def iv(self, channel, start=0, stop=3, step=0.2, delay=0.2):
'''
Take an IV on channel chan:
- start / stop in V
- steps
'''
biaspar = 'bias%d' % channel
vmeaspar = 'vmeas%d' % channel
r = self.get_resistance() / 1000.0 # Not sure why this is dividing. Bug?
n = (int(abs(stop - start) / step)) + 1
data = qt.Data(name='iv')
data.add_coordinate('Vbias', units='V')
data.add_value('Vmeas', units='V')
data.create_file()
for i in range(n):
v_out = start + i * step
current = v_out/r
self.set(biaspar, v_out, check=False)
qt.msleep(delay)
v_meas = self.get(vmeaspar)
print 'v_out, current_out, v_meas: %f, %f, %f' %(v_out, current, v_meas)
data.add_data_point(v_out, v_meas)
self.set(biaspar, 0)
qt.plot(data, name='iv', clear=True)
return data
def plot_last_histogram(self):
y, x = self._hist, self._hist_bins[
1:] * self._hist_binsize_ns #np.histogram(self._dts_ns, bins = np.linspace(self.get_roi_min(), self.get_roi_max(),pts))#np.min(dts[dts>0]),np.max(dts),pts))
plotname = self.get_name() + '_histogram'
qt.plot(x, y, name=plotname, clear=True)
f = common.fit_exp_decay_shifted_with_offset
#A * exp(-(x-x0)/tau) + a
#['g_a', 'g_A', 'g_tau', 'g_x0']
args = [1, np.max(y) * 0.1, 12, x[np.argmax(y) + 2.]]
first_fit_bin = int(
np.round(self._plot_extra_range / self._hist_binsize_ns))
xf, yf = x[first_fit_bin:], y[first_fit_bin:]
fitres = fit.fit1d(xf,
yf,
f,
*args,
fixed=[0],
do_print=False,
ret=True,
maxfev=100)
plot_pts = 200
x_p = np.linspace(min(xf), max(xf), plot_pts)
if fitres['success']:
y_p = fitres['fitfunc'](x_p)
print 'fit success'
else:
y_p = f(*args)[1](x_p)
print 'fit failed'
print fitres['params_dict']
qt.plot(x_p, y_p, 'b', name=plotname, clear=False)
self.y = y
self.x = x
def plot_trace(self):
'''
performs a measurement and plots the data.
'''
freqs, reply = self.get_trace()
qt.plot(freqs, reply, name='netan',
xlabel='freq [Hz]', ylabel='S_ij [dB]',
clear=True)
def save_spectrum(self, ret=False):
spec = andor.get_spectrum()
specd = qt.Data(name='spectrum')
specd.add_value('Counts')
specd.create_file()
specd.add_data_point(spec)
specd.close_file()
qt.plot(specd, name='saved_spectrum', clear=True)
if ret:
return spec
def save_spectrum(self, ret=False):
spec = andor.get_spectrum()
specd = qt.Data(name='spectrum')
specd.add_value('Counts')
specd.create_file()
specd.add_data_point(spec)
specd.close_file()
qt.plot(specd, name='saved_spectrum', clear=True)
if ret:
return spec
def save_spectrum(self, ret=False):
spec = winspec.get_spectrum()
specd = qt.Data(name='spectrum')
specd.add_coordinate('Wavelength', units='nm')
specd.add_value('Counts')
specd.create_file()
specd.add_data_point(spec)
specd.close_file()
qt.plot(specd, name='saved_spectrum', clear=True)
if ret:
return spec
def save_spectrum(self, ret=False):
spec = winspec.get_spectrum()
specd = qt.Data(name='spectrum')
specd.add_coordinate('Wavelength', units='nm')
specd.add_value('Counts')
specd.create_file()
specd.add_data_point(spec)
specd.close_file()
qt.plot(specd, name='saved_spectrum', clear=True)
if ret:
return spec
def save_spectrum(self, ret=False):
spec = winspec.get_spectrum()
specd = qt.Data(name="spectrum")
specd.add_coordinate("Wavelength", units="nm")
specd.add_value("Counts")
specd.create_file()
specd.add_data_point(spec)
specd.close_file()
qt.plot(specd, name="saved_spectrum", clear=True)
if ret:
return spec
def iv_counts_disc_sr400(self, channel, start=0, stop=10, step=0.25, delay=0.2, discarray = [0.2]):
'''
Take an IV on channel chan and measure count rate:
- start / stop in V
- steps
'''
print ''
sr400 = qt.instruments['sr400']
biaspar = 'bias%d' % channel
vmeaspar = 'vmeas%d' % channel
r = self.get_resistance() / 1000.0
n = (int(abs(stop - start) / step)) + 1
data = qt.Data(name='iv')
data.add_coordinate('Vbias', units='V')
data.add_value('Vmeas', units='V')
data.add_value('Counts', units='')
data.create_file()
plot3d = qt.Plot3D(data, name='3D', style='image', coorddims=(1,0), valdim=2)
for disc in discarray:
if (msvcrt.kbhit() and (msvcrt.getch() == 'q')): break
sr400.set_disc_levelA(disc)
sr400.set_disc_levelB(disc)
for i in range(n):
if (msvcrt.kbhit() and (msvcrt.getch() == 'q')): break
v_out = start + i * step
current = v_out/r
self.set(biaspar, v_out, check=False)
time.sleep(delay)
v_meas = self.get(vmeaspar)
if channel == 0:
counts = sr400.get_countA()
else:
counts = sr400.get_countB()
print 'v_out, current_out, v_meas, counts: %f, %f, %f, %d' % (v_out, current, v_meas, counts)
data.add_data_point(v_out, v_meas, counts)
data.add_data_point(v_out, disc, counts)
if v_meas > 0.5:
break
self.set(biaspar, 0)
qt.plot(data, name='ivcounts', clear=True)
qt.plot(data, name='ivcounts', valdim=2, right=True)
return data
def optimize(self, plot=0, dims='Vdim', cycles=1):
if 'laserscan_plot' in qt.plots:
qt.plots['laserscan_plot'].clear()
qt.plot(name='laserscan_plot',clear=True,needtempfile=False)
for c in range(cycles):
ret = True
#print '%s' % self.dimensions['V']
for d in self.dimensions[dims]:
#print 'dims is %s d is %s' % (dims, d)
scan_length = self.dimensions[d]['scan_length']
nr_of_points = self.dimensions[d]['nr_of_points']
if d == 'V':
# Get the current voltage from the Toptica
cur_V = self._topt.get_piezo_voltage()
if cur_V == None:
logging.warning(__name__ + 'Current position is none! Toptica voltage not initialized?')
