incorprated changes since August

Scripts/Hahn_Echo/op_hahn_exp.py

@@ -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

Scripts/Saturation_Recovery_with_Solid_Echo_Detection/op_satrec2_exp.py

@@ -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 

Scripts/Solid_Echo/op_solidecho_exp.py

@@ -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
@@ -144,4 +144,4 @@ def solidecho_experiment(pars, run):
     e.set_description('run', run)		# current scan
     e.set_description('rec_phase', -PH2)	# current receiver phase
 
-    return e
+    return e

Scripts/Spin_Alignment/op_spinal_exp.py

@@ -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['SW'] = 10e6    	# spectral window (Hz)
-    pars['SI'] = 1*512  	# number of acquisition points
+    pars['SI'] = 1*1024  	# number of acquisition points
-    pars['NS'] = 8		# number of scans
+    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['PH1'] = [0,  270,   0, 270,   180,  90, 180,  90] # 1st (90-degree) pulse
-    pars['PH3'] = [90,180,  90, 180,    180, 180,  90,  90 ] # 2nd (45-degree) pulse
+    pars['PH3'] = [90, 180,  90, 180,    90, 180,  90, 180] # 2nd (90-degree) pulse
-    pars['PH4'] = [90, 90, 270, 270,    180,   0,   0, 180 ] # 3rd (45-degree) pulse
+    pars['PH4'] = [90,  90, 270, 270,     0,   0, 180, 180]  # 3rd (90-degree) pulse
-    pars['PH2'] = [0, 180, 180,   0,     90, 270,  90, 270 ] # receiver
+    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:

Scripts/Spin_Alignment_Spin32/op_spinal32_exp.py

@@ -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)		

Scripts/Steady_Gradient_Spin_Echo/op_sgse_exp.py

@@ -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)		

Scripts/Steady_Gradient_Spin_Echo_with_CPMG_Detection/op_sgse2_exp.py

@@ -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['P90'] = 0.8e-6	# 90-degree pulse length (s)
-    pars['SF'] = 338.7e6  	# spectrometer frequency (Hz)
+    pars['SF'] = 161.85e6  	# spectrometer frequency (Hz)
-    pars['O1'] = -60e3		# offset from SF (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['D2'] = 20e-6		# delay after second STE pulse (s) 
-    pars['NECH'] = 16   	# number of 180-degree pulses in the CPMG train
+    pars['D4'] = 2.5e-6         # pre-acquisition delay (s) 
-    pars['TAU'] = 40e-6         # half pulse period in the CPMG train (s)
+    pars['NECH'] = 128   	# number of 180-degree pulses in the CPMG train
-    pars['PHA'] = -127   	# receiver phase (degree) 
+    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
+    stop = 3e-1			# end value
-    steps = 3			# number of values
+    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()                                	# --------------------------------------
 

Scripts/Steady_Gradient_Spin_Echo_with_CPMG_Detection/op_sgse2_res.py

@@ -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

Scripts/T1Q/op_t1q_exp.py

@@ -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['D2'] = 30e-1		# delay after second pulse or 'long tau' (s) 
-    pars['PHA'] = -27		# receiver phase (degree)
+    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
@@ -124,6 +123,9 @@ def t1q_experiment(pars, run):
     PH5 = pars['PH5'][run%len(pars['PH5'])]
     PH2 = pars['PH2'][run%len(pars['PH2'])]
     PHA = pars['PHA']
+   
+    if (run/8)%2 != 0:
+        PH5 += 180
 
     # set sampling parameters:
     SI = pars['SI']
@@ -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:  

Scripts/T2_Filtered_ZZ-Exchange/op_t2zz_exp.py

@@ -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)		

Scripts/Zeeman_Order/op_zeeman_exp.py

@@ -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)
@@ -156,4 +156,4 @@ def zeeman_experiment(pars, run):
     e.set_description('run', run)		# current scan
     e.set_description('rec_phase', -PH2)	# current receiver phase
 
-    return e
+    return e