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Commit 70833171 authored by syz's avatar syz
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Inference now corrects for r_extra. Restructured output of inference on... 

Inference now corrects for r_extra. Restructured output of inference on period. Added plot for I reconstructed
parent e779009a
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pycroscopy/processing/giv_utils.py
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......@@ -14,14 +14,13 @@ from ..io.hdf_utils import getAuxData
from ..viz.plot_utils import set_tick_font_size
def do_bayesian_inference(i_meas, bias, freq, num_x_steps=251, gam=0.03, e=10.0, sigma=10., sigmaC=1.,
def do_bayesian_inference(i_meas, bias, freq, num_x_steps=251, r_extra=110, gam=0.03, e=10.0, sigma=10., sigmaC=1.,
num_samples=2E3, show_plots=False, econ=False):
"""
this function accepts a Voltage vector and current vector
and returns a Bayesian inferred result for R(V) and capacitance
Used for solving the situation I = V/R(V) + CdV/dt
to recover R(V) and C, where C is constant.
Parameters
----------
i_meas : 1D array or list
......@@ -32,6 +31,8 @@ def do_bayesian_inference(i_meas, bias, freq, num_x_steps=251, gam=0.03, e=10.0,
frequency of applied waveform
num_x_steps : unsigned int (Optional, Default = 251)
Number of steps in x vector (interpolating V)
r_extra : float (Optional, default = 220 [Ohms])
Extra resistance in the RC circuit that will provide correct current and resistance values
gam : float (Optional, Default = 0.03)
gamma value for reconstruction
e : float (Optional, Default = 10.0)
......@@ -46,7 +47,6 @@ def do_bayesian_inference(i_meas, bias, freq, num_x_steps=251, gam=0.03, e=10.0,
Whether or not to show plots
econ : Boolean (Optional, Default = False)
Whether or not extra datasets are returned. Turn this on when running on multiple datasets
Returns
-------
results_dict : Dictionary
......@@ -60,9 +60,7 @@ def do_bayesian_inference(i_meas, bias, freq, num_x_steps=251, gam=0.03, e=10.0,
'cValue' : float. Capacitance value
'm2R' : Ask Kody
'SI' : Ask Kody
Written by Kody J. Law (Matlab) and translated to Python by Rama K. Vasudevan
"""
num_samples = int(num_samples)
num_x_steps = int(num_x_steps)
......@@ -86,12 +84,12 @@ def do_bayesian_inference(i_meas, bias, freq, num_x_steps=251, gam=0.03, e=10.0,
A = np.zeros(shape=(num_volt_points, num_x_steps + 1))
for j in range(num_volt_points):
ix = int(round(np.floor((bias[j] + max_volts) / dx) + 1))
ix = min(ix, len(x)-1)
ix = min(ix, len(x) - 1)
ix = max(ix, 1)
A[j, ix] = bias[j] * (bias[j] - x[ix - 1]) / (x[ix] - x[ix - 1])
A[j, ix - 1] = bias[j] * (1. - (bias[j] - x[ix - 1]) / (x[ix] - x[ix - 1]))
A[:, num_x_steps] = dv
A[:, num_x_steps] = dv + r_extra * bias
# generate simulated observations
Lapt = (-1. * np.diag((t[:-1]) ** 0, -1) - np.diag(t[:-1] ** 0, 1) + 2. * np.diag(t ** 0, 0)) / dt / dt
......@@ -175,7 +173,7 @@ def do_bayesian_inference(i_meas, bias, freq, num_x_steps=251, gam=0.03, e=10.0,
return results_dict
def bayesian_inference_on_period(i_meas, excit_wfm, ex_freq, r_extra=220, num_x_steps=500, show_plots=False,
def bayesian_inference_on_period(i_meas, excit_wfm, ex_freq, r_extra=110, num_x_steps=500, show_plots=False,
r_max=None, **kwargs):
"""
Performs Bayesian Inference on a single I-V curve.
