Adapt to binder
imperator
1 year ago
parent
73a79a1627
commit
3afad8c32d
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scipy
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scipy
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numpy
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numpy
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matplotlib
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matplotlib
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hdf5storage
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ipympl
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ipympl
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mat73
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from itertools import product
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import numpy as np
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from scipy.integrate import trapezoid
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import matplotlib.pyplot as plt
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from matplotlib.lines import Line2D
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from IPython.display import display
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from ipywidgets import interact, interact_manual, IntSlider, FloatSlider, IntRangeSlider, ToggleButton, ToggleButtons, Layout
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from scipy.io import loadmat as sp_loadmat
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from mat73 import loadmat as mat73_loadmat
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def in_colab():
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"""Check if the code is running in Google Colab."""
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try:
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import google.colab
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return True
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except ImportError:
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return False
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is_colab = in_colab()
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continuous_update = not is_colab
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if is_colab:
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from google.colab import output
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output.enable_custom_widget_manager()
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def setup_matplotlib_magic():
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get_ipython().run_line_magic('matplotlib', 'inline' if is_colab else 'widget')
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def draw_figure(fig):
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if not is_colab:
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fig.canvas.draw_idle()
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else:
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plt.show()
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def maybe_setup(setup_fun, state):
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if not is_colab:
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return
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elif 'needs_setup' not in state:
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state['needs_setup'] = True
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else:
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state.update(setup_fun())
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def loadmat(mat_file):
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try:
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return sp_loadmat(mat_file)
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except Exception:
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return mat73_loadmat(mat_file)
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def generate_sims(C, k, alpha, sigma_a, sigma_s, lambda_, n_sim=100, tau=100, dt_total=11 / 85):
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dt = dt_total / tau
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# discretize C
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if isinstance(k, np.ndarray):
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C_scaled = np.repeat(C * k[:, np.newaxis], tau, axis=1)
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n_sim = len(k)
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else:
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C_scaled = np.repeat(C * k, tau)[np.newaxis, :]
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T = C_scaled.shape[-1]
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# noise terms
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xiR = np.random.randn(n_sim) * alpha / k
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xiL = np.random.randn(n_sim) * alpha / k
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directional_noise = (
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xiR[:, np.newaxis] * (C_scaled > 0) +
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xiL[:, np.newaxis] * (C_scaled < 0)
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)
