Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix docstrings and rerun #7

Merged
merged 1 commit into from
Jun 18, 2021
Merged

Fix docstrings and rerun #7

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
26 changes: 13 additions & 13 deletions notebooks/complexity_corr_membrane_potential.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -75,7 +75,7 @@
" Time point marking the start of stimulus input [ms]\n",
" t_stop : number\n",
" Time point marking the end of stimulus input [ms]\n",
" kwargs : dict\n",
" args : list\n",
" g_Na : number\n",
" Sodium (Na) maximum conductance [mS/cm^2]\n",
" g_K : number\n",
Expand All @@ -94,9 +94,13 @@
" Returns\n",
" -------\n",
" numpy.ndarray\n",
" State variables dynamics of shape (`t.size`, 4).\n",
" State variables dynamics of shape (`t.size`, 4)\n",
" \"\"\"\n",
" Vm, m, h, n = y0\n",
" if args:\n",
" g_Na, g_K, g_L, Cm, E_Na, E_K, E_L = args\n",
" else:\n",
" g_Na, g_K, g_L, Cm, E_Na, E_K, E_L = 120, 36, 0.3, 50, -77, -54.4\n",
" dVmdt = ((synaptic_current(t, A, t_start, t_stop)\n",
" - g_Na * m ** 3 * h * (Vm - E_Na)\n",
" - g_K * n ** 4 * (Vm - E_K)\n",
Expand Down Expand Up @@ -139,13 +143,13 @@
"source": [
"# Solve the ODE system\n",
"I = synaptic_current(t, A, t_start, t_stop)\n",
"args = (A, t_start, t_stop, g_Na, g_K, g_L, Cm, E_Na, E_K, E_L)\n",
"Vm = odeint(hodgkin_huxley_model, y0, t, args=args)[:, 0]\n",
"params = (A, t_start, t_stop, g_Na, g_K, g_L, Cm, E_Na, E_K, E_L)\n",
"Vm = odeint(hodgkin_huxley_model, y0, t, args=params)[:, 0]\n",
"\n",
"# Cunt the number of spikes...\n",
"# Count the number of spikes...\n",
"thresh = -40\n",
"n_spikes = find_peaks(Vm, height=thresh)[0].size\n",
"# ... and propose a sampling frequency\n",
"# ... and define a sampling frequency\n",
"sf = (n_spikes + 1) * 2"
]
},
Expand All @@ -171,7 +175,7 @@
}
],
"source": [
"# Generate 100 voltage traces with increasing noise...\n",
"# Generate 100 voltage traces with increasing noise\n",
"np.random.seed(42)\n",
"n_simulations = 100\n",
"noise_factor = np.linspace(0, 10, n_simulations)\n",
Expand All @@ -180,20 +184,16 @@
"for i in range(n_simulations):\n",
" traces[i] = Vm + noise_factor[i] * neural_noise[i, :]\n",
" \n",
"# ...and plot the first and last traces\n",
"# Plot the first and last voltage trace\n",
"fig, ax = plt.subplots(2, 1, sharex=True, sharey=False,\n",
" gridspec_kw={'height_ratios': [3, 1]}, figsize=(8, 5))\n",
"\n",
"ax[0].plot(t, traces[0], label=f'noise factor = {noise_factor[0]}', zorder=2)\n",
"ax[0].plot(t, traces[-1], label=f'noise factor = {noise_factor[-1]}', zorder=1)\n",
"ax[0].set_ylabel('$V_m$ [mV]')\n",
"ax[0].legend()\n",
"\n",
"ax[1].plot(t, I, 'C2')\n",
"ax[1].set_xlabel('$t$ [ms]')\n",
"ax[1].set_ylabel('$I$ [nA]')\n",
"\n",
"plt.show()"
"ax[1].set_ylabel('$I$ [nA]');"
]
},
{
Expand Down