Add option to suppress ringing in Saturation Recovery script

A parameter option "suppress_ringing" has been added to the Saturation Recovery script. This option modifies phase lists and allows the application of a phase cycle that compensates for ringing but reduces signal-to-noise ratio by half. This gives users the option to prioritize either reduced ringing or higher SNR as per their requirements.

Scripts/Saturation_Recovery/satrec_exp.py

@@ -11,22 +11,21 @@ def experiment(): # saturation-recovery experiment
     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['SW'] = 200e3		# spectral window (Hz)
+    pars['SW'] = 200e3		# sampling rate (Hz)
     pars['SI'] = 1*256		# number of acquisition points
     pars['NS'] = 8		# number of scans
     pars['DS'] = 0		# number of dummy scans
     pars['TAU'] = 1		# delay for recovery (s)
     pars['DEAD1'] = 5e-6	# receiver dead time (s)
-    pars['PHA'] = 100		# receiver phase (degree) 
+    pars['PHA'] = 0		# receiver phase (degree)
       # -*- these aren't variable: -*-
-    pars['NECH'] = 40		# number of saturation pulses
+    pars['NECH'] = 7		# number of saturation pulses
     pars['D1'] = 100e-3		# starting interval in saturation sequence (s) 
     pars['D2'] = 1e-4		# end interval in saturation sequence (s) 
     pars['DATADIR'] = '/home/fprak/Students/'	# data directory
     pars['OUTFILE'] = None			# output file name
 
-  # specify a variable parameter (optional):
+    # specify a variable parameter (optional):
     pars['VAR_PAR'] = 'TAU'	# variable parameter name (a string)   
     start = 1e-3		# starting value
     stop = 5e-0			# end value
@@ -34,7 +33,7 @@ def experiment(): # saturation-recovery experiment
     log_scale = True		# log scale flag 
     stag_range = False		# staggered range flag
 
-  # check parameters for safety: 
+    # check parameters for safety:
     if pars['PHA'] < 0:
         pars['PHA'] = 360 + pars['PHA']
 
@@ -47,8 +46,7 @@ def experiment(): # saturation-recovery experiment
         raise Exception("Pulse too long!!!")
 
     if pars['NS']%4 != 0:
-        pars['NS'] = int(round(pars['NS'] / 4) + 1) * 4 
-        print 'Number of scans changed to ',pars['NS'],' due to phase cycling' 
+        print 'Number of scans should be changed to ',pars['NS'],' due to phase cycling'
 
     if pars['D1'] < pars['D2']:
         raise Exception("D1 must be greater than D2")
@@ -57,7 +55,7 @@ def experiment(): # saturation-recovery experiment
     if sat_length > 1.:
         raise Exception("Saturation sequence too long!!!")   
 
-  # start the experiment:
+    # start the experiment:
     if var_key: 
         # this is an arrayed experiment:
         if log_scale:
@@ -117,8 +115,7 @@ def satrec_experiment(pars, run):
     # read in variables:
     P90 = pars['P90']
     SF =  pars['SF']
-    O1 =  pars['O1']
-    DEAD1 = pars['DEAD1'] 
+    DEAD1 = pars['DEAD1']
     NECH = pars['NECH']
     D1 =  pars['D1']
     D2 =  pars['D2']
@@ -127,21 +124,15 @@ def satrec_experiment(pars, run):
     PH3 = pars['PH3'][run%len(pars['PH3'])]
     PH2 = pars['PH2'][run%len(pars['PH2'])]
     PHA = pars['PHA']
-
-    # set sampling parameters:
-    SI = pars['SI']
-    SW = pars['SW']
-    while SW <= 10e6 and SI < 256*1024:
-        SI *= 2
-        SW *= 2
-
-    # set variable delay list for saturation pulses: 
+    SI = pars["SI"]
+    SW = pars["SW"]
+    # set variable delay list for saturation pulses:
     vdlist = log_range(D2, D1, NECH-1)
 
     # run the pulse sequence:
 
     # saturation:
-    e.set_frequency(SF+O1, phase=PH1)				# set frequency and phase for saturation pulses
+    e.set_frequency(SF, phase=PH1)				# set frequency and phase for saturation pulses
     e.ttl_pulse(TXEnableDelay, value=TXEnableValue)		# enable RF amplifier
     e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue)		# apply 90-degree pulse
     for delay in vdlist[::-1]:
@@ -149,15 +140,15 @@ def satrec_experiment(pars, run):
         e.ttl_pulse(TXEnableDelay, value=TXEnableValue)		# enable RF amplifier
         e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue)	# apply 90-degree pulse
 
-    # recovery:
-    e.wait(TAU)							# recovery time
     e.set_phase(PH3)						# set phase for measuring pulse
+    # recovery:
+    e.wait(TAU-5e-7)							# recovery time
 