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dW = np.sqrt(dt) * np.random.randn(n_sim, T)
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eta = 1 + np.random.randn(n_sim, T) * (sigma_s * np.sqrt(tau))
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# accumulated evidence
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a = np.zeros((n_sim, T + 1))
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mE = np.zeros((n_sim, T + 1))
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for t in range(T):
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a[:, t + 1] = a[:, t] + (
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directional_noise[:, t] * C_scaled[:, t] * (dt_total / tau) +
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lambda_ * a[:, t] * (dt_total / tau) +
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sigma_a * dW[:, t] +
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eta[:, t] * C_scaled[:, t] * (dt_total / tau)
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)
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# momentary evidence
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mE[:, t+1] = eta[:, t] * C_scaled[:, t] * (dt_total / tau) + lambda_ * a[:, t] * (dt_total / tau)
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return a[:, 1:], mE, tau, dt
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def generate_sims_conditions(ks, directions, sim_parameters, num_sims_per_condition):
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simulation_combinations = list(product(ks, directions))
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a_all = []
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mE_all = []
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k_idx_all = []
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direction_all = []
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for idx, (k, direction) in enumerate(simulation_combinations):
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C = sim_parameters['C'] * direction
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dir_label = 1 if direction == 1 else 0
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a_temp, mE_temp, tau, dt = generate_sims(**{
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**sim_parameters,
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'C': C,
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'k': k,
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'n_sim': num_sims_per_condition
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})
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# subsample at every tau steps
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a_sampled = a_temp[:, tau-1::tau]
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mE_sampled = mE_temp[:, tau-1::tau] / dt
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a_all.append(a_sampled)
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mE_all.append(mE_sampled)
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k_idx_all.extend([k] * num_sims_per_condition)
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direction_all.extend([dir_label] * num_sims_per_condition)
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a_all = np.vstack(a_all)
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mE_all = np.vstack(mE_all)
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k_idx_all = np.array(k_idx_all)
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direction_all = np.array(direction_all)
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choices = (a_all > 0).astype(int) # 1 is right, 0 is left
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is_correct = (choices == direction_all[:, np.newaxis]).astype(int)
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time = np.arange(len(C))
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return time, a_all, mE_all, k_idx_all, choices, is_correct
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def plot_sims(C_size=11, num_sims=30 if not is_colab else 5):
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setup_matplotlib_magic()
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def setup():
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fig, axes = plt.subplots(figsize=(6.5, 5))
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evidence_line = axes.plot([], [], color='C2', alpha=1)[0]
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sim_lines = []
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for i in range(num_sims):
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sim_line = axes.plot([], [], color='C0', alpha=0.3)[0]
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sim_lines += [sim_line]
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axes.set(
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title=f"{num_sims} Simulations",
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ylabel="value",
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xlabel="time $t$",
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xlim=(0, 11),
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ylim=(-1.5, 1.5)
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)