......@@ -202,78 +200,75 @@ def bayesian_inference_on_period(i_meas, excit_wfm, ex_freq, r_extra=220, num_x_
Other parameters that will be passed on to the do_bayesian_inference function
Returns
-------
capacitance : array-like - 2 elements
Capacitance on the forward and reverse sections
triangular_bias : array-like
Interpolated bias from bayesian inference of length num_x_steps
resistance : array-like
Resistance of sample infered by Bayesian Inference of length num_x_steps
variance : array-like
Variance of the inferred resistance of length num_x_steps
i_corr_sine : array-like
Measured current with the capacitance correctly subtracted.
results : dictionary
Dictionary iterms are
'cValue' : array-like - 2 elements
Capacitance on the forward and reverse sections
'x' : array-like
Interpolated bias from bayesian inference of length num_x_steps
'mR' : array-like
Resistance of sample infered by Bayesian Inference of length num_x_steps
'vR' : array-like
Variance of the inferred resistance of length num_x_steps
'IcorrSine' : array-like
Measured current with the capacitance correctly subtracted.
'Irec' : array-like
Current reconstructed via Bayesian Inference
"""
roll_val = -0.25
num_v_steps = excit_wfm.size
cos_omega_t = np.roll(excit_wfm, int(num_v_steps * roll_val))
y_val = np.roll(i_meas, int(num_v_steps * roll_val))
half_x_steps = num_x_steps // 2
rev_results = do_bayesian_inference(y_val[:int(0.5 * num_v_steps)], cos_omega_t[:int(0.5 * num_v_steps)],
rev_results = do_bayesian_inference(y_val[:int(0.5 * num_v_steps)] * -1,
cos_omega_t[:int(0.5 * num_v_steps)] * -1,
ex_freq, num_x_steps=half_x_steps,
econ=True, show_plots=False, **kwargs)
econ=True, show_plots=False, r_extra=r_extra, **kwargs)
forw_results = do_bayesian_inference(y_val[int(0.5 * num_v_steps):], cos_omega_t[int(0.5 * num_v_steps):],
ex_freq, num_x_steps=half_x_steps,
econ=True, show_plots=False, **kwargs)
econ=True, show_plots=False, r_extra=r_extra, **kwargs)
# putting the split inference together:
full_results = dict()
for item in ['Irec', 'cValue']:
full_results[item] = np.hstack((forw_results[item], rev_results[item]))
# print(item, full_results[item].shape)
# Rolling back Irec - (this is the only one in cosine):
# A wasteful quantity since it is a duplicate of i_meas
# full_results['Irec'] = np.roll(full_results['Irec'], int(num_v_steps * roll_val * -1))
# Capacitance is always doubled - halve it now:
full_results['cValue'] *= 0.5
cap_val = np.mean(full_results['cValue'])
# Compensating the resistance..
omega = 2 * np.pi * ex_freq
# omega = 2 * np.pi * ex_freq
"""t_max = 1. / ex_freq
t = np.linspace(0, t_max, len(excit_wfm))
dt = t[2] - t[1]"""
# dt = period time / points per period
dt = 1 / (ex_freq * excit_wfm.size)
dv = np.diff(excit_wfm) / dt
dv = np.append(dv, dv[-1])
i_meas = i_meas # from nA to A
i_cap = cap_val * omega * cos_omega_t # from nF to F
i_extra = r_extra * cap_val * excit_wfm # from nF to F, ohms to ohms (1)
i_cap = cap_val * dv # from nF to F
i_extra = r_extra * 2 * cap_val * excit_wfm # from nF to F, ohms to ohms (1)