     # detection:
     e.ttl_pulse(TXEnableDelay, value=TXEnableValue)		# enable RF amplifier
     e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue)  	# apply 90-degree pulse  
     e.set_phase(PHA)						# set phase for receiver
-    e.wait(DEAD1)                                               # wait for coil ringdown  
+    e.wait(DEAD1-5e-7)                                               # wait for coil ringdown
     e.record(SI, SW, sensitivity=ADCSensitivity)		# acquire signal
 
     # write experiment parameters:  

Scripts/Saturation_Recovery/satrec_res.py

@@ -29,42 +29,6 @@ def result():
         # 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'])
 

Scripts/Saturation_Recovery_with_Solid_Echo_Detection/satrec2_exp.py

@@ -11,23 +11,23 @@ def experiment(): # saturation-recovery with soild-echo detection
     pars = {}
     pars['P90'] = 2.3e-6	# 90-degree pulse length (s)
     pars['SF'] = 46.7e6		# spectrometer frequency (Hz)
-    pars['O1'] = 5.6e3		# 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['TAU'] = 1		# delay for recovery (s)
     pars['D3'] = 20e-6		# echo delay (s)
-    pars['D4'] = 0			# echo pre-aquisition delay (s)
+    pars['D4'] = 0			# pre-aquisition delay (s), use negative values
     pars['PHA'] = -30		# receiver phase (degree)
      # -*- these ain't variable: -*-
-    pars['NECH'] = 40		# number of saturation pulses
+    pars['NECH'] = 7		# number of saturation pulses
     pars['D1'] = 100e-3		# starting interval in saturation sequence (s) 
     pars['D2'] = 1e-4		# end interval in saturation sequence (s) 
     pars['DATADIR'] = '/home/fprak/Students/'	# data directory
     pars['OUTFILE'] = None			# output file name
+    pars["suppress_ringing"] = False # 16 Phase cycle, reduces ringing but halves SNR
 
-  # specify a variable parameter (optional):
+    # specify a variable parameter (optional):
     pars['VAR_PAR'] = 'TAU'	# variable parameter name (a string)   
     start = 1e-4		# starting value
     stop = 1e-0			# end value
@@ -48,8 +48,7 @@ def experiment(): # saturation-recovery with soild-echo detection
         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'
+        print 'Number of scans should be ',pars['NS'],' due to phase cycling'
 
     if pars['D1'] < pars['D2']:
         raise Exception("D1 must be greater than D2!")
@@ -111,16 +110,21 @@ def satrec2_experiment(pars, run):
 
     pars['PROG'] = 'satrec2_experiment'
 
-    # phase lists:
-    pars['PH1'] = [  0] 					# saturation pulses
-    pars['PH3'] = [ 0, 180,   0, 180, 90, 270,  90, 270]	# 1st 90-degree pulse
-    pars['PH4'] = [90,  90, 270, 270,  0,   0, 180, 180]	# 2nd 90-degree pulse
-    pars['PH2'] = [ 0, 180,   0, 180, 90, 270,  90, 270]	# receiver
+    if pars["suppress_ringing"]:
+        # phase cycle to compensate ringing (loss of half the signal!)
+        pars['PH3'] = [ 0,   0,   0,   0,   90,  90,  90,  90,  180, 180, 180, 180, 270, 270, 270, 270]	# 1st 90-degree pulse
+        pars['PH4'] = [ 0,   90,  180, 270, 90,  180, 270, 0,   180, 270, 0,   90,  270, 0,   90,  180]	# 2nd 90-degree pulse
+        pars['PH2'] = [ 180, 0,   180, 0,   270, 90,  270, 90,  0,   180, 0,   180, 90,  270, 90,  270]	# receiver
+    else:
+        # simple phase cycle:
+        pars['PH1'] = [0]  # saturation pulses
+        pars['PH3'] = [0, 180, 0, 180, 90, 270, 90, 270]  # 1st 90-degree pulse
+        pars['PH4'] = [90, 90, 270, 270, 0, 0, 180, 180]  # 2nd 90-degree pulse
+        pars['PH2'] = [0, 180, 0, 180, 90, 270, 90, 270]  # receiver
 
     # read in variables:
     P90 = pars['P90']
     SF =  pars['SF']
-    O1 =  pars['O1']
     NECH = pars['NECH']
     D1 =  pars['D1']
     D2 =  pars['D2']
@@ -132,21 +136,16 @@ def satrec2_experiment(pars, run):
     PH4 = pars['PH4'][run%len(pars['PH4'])]
     PH2 = pars['PH2'][run%len(pars['PH2'])]
     PHA = pars['PHA']
+    SI = pars['SI']
+    SW = pars['SW']
 
     # set variable delay list for saturation pulses: 
     vdlist = log_range(D2, D1, NECH-1)
 
-    # set sampling parameters:
-    SI = pars['SI']
-    SW = pars['SW']
-    while SW <= 10e6 and SI < 256*1024:
-        SI *= 2
-        SW *= 2
-
-    # the pulse sequence: 
+    # the pulse sequence:
 