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plt.axhline(0., color='black', alpha=0.3)
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plt.tight_layout()
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legend_elements = [
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Line2D([], [], color='C2', label='evidence pulse'),
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Line2D([], [], color='C0', label='accumulator $a$ (decision: right)'),
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Line2D([], [], color='C1', label='accumulator $a$ (decision: left)')
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]
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axes.legend(handles=legend_elements, loc='upper right')
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return {'fig': fig, 'axes': axes, 'evidence_line': evidence_line, 'sim_lines': sim_lines}
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state = setup()
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state['random_seed'] = 42
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def update_plot(C_dir, C, k, alpha, sigma_a, sigma_s, lambda_, fixed_noise):
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maybe_setup(setup, state)
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if fixed_noise == 'redraw noise':
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state['random_seed'] = np.random.randint(0, 2**32)
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np.random.seed(state['random_seed'])
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C = np.concatenate([np.zeros(C[0]), np.ones(C[1] - C[0]), np.zeros(C_size - C[1])])
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C *= 1 if C_dir == 'pulse right' else -1
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sims, *_ = generate_sims(C, k, alpha, sigma_a, sigma_s, lambda_, n_sim=num_sims)
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for sim, sim_line in zip(sims, state['sim_lines']):
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sim_line.set_data(np.linspace(0, len(C), len(sim)), sim)
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sim_line.set_color('C0' if sim[-1] > 0 else 'C1')
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state['evidence_line'].set_data(np.linspace(0., len(C), len(C) * 1_000), np.repeat(C, 1_000) * k)
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draw_figure(state['fig'])
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style = {'description_width': '150px'}
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layout = Layout(width='600px')
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sliders = {
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'C_dir': ToggleButtons(options=['pulse left', 'pulse right'], value='pulse right', description=' '),
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'C': IntRangeSlider(min=0, max=C_size, value=[3, 7], description='evidence pulse timing', style=style, layout=layout, continuous_update=continuous_update),
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'k': FloatSlider(min=1e-6, max=1., step=0.01, value=0.5, description='coherence', style=style, layout=layout, continuous_update=continuous_update),
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'sigma_s': FloatSlider(min=0, max=3, step=0.01, value=0., description='fast noise (input)', style=style, layout=layout, continuous_update=continuous_update),
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'alpha': FloatSlider(min=0, max=1, step=0.01, value=0., description='slow noise (brain)', style=style, layout=layout, continuous_update=continuous_update),
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'sigma_a': FloatSlider(min=0, max=1, step=0.01, value=0., description='fast inner noise (brain)', style=style, layout=layout, continuous_update=continuous_update),
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'lambda_': FloatSlider(min=-5, max=5, step=0.01, value=0., description='leakiness', style=style, layout=layout, continuous_update=continuous_update),
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'fixed_noise': ToggleButtons(options=['fix noise', 'redraw noise'], value='fix noise', description=' '),
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}
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interact(update_plot, **sliders)
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def update_errorbar(err_container, x, y, yerr):
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err_container.lines[0].set_data(x, y)
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linecol = err_container.lines[2][0]
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segments = []
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for xi, yi, yerri in zip(x, y, yerr):
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segments.append([[xi, yi - yerri], [xi, yi + yerri]])
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linecol.set_segments(segments)
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def plot_model_free_analysis_conditions(C, ks, num_sims_per_condition=2_000):
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setup_matplotlib_magic()
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def setup():
