Merge branch 'master' of ssh://chaos3.fkp.physik.tu-darmstadt.de/diffusion/DSL/damaris-script-library

README.md

@@ -7,4 +7,30 @@ You can get a clone of this repository via:
 
 Details of the pulse programs can be found [[https://chaos3.fkp.physik.tu-darmstadt.de/diffusion/DSL/browse/master/The%20DAMARIS%20Script%20Library.pdf | here]].
 
+
+## For people working with this and thy want to revert the local changes:
+
+(This is from [[https://stackoverflow.com/questions/1146973/how-do-i-revert-all-local-changes-in-git-managed-project-to-previous-state|from StackOverflow]])
+If you want to revert changes made to your working copy, do this:
+
+    git checkout .
+
+If you want to revert changes made to the index (i.e., that you have added), do this. Warning this will reset all of your unpushed commits to master!:
+
+    git reset
+
+If you want to revert a change that you have committed, do this:
+
+    git revert <commit 1> <commit 2>
+
+If you want to remove untracked files (e.g., new files, generated files):
+
+    git clean -f
+
+Or untracked directories (e.g., new or automatically generated directories):
+
+    git clean -fd
+
+
+
 Current maintainer of this library is @markusro.

Scripts/Miscellaneous/PhaseTest/README.md

@@ -0,0 +1,7 @@
+Phase Test
+==========
+This script helps in testing the correct function of the phase programming 
+of RF sources. It measures a first and second, albeit phase shifted, 
+interval and calculatets the dot product of these to intervals. 
+The result should be a smooth full period of a cosine.
+

Scripts/Miscellaneous/PhaseTest/phase_exp.py

@@ -0,0 +1,25 @@
+import numpy as N
+# connect PTS RF source to ADC card, set to generate a few MHz
+# result should be a fulle period of sine/cosine
+def experiment():
+    #step = 0.36 # for PTS 500
+    step = 0.225 # for PTS 310
+    for i in list(xrange(1)): # number of periods
+        samples = 2048
+        print samples
+        for phase in N.arange(0,360,step):
+            #phase=ph
+            e=Experiment()
+            #e.set_frequency(1e6,0)
+            e.wait(20e-6)
+            e.set_description("phase", phase)
+            e.set_description("i", i)
+            e.set_phase(0.0)
+            #e.loop_start(1)
+            e.wait(20e-6)
+            e.record(samples, 20e6,sensitivity=10)
+            e.set_phase(phase)
+            e.wait(20e-6)
+            #e.loop_end()
+            e.record(samples, 20e6,sensitivity=10)
+            yield e

Scripts/Miscellaneous/PhaseTest/phase_res.py

@@ -0,0 +1,23 @@
+import numpy
+
+def result():
+    o=MeasurementResult("overview")
+    for r in results:
+        if r is None: continue
+        #print r
+        data["single scan"]=r
+        phase = r.get_description("phase")
+        i = int(r.get_description("i"))
+        r1=numpy.array(r.get_result_by_index(0).y[0], dtype="Float64")
+        r2=numpy.array(r.get_result_by_index(1).y[0], dtype="Float64")
+        #print r1
+        r1-=r1.mean()
+        r1/=r1.std()
+        r2-=r2.mean()
+        r2/=r2.std()
+        
+        c = numpy.dot(r1, r2)
+        print c
+        o[phase+360*i]=AccumulatedValue(c)
+        
+        data["overview"]=o