i_corr_sine = i_meas - i_cap - i_extra
# It is a lot simpler to correct the bayesian current,
# since the capacitance contribution has already been removed, and
# i_extra when plotted against bias is just a straight line!
"""i_extra = r_extra * cap_val * forw_results['x']
i_forw = (forw_results['x']/forw_results['mR']) - i_extra
i_rev = (rev_results['x']/rev_results['mR']) - i_extra"""
# Now also correct the inferred resistance
# old_resistance = np.hstack((forw_results['mR'], np.flipud(rev_results['mR'])))
old_r_forw = forw_results['mR']
old_r_rev = rev_results['mR']
forw_results['mR'] = forw_results['mR'] / (1 - (forw_results['mR'] * r_extra * cap_val))
rev_results['mR'] = rev_results['mR'] / (1 - (rev_results['mR'] * r_extra * cap_val))
full_results['IcorrSine'] = i_corr_sine
# by default Bayesian inference will sort bias in ascending order
for item in ['x', 'mR', 'vR']:
full_results[item] = np.hstack((forw_results[item], np.flipud(rev_results[item])))
rev_results['x'] *= -1
rev_results['Irec'] *= -1
for item in ['x', 'mR', 'vR', 'Irec']:
full_results[item] = np.hstack((forw_results[item], rev_results[item]))
# print(item, full_results[item].shape)
full_results['Irec'] = np.roll(full_results['Irec'], int(num_v_steps * roll_val))
# Plot to make sure things are indeed correct:
if show_plots:
fig, axis = plt.subplots(figsize=(8, 8))
axis.plot(excit_wfm, i_meas, color='green', label='Meas')
axis.plot(excit_wfm, i_corr_sine, color='k', label='Sine corr') # should not be able to see this.
axis.plot(excit_wfm, i_extra, '--', color='grey', label='I extra')
# axis.plot(full_results['x'], full_results['x'] / old_resistance, label='Bayes orig')
# axis.plot(full_results['x'], full_results['x'] / full_results['mR'], label='Bayes corr')
axis.plot(forw_results['x'], forw_results['x'] / old_r_forw, '--', color='cyan', label='Bayes orig F')
axis.plot(rev_results['x'], rev_results['x'] / old_r_rev, '--', color='orange', label='Bayes orig R')
axis.plot(excit_wfm, full_results['Irec'], '--', color='orange', label='I rec')
axis.plot(forw_results['x'], forw_results['x'] / forw_results['mR'], color='blue', label='Bayes corr F')
axis.plot(rev_results['x'], rev_results['x'] / rev_results['mR'], color='red', label='Bayes corr R')
axis.set_xlabel('Bias (V)')
......@@ -285,7 +280,7 @@ def bayesian_inference_on_period(i_meas, excit_wfm, ex_freq, r_extra=220, num_x_
def _plot_resistance(axis, bias_triang, res_vec, variance_vec, forward=True):
st_dev = np.sqrt(variance_vec)
good_pts = np.where(st_dev < 10)[0]
good_pts = good_pts[np.where(good_pts < old_r_forw.size)[0]]
good_pts = good_pts[np.where(good_pts < forw_results['x'].size)[0]]
pos_limits = res_vec + st_dev
neg_limits = res_vec - st_dev
if forward:
......@@ -297,14 +292,11 @@ def bayesian_inference_on_period(i_meas, excit_wfm, ex_freq, r_extra=220, num_x_
axis.fill_between(bias_triang[good_pts], pos_limits[good_pts], neg_limits[good_pts],
alpha=0.25, color=cols_set[1], label='R(V)+-$\sigma$')
fig, axes = plt.subplots(ncols=2, nrows=2, figsize=(10, 10))
fig, axes = plt.subplots(ncols=2, nrows=1, figsize=(10, 5))
for axis, res_vec, variance_vec, name, direction in zip(axes.flat,
[old_r_forw, old_r_rev, forw_results['mR'],
rev_results['mR']],
[forw_results['vR'], rev_results['vR'],
forw_results['vR'], rev_results['vR']],
['Forw Orig', 'Rev Orig', 'Forw Corr', 'Rev Corr'],