     # saturation:
-    e.set_frequency(SF+O1, phase=PH1)			# set frequency and phase for saturation pulses
+    e.set_frequency(SF, phase=PH1)			# set frequency and phase for saturation pulses
     e.ttl_pulse(TXEnableDelay, value=TXEnableValue)	# enable RF amplifier
     e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue)	# apply 90-degree pulse
     for delay in vdlist[::-1]:
@@ -154,19 +153,19 @@ def satrec2_experiment(pars, run):
         e.ttl_pulse(TXEnableDelay, value=TXEnableValue)	# enable RF amplifier
         e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue) # apply 90-degree pulse
 
-    # recovery:
-    e.wait(TAU)						# wait for tau
     e.set_phase(PH3)					# set phase for next pulse
-     
+    # recovery:
+    e.wait(TAU-5e-7)						# wait for tau
+
     # 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-TXEnableDelay)			# echo delay
     e.set_phase(PH4)					# set phase for next pulse
+    e.wait(D3-P90-TXEnableDelay-5e-7)			# echo delay
     e.ttl_pulse(TXEnableDelay, value=TXEnableValue)	# enable RF amplifier
     e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue)	# apply 90-degree pulse 
     e.set_phase(PHA)					# set phase for receiver
-    e.wait(D3-P90/2+D4)					# echo delay    
+    e.wait(D3-P90/2+D4-5e-7)					# echo delay
     e.record(SI, SW, sensitivity=ADCSensitivity)	# acquisition
 
     # write experiment attributes:  

Scripts/Saturation_Recovery_with_Solid_Echo_Detection/satrec2_res.py

@@ -29,40 +29,6 @@ def result():
         # 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:

Scripts/Spin_Alignment/spinal_exp.py

@@ -105,7 +105,7 @@ def spinal_experiment(pars, run):
                        
    # 8-step phase cycle (Schaefer et al. J Magn Res A 115 (1995))
     pars['PH1'] = [ 0,   0, 180, 180,  90, 90, 270, 270] # 1st (90-degree) pulse
-    pars['PH3'] = [90, 270,  90, 270, 180, 90, 180,  90] # 2nd (90-degree) pulse
+    pars['PH3'] = [90, 270, 270,  90, 180,  0,   0, 180] # 2nd (90-degree) pulse
     pars['PH4'] = [90]  # 3rd (90-degree) pulse
     pars['PH2'] = [90, 270]  # receiver
         

Scripts/Spin_Alignment_Four_Pulses/spinal4pulses_exp.py

@@ -106,7 +106,7 @@ def spinal4pulses_experiment(pars, run):
                        
    # 8-step phase cycle (Schaefer et al. J Magn Res A 115 (1995))
     pars['PH1'] = [0,    0, 180, 180,  90, 90, 270, 270] # 1st (90-degree) pulse
-    pars['PH3'] = [90, 270,  90, 270, 180, 90, 180,  90] # 2nd (90-degree) pulse
+    pars['PH3'] = [90, 270, 270,  90, 180,  0,   0, 180] # 2nd (90-degree) pulse
     pars['PH4'] = [90] # 3rd (90-degree) pulse
     pars['PH5'] = [90] * 8 + [270] * 8
     pars['PH2'] = [90, 270]  # receiver

Scripts/Zeeman_Order/zeeman_exp.py

@@ -103,8 +103,8 @@ def zeeman_experiment(pars, run):
 
    # 8-step phase cycle (Schaefer et al. J Magn Res A 115 (1995))
     pars['PH1'] = [0,   0, 180, 180, 90,  90, 270, 270] # 1st (90-degree) pulse
-    pars['PH3'] = [0, 180,   0, 180, 90, 180,  90, 180] # 2nd (90-degree) pulse
-    pars['PH4'] = [90]  # 3rd (90-degree) pulse
+    pars['PH3'] = [0, 180, 180,   0, 90, 270, 270,  90] # 2nd (90-degree) pulse
+    pars['PH4'] = [0]  # 3rd (90-degree) pulse
     pars['PH2'] = [90, 270]  # receiver
 
    # read in variables:

Scripts/Zeeman_Order_Four_Pulses/zeeman4pulses_exp.py

@@ -104,7 +104,7 @@ def zeeman4pulses_experiment(pars, run):
     
     # ok 8-step phase cycle (Schaefer et al. J Magn Res A 115 (1995))
     pars['PH1'] = [0,   0, 180, 180, 90,  90, 270, 270] # 1st (90-degree) pulse
-    pars['PH3'] = [0, 180,   0, 180, 90, 180,  90, 270] # 2nd (90-degree) pulse
+    pars['PH3'] = [0, 180, 180,   0, 90, 270, 270,  90] # 2nd (90-degree) pulse
     pars['PH4'] = [0]  # 3rd (90-degree) pulse
     pars['PH5'] = [90] * 8 + [270] * 8
     pars['PH2'] = [90, 270]  # receiver