def getting_amplitude_and_dt(ax: plt.Axes, x: np.ndarray, cold: np.ndarray,
hot: np.ndarray) -> plt.Axes:
"""Adds hot and cold trace to axes with a straight line before and after transition to emphasise amplitude etc"""
ax.set_title("Hot and cold part of transition")
ax.set_xlabel('Sweep Gate (mV)')
ax.set_ylabel('I (nA)')
ax.plot(x, cold, color='blue', label='Cold', linewidth=1)
ax.plot(x, hot, color='red', label='Hot', linewidth=1)
# Add straight lines before and after transition to emphasise amplitude
transition_width = 0.30
before_transition_id = U.get_data_index(x,
np.mean(x) - transition_width,
is_sorted=True)
after_transition_id = U.get_data_index(x,
np.mean(x) + transition_width,
is_sorted=True)
line = lm.models.LinearModel()
top_line = line.fit(cold[:before_transition_id],
x=x[:before_transition_id],
nan_policy='omit')
bottom_line = line.fit(cold[after_transition_id:],
x=x[after_transition_id:],
nan_policy='omit')
ax.plot(x, top_line.eval(x=x), linestyle=':', color='black')
ax.plot(x, bottom_line.eval(x=x), linestyle=':', color='black')
# Add vertical arrow between dashed lines
# x_val = (np.mean(x) + x[-1]) / 2 # 3/4 along
x_val = 0.20
y_bot = bottom_line.eval(x=x_val)
y_top = top_line.eval(x=x_val)
arrow = ax.annotate(text='',
xy=(x_val, y_bot),
xytext=(x_val, y_top),
arrowprops=dict(arrowstyle='<|-|>', lw=1))
text = ax.text(x=x_val + 0.02, y=(y_top + y_bot) / 2, s='dI/dN')
ax.set_xlim(-0.5, 0.5)
ax.legend(loc='center left')
# Add horizontal lines to show thetas
# TODO: should decide if I want to do this from fit results, or if it is just to give an idea theta..
return ax
def one_d_data_vs_n(self):
if self.datnum:
self.which = ['i_sense_cold', 'dndt', 'occupation']
try:
x, data_dndt = _get_x_and_data(self.datnum, self.experiment_name, 'dndt')
except NotFoundInHdfError:
logger.warning(f'Dat{self.datnum}: dndt data not found, probably a transition only dat')
return go.Figure()
nrg_func = NRG_func_generator(which='dndt')
nrg_dndt = nrg_func(x, self.mid, self.g, self.theta, self.amp, self.lin, self.const, self.occ_lin)
nrg_func = NRG_func_generator(which='occupation')
occupation = nrg_func(x, self.mid, self.g, self.theta, self.amp, self.lin, self.const, self.occ_lin)
# Rescale dN/dTs to have a peak at 1
nrg_dndt = nrg_dndt * (1 / np.nanmax(nrg_dndt))
x_max = x[get_data_index(data_dndt, np.nanmax(data_dndt))]
x_range = abs(x[-1] - x[0])
indexs = get_data_index(x, [x_max - x_range / 50, x_max + x_range / 50])
avg_peak = np.nanmean(data_dndt[indexs[0]:indexs[1]])
# avg_peak = np.nanmean(data_dndt[np.nanargmax(data_dndt) - round(x.shape[0] / 50):
# np.nanargmax(data_dndt) + round(x.shape[0] / 50)])
data_dndt = data_dndt * (1 / avg_peak)
if (new_max := np.nanmax(np.abs([np.nanmax(data_dndt), np.nanmin(data_dndt)]))) > 5: # If very noisy
data_dndt = data_dndt / (new_max / 5) # Reduce to +-5ish
interp_range = np.where(np.logical_and(occupation < 0.99, occupation > 0.01))
if len(interp_range[0]) > 5: # If enough data to actually plot something
interp_data = occupation[interp_range]
interp_x = x[interp_range]
interper = interp1d(x=interp_x, y=interp_data, assume_sorted=True, bounds_error=False)
occ_x = interper(x)
plotter = OneD(dat=None)
fig = plotter.figure(xlabel='Occupation', ylabel='Arbitrary',
title=f'dN/dT vs N: G={self.g:.2f}mV, '
f'{THETA}={self.theta:.2f}mV, '
f'{THETA}/G={self.theta / self.g:.2f}'
f' -- Dat{self.datnum}')
fig.add_trace(plotter.trace(x=occ_x, data=data_dndt, name='Data dN/dT', mode='lines+markers'))