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fig, axes = plt.subplots(1, 2, figsize=(10, 5), sharex=True)
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accuracy_lines = [axes[0].errorbar([], [], yerr=[], label=f'$k = {k}$') for k in ks]
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kernel_lines = [axes[1].plot([], [], label=f'$k = {k}$')[0] for k in ks]
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axes[0].set(
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title="accuracy",
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xlabel="$t$",
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xlim=(0, len(C) - 1),
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ylim=(0, 1)
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)
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axes[0].legend(loc='lower right', fontsize='small')
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axes[1].set(
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title="psychophysical kernel",
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xlabel="$t$",
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ylim=(-3, 3)
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)
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axes[1].legend(loc='lower left', fontsize='small')
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fig.tight_layout()
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return {'fig': fig, 'axes': axes, 'accuracy_lines': accuracy_lines, 'kernel_lines': kernel_lines}
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state = setup() if not is_colab else {'needs_setup': True}
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def update_plot(sigma_s, alpha, sigma_a, lambda_):
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maybe_setup(setup, state)
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sim_parameters = {
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'C': C,
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'sigma_s': sigma_s,
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'alpha': alpha,
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'sigma_a': sigma_a,
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'lambda_': lambda_
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}
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directions = [1, -1]
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time, a_all, mE_all, k_idx_all, choices, is_correct = generate_sims_conditions(
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ks, directions, sim_parameters, num_sims_per_condition
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)
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for i, k in enumerate(ks):
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mask = (k_idx_all == k)
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is_corr_k = is_correct[mask, :]
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perf = is_corr_k.mean(axis=0)
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ci95 = 1.96 * is_corr_k.std(axis=0) / np.sqrt(mask.sum())
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update_errorbar(state['accuracy_lines'][i], time, perf, yerr=ci95)
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psy_kernel = (
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mE_all[ (choices[:, -1] == 1) & mask ].mean(axis=0) -
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mE_all[ (choices[:, -1] != 1) & mask ].mean(axis=0)
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)
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state['kernel_lines'][i].set_data(time, psy_kernel)
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state['fig'].tight_layout()
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draw_figure(state['fig'])
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style = {'description_width': '150px'}
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layout = Layout(width='600px')
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sliders = {
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'sigma_s': FloatSlider(min=0, max=5, step=0.01, value=0., description='fast noise (input)', style=style, layout=layout),
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'alpha': FloatSlider(min=0, max=1, step=0.01, value=0., description='slow noise (brain)', style=style, layout=layout),
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'sigma_a': FloatSlider(min=0, max=2, step=0.01, value=0., description='fast inner noise (brain)', style=style, layout=layout),
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'lambda_': FloatSlider(min=-5, max=5, step=0.01, value=0., description='leakiness', style=style, layout=layout)
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}
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interact_manual.options(manual_name='run simulations')(
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update_plot,
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**sliders
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)
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def model_free_analysis(dataset):
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is_correct = dataset['choices'] == dataset['direction'].flatten()
