def runExperiment():
global my_SRS
#Plotting setup, xs is the frequencies, ys is the average intensities for the signal, bys is avg intensities for background
style.use("fivethirtyeight")
fig = plt.figure()
ax1 = fig.add_subplot(1, 1, 1)
xs = []
ys = []
bys = []
initPB()
#initiate RF generator with channel and model type; set amplitude
my_SRS = SRSctl.initSRS(27, 'SG386')
SRSctl.setSRS_RFAmplitude(my_SRS, .14, units="Vpp")
#set test frequency and modulation
SRSctl.setSRS_Freq(my_SRS, config['START_FREQUENCY'], 'GHz')
SRSctl.setupSRSmodulation(my_SRS, config['sequence_name'])
#Get the instruction Array
instructionArray = PBctl.programPB(config['sequence_name'],
[config['t_AOM']])
print(instructionArray)
#Program the PulseBlaster
status = pb_start_programming(PULSE_PROGRAM)
for i in range(0, len(instructionArray)):
PBctl.pb_inst_pbonly(instructionArray[i][0], instructionArray[i][1],
instructionArray[i][2], instructionArray[i][3])
pb_stop_programming()
#Configure the DAQ
global task
task = DAQ.configureDAQ(ESR.Nsamples)
#turn on the microwave excitation - changed the sequence here, zhao, 02/24/2020
SRSctl.enableSRS_RFOutput(my_SRS)
global f
#Set f to be the start frequency
f = config['START_FREQUENCY']
#start the pulse blaster # you can start pulseblaster at the beginning the experiment and turn it off until everything is done -- Zhao, 6/11/2020
pb_start()
#Throw away the first NThrow samples to get the photodiode warmed up
for i in range(NThrow):
DAQ.readDAQ(task, ESR.Nsamples * 2, 10)
#Begin the animation - All of the experiment work is done in the animate function. FuncAnimation runs animate in a loop automatically
ani = animation.FuncAnimation(
fig, animate, fargs=(xs, ys, bys), interval=200
) ## not sure if this is the best approach. maybe try to use the "frames" variable for this function -- Zhao, 6/11/2020
def runExperiment(expConfigFile):
# This function runs the experiment with input parameters configured by the user in the experiment config file (e.g. ESRconfig, Rabiconfig, etc) and plots and saves the data.
try:
'''Runs the experiment.'''
expCfg = import_module(expConfigFile)
expCfg.N_scanPts = len(expCfg.scannedParam) #protection against non-integer user inputs for N_scanPts.
validateUserInput(expCfg)
#Check if save directory exists, and, if not, creates a "Saved Data" folder in the current directory, where all data will be saved.
if not (isdir(expCfg.savePath)):
makedirs(expCfg.savePath)
print('Warning: Save directory did not exist, creating folder named Saved_Data in the working directory. Data will be saved to this directory.')
#Initialise SRS and program PulseBlaster
SRS = SRSctl.initSRS(conCfg.GPIBaddr,conCfg.modelName)
SRSctl.setSRS_RFAmplitude(SRS,expCfg.microwavePower)
SRSctl.setupSRSmodulation(SRS,expCfg.sequence)
sequenceArgs = expCfg.updateSequenceArgs()
expParamList = expCfg.updateExpParamList()
if expCfg.sequence != 'ESRseq':
SRSctl.setSRS_Freq(SRS, expCfg.microwaveFrequency)
#Program PB
seqArgList = [expCfg.scannedParam[-1]]
seqArgList.extend(sequenceArgs)
instructionArray=PBctl.programPB(expCfg.sequence,seqArgList)
else:
SRSctl.setSRS_Freq(SRS, expCfg.scannedParam[0])
#Program PB
instructionArray=PBctl.programPB(expCfg.sequence,sequenceArgs)
SRSctl.enableSRS_RFOutput(SRS)
#Configure DAQ
DAQclosed = False
DAQtask = DAQctl.configureDAQ(expCfg.Nsamples)
if expCfg.plotPulseSequence:
# Plot sequence
plt.figure(0)
[t_us,channelPulses,yTicks]=seqCtl.plotSequence(instructionArray,expCfg.PBchannels)
for channel in channelPulses:
plt.plot(t_us, list(channel))
plt.yticks(yTicks)
plt.xlabel('time (us)')
plt.ylabel('channel')
# If we are plotting a Rabi with pulse length <5*t_min, warn the user in the sequence plot title that the instructions sent to the PulseBlaster microwave channel are for a 5*t_min pulse, but that the short pulse flags are simultaneously pulsed to produce the desired pulse length
if expCfg.sequence == 'RabiSeq' and (seqArgList[0]<(5*t_min)):
plt.title('Pulse Sequence plot (at last scan point). Close to proceed with experiment...\n(note: we plot the instructions sent to the PulseBlaster (PB) for each channel. For microwave pulses<',5*t_min,'ns, the microwave\nchannel (PB_MW) is instructed to pulse for',5*t_min,'ns, but the short-pulse flags of the PB are pulsed simultaneously (not shown) to\nproduce the desired output pulse length at PB_MW. This can be verified on an oscilloscope.)', fontsize=7)
else:
plt.title('Pulse Sequence plot (at last scan point)\n close to proceed with experiment...')