break
self._opt_pos_prev['V'] = cur_V
# Create the desired array of points to measure
point_array = np.linspace(cur_V-scan_length/2.0,cur_V+scan_length/2.0,nr_of_points)
count_array = self.sweep_laser_and_count(point_array)
# Find the difference between readouts to get the counts measured
# at a certain point, then divide by the period to get the estimate
# of the counts per second
# Call the fitting routine to determine optimal position
# and set it as self._opt_pos['x'], in this case.
ret = self.process_fit(point_array, count_array, 'V', 10.0)
print 'Previous V/sigma: %.3f/%.3f, new optimum V: %.3f (delta %.1f V)' % (self._opt_pos_prev['V'], self._opt_sigma_prev['V'], self._opt_pos['V'], self._opt_pos['V']-self._opt_pos_prev['V'])
#
if np.array(point_array).min() < self._opt_pos['V'] < np.array(point_array).max():
self._topt.set_piezo_voltage(self._opt_pos['V'])
else:
self._topt.set_piezo_voltage(self._opt_pos_prev['V'])
self._opt_pos['V'] = self._opt_pos_prev['V']
print 'Optimum outside scan range: Position is set to previous maximum'
ret = False
qt.msleep(0.05)
if msvcrt.kbhit():
kb_char=msvcrt.getch()
if kb_char == "q" : break
return ret
def focus_plot(self):
samples = 12000
rate = 240000
channel = self.FP_params['aiport']
while True:
rsamples = self.read_sweep(samples, rate, channel)
time_axis = np.linspace(0.0,float(np.size(rsamples))/rate,np.size(rsamples))
qt.plot(time_axis,rsamples,name='fp_focusplot',traceofs=0.2, clear=True,linewidth=6)
time.sleep(0.5)
if msvcrt.kbhit():
kb_char=msvcrt.getch()
if kb_char == "q" : break
return
def iv_counts_sr400(self, channel, start=0, stop=10, step=0.25, delay=0.2):
'''
Take an IV on channel chan and measure count rate:
- start / stop in V
- steps
'''
print ''
sr400 = qt.instruments['sr400']
biaspar = 'bias%d' % channel
vmeaspar = 'vmeas%d' % channel
r = self.get_resistance() / 1000.0
n = (int(abs(stop - start) / step)) + 1
data = qt.Data(name='iv')
data.add_coordinate('Vbias', units='V')
data.add_value('Vmeas', units='V')
data.add_value('Counts', units='')
data.create_file()
for i in range(n):
v_out = start + i * step
current = v_out/r
self.set(biaspar, v_out, check=False)
time.sleep(delay)
v_meas = self.get(vmeaspar)
if channel == 0:
counts = sr400.get_countA()
else:
counts = sr400.get_countB()
print 'v_out, current_out, v_meas, counts: %f, %f, %f, %d' % (v_out, current, v_meas, counts)
data.add_data_point(v_out, v_meas, counts)
if v_meas > 0.5:
break
self.set(biaspar, 0)
qt.plot(data, name='ivcounts', clear=True)
qt.plot(data, name='ivcounts', valdim=2, right=True)
return data
def find_initial_values_lorentzian(x_data,
y_data,
moving_average=2,
plot_res=False):
'''
finds the initial values for a lorentzian dip or peak
p[0] = x0
p[1] = 2*HM dip height
p[2] = dx width
p[3] = y0 offset
'''
p = 4 * [0]
diffy = mva.movingaverage(diff(y_data), moving_average)
if plot_res:
pl = plot(name='find_resonance')
pl.clear()
plot(diffy, title='moving_average of diff_y', name='find_resonance')
plot(y_data, title='y_data', name='find_resonance')
dymax = max(diffy)
i_dymax = diffy.tolist().index(dymax)
dymin = min(diffy)
i_dymin = diffy.tolist().index(dymin)
if i_dymin > i_dymax:
'''
means its a peak
'''
peak = 1
y0 = min(y_data)
else:
'''
means its a dip
'''
peak = -1
y0 = max(y_data)
dx = abs(x_data[i_dymin] - x_data[i_dymax])
x0 = (x_data[i_dymin] + x_data[i_dymax]) / 2
HM = peak * abs(y_data[i_dymax] - y_data[floor((i_dymin + i_dymax) / 2)])
p[0] = x0
p[1] = 2 * HM
p[2] = dx
p[3] = y0
return p
def find_initial_values_lorentzian(x_data,y_data,moving_average = 2, plot_res = False):
'''
finds the initial values for a lorentzian dip or peak
p[0] = x0
p[1] = 2*HM dip height
p[2] = dx width
p[3] = y0 offset
'''
p=4*[0]