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time = np.arange(dataset['a'].shape[1])
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perfs = []
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ci95s = []
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psy_kernels = []
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for k_idx in [1, 2, 3]:
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mask = (dataset['kIdx'].flatten() == k_idx)
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is_corr_k = is_correct[:, mask]
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perf = is_corr_k.mean(axis=1)
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ci95 = 1.96 * is_corr_k.std(axis=1) / np.sqrt(mask.sum())
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psy_kernel = (
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dataset['mE'][ (dataset['choices'][-1, :] == 1) & mask ].mean(axis=0) -
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dataset['mE'][ (dataset['choices'][-1, :] != 1) & mask ].mean(axis=0)
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)
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perfs += [perf]
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ci95s += [ci95]
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psy_kernels += [psy_kernel]
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return time, perfs, ci95s, psy_kernels
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def plot_model_free_analysis_conditions_vs_baseline(baseline_data, num_sims_per_condition=2_000):
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setup_matplotlib_magic()
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C = np.concatenate(([0], np.ones(10)))
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ks = [0.2, 0.4, 0.8]
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def setup():
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fig, axes = plt.subplots(1, 2, figsize=(10, 5), sharex=True)
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accuracy_lines = [axes[0].errorbar([], [], yerr=[], label=f'$k = {k}$') for k in ks]
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kernel_lines = [axes[1].plot([], [], label=f'$k = {k}$')[0] for k in ks]
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axes[0].set(
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title="accuracy",
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xlabel="$t$",
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xlim=(0, len(C) - 1),
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ylim=(0, 1)
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)
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axes[1].set(
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title="psychophysical kernel",
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xlabel="$t$",
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ylim=(-3, 3)
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)
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time, perfs, ci95s, psy_kernels = model_free_analysis(baseline_data)
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||||||
|
for i, (perf, ci95, psy_kernel) in enumerate(zip(perfs, ci95s, psy_kernels, strict=True)):
|
||||||
|
axes[0].errorbar(time, perf, yerr=ci95, color=f'C{i}', label=f'$k = {ks[i]}$ (baseline)', linestyle='--', alpha=0.3)
|
||||||
|
axes[1].plot(time, psy_kernel, color=f'C{i}', label=f'$k = {ks[i]}$ (baseline)', linestyle='--', alpha=0.3)
|
||||||
|
|
||||||
|
axes[0].legend(loc='lower right', fontsize='small')
|
||||||
|
axes[1].legend(loc='lower left', fontsize='small')
|
||||||
|
|
||||||
|
fig.tight_layout()
|
||||||
|
|
||||||
|
return {'fig': fig, 'axes': axes, 'accuracy_lines': accuracy_lines, 'kernel_lines': kernel_lines}
|
||||||
|
|
||||||
|
state = setup() if not is_colab else {'needs_setup': True}
|
||||||
|
|
||||||
|
def update_plot(sigma_s, alpha, sigma_a, lambda_):
|
||||||
|
maybe_setup(setup, state)
|
||||||
|
|
||||||
|
sim_parameters = {
|
||||||
|
'C': C,
|
||||||
|
'sigma_s': sigma_s,
|
||||||
|
'alpha': alpha,
|
||||||
|
'sigma_a': sigma_a,
|
||||||
|
'lambda_': lambda_
|
||||||
|
}
|
||||||
|
|
||||||
|
directions = [1, -1]
|
||||||
|
time, a_all, mE_all, k_idx_all, choices, is_correct = generate_sims_conditions(
|
||||||
|
ks, directions, sim_parameters, num_sims_per_condition
|
||||||
|
)
|
||||||
|
|
||||||
|
for i, k in enumerate(ks):
|
||||||
|
mask = (k_idx_all == k)
|
||||||
|
is_corr_k = is_correct[mask, :]
|
||||||
|
perf = is_corr_k.mean(axis=0)
|
||||||
|
ci95 = 1.96 * is_corr_k.std(axis=0) / np.sqrt(mask.sum())
|
||||||
|
|
||||||
|
update_errorbar(state['accuracy_lines'][i], time, perf, yerr=ci95)
|
||||||
|
|
||||||
|
psy_kernel = (
|
||||||
|
mE_all[ (choices[:, -1] == 1) & mask ].mean(axis=0) -
|
||||||
|
mE_all[ (choices[:, -1] != 1) & mask ].mean(axis=0)
|
||||||
|
)
|
||||||
|
|
||||||
|
state['kernel_lines'][i].set_data(time, psy_kernel)
|
||||||
|
|
||||||
|
state['fig'].tight_layout()
|
||||||
|
draw_figure(state['fig'])
|
||||||
|
|
||||||
|
|
||||||
|
style = {'description_width': '150px'}
|
||||||
|
layout = Layout(width='600px')
|
||||||
|
sliders = {
|
||||||
|