Scripts/PFG/Stimulated_Echo/pfg_ste_exp.py

@@ -0,0 +1,174 @@
+# -*- coding: iso-8859-1 -*-
+
+TXEnableDelay = 2e-6 # test
+TXEnableValue = 0b0001	# TTL line enabling RF amplifier (bit 0)
+TXPulseValue  = 0b0010	# TTL line triggering RF pulses  (bit 1)
+ADCSensitivity = 2	# voltage span for ADC
+DAC_conv = 6.32e-5 # T/dac_value
+
+def experiment(): # stimulated echo experiment
+
+  # set up acquisition parameters:
+    pars = {}
+    pars['P90'] = 3.2e-6	# 90-degree pulse length (s)
+    pars['SF'] = 338.7e6	# spectrometer frequency (Hz)
+    pars['O1'] = -87e3		# offset from SF (Hz)
+    pars['SW'] = 500e3		# spectrum width (Hz)
+    pars['SI'] = 8*1024		# number of acquisition points
+    pars['NS'] = 16*2		# number of scans
+    pars['DS'] = 0		# number of dummy scans
+    pars['RD'] = 3*7.7		# delay between scans (s)
+    pars['D1'] = 1e-3		# delay after first pulse (short tau) (s)
+    pars['D2'] = 50e-3		# delay after second pulse (long tau) (s) 
+    pars['D4'] = 0e-6		# echo pre-acquisition delay (s)
+    pars["DAC1"] = 1000		# DAC value (PFG)
+    pars["D5"] = 0.9e-3	# PFG pulse length
+    pars['PHA'] = 30+180		# receiver phase (degree) 
+    pars['DATADIR'] = '/home/markusro/STE'	# data directory
+    pars['OUTFILE'] = ""			# output file name
+
+  # specify a variable parameter (optional):
+    pars['VAR_PAR'] = "DAC1"	# variable parameter name (a string)   
+    start = 0		# starting value
+    stop = int(5/DAC_conv) #1.5e5			# end value
+    steps = 21			# number of values
+    log_scale = False		# log scale flag 
+    stag_range = False		# staggered range flag
+
+  # check parameters for safety: 
+    if pars['PHA'] < 0:
+        pars['PHA'] = 360 + pars['PHA']
+
+    if pars['P90'] > 20e-6:
+        raise Exception("Pulse too long!!!")
+
+    # check whether a variable parameter is named: 
+    var_key = pars.get('VAR_PAR')
+    if var_key == 'P90' and (start > 20e-6 or stop > 20e-6):
+        raise Exception("Pulse too long!!!")
+
+    if pars['NS']%16 != 0:
+        pars['NS'] = int(round(pars['NS'] / 16) + 1) * 16 
+        print 'Number of scans changed to ',pars['NS'],' due to phase cycling'
+
+   # start the experiment:
+
+    # check if a variable parameter is named: 
+    var_key = pars.get('VAR_PAR')
+    if var_key: 
+        # this is an arrayed experiment:
+        if log_scale:
+            array = log_range(start,stop,steps)
+        else:
+            array = lin_range(start,stop,steps)
+
+        if stag_range:
+            array = staggered_range(array, size = 2)
+
+        # estimate the experiment time:
+        if var_key == 'D1':
+            seconds = (sum(array)*2 + (pars['D2'] + pars['RD']) * steps) * (pars['NS'] + pars['DS'])
+        elif var_key == 'D2':
+            seconds = (sum(array) + (pars['D1']*2 + pars['RD']) * steps) * (pars['NS'] + pars['DS'])
+        elif var_key == 'RD':
+            seconds = (sum(array) + (pars['D1']*2 + pars['D2']) * steps) * (pars['NS'] + pars['DS'])
+        else:
+            seconds = (pars['D1']*2 + pars['D2'] + pars['RD']) * steps * (pars['NS']+ pars['DS'])
+        m, s = divmod(seconds, 60)
+        h, m = divmod(m, 60)