diffy = mva.movingaverage(diff(y_data),moving_average)
if plot_res:
pl = plot(name='find_resonance')
pl.clear()
plot(diffy,title='moving_average of diff_y',name='find_resonance')
plot(y_data,title='y_data',name='find_resonance')
dymax = max(diffy)
i_dymax = diffy.tolist().index(dymax)
dymin = min(diffy)
i_dymin = diffy.tolist().index(dymin)
if i_dymin>i_dymax:
'''
means its a peak
'''
peak = 1
y0 = min(y_data)
else:
'''
means its a dip
'''
peak = -1
y0 = max(y_data)
dx = abs(x_data[i_dymin] - x_data[i_dymax])
x0 = (x_data[i_dymin] + x_data[i_dymax])/2
HM = peak*abs(y_data[i_dymax] - y_data[floor((i_dymin+i_dymax)/2)])
p[0] = x0
p[1] = 2*HM
p[2] = dx
p[3] = y0
return p
def save_ROI_data(self, x, y, z, sweepname='sweep_value'):
roix = y
roiy = z[:,self.ROI_min:self.ROI_max].sum(axis=1)
np.savetxt(os.path.join(self.save_folder,
self.save_filebase+'_ROI_sum.dat'), np.vstack((roix,roiy)).T)
p = qt.plot(roix, roiy, 'rO-', name='ROI_summed', clear=True,
xlabel=sweepname, ylabel='counts', title='ROI summed')
p.reset()
h,ts = os.path.split(self.save_folder)
h,date = os.path.split(h)
p.set_plottitle(date+'/'+ts+': '+'ROI_summed')
p.save_png(os.path.join(self.save_folder, self.save_filebase))
def optimize(self):
self.initialize()
for i in range(int(self._iterations)):
print 'Iteration %d, cur_f %.2f' % (i, self._cur_f)
self.iterate()
print 'Current x location is: %s, %s' % (np.array(self._cur_x), self._cur_f)
time.sleep(0.1)
print 'Done!'
self._optimization_is_on = False
if self._complete_poll == True:
hist = np.array(self._history)
plot2d_1 = qt.plot(np.arange(hist.size),hist,name='mads_optimize',clear=True)
#plot2d = qt.plot(self._hypd, coorddim=0, valdim=1,name='optT4',clear=True)
#plot2d.add_data(self._hypd, coorddim=0, valdim=2, maxtraces=1)
#plot2d.add_data(self._hypd, coorddim=0, valdim=3, maxtraces=1)
#
# plota1 = qt.plot(self._hypd, coorddim=0, valdim=4,name='angle1',clear=True)
# plota2 = qt.plot(self._hypd, coorddim=0, valdim=5,name='angle2',clear=True)
# plotcmax = qt.plot(self._hypd, coorddim=0, valdim=6,name='cmax',clear=True)
# plotfevals = qt.plot(self._hypd, coorddim=0, valdim=8, maxtraces=1, clear=True)
# plotmmax = qt.plot(self._hypd, coorddim=0, valdim=9, name='mmax', maxtraces=1, clear=True)
else:
hist = np.array(self._history)
plot2d_1 = qt.plot(np.arange(hist.size),hist,name='mads_optimize',clear=True)
#
# plota1 = qt.plot(self._hypd, coorddim=0, valdim=1,name='angle1',clear=True)
# plota2 = qt.plot(self._hypd, coorddim=0, valdim=2,name='angle2',clear=True)
# plotcmax = qt.plot(self._hypd, coorddim=0, valdim=3,name='cmax',clear=True)
# plotfevals = qt.plot(self._hypd, coorddim=0, valdim=5, maxtraces=1, clear=True)
# plotmmax = qt.plot(self._hypd, coorddim=0, valdim=6, maxtraces=1, clear=True, name='mmax')
print 'Total function evals: %d' % self._nfeval
# plotff = qt.plot(self._fed, coorddim=0, valdim=1, maxtraces=1, name='fevalp', clear=True)
return np.array(self._cur_x)
def max_intensity_plot(self):
samples = 500
rate = 10000
channel = self.FP_params['aiport']
data = qt.Data(name='max_int_data')
data.add_coordinate('time')
data.add_value('intensity')
t0 = time.time()
miplot = qt.plot(data,name='maxintplot',traceofs=0.2, coorddim=0, valdim=1, maxpoints=100, linewidth=6, clear=True)
while True:
rsamples = self.read_sweep(samples, rate, channel)
data.add_data_point((time.time()-t0),np.max(rsamples))
miplot.update()
time.sleep(0.5)
if msvcrt.kbhit():
kb_char=msvcrt.getch()
if kb_char == "q" : break
return
def save_trace(self, filepath=None, plot=True):
'''
runs 'get_trace()' and saves the output to a file.
Input:
filepath (string): Path to where the file should be saved.(optional)
Output:
filepath (string): The filepath where the file has been created.
