Merge 7a89850 into 8a9d06e

examples/hh_nevergrad_errorevolution.py

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+from brian2 import *
+from brian2modelfitting import *
+import pandas as pd
+from mpl_toolkits.mplot3d import Axes3D
+from matplotlib.animation import FuncAnimation
+
+
+# load data
+df_inp_traces = pd.read_csv('input_traces_hh.csv')
+df_out_traces = pd.read_csv('output_traces_hh.csv')
+inp_traces = df_inp_traces.to_numpy()
+inp_traces = inp_traces[:-1, 1:]
+out_traces = df_out_traces.to_numpy()
+out_traces = out_traces[:-1, 1:]
+
+# model parameters
+area = 20000. * umetre ** 2
+Cm = 1. * ufarad * cm ** -2 * area
+E_l = -65. * mV
+E_k = -90. * mV
+E_na = 50. * mV
+Vt = -63. * mV
+init_v = {'v': -65. * mV}
+dt = 0.01 * ms
+defaultclock.dt = dt
+
+# model definition
+hodgkin_huxley = Equations(
+'''dv/dt = (
+        (g_l * (E_l - v)
+        - g_na * (m ** 3) * h * (v - E_na)
+        - g_k * (n ** 4) * (v - E_k) + I) / Cm) : volt
+    dm/dt = (
+        0.32 * (mV ** -1 ) * (13.0 * mV - v + Vt) 
+        / (exp((13.0 * mV - v + Vt) / (4.0 * mV)) - 1.0) / ms * (1 - m)
+        - 0.28 * (mV ** -1) * (v - Vt - 40.0 * mV) 
+        / (exp((v - Vt - 40.0 * mV) / (5.0 * mV)) - 1.0) / ms * m) : 1
+    dn/dt = (
+        0.032 * (mV ** -1) * (15.0 * mV - v + Vt) 
+        / (exp((15.0 * mV - v + Vt) / (5.0 * mV)) - 1.0) / ms * (1.0 - n)
+        - 0.5 * exp((10.0 * mV - v + Vt) / (40.0 * mV)) / ms * n) : 1
+    dh/dt = (
+        0.128 * exp((17.0 * mV - v + Vt) / (18.0 * mV)) / ms * (1.0 - h)
+        - 4.0 / (1 + exp((40.0 * mV - v + Vt) / (5.0 * mV))) / ms * h) : 1
+    g_na : siemens (constant)
+    g_k : siemens (constant)
+    g_l : siemens (constant)''')
+
+# optimizer instantiation
+optimizer = NevergradOptimizer()
+
+# metric instantiation
+metric = MSEMetric()
+
+# fitter definition and fitting procedure
+n_samples = 40
+fitter = TraceFitter(
+    model=hodgkin_huxley,
+    input_var='I', input=inp_traces * amp,
+    output_var='v', output=out_traces * mV,
+    dt=dt,
+    n_samples=n_samples,
+    method='exponential_euler',
+    param_init=init_v)
+
+
+def callback(params, errors, best_params, best_error, index):
+    """Custom callback"""
+    print(f'[round {index + 1}]\t{np.min(errors)}')
+
+
+# fitting procedure
+n_rounds = 25
+res, error = fitter.fit(
+    optimizer=optimizer,
+    metric=metric,
+    n_rounds=n_rounds,
+    callback=callback,
+    g_l=[1.e-09 * siemens, 1.e-07 * siemens],
+    g_na=[2.e-06 * siemens, 2.e-04 * siemens],
+    g_k=[6.e-07 * siemens, 6.e-05 * siemens])
+
+# visualization of best fitted traces
+start_scope()
+fit_traces = fitter.generate_traces(params=res, param_init=init_v)
+
+nrows = 2
+ncols = fit_traces.shape[0]
+fig, axs = plt.subplots(
+    nrows=nrows, ncols=ncols, sharex=True,
+    gridspec_kw={'height_ratios': [3, 1]}, figsize=(15, 4))
+for idx in range(ncols):