+        print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
+
+        # loop for a variable parameter:
+        for index, pars[var_key] in enumerate(array):
+            print 'Arrayed experiment for '+var_key+': run = '+str(index+1)+\
+                             ' out of '+str(array.size)+': value = '+str(pars[var_key])
+            # loop for accumulation:
+            for run in xrange(pars['NS']+pars['DS']):
+                yield ste_experiment(pars, run) 
+            synchronize()
+    else:
+        # estimate the experiment time:
+        seconds = (pars['D1']*2 + pars['D2'] + pars['RD']) * (pars['NS']+ pars['DS'])
+        m, s = divmod(seconds, 60)
+        h, m = divmod(m, 60)
+        print '%s%02d:%02d:%02d' % ('Experiment time estimated: ', h, m, s)
+
+        # loop for accumulation:
+        for run in xrange(pars['NS']+pars['DS']):
+            yield ste_experiment(pars, run)
+
+
+# the pulse program:
+
+def ste_experiment(pars, run):
+    e=Experiment()
+
+    dummy_scans = pars.get('DS')
+    if dummy_scans:
+        run -= dummy_scans
+
+    pars['PROG'] = 'ste_experiment'
+
+    # phase lists [16-phase cycle from JMR 157, 31 (2002)]:
+    pars['PH1'] = [0, 180,   0, 180,   0, 180,   0, 180,  90, 270,  90, 270,  90, 270,  90, 270] # 1st 90-degree pulse
+    pars['PH3'] = [0,   0, 180, 180,   0,   0, 180, 180,   0,   0, 180, 180,   0,   0, 180, 180] # 2nd 90-degree pulse
+    pars['PH4'] = [0,   0,   0,   0, 180, 180, 180, 180,   0,   0,   0,   0, 180, 180, 180, 180] # 3nd 90-degree pulse
+    pars['PH2'] = [0, 180, 180,   0, 180,   0,   0, 180, 270,  90,  90, 270,  90, 270, 270,  90] # receiver
+
+    # read in variables:
+    P90 = pars['P90']
+    SF =  pars['SF']
+    O1 =  pars['O1']
+    RD =  pars['RD']
+    D1 =  pars['D1']
+    D2 =  pars['D2']
+    D4 =  pars['D4']
+    D5 =  pars['D5']
+    DAC1 =  pars['DAC1']
+    PH1 = pars['PH1'][run%len(pars['PH1'])]
+    PH3 = pars['PH3'][run%len(pars['PH3'])]
+    PH4 = pars['PH4'][run%len(pars['PH4'])]
+    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
+
+   # run the pulse sequence: 
+    e.wait(RD)						# delay between scans
+    e.set_frequency(SF+O1, phase=PH1)
+    e.ttl_pulse(TXEnableDelay, value=TXEnableValue)
+    e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue)	# 90-degree pulse 
+
+    e.set_phase(PH3)
+    
+    e.set_pfg(dac_value=DAC1, length=D5, shape=("rec",100e-6))
+    e.wait(D1-P90/2-TXEnableDelay - D5)			# 'short tau'
+
+    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.set_phase(PH4)
+
+    e.ttl_pulse(TXEnableDelay, value=TXEnableValue)		
+    e.ttl_pulse(P90, value=TXEnableValue|TXPulseValue)	# 90-degree pulse
+
+    e.set_phase(PHA)
+    
+    e.set_pfg(dac_value=DAC1, length=D5, shape=("rec",100e-6))
+    e.wait(D1-P90/2-TXEnableDelay+D4-D5)      		# 'short tau'
+    e.record(SI, SW, sensitivity=ADCSensitivity)	# acquisition
+
+
+    # write experiment parameters:  
+    for key in pars.keys():
+        e.set_description(key, pars[key])		# acquisition parameters
+    e.set_description('run', run)			# current scan
+    e.set_description('rec_phase', -PH2)		# current receiver phase
+
+    return e