'''
#TODO: change value label 'S_ij' to represent actual measurement
freqs, reply = self.get_trace()
d = qt.Data(name='netan')
d.add_coordinate('freq [Hz]')
d.add_value('S_ij [dB]')
d.create_file(filepath=filepath)
d.add_data_point(zip(freqs, reply))
d.close_file()
if plot:
p = qt.plot(d, name='netan', clear=True)
p.save_png()
p.save_gp()
return d.get_filepath()
def save_ROI_data(self, x, y, z, sweepname='sweep_value'):
roix = y
roiy = z[:, self.ROI_min:self.ROI_max].sum(axis=1)
np.savetxt(
os.path.join(self.save_folder,
self.save_filebase + '_ROI_sum.dat'),
np.vstack((roix, roiy)).T)
p = qt.plot(roix,
roiy,
'rO-',
name='ROI_summed',
clear=True,
xlabel=sweepname,
ylabel='counts',
title='ROI summed')
p.reset()
h, ts = os.path.split(self.save_folder)
h, date = os.path.split(h)
p.set_plottitle(date + '/' + ts + ': ' + 'ROI_summed')
p.save_png(os.path.join(self.save_folder, self.save_filebase))
def avg_max_intensity_plot(self):
samples = 500
rate = 10000
channel = self.FP_params['aiport']
data = qt.Data(name='avg_max_int_data')
data.add_coordinate('time')
data.add_value('intensity')
t0 = time.time()
miplot = qt.plot(data,name='avgmaxintplot',traceofs=0.2, coorddim=0, valdim=1, maxpoints=100,linewidth=7,clear=True)
while True:
rsamples = self.read_sweep(samples, rate, channel)
time_axis = np.linspace(0.0,float(np.size(rsamples))/rate,np.size(rsamples))
p = pf.PeakFinder(time_axis,rsamples, maxpeaks = 4,threshold = 4,fitwidth=35,fitfunc='FIT_LORENTZIAN',amp_threshold=0.2)
peaks = p.find(sign=1, bgorder=1)
peak_array = np.array(peaks)
data.add_data_point((time.time()-t0),np.mean(peak_array[:,1]))
miplot.update()
time.sleep(0.5)
if msvcrt.kbhit():
kb_char=msvcrt.getch()
if kb_char == "q" : break
return
def save_trace(self, filepath=None, plot=True):
'''
runs 'get_trace()' and saves the output to a file.
Input:
filepath (string): Path to where the file should be saved.(optional)
Output:
filepath (string): The filepath where the file has been created.
'''
#TODO: change value label 'S_ij' to represent actual measurement
freqs, reply = self.get_trace()
d = qt.Data(name='netan')
d.add_coordinate('freq [Hz]')
d.add_value('S_ij [dB]')
d.create_file(filepath=filepath)
d.add_data_point(zip(freqs, reply))
d.close_file()
if plot:
p = qt.plot(d, name='netan', clear=True)
p.save_png()
p.save_gp()
return d.get_filepath()
import numpy as np
import qt
x = np.arange(-10, 10, 0.2)
y = np.sinc(x)
yerr = 0.1 * np.random.rand(len(x))
d = qt.Data()
d.add_coordinate("x")
d.add_coordinate("y")
d.add_coordinate("yerr")
d.create_file()
d.add_data_point(x, y, yerr)
p = qt.Plot2D()
p.add_data(d, coorddim=0, valdim=1, yerrdim=2)
# or:
qt.plot(x, y, yerr=yerr, name="test2")
def plot(self):
if not self._dev:
return
import qt
x, trace = self._dev.get_block()
qt.plot(trace, name='picoharp', clear=True)
def process_fit(self, p, cr, dimension):
# p is position array
# cr is countrate array
# d is a string corresponding to the dimension
# Get the Gaussian width sigma guess from the dimensions dictionary
sigma_guess = self.dimensions[dimension]['sigma']
# Always do a Gaussian fit, for now
self._gaussian_fit = True
if self._gaussian_fit:
# Come up with some robust estimates, for low signal/noise conditions
a_guess = np.array(cr).min()
A_guess = np.array(cr).max()-np.array(cr).min()
p_size = np.size(p)
x0_guess = p[np.round(p_size/2.0)] #np.sum(np.array(cr) * np.array(p))/np.sum(np.array(cr)**2)
#sigma_guess = 1.0#np.sqrt(np.sum(((np.array(cr)-x0_guess)**2)*(np.array(p))) / np.sum((np.array(p))))
#print 'Guesses: %r %r %r %r' % (a_guess, x0_guess,A_guess,sigma_guess)
gaussian_fit = fit.fit1d(np.array(p,dtype=float), np.array(cr,dtype=float),common.fit_gauss, a_guess,
x0_guess,A_guess, sigma_guess, do_print=False,ret=True)
ababfunc = a_guess + A_guess*np.exp(-(p-x0_guess)**2/(2.0*sigma_guess**2))
if type(gaussian_fit) != dict:
pamax = np.argmax(cr)
self._opt_pos[dimension] = p[pamax]
ret = False
print '(%s) fit failed! Set to maximum.' % dimension
else:
if gaussian_fit['success'] != False:
self._fit_result = [gaussian_fit['params'][1],
gaussian_fit['params'][2],
gaussian_fit['params'][3],
gaussian_fit['params'][0] ]
self._fit_error = [gaussian_fit['error'][1],
gaussian_fit['error'][2],
gaussian_fit['error'][3],
gaussian_fit['error'][0] ]
self._opt_pos[dimension] = self._fit_result[0]
ret = True
final_fit_func = gaussian_fit['params'][0] + gaussian_fit['params'][2]*np.exp(-(p-gaussian_fit['params'][1])**2/(2.0*gaussian_fit['params'][3]**2))
