op_spinal_exp.py
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@ -1,25 +1,25 @@
# -*- coding: iso-8859-1 -*-
TXEnableDelay = 2e-6
TXEnableDelay = 1e-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 = 1 # voltage span for ADC
def experiment(): # Jeener-Broekaert echo sequence (a.k.a. spin-alignment)
# set up acquisition parameters:
pars = {}
pars['P90'] = 2.3e-6 # 90-degree pulse length (s)
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'] = 1e6 # spectral window (Hz)
pars['SI'] = 1*512 # number of acquisition points
pars['NS'] = 8 # number of scans
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'] = 3 # delay between scans (s)
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['PHA'] = -36 # receiver phase (degree)
pars['PHA'] = -52 # receiver phase (degree)
pars['DATADIR'] = '/home/fprak/Students/' # data directory
pars['OUTFILE'] = None # output file name
@ -104,10 +104,10 @@ def spinal_experiment(pars, run):
pars['PROG'] = 'spinal_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, 90, 90, 180, 180 ] # 1st (90-degree) pulse
pars['PH3'] = [90,180, 90, 180, 180, 180, 90, 90 ] # 2nd (45-degree) pulse
pars['PH4'] = [90, 90, 270, 270, 180, 0, 0, 180 ] # 3rd (45-degree) pulse
pars['PH2'] = [0, 180, 180, 0, 90, 270, 90, 270 ] # receiver
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['PH2'] = [0, 180, 180, 0, 90, 270, 270, 90] # receiver
# read in variables:
P90 = pars['P90']
@ -137,13 +137,13 @@ def spinal_experiment(pars, run):
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
e.wait(D1-P90/2-TXEnableDelay) # 'short tau'
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-TXEnableDelay) # 'long tau'
e.wait(D2-P45-TXEnableDelay) # 'long tau'
e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
@ -151,7 +151,7 @@ def spinal_experiment(pars, run):
e.wait(TXEnableDelay)
e.set_phase(PHA)
e.wait(5e-6)#D1-P45/2-TXEnableDelay) # 'short tau'
e.wait(D1-P45/2-TXEnableDelay) # 'short tau'
e.record(SI, SW, sensitivity=ADCSensitivity) # acquisition
# write experiment parameters:

4
Scripts/Spin_Alignment_Spin32/op_spinal32_exp.py
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@ -137,13 +137,13 @@ def spinal32_experiment(pars, run):
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
e.wait(D1-P90/2-TXEnableDelay) # 'short tau'
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-TXEnableDelay) # 'long tau'
e.wait(D2-P45-TXEnableDelay) # 'long tau'
e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)

4
Scripts/Steady_Gradient_Spin_Echo/op_sgse_exp.py
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@ -134,13 +134,13 @@ def ste_experiment(pars, run):
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
e.wait(D1-P90/2-TXEnableDelay) # 'short tau'
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-P90/2-TXEnableDelay) # 'long tau'
e.wait(D2-P90-TXEnableDelay) # 'long tau'
e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)

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

20
Scripts/T1Q/op_t1q_exp.py
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@ -9,22 +9,22 @@ def experiment(): # Jeener-Broekaert sequence with solid-echo detection to measu
# set up acquisition parameters:
pars = {}
pars['P90'] = 2.3e-6 # 90-degree pulse length (s)
pars['P90'] = 4.2e-6 # 90-degree pulse length (s)
pars['SF'] = 46.7e6 # spectrometer frequency (Hz)
pars['O1'] = 5.6e3 # offset from SF (Hz)
pars['SW'] = 200e3 # spectrum width (Hz)
pars['SI'] = 1*256 # number of acquisition points
pars['NS'] = 32 # number of scans
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'] = 30e-6 # delay after second pulse or 'long tau' (s)
pars['PHA'] = -27 # receiver phase (degree)
pars['D2'] = 30e-1 # delay after second pulse or 'long tau' (s)
pars['PHA'] = -40 # 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)
pars['VAR_PAR'] = None#'D2' # variable parameter name (a string)
start = 30e-6 # starting value
stop = 2e-0 # end value
steps = 16 # number of values
@ -109,7 +109,6 @@ def t1q_experiment(pars, run):
pars['PH5'] = [0, 0, 180, 180, 270, 90, 90, 270] # refocucing 90-deg pulse
pars['PH2'] = [0, 180, 0, 180, 180, 0, 180, 0] # receiver
# read in variables:
P90 = pars['P90']
P45 = pars['P90']*0.5
@ -125,6 +124,9 @@ def t1q_experiment(pars, run):
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']
@ -138,13 +140,13 @@ def t1q_experiment(pars, run):
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
e.wait(D1-P90/2-TXEnableDelay) # 'short tau'
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-TXEnableDelay) # 'long tau'
e.wait(D2-P45-TXEnableDelay) # 'long tau'
e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
@ -157,7 +159,7 @@ def t1q_experiment(pars, run):
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
e.set_phase(PHA)
e.wait(13e-6)
e.wait(12e-6)
e.record(SI, SW, sensitivity=ADCSensitivity) # acquisition
# write experiment attributes:

6
Scripts/T2_Filtered_ZZ_Exchange/op_t2zz_exp.py → Scripts/T2_Filtered_ZZ-Exchange/op_t2zz_exp.py
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@ -141,19 +141,19 @@ def t2zz_experiment(pars, run):
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 1st pulse
e.wait(D1-P90/2-TXEnableDelay) # echo delay
e.wait(D1-P90-TXEnableDelay) # echo delay
e.set_phase(PH3)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 2nd pulse (90- or 180-degree)
e.wait(D1-P90/2-TXEnableDelay) # echo delay
e.wait(D1-P90-TXEnableDelay) # echo delay
e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 3rd pulse (z-storage pulse)
e.wait(D2-P90/2-TXEnableDelay) # mixing time
e.wait(D2-P90-TXEnableDelay) # mixing time
e.set_phase(PH5)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)

0
Scripts/T2_Filtered_ZZ_Exchange/op_t2zz_res.py → Scripts/T2_Filtered_ZZ-Exchange/op_t2zz_res.py
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4
Scripts/Zeeman_Order/op_zeeman_exp.py
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@ -133,13 +133,13 @@ def zeeman_experiment(pars, run):
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # 90-degree pulse
e.wait(D1-P90/2-TXEnableDelay) # 'short tau'
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-P90/2-TXEnableDelay) # 'long tau'
e.wait(D2-P90-TXEnableDelay) # 'long tau'
e.set_phase(PH4)
e.ttl_pulse(TXEnableDelay, value=TXEnableValue)