Scripts/PFG/Stimulated_Echo/pfg_ste_res.py

@@ -0,0 +1,209 @@
+# -*- coding: iso-8859-1 -*-
+
+from numpy import *
+from scipy.signal import *
+from scipy.optimize import *
+from os import path, rename
+
+def result():
+
+    measurement = MeasurementResult('Magnetization')
+
+    measurement_range = [0.0, 10e-6]
+    measurement_ranging = False
+
+    suffix = '' 	# output file name's suffix and...
+    counter = 1		# counter for arrayed experiments
+    var_key = ''	# variable parameter name
+
+    # loop over the incoming results: 
+    for timesignal in results:
+        if not isinstance(timesignal,ADC_Result): 
+            continue
+
+        # read experiment parameters:
+        pars = timesignal.get_description_dictionary()
+
+        # ---------------- digital filter ------------------ 
+             
+        # 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: # otherwise no filter applied
+
+            # 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)
+
+        # ----------------------------------------------------
+
+        # phase timesignal according to current rec_phase:
+        timesignal.phase(pars['rec_phase'])
+
+        # provide timesignal to the display tab:
+        data['Current scan'] = timesignal
+
+        # accumulate...
+        if not locals().get('accu'):
+            accu = Accumulation()
+
+        # skip dummy scans, if any:
+        if pars['run'] < 0: continue
+
+        # add up:
+        accu += timesignal
+
+        # provide accumulation to the display tab:
+        data['Accumulation'] = accu
+
+        # check how many scans are done:
+        if accu.n == pars['NS']: # accumulation is complete
+
+            # make a copy:
+            echo = accu + 0
+
+            # compute the initial phase of the signal:
+            phi0 = arctan2(accu.y[1][0], accu.y[0][0]) * 180 / pi
+            if not locals().get('ref'): ref = phi0   
+            print 'phi0 = ', phi0
+
+            # rotate the signal to maximize Re (optional):     
+            #echo.phase(-phi0) 
+
+            # do FFT: 
+            echo.exp_window(line_broadening=10)
+            spectrum = echo.fft(samples=2*pars['SI'])
+
+            # try zero-order phase correction:
+            spectrum.phase(-phi0)
+
+            # provide spectrum to the display tab:
+            data['Spectrum'] = spectrum
+
+            # check whether it is an arrayed experiment:
+            var_key = pars.get('VAR_PAR')
+            if var_key:
+                # get variable parameter's value:
+                var_value = pars.get(var_key)
+
+                # provide signal recorded with var_value to the display tab:
+                data['Accumulation'+"/"+var_key+"=%e"%(var_value)] = accu                
+
+                # measure signal intensity vs. var_value:
+                if measurement_ranging == True:
+                   [start, stop] = accu.get_sampling_rate() * array(measurement_range)
+                   measurement[var_value] = sum(accu.y[0][int(start):int(stop)]) 
+                   
+                else:
+                   measurement[var_value] = sum(accu.y[0][0:31])
+
+                # provide measurement to the display tab:
+                data[measurement.get_title()] = measurement
+
+                # update the file name suffix:
+                suffix = '_' + str(counter)
+                counter += 1
+
+            # save accu if required:
+            outfile = pars.get('OUTFILE')
+            if outfile:
+                datadir = pars.get('DATADIR')
+
+                # write raw data in Simpson format:
+                filename = datadir+outfile+suffix+'.dat'
+                if path.exists(filename):
+                    rename(filename, datadir+'~'+outfile+suffix+'.dat')
+                accu.write_to_simpson(filename)
+
+                # write raw data in Tecmag format:
+                # filename = datadir+outfile+'.tnt'
+                # accu.write_to_tecmag(filename, nrecords=20)
+
+                # write parameters in a text file:
+                filename = datadir+outfile+suffix+'.par' 
+                if path.exists(filename):
+                    rename(filename, datadir+'~'+outfile+suffix+'.par')
+
+                fileobject = open(filename, 'w')
+                for key in sorted(pars.iterkeys()):
+                    if key=='run': continue
+                    if key=='rec_phase': continue
+                    fileobject.write('%s%s%s'%(key,'=', pars[key]))
+                    fileobject.write('\n')
+                fileobject.close()
+
+            # reset accumulation:
+            del accu
+
+    if var_key == 'D2':
+        # mono-exponential decay fit:
+        xdata = measurement.get_xdata()
+        ydata = measurement.get_ydata()
+        [amplitude, rate, offset] = fitfunc(xdata, ydata)
+        print '%s%02g' % ('Amplitude = ', amplitude)
+        print '%s%02g' % ('T1 [s] = ', 1./rate)
+        print '%s%02g' % ('Offset = ', offset)
+
+        # update display for the fit:
+        measurement.y = func([amplitude, rate, offset], xdata)
+        data[measurement.get_title()] = measurement
+
+# the fitting procedure:
+def fitfunc(xdata, ydata):
+
+    # initialize variable parameters:
+    try: 
+        # solve Az = b:
+        A = array((ones(xdata.size/2), xdata[0:xdata.size/2]))
+        b = log(abs(ydata[0:xdata.size/2]))
+        z = linalg.lstsq(transpose(A), b)
+        amplitude = exp(z[0][0])
+        rate = -z[0][1]
+    except:
+        amplitude = abs(ydata[0])
+        rate = 1./(xdata[-1] - xdata[0])
+    offset = min(ydata)
+    p0 = [amplitude, rate, offset]
+
+    # run least-squares optimization:
+    plsq = leastsq(residuals, p0, args=(xdata, ydata))
+
+    return plsq[0] # best-fit parameters
+
+def residuals(p, xdata, ydata):
+    return ydata - func(p, xdata)
+
+# here is the function to fit:
+def func(p, xdata):
+    return p[0]*exp(-p[1]*xdata) + p[2]
+
+
+pass