qt.plot(p,cr,p,ababfunc,p,final_fit_func,name='fbl_plot',needtempfile=False)
#print '(%s) optimize succeeded!' % self.get_name()
else:
self.set_data('fit', zeros(len(p)))
ret = False
print '(%s) optimize failed! Set to maximum.' % dimension
self._opt_pos[dimension] = p[np.argmax(cr)]
qt.plot(p,cr,p,ababfunc,name='fbl_plot',clear=True,needtempfile=False)
return ret
def num2str(num, precision):
return "%0.*f" % (precision, num)
A = fit.Parameter(max(measured_power - BG) / 2)
B = fit.Parameter(max(measured_power - BG) / 2)
f = fit.Parameter(1 / 2.5)
phi = fit.Parameter(0)
def fit_cos(x):
return A() + B() * cos(2 * pi * f() * x + phi())
ret = fit.fit1d(V_EOM.reshape(-1),
measured_power.reshape(-1) - BG,
None,
fitfunc=fit_cos,
p0=[A, B, f, phi],
do_plot=True,
do_print=True,
ret=True)
p = qt.plots['EOM Calibration curve']
V = linspace(EOM_min_voltage, EOM_max_voltage, V_step_size / 10)
qt.plot(V, fit_cos(V), 'r-', name='EOM Calibration curve')
plt.save_png(file_directory[0:65] + 'calibration_EOM_curve.png')
print 'Extinction = max/min = ' + num2str(
max(measured_power - BG) / min(measured_power - BG), 0)
print 'Done'
def plot(self):
if not self._dev:
return
import qt
x, trace = self._dev.get_block()
qt.plot(trace, name='picoharp', clear=True)
def optimize(self, plot=0, dims='xyz', cycles=1):
if 'fbl_plot' in qt.plots:
qt.plots['fbl_plot'].clear()
qt.plot(name='fbl_plot',clear=True,needtempfile=False)
for c in range(cycles):
ret = True
for d in self.dimensions[dims]:
scan_length = self.dimensions[d]['scan_length']
nr_of_points = self.dimensions[d]['nr_of_points']
if d == 'x':
# Get the current position from the FSM - only works if the
# FSM has been written to at least once!
cur_pos = self._fsm.get_abs_positionX()
if cur_pos == None:
print 'Current position is none! FSM not initialized?'
break
self._opt_pos_prev['x'] = cur_pos
# Create the desired array of points to measure
point_array = np.linspace(cur_pos-scan_length/2.0,cur_pos+scan_length/2.0,nr_of_points)
# Add the beginning point so that it's in the array twice
# at the beginning. This is because we're looking for the
# difference between counter reads to get the counts per
# second at a position.
temp_point_array = np.insert(point_array,0,cur_pos-scan_length/2.0,axis=0)
# Use AO Smooth Goto code to smoothly go to the beginning point
self._fsm.AO_smooth(cur_pos, cur_pos-scan_length/2.0, 'X')
# Now write the points and get the counts
fsm_rate = 40.0 # Hz
counts = self._fsm.sweep_and_count(temp_point_array,fsm_rate, 'ctr0','PFI0','X')
# Find the difference between readouts to get the counts measured
# at a certain point, then divide by the period to get the estimate
# of the counts per second
cps = np.diff(counts)*fsm_rate
# Call the fitting routine to determine optimal position
# and set it as self._opt_pos['x'], in this case.
ret = self.process_fit(point_array, np.diff(counts), 'x', fsm_rate)
print 'Previous x: %.3f, new optimum: %.3f (delta %.1f nm)' % (self._opt_pos_prev['x'], self._opt_pos['x'], self._opt_pos['x']*1E3-self._opt_pos_prev['x']*1E3)
#
if np.array(point_array).min() < self._opt_pos['x'] < np.array(point_array).max():
self._fsm.set_abs_positionX(self._opt_pos['x'])
else:
self._fsm.set_abs_positionX(self._opt_pos_prev['x'])
self._opt_pos['x'] = self._opt_pos_prev['x']
print'Optimum outside scan range: Position is set to previous maximum'
ret = False
#print 'Position changed %d nm' % (self._opt_pos['x']*1E3-self._opt_pos_prev['x']*1E3)
if d == 'y':
# Get the current position from the FSM - only works if the
# FSM has been written to at least once!
cur_pos = self._fsm.get_abs_positionY()
self._opt_pos_prev['y'] = cur_pos
# Create the desired array of points to measure
point_array = np.linspace(cur_pos-scan_length/2.0,cur_pos+scan_length/2.0,nr_of_points)
# Add the beginning point so that it's in the array twice
# at the beginning. This is because we're looking for the
# difference between counter reads to get the counts per
# second at a position.
temp_point_array = np.insert(point_array,0,cur_pos-scan_length/2.0,axis=0)
##print 'y temp point array %s' % temp_point_array
# Use AO Smooth Goto code to smoothly go to the beginning point
self._fsm.AO_smooth(cur_pos, cur_pos-scan_length/2.0, 'Y')
# Now write the points and get the counts
fsm_rate = 40.0 # Hz
counts = self._fsm.sweep_and_count(temp_point_array,fsm_rate, 'ctr0','PFI0','Y')