+    axs[0, idx].plot(out_traces[idx, :].T, 'k-', label='$V_m^{measured}(t)$')
+    axs[0, idx].plot(fit_traces[idx, :].T / mV, 'r--', label='$V_m^{fit}(t)$')
+    axs[1, idx].plot(inp_traces[idx, :].T / amp, 'k-', label='$I(t)$')
+    axs[0, idx].grid()
+    axs[1, idx].grid()
+    axs[1, idx].set_xlabel('t [ms]')
+    if idx == 0:
+        axs[0, idx].set_ylabel('$V_m$ [mV]')
+        axs[1, idx].set_ylabel('$I$ [A/cm$^2$]')
+handles, labels = [
+    (h + l) for h, l
+    in zip(axs[0, idx].get_legend_handles_labels(),
+           axs[1, idx].get_legend_handles_labels())]
+fig.legend(handles, labels, loc='upper right')
+plt.tight_layout()
+plt.show()
+# fig.savefig('traces.png', format='png', bbox_inches='tight', dpi=220)
+
+# visualization of errors and parameters evolving over time
+full_output = fitter.results(format='dataframe', use_units=False)
+g_k = full_output['g_k'].to_numpy()
+g_na = full_output['g_na'].to_numpy()
+g_l = full_output['g_l'].to_numpy()
+error = full_output['error'].to_numpy()
+
+fig = plt.figure(figsize=(15, 5))
+ax1 = fig.add_subplot(1, 2, 1, projection='3d')
+ax2 = fig.add_subplot(1, 2, 2)
+ax1.set_xlabel('$g_K$ [S]')
+ax1.set_ylabel('$g_{Na}$ [S]')
+ax1.set_zlabel('$g_l$ [S]')
+ax2.set_xlabel('round')
+ax2.set_ylabel('error')
+ax1.w_xaxis.set_pane_color((0, 0, 0))
+ax1.w_yaxis.set_pane_color((0, 0, 0))
+ax1.w_zaxis.set_pane_color((0, 0, 0))
+ax1.set_xlim3d(0, g_k.max() * 1.01)
+ax1.set_ylim3d(0, g_na.max() * 1.01)
+ax1.set_zlim3d(0, g_l.max() * 1.01)
+ax1.ticklabel_format(useOffset=True, style='scientific', scilimits=(0, 0))
+ax1.grid()
+ax2.grid()
+
+
+def init():
+    ax1.plot3D(g_k[:n_samples], g_na[:n_samples], g_l[:n_samples],
+               'b*', markersize=4, label='init population')
+    ax2.plot([0], np.min(error[:n_samples]),
+             'b*', markersize=8, label='init best error')
+    ax1.legend()
+    ax2.legend()
+
+
+def animate(frame):
+    istart = frame * n_samples
+    iend = istart + n_samples
+    if (res['g_k'] / siemens in g_k[istart:iend]
+            and res['g_na'] / siemens in g_na[istart:iend]
+            and res['g_l'] / siemens in g_l[istart:iend]):
+        ax1.plot3D([res['g_k']], [res['g_na']], [res['g_l']],
+                  'r*', markersize=8, label='best params')
+        ax2.plot(frame, np.min(error[istart:iend]),
+                'r*', markersize=8, label='best error')
+        ax1.legend()
+        ax2.legend()
+    else:
+        ax1.plot3D(g_k[istart:iend], g_na[istart:iend], g_l[istart:iend],
+                   'ko', markersize=4, zorder=-1, alpha=0.3)
+        ax2.plot(frame, np.min(error[istart:iend]), 'ko',
+                 markersize=4, zorder=-1)
+
+
+anim = FuncAnimation(
+    fig, animate, init_func=init, frames=np.arange(1, n_rounds), repeat=False)
+plt.tight_layout()
+plt.show()
+# anim.save('evolution.gif', writer='pillow', fps=5)