[True, False, True, False]):
[forw_results['mR'], rev_results['mR']],
[forw_results['vR'], rev_results['vR']],
['Forw', 'Rev'], [True, False, ]):
_plot_resistance(axis, forw_results['x'], res_vec, variance_vec, forward=direction)
y_lims = axis.get_ylim()
if r_max is not None:
......@@ -317,7 +309,7 @@ def bayesian_inference_on_period(i_meas, excit_wfm, ex_freq, r_extra=220, num_x_
axis.legend()
fig.tight_layout()
return full_results['cValue'], full_results['x'], full_results['mR'], full_results['vR'], i_corr_sine
return full_results
def plot_bayesian_spot_from_h5(h5_bayesian_grp, h5_resh, pix_ind, **kwargs):
......@@ -353,7 +345,7 @@ def plot_bayesian_spot_from_h5(h5_bayesian_grp, h5_resh, pix_ind, **kwargs):
pix_pos=h5_pos[pix_ind], **kwargs)
def plot_bayesian_results(bias_sine, i_meas, i_corrected, bias_triang, resistance, r_variance,
def plot_bayesian_results(bias_sine, i_meas, i_corrected, bias_triang, resistance, r_variance, i_recon=None,
pix_pos=[0, 0], broken_resistance=True, r_max=None, res_scatter=False, **kwargs):
"""
Plots the basic Bayesian Inference results for a specific pixel
......@@ -364,6 +356,8 @@ def plot_bayesian_results(bias_sine, i_meas, i_corrected, bias_triang, resistanc
i_meas : 1D float numpy array
Current measured from experiment
i_corrected : 1D float numpy array
current with capacitance and R extra compensated
i_recon : 1D float numpy array
Reconstructed current
bias_triang : 1D float numpy array
Interpolated bias
......@@ -418,7 +412,6 @@ def plot_bayesian_results(bias_sine, i_meas, i_corrected, bias_triang, resistanc
axes[0].set_ylabel('Resistance (G$\Omega$)', fontsize=font_size_2)
pts_to_plot = [good_forw, good_rev]
for type_ind, axis, pts_list, cols_set, sym_set, set_name in zip(range(len(names)),
......@@ -447,7 +440,7 @@ def plot_bayesian_results(bias_sine, i_meas, i_corrected, bias_triang, resistanc
axis.fill_between(bias_triang[cur_range], pos_limits[cur_range], neg_limits[cur_range],
alpha=0.25, color=cols_set[1])
if ind == 1:
axis.legend(['R(V)', 'R(V)+-$\sigma$'], loc='best', fontsize=font_size_1)
axis.legend(['R(V)', 'R(V)+-$\sigma$'], loc='upper center', fontsize=font_size_1)
else:
if res_scatter:
axis.scatter(bias_triang[pts_list], resistance[pts_list],
......@@ -457,7 +450,7 @@ def plot_bayesian_results(bias_sine, i_meas, i_corrected, bias_triang, resistanc
linestyle=sym_set[0], linewidth=3, label='R(V)')
axis.fill_between(bias_triang[pts_list], pos_limits[pts_list], neg_limits[pts_list],
alpha=0.25, color=cols_set[1], label='R(V)+-$\sigma$')
axis.legend(loc='upper left', fontsize=font_size_1)
axis.legend(loc='upper center', fontsize=font_size_1)
axis.set_xlabel('Voltage (V)', fontsize=font_size_2)
axis.set_xlim((-ex_amp, ex_amp))
......@@ -465,6 +458,8 @@ def plot_bayesian_results(bias_sine, i_meas, i_corrected, bias_triang, resistanc
# ################### CURRENT PLOT ##########################
axes[2].plot(bias_sine, i_meas, 'green', linewidth=3, label='I$_{meas}$')
if i_recon is not None:
axes[2].plot(bias_sine, i_recon, 'k--', linewidth=3, label='I$_{recon}$')
axes[2].plot(cos_omega_t[orig_half_pt:], i_correct_rolled[orig_half_pt:],
'blue', linewidth=3, label='I$_{Bayes} Forw$')
axes[2].plot(cos_omega_t[:orig_half_pt], i_correct_rolled[:orig_half_pt],
......
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