# Find the difference between readouts to get the counts measured
# at a certain point, then divide by the period to get the estimate
# of the counts per second
cps = np.diff(counts)*fsm_rate
# Call the fitting routine to determine optimal position
# and set it as self._opt_pos['y'], in this case.
ret = self.process_fit(point_array, np.diff(counts), 'y', fsm_rate)
print 'Previous y: %.3f, new optimum: %.3f (delta %.1f nm)' % (self._opt_pos_prev['y'], self._opt_pos['y'], self._opt_pos['y']*1.0E3-self._opt_pos_prev['y']*1.0E3)
if np.array(point_array).min() < self._opt_pos['y'] < np.array(point_array).max():
self._fsm.set_abs_positionY(self._opt_pos['y'])
else:
self._fsm.set_abs_positionY(self._opt_pos_prev['y'])
self._opt_pos['y'] = self._opt_pos_prev['y']
print 'Optimum outside scan range: Position is set to previous maximum'
ret = False
#print 'Position changed %d nm' % (self._opt_pos['y']*1.0E3-self._opt_pos_prev['y']*1.0E3)
if d == 'z':
# Get the current position from the FSM - only works if the
# FSM has been written to at least once!
cur_pos = self._xps.get_abs_positionZ() # In mm, not um!
self._opt_pos_prev['z'] = cur_pos # In mm
# Create the desired array of points to measure
# Note 0.001 converts from mm to um!
point_array = np.linspace(cur_pos-scan_length*0.001/2.0,cur_pos+scan_length*0.001/2.0,nr_of_points)
# No need to double up on initial position in the point array
# since the counts will be read out step-by-step and not in
# a synchronized DAQ read.
# Set the position on the XPS to the initial point; sort of redundant
self._xps.set_abs_positionZ((cur_pos-0.001*scan_length/2.0))
# Now write the points and get the counts
counts = np.zeros(nr_of_points)
# HARDCODED SETUP FOR COUNT READING
xps_rate = 40.0 # Hz
xps_settle_time = 10.0*0.001 # 10 ms
prev_ctr0_src = self._ni63.get_ctr0_src()
self._ni63.set_ctr0_src('PFI0')
prev_count_time = self._ni63.get_count_time()
self._ni63.set_count_time(1.0/xps_rate)
for i in range(nr_of_points):
# Point array is in mm, so this should work
self._xps.set_abs_positionZ((point_array[i]))
qt.msleep(xps_settle_time)
counts[i] = self._ni63.get_ctr0()
self._ni63.set_count_time(prev_count_time)
self._ni63.set_ctr0_src(prev_ctr0_src)
# Find the difference between readouts to get the counts measured
# at a certain point, then divide by the period to get the estimate
# of the counts per second
cps = counts*xps_rate
# Call the fitting routine to determine optimal position
# and set it as self._opt_pos['z'], in this case.
ret = self.process_fit(point_array, counts, 'z', xps_rate)
print 'Previous z: %.6f, new optimum is %.6f (delta %.1f nm)' % (self._opt_pos_prev['z'], self._opt_pos['z'], self._opt_pos['z']*1.0E6-self._opt_pos_prev['z']*1.0E6)
#
if np.array(point_array).min() < self._opt_pos['z'] < np.array(point_array).max():
self._xps.set_abs_positionZ(self._opt_pos['z'])
else:
self._xps.set_abs_positionZ(self._opt_pos_prev['z'])
print 'Optimum outside scan range: Position is set to previous maximum'
self._opt_pos['z'] = self._opt_pos_prev['z']
ret = False
# Use 10^6 instead of 10^3 to convert from mm to nm
qt.msleep(0.1)
qt.msleep(0.05)
if msvcrt.kbhit():
kb_char=msvcrt.getch()
if kb_char == "q" : break
return ret
def num2str(num, precision):
return "%0.*f" % (precision, num)
A = fit.Parameter(max(measured_power - BG) / 2)
B = fit.Parameter(max(measured_power - BG) / 2)
f = fit.Parameter(1 / 2.5)
phi = fit.Parameter(0)
def fit_cos(x):
return A() + B() * cos(2 * pi * f() * x + phi())
ret = fit.fit1d(
V_EOM.reshape(-1),
measured_power.reshape(-1) - BG,
None,
fitfunc=fit_cos,
p0=[A, B, f, phi],
do_plot=True,
do_print=True,
ret=True,
)
p = qt.plots["EOM Calibration curve"]
V = linspace(EOM_min_voltage, EOM_max_voltage, V_step_size / 10)
qt.plot(V, fit_cos(V), "r-", name="EOM Calibration curve")
plt.save_png(file_directory[0:65] + "calibration_EOM_curve.png")