plt.show()
#Initialize data arrays
meanSignalCurrentRun = np.zeros(expCfg.N_scanPts)
meanBackgroundCurrentRun = np.zeros(expCfg.N_scanPts)
contrastCurrentRun = np.zeros(expCfg.N_scanPts)
signal = np.zeros([expCfg.N_scanPts,expCfg.Navg])
background = np.zeros([expCfg.N_scanPts,expCfg.Navg])
contrast = np.zeros([expCfg.N_scanPts,expCfg.Navg])
#Run experiment
for i_run in range (0,expCfg.Navg):
print('Run ',i_run+1,' of ',expCfg.Navg)
if expCfg.randomize:
if i_run>0:
shuffle(expCfg.scannedParam)
for i_scanPoint in range (0, expCfg.N_scanPts):
#setup next scan iteration (e.g. for ESR experiment, change microwave frequency; for T2 experiment, reprogram pulseblaster with new delay)
if expCfg.sequence == 'ESRseq':
SRSctl.setSRS_Freq(SRS, expCfg.scannedParam[i_scanPoint])
else:
seqArgList[0] = expCfg.scannedParam[i_scanPoint]
instructionArray= PBctl.programPB(expCfg.sequence,seqArgList)
print('Scan point ',i_scanPoint+1,' of ',expCfg.N_scanPts)
#read DAQ
cts=DAQctl.readDAQ(DAQtask,2*expCfg.Nsamples,expCfg.DAQtimeout)
#Extract signal and background counts
sig = cts[0::2]
bkgnd = cts[1::2]
#Take average of counts
meanSignalCurrentRun[i_scanPoint] = np.mean(sig)
meanBackgroundCurrentRun[i_scanPoint] = np.mean(bkgnd)
if expCfg.shotByShotNormalization:
contrastCurrentRun[i_scanPoint] = np.mean(calculateContrast(expCfg.contrastMode,sig,bkgnd))
else:
contrastCurrentRun[i_scanPoint] = calculateContrast(expCfg.contrastMode,meanSignalCurrentRun[i_scanPoint],meanBackgroundCurrentRun[i_scanPoint])
if i_run==0:
if expCfg.livePlotUpdate:
xValues=expCfg.scannedParam[0:i_scanPoint+1]
plt.plot([x/expCfg.plotXaxisUnits for x in xValues],contrastCurrentRun[0:i_scanPoint+1], 'b-')
plt.ylabel('Contrast')
plt.xlabel(expCfg.xAxisLabel)
plt.draw()
plt.pause(0.0001)
# Save data at intervals dictated by saveSpacing_inPulseLengthPts and at final delay point
if (i_scanPoint%expCfg.saveSpacing_inScanPts == 0) or (i_scanPoint==expCfg.N_scanPts-1):
data = np.zeros([i_scanPoint+1,3])
data[:,0] = expCfg.scannedParam[0:i_scanPoint+1]
data[:,1] = meanSignalCurrentRun[0:i_scanPoint+1]
data[:,2] = meanBackgroundCurrentRun[0:i_scanPoint+1]
dataFile = open(expCfg.dataFileName, 'w')
for line in data:
dataFile.write("%.0f\t%.8f\t%.8f\n" % tuple(line))
paramFile = open(expCfg.paramFileName, 'w')
expParamList[1] = i_scanPoint+1
paramFile.write(expCfg.formattingSaveString % tuple(expParamList))
dataFile.close()
paramFile.close()
#Sort current run counts in order of increasing delay
dataCurrentRun = np.transpose(np.array([expCfg.scannedParam,meanSignalCurrentRun,meanBackgroundCurrentRun,contrastCurrentRun]))
sortingIndices = np.argsort(dataCurrentRun[:,0])
dataCurrentRun = dataCurrentRun[sortingIndices]
#Fill in current run data:
sortedScanParam = dataCurrentRun[:,0]
signal[:,i_run] = dataCurrentRun[:,1]
background[:,i_run] = dataCurrentRun[:,2]
contrast[:,i_run] = dataCurrentRun[:,3]
#Update quantities for plotting
updatedSignal = np.mean(signal[:,0:i_run+1],1)
updatedBackground = np.mean(background[:,0:i_run+1],1)
updatedContrast = np.mean(contrast[:,0:i_run+1],1)
#Update plot:
if expCfg.livePlotUpdate:
plt.clf()
plt.plot([x/expCfg.plotXaxisUnits for x in sortedScanParam] ,updatedContrast,'b-')
plt.ylabel('Contrast')