fig.add_trace(plotter.trace(x=occ_x, data=nrg_dndt, name='NRG dN/dT', mode='lines'))
return fig
def get_dats_closest_to_temp(self, temp: float) -> SingleTraceData:
"""Return the dats at the closest temperature to requested. If it is more than 10% off then warn user"""
v = list(self.temp_dat_dict.keys())[U.get_data_index(
list(self.temp_dat_dict.keys()), temp)]
if v not in self._single_trace_datas.keys():
if (diff := abs(temp - v)) > temp / 10:
logging.warning(
f'Closest temperature to requested is {v:.2f} which is {diff:.2f} from requested {temp:.2f}'
)
dats = self.temp_dat_dict[v]
self._single_trace_datas[v] = SingleTraceData(dats, temperature=v)
def plot_csq_trace(dat: DatHDF, cutoff: Optional[float] = None) -> Data1D:
plotter = OneD(dat=dat)
plotter.TEMPLATE = 'simple_white'
fig = plotter.figure(xlabel='CSQ Gate (mV)',
ylabel='Current (nA)',
title='CS current vs CSQ gate')
x = dat.Data.x
data = dat.Data.i_sense
if cutoff:
upper_lim = U.get_data_index(x, cutoff)
x, data = x[:upper_lim], data[:upper_lim]
fig.add_trace(plotter.trace(data=data, x=x))
fig.show()
return Data1D(x=x, data=data)
def do_calc(datnum):
dat = get_dat(datnum)
fit = dat.Transition.avg_fit
mid = fit.best_values.mid
width = fit.best_values.theta * 15
x1, x2 = U.get_data_index(dat.Transition.avg_x, [mid - width, mid + width],
is_sorted=True)
x = dat.Transition.avg_x[x1:x2]
data = dat.Transition.avg_data[x1:x2]
new_fit = dat.Transition.get_fit(which='avg',
name='narrow_centered',
overwrite=True,
x=x,
data=data)
print(f'Fitting Dat{dat.datnum} from {x[0]:.2f} -> {x[-1]:.2f}mV')
return new_fit
def vp_transition_fit(self) -> DataInfo:
dat = self.vp_dat
self.vp_info = self.DataInfo(dat, xlabel='V_P (mV)')
vp = self.vp_info
vp.full_data = dat.Data.i_sense
vp.full_x = dat.Data.x
vp.smoothed_data, vp.smoothed_x = U.resample_data(vp.full_data, vp.full_x, max_num_pnts=100,
resample_method='bin')
vp.rough_center = vp.smoothed_x[np.nanargmin(np.diff(vp.smoothed_data))]
ids = U.get_data_index(vp.full_x, [vp.rough_center - 4, vp.rough_center + 4])
vp.fit_data = vp.full_data[ids[0]:ids[1]]
vp.fit_x = vp.full_x[ids[0]:ids[1]]
vp.fit = self._fit(vp.fit_data, vp.fit_x)
return self.vp_info
def plot_slice(datnum, data_name, slice_val) -> go.Figure:
if datnum:
dat = get_dat(datnum)
data = dat.Data.get_data(data_name)
if data.ndim > 1:
x = dat.Data.get_data('x')
y = dat.Data.get_data('y')
if slice_val is None:
slice_val = y[0]
slice_val = U.get_data_index(y, slice_val)
z = dat.Data.get_data('i_sense')[slice_val]
x, z = [U.bin_data_new(arr, int(round(z.shape[-1] / 500))) for arr in (x, z)]
plotter = DashOneD(dat=dat)
fig = plotter.plot(data=z, x=x, mode='lines', title=f'Dat{datnum}: Slice at y = {y[slice_val]:.1f}')
return fig
return go.Figure()
def _center_2d_data(x, data2d, occupation2d) -> Data2D:
assert all(a.ndim == 2 for a in [data2d, occupation2d])
new_data = []
for data, occupation in zip(data2d, occupation2d):
idx = U.get_data_index(occupation,
0.5) # Get values near to occ = 0.5
interper = interp1d(occupation[idx - 1:idx + 2],
x[idx - 1:idx + 2],
bounds_error=False,
fill_value=(0, 1)) # will include occ = 0.5
half_x = interper(0.5)
new_x = x - half_x
data_interper = interp1d(new_x,
data,
bounds_error=False,
fill_value=(data[0], data[-1]))
new_data.append(data_interper(x))
return Data2D(x=x, y=np.arange(len(new_data)), data=np.array(new_data))
def plot_slice(fig, slice_val, slice_tog):
if slice_tog == [True]:
if not slice_val:
slice_val = 0
d = fig.get('data', None)
if d:
d = d[0]
x = d.get('x', None)
y = d.get('y', None)
z = d.get('z', None)
if all([a is not None for a in [x, y, z]]):
# x, z = [U.bin_data_new(arr, int(round(z.shape[-1] / 500))) for arr in (x, z)]
slice_index = U.get_data_index(y, slice_val)
data = z[slice_index]
fig = go.Figure()
fig.add_trace(go.Scatter(mode='lines', x=x, y=data))
fig.update_layout(title=f'Slice at y = {y[slice_index]:.1f}')
return fig
return go.Figure()
def plotting_center_shift():
nrg_func = NRG_func_generator('occupation')
params = lm.Parameters()
params.add_many(
('mid', 0, True, -200, 200, None, 0.001),
('theta', 3.9, False, 1, 500, None, 0.001),
('amp', 1, True, 0, 3, None, 0.001),
('lin', 0, True, 0, 0.005, None, 0.00001),
('occ_lin', 0, True, -0.0003, 0.0003, None, 0.000001),
('const', 0, True, -2, 10, None, 0.001),
('g', 1, True, 0.2, 2000, None, 0.01),
)
model = lm.Model(nrg_func)
x = np.linspace(-10, 5000, 10000)
gs = np.linspace(0, 200, 201)
thetas = np.logspace(0.1, 2, 20)
# thetas = np.linspace(1, 500, 10)
# thetas = [1, 2, 5, 10, 20]
all_mids = []
for theta in thetas:
params['theta'].value = theta
mids = []
for g in gs:
params['g'].value = g
occs = model.eval(x=x, params=params)
mids.append(x[U.get_data_index(occs, 0.5, is_sorted=True)])
all_mids.append(mids)
plotter = OneD(dat=None)
fig = plotter.figure(xlabel='Gamma /mV',
ylabel='Shift of 0.5 OCC',
title='Shift of 0.5 Occupation vs Theta and G')
fig.update_layout(legend=dict(title='Theta /mV'))
for mids, theta in zip(all_mids, thetas):
fig.add_trace(
plotter.trace(data=mids, x=gs, name=f'{theta:.1f}', mode='lines'))
fig.show()
return fig
def do_calc(datnum):
"""Just a function which can be passed to a process pool for faster calculation"""
save_name = 'SPS.0045'
dat = get_dat(datnum)
setpoints = [0.0045, None]
# Get other inputs
setpoint_times = square_wave_time_array(dat.SquareEntropy.square_awg)
sp_start, sp_fin = [U.get_data_index(setpoint_times, sp) for sp in setpoints]
logger.debug(f'Setpoint times: {setpoints}, Setpoint indexs: {sp_start, sp_fin}')
# Run Fits
pp = dat.SquareEntropy.get_ProcessParams(name=None, # Start from default and modify from there
setpoint_start=sp_start, setpoint_fin=sp_fin,
transition_fit_func=i_sense,
save_name=save_name)
out = dat.SquareEntropy.get_Outputs(name=save_name, inputs=None, process_params=pp, overwrite=False)
dat.Entropy.get_fit(which='avg', name=save_name, data=out.average_entropy_signal, x=out.x, check_exists=False)
[dat.Entropy.get_fit(which='row', row=i, name=save_name,
data=row, x=out.x, check_exists=False) for i, row in enumerate(out.entropy_signal)]
for dat in all_dats:
w_val = 100
strong_fit = dat.NrgOcc.get_fit(name=strong_fit_name)
if strong_fit.best_values.g > strong_gamma_cutoff:
fit_name = strong_fit_name
else:
fit_name = weak_fit_name
int_data = get_integrated_data(
dat,
fit_name=fit_name,
zero_point=-w_val,
csq_datnum=csq_datnum,
which_linear_theta_fit=which_linear_theta_fit)
idx = U.get_data_index(int_data.x, w_val) # Measure entropy at x = xxx
if idx >= int_data.x.shape[
-1] - 1: # or the end if it doesn't reach xxx
idx -= 10
int_entropy = np.nanmean(int_data.data[idx - 10:idx + 10])
avg_dndt = get_avg_entropy_data(dat,
center_func=_center_func,
csq_datnum=csq_datnum)
fit = dat.Entropy.get_fit(calculate_only=True,
data=avg_dndt.data,
x=avg_dndt.x)
cg_vals.append(dat.Logs.dacs['ESC'])
int_entropies.append(int_entropy)
fit_entropies.append(fit.best_values.dS)