print "Extinction = max/min = " + num2str(max(measured_power - BG) / min(measured_power - BG), 0)
print "Done"
def take_spectrum(self, ret=False):
spec = winspec.get_spectrum()
qt.plot(spec, name='winspec_spectrum', clear=True)
if ret:
return spec
def take_spectrum(self, ret=False):
spec = winspec.get_spectrum()
qt.plot(spec, name='winspec_spectrum', clear=True)
if ret:
return spec
def take_spectrum(self, ret=False):
spec = andor.get_spectrum()
qt.plot(spec, name='andor_spectrum', clear=True)
if ret:
return spec
def fit1D(x,y,fit_func, **kw):
'''
parameters
x : tuple of indep. variables
y : dep. var. (data)
fit_func : function to be fitted structure fit_fun(x, p0) with p0 parameters
known KW
init_guess : vector of initial estimates for p0
guess_func : function that guesses the initial parameters p0
full_output : True by default
onscreen : print reuslts on screen
ret_fit : return an array fit_func(x, Pfit)
plot_results=False
'''
full_output = kw.pop('full_output',True)
onscreen = kw.pop('onscreen',True)
kw_c=kw.copy()
qt.mstart()
try:
p0 = kw_c.pop('init_guess')
except KeyError:
print('No initial guess given, trying guess func instead')
p0 = kw_c.pop('guess_func')(x,y)
if type(x)==type((0,)):
var = x+(y,)
else :
x=(x,)
var=x+(y,)
if type(p0)==type((0,)):
pass
else :
p0=tuple(p0)
plres=kw.pop('plot_results', False)
if plres:
pltr=plot(name='fit monitor')
pltr.clear()
init_guess_arr = fit_func(*(x+tuple(p0)))
plot(x[0], init_guess_arr, title = 'initial guess',name='fit monitor')
plot(x[0], y, title = 'data',name='fit monitor')
plsq,cov,info,mesg,success = leastsq(_residuals_m, \
p0, args=(fit_func,)+var, full_output = 1, maxfev=10000)#,xtol=kw.pop('xtol',1.e-10))
try :
len(plsq)
except TypeError :
plsq=[plsq]
if onscreen:
print('plsq',plsq)
print('mesg',mesg)
print(cov)
#print 'info: ',info
dof = max(np.shape(y)) - len(plsq)
errors = estimate_errors(plsq,info,cov,dof)
k=0
if plres:
fresarr = fit_func(*(x+tuple(plsq)))
plot(x[0],fresarr , title = 'fit',name='fit monitor')
if onscreen:
for p in plsq:
print('p%s = %s +/- %s'%(k,p,errors[k]))
k+=1
if kw.pop('ret_fit',False):
return plsq, errors, fit_func(*(x+tuple(plsq))),cov,info
else:
return plsq, errors
qt.mstop()
import numpy as np
import qt
x = np.arange(-10, 10, 0.2)
y = np.sinc(x)
yerr = 0.1*np.random.rand(len(x))
d = qt.Data()
d.add_coordinate('ixs')
d.add_coordinate('ylon')
d.add_coordinate('yerr')
d.create_file()
d.add_data_point(x,y,yerr)
p = qt.Plot2D()
p.add_data(d, coorddim=0, valdim=1, yerrdim=2)
# or: ('ok' is style for black circles)
qt.plot(x, y, 'ok', yerr=yerr, name='test2')
def process_fit(self, p, cr, dimension, rate):
# p is position array
# cr is countrate array
# d is a string corresponding to the dimension
# Get the Gaussian width sigma guess from the dimensions dictionary
sigma_guess = self.dimensions[dimension]['sigma']
# Always do a Gaussian fit, for now
self._gaussian_fit = True
if self._gaussian_fit:
# Come up with some robust estimates, for low signal/noise conditions
a_guess = np.array(cr).min()*0.9
A_guess = np.array(cr).max()-np.array(cr).min()
p_size = np.size(p)
x0_guess = p[np.round(p_size/2.0)] #np.sum(np.array(cr) * np.array(p))/np.sum(np.array(cr)**2)
#sigma_guess = 1.0#np.sqrt(np.sum(((np.array(cr)-x0_guess)**2)*(np.array(p))) / np.sum((np.array(p))))
#print 'Guesses: %r %r %r %r' % (a_guess, x0_guess,A_guess,sigma_guess)
# The following statement is that if the old sigma is within a factor of 2 of the initial fixed value
# then use the old sigma as the guess for the fit.
if np.abs(self._opt_sigma_prev[dimension]/self.dimensions[dimension]['sigma']) < 2.0 and np.abs(self._opt_sigma_prev[dimension]/self.dimensions[dimension]['sigma']) > 0.3:
sigma_guess = self._opt_sigma_prev[dimension]
else:
sigma_guess = self.dimensions[dimension]['sigma']
ababfunc = (a_guess + A_guess*np.exp(-(p-x0_guess)**2/(2.0*sigma_guess**2)))*rate