plt.xlabel(expCfg.xAxisLabel)
plt.draw()
plt.pause(0.001)
# Save data at intervals dictated by saveSpacing_inAverages and after final scan
if (i_run%expCfg.saveSpacing_inAverages == 0) or (i_run==expCfg.Navg-1):
data = np.zeros([expCfg.N_scanPts,3])
data[:,0] = sortedScanParam
data[:,1] = updatedSignal
data[:,2] = updatedBackground
dataFile = open(expCfg.dataFileName, 'w')
for item in data:
dataFile.write("%.0f\t%.8f\t%.8f\n" % tuple(item))
paramFile = open(expCfg.paramFileName, 'w')
expParamList[3] = i_run+1
paramFile.write(expCfg.formattingSaveString % tuple(expParamList))
dataFile.close()
paramFile.close()
#Turn off SRS output
SRSctl.disableSRS_RFOutput(SRS)
#Close DAQ task:
DAQctl.closeDAQTask(DAQtask)
DAQclosed=True
plt.show()
except KeyboardInterrupt:
print('User keyboard interrupt. Quitting...')
sys.exit()
finally:
if 'SRS' in vars():
#Turn off SRS output
SRSctl.disableSRS_RFOutput(SRS)
if ('DAQtask' in vars()) and (not DAQclosed):
#Close DAQ task:
DAQctl.closeDAQTask(DAQtask)
DAQclosed=True
# Configure the core clock
pb_core_clock(500.0)
#Get the first instruction Array
instructionArray = PBctl.programPB(sequence_name, sequenceArgs)
print(instructionArray)
#Program the PulseBlaster
status = pb_start_programming(PULSE_PROGRAM)
for i in range(0, len(instructionArray)):
PBctl.pb_inst_pbonly(instructionArray[i][0], instructionArray[i][1],
instructionArray[i][2], instructionArray[i][3])
pb_stop_programming()
#Configure the DAQ
task = DAQ.configureDAQ(RABI.Nsamples)
#turn on the microwave excitation - changed the sequence here, zhao, 02/24/2020
#SRSctl.enableSRS_RFOutput(my_SRS) UNCOMMENT THIS!
#Set t to be the start time and initalize the average variable to 0
t = START_LENGTH
average = 0
#Throw away the first NThrow samples to get the photodiode warmed up
for i in range(NThrow):
pb_start()
DAQ.readDAQ(task, RABI.Nsamples * 2, 10)
pb_stop()
print('Error: startDelay is too short. Please set startDelay>',5*t_min,'ns.')
sys.exit()
if startDelay%(t_min):
startDelay = t_min*round(startDelay/t_min)
print('Warning: startDelay is not a multiple of',t_min,'ns. Rounding...\nstartDelay now set to:',startDelay,'ns.')
t_readoutDelay = np.linspace(startDelay,endDelay, N_scanPts, endpoint=True)
stepSize = t_readoutDelay[1]-t_readoutDelay[0]
if (stepSize%t_min):
roundedStepSize = t_min*round(stepSize/t_min)
endDelay = (N_scanPts-1)*roundedStepSize + startDelay
print('Warning: requested time step is ',stepSize,'ns, which is not an integer multiple of ',t_min,'ns. Rounding step size to the nearest multiple of ',t_min,':\nStep size is now',roundedStepSize,'.\nstartDelay=',startDelay,' and \nendDelay=',endDelay)
t_readoutDelay = np.linspace(startDelay,endDelay, N_scanPts, endpoint=True)
#Configure DAQ
DAQclosed = False
DAQtask = DAQctl.configureDAQ(Nsamples)
fluorescence = np.zeros(N_scanPts)
if plotPulseSequence:
instructionArray= PBctl.programPB('optimReadoutSeq', [t_readoutDelay[-1],t_AOM])
[t_us,channelPulses,yTicks]=seqCtl.plotSequence(instructionArray,PBchannels)
plt.figure(0)
for channel in channelPulses:
plt.plot(t_us, list(channel))
plt.yticks(yTicks)
plt.xlabel('time (us)')
plt.ylabel('channel')
plt.title('Pulse Sequence plot (at last scan point)')
#Run readout delay scan:
for i in range (0, N_scanPts):