# New method for fitting
# Purpose of this new method is to improve the robustness of both the numerical optimization and the 'mistracks'
# that can occur because of nearby luminescence.
# I think that the numerical robustness can be improved by using a
# multiple start technique -- start the optimization at a series of
# guesses across the frequency range, and note the 'best fit' value
# of each. Pick the one with the best fit of each of these fits, and
# return it, subject to the condition that the center of the peak is
# within the min/max of the scan range. This way, it will be no
# worse than the existing method and significantly more robust to
# finding the global minimum.
# The second modification is to reduce the probability of a fit to
# a nearby peak that isn't the one we want, which I call a 'mistrack'.
# This can be done by multiplying the likelihood by a prior, making
# it a Bayesian method, that incorporates our knowledge that the
# peak we want will not drift too far from scan to scan. Therefore,
# given two peaks that fit equally well, the one nearest to the old
# peak location should be selected preferentially. The exception to
# this is if the other peak fits exceedingly well; these statements
# are quantified by the exact prior probability distribution used.
bf_ret = self.bayesian_fit(p, cr, np.array((A_guess, x0_guess, sigma_guess, a_guess)),self.dimensions[dimension]['drift_prior'])
# check if fit result is in range, process it accordingly
if not (bf_ret[1] > np.min(p)) and (bf_ret[1] < np.max(p)):
# fit out of range, set location to max
pamax = np.argmax(cr)
self._opt_pos[dimension] = p[pamax]
ret = False
print '(%s) fit failed! Set to maximum.' % dimension
else:
self._opt_pos[dimension] = bf_ret[1]
self._opt_sigma_prev[dimension] = bf_ret[2]
ret = True
final_fit_func = (bf_ret[3] + bf_ret[0]*np.exp(-(p-bf_ret[1])**2/(2.0*bf_ret[2]**2)))*rate
qt.plot(p,cr*rate,p,ababfunc,p,final_fit_func,name='fbl_plot',needtempfile=False)
#print '(%s) optimize succeeded!' % self.get_name()
return ret
def read_sweep_plot(self, samples, rate, channel):
rsamples = self.read_sweep(samples, rate, channel)
time_axis = np.linspace(0.0,float(np.size(rsamples))/rate,np.size(rsamples))
qt.plot(time_axis,rsamples,name='fpplot1',traceofs=0.2, maxtraces=20)
return
import numpy as np
import qt
x = np.arange(-10, 10, 0.2)
y = np.sinc(x)
yerr = 0.1 * np.random.rand(len(x))
d = qt.Data()
d.add_coordinate('x')
d.add_coordinate('y')
d.add_coordinate('yerr')
d.create_file()
d.add_data_point(x, y, yerr)
p = qt.Plot2D()
p.add_data(d, coorddim=0, valdim=1, yerrdim=2)
# or:
qt.plot(x, y, yerr=yerr, name='test2')
def save_2D_data(self, timename='t (ns)', sweepname='sweep_value', ret=False):
grp=h5.DataGroup('p7889_raw_data',self.h5data,base=self.h5base)
self.save_params(grp=grp.group)
x,yint,z = self._get_p7889_data()
#### convert x to bins.... because this is what we see on the
y=self.params['sweep_pts']
xx, yy = np.meshgrid(x,y)
#dat=h5.HDF5Data(name=self.name)
grp.add_coordinate(name='t (ns)',data=x, dtype='f8')
grp.add_coordinate(name=self.params['sweep_name'],data=y)
grp.add_value(name='Counts',data=z)
# m2.save_instrument_settings_file(grp.group)
#do post-processing
grp1=h5.DataGroup('processed data',self.h5data,base=self.h5base)
if self.params['Eval_ROI_start']<np.amin(x):
startind=[0]
else:
startind=np.where(x==self.params['Eval_ROI_start'])
if self.params['Eval_ROI_end']>np.amax(x):
endind=[x.size-1]
else:
endind=np.where(x==self.params['Eval_ROI_end'])
#strip the count array of points in time that lie outside of the specified ROIs
# print x
# print startind,endind
sliced=z[:,startind[0]:endind[0]]
# print sliced
summation=np.array(range(self.params['pts']))
for i,row in enumerate(sliced):
summation[i]=np.sum(row)
grp1.add_coordinate(name=self.params['sweep_name'],data=y)
grp1.add_value(name='Counts in ROI',data=summation)
plt=qt.plot(name=self.mprefix+self.name,clear=True)
plt.add(y,summation,'rO',yerr=np.sqrt(summation))
plt.add(y,summation,'r-')
plt.set_plottitle(self.name)
plt.set_legend(False)
plt.set_xlabel(self.params['sweep_name'])
plt.set_ylabel('counts')
plt.save_png(self.datafolder+'\\'+self.name+'.png')
self.h5data.flush()
if ret:
return x,y,z
else:
self.h5data.flush()
def updated_measurement(self):
"""
Incorporates live plotting for the p7889.
"""
self.p7889.Start()
qt.msleep(0.5)
self.awg.start()
counter = 0
opt_ins = qt.instruments['optimiz0r'] # added for long measurements MJD
GreenAOM = qt.instruments['GreenAOM']
last_time = time.time()
sample_time = 5.0
while self.p7889.get_state():
qt.msleep(0.1)
counter += 1
if counter % 1500 == 0: # idem added for long measurement
GreenAOM.set_power(self.params['GreenAOM_power'])
opt_ins.optimize(dims=['x','y','z'], cycles=1)
opt_ins.optimize(dims=['x','y','z'], cycles=1)
GreenAOM.turn_off()
elif msvcrt.kbhit():
kb_char=msvcrt.getch()
if kb_char == "q":
stop = True
break
if (time.time() - last_time) > sample_time:
last_time = time.time()
x,z = self.p7889.get_P7889data()
y=self.params['sweep_pts']
if self.params['Eval_ROI_start']<np.amin(x):
startind=[0]
else:
startind=np.where(x==self.params['Eval_ROI_start'])
if self.params['Eval_ROI_end']>np.amax(x):
endind=[x.size-1]
else:
endind=np.where(x==self.params['Eval_ROI_end'])
#strip the count array of points in time that lie outside of the specified ROIs
# print x
# print startind,endind
sliced=z[:,startind[0]:endind[0]]
# print sliced
summation=np.array(range(self.params['pts']))
for i,row in enumerate(sliced):
summation[i]=np.sum(row)
plt=qt.plot(name=self.mprefix+self.name,clear=True)
plt.add(y,summation,'rO',yerr=np.sqrt(summation))
plt.add(y,summation,'r-')
plt.set_plottitle(self.name)
plt.set_legend(False)
plt.set_xlabel(self.params['sweep_name'])
plt.set_ylabel('counts')
self.stop_sequence()
def take_spectrum(self, ret=False):
spec = andor.get_spectrum()
qt.plot(spec, name='andor_spectrum', clear=True)
if ret:
return spec