'sigma_s': FloatSlider(min=0, max=5, step=0.01, value=0., description='fast noise (input)', style=style, layout=layout),
|
||||||
|
'alpha': FloatSlider(min=0, max=1, step=0.01, value=0., description='slow noise (brain)', style=style, layout=layout),
|
||||||
|
'sigma_a': FloatSlider(min=0, max=2, step=0.01, value=0., description='fast inner noise (brain)', style=style, layout=layout),
|
||||||
|
'lambda_': FloatSlider(min=-5, max=5, step=0.01, value=0., description='leakiness', style=style, layout=layout)
|
||||||
|
}
|
||||||
|
|
||||||
|
interact_manual.options(manual_name='run simulations')(
|
||||||
|
update_plot,
|
||||||
|
**sliders
|
||||||
|
)
|
||||||
|
|
||||||
|
|
||||||
|
def bin_spikes(raw_spike_matrix, bin_size=50):
|
||||||
|
num_bins = raw_spike_matrix.shape[1] // bin_size
|
||||||
|
|
||||||
|
truncated_raw_spike_matrix = raw_spike_matrix[:, :num_bins * bin_size, :]
|
||||||
|
binned_spike_matrix = truncated_raw_spike_matrix.reshape([
|
||||||
|
truncated_raw_spike_matrix.shape[0],
|
||||||
|
num_bins,
|
||||||
|
-1,
|
||||||
|
truncated_raw_spike_matrix.shape[2]
|
||||||
|
]).sum(axis=2)
|
||||||
|
|
||||||
|
return binned_spike_matrix
|
||||||
|
|
||||||
|
|
||||||
|
def get_binned_spike_matrix(mat_data):
|
||||||
|
raw_spike_matrix = mat_data['RawSpikeMatrix1'][:, 149:1000, :]
|
||||||
|
binned_spike_matrix = bin_spikes(raw_spike_matrix)
|
||||||
|
binned_spike_matrix = np.sqrt(binned_spike_matrix)
|
||||||
|
time = np.arange(binned_spike_matrix.shape[1]) * 50
|
||||||
|
return time, binned_spike_matrix
|
||||||
|
|
||||||
|
|
||||||
|
def plot_single_neuron(mat_data):
|
||||||
|
setup_matplotlib_magic()
|
||||||
|
|
||||||
|
time, binned_spike_matrix = get_binned_spike_matrix(mat_data)
|
||||||
|
|
||||||
|
def setup():
|
||||||
|
fig, axes = plt.subplots(figsize=(6.5, 4.5))
|
||||||
|
|
||||||
|
neuron_line = axes.plot([], [])[0]
|
||||||
|
|
||||||
|
axes.set(
|
||||||
|
ylabel=r'$\sqrt{N_\mathrm{spikes}}$',
|
||||||
|
xlabel='time [ms]',
|
||||||
|
xlim=(0, 800)
|
||||||
|
)
|
||||||
|
|
||||||
|
return {'fig': fig, 'axes': axes, 'neuron_line': neuron_line}
|
||||||
|
|
||||||
|
state = setup()
|
||||||
|
|
||||||
|
def update_plot(neuron_idx):
|
||||||
|
maybe_setup(setup, state)
|
||||||
|
|
||||||
|
state['neuron_line'].set_data(time, binned_spike_matrix.mean(axis=0)[:, neuron_idx])
|
||||||
|
|
||||||
|
state['axes'].relim()
|
||||||
|
state['axes'].autoscale(axis='y')
|
||||||
|
state['axes'].set_title(f'Neuron #{neuron_idx}', fontsize='small')
|
||||||
|
state['fig'].tight_layout()
|
||||||
|
draw_figure(state['fig'])
|
||||||
|
|
||||||
|
sliders = {
|
||||||
|
'neuron_idx': IntSlider(min=0, max=binned_spike_matrix.shape[2] - 1, description='neuron #', layout=Layout(width='800px'), continuous_update=continuous_update)
|
||||||
|
}
|
||||||
|
|
||||||
|
interact(update_plot, **sliders)
|
||||||
|
|
||||||
|
|
||||||
|
def plot_neuron_by_choice(mat_data):
|
||||||
|
setup_matplotlib_magic()
|
||||||
|
|
||||||
|
time, binned_spike_matrix = get_binned_spike_matrix(mat_data)
|
||||||
|
|
||||||
|
correct_trials_mask = (mat_data['targ_cho'].flatten() == mat_data['targ_cor'].flatten())
|
||||||
|
right_choice = (mat_data['targ_cho'].flatten() == 1)
|
||||||
|
|
||||||
|
def setup():
|
||||||
|
fig, axes = plt.subplots(1, 2, figsize=(8, 4), sharex=True)
|
||||||
|
|
||||||
|
choices = ['right choice', 'left choice']
|
||||||
|
correct_lines = []
|
||||||
|
for choice in choices:
|
||||||
|
correct_line = axes[0].plot([], [], label=choice)[0]
|
||||||
|
correct_lines += [correct_line]
|
||||||
|
|
||||||
|
incorrect_lines = []
|
||||||
|
for choice in choices:
|
||||||
|
incorrect_line = axes[1].plot([], [], label=choice)[0]
|
||||||
|
incorrect_lines += [incorrect_line]
|
||||||
|
|
||||||
|
axes[0].set(
|
||||||
|
title='correct trials',
|
||||||
|
ylabel=r'$\sqrt{N_\mathrm{spikes}}$',
|
||||||
|
xlabel='time [ms]',
|
||||||
|
xlim=(0, 800)
|
||||||
|
)
|
||||||
|
axes[1].set(
|
||||||
|
title='incorrect trials',
|
||||||
|
xlabel='time [ms]'
|
||||||
|
)
|
||||||
|
axes[0].legend(loc='upper right')
|
||||||
|
axes[1].legend(loc='upper right')
|
||||||
|
|
||||||
|
return {'fig': fig, 'axes': axes, 'correct_lines': correct_lines, 'incorrect_lines': incorrect_lines}
|
||||||
|
|
||||||
|
state = setup()
|
||||||
|
|
||||||
|
def update_plot(neuron_idx):
|
||||||
|
maybe_setup(setup, state)
|
||||||
|
|
||||||
|
state['correct_lines'][0].set_data(time, binned_spike_matrix[correct_trials_mask & right_choice].mean(axis=0)[:, neuron_idx])
|
||||||
|
state['correct_lines'][1].set_data(time, binned_spike_matrix[correct_trials_mask & ~right_choice].mean(axis=0)[:, neuron_idx])
|
||||||
|
state['incorrect_lines'][0].set_data(time, binned_spike_matrix[~correct_trials_mask & right_choice].mean(axis=0)[:, neuron_idx])
|
||||||
|
state['incorrect_lines'][1].set_data(time, binned_spike_matrix[~correct_trials_mask & ~right_choice].mean(axis=0)[:, neuron_idx])
|
||||||
|
|
||||||
|
state['axes'][0].relim()
|
||||||
|
state['axes'][1].relim()
|
||||||
|
state['axes'][0].autoscale(axis='y')
|
||||||
|
state['axes'][1].autoscale(axis='y')
|
||||||
|
state['fig'].suptitle(f'Neuron #{neuron_idx}', fontsize='small')
|
||||||
|
state['fig'].tight_layout()
|
||||||
|
draw_figure(state['fig'])
|
||||||
|
|
||||||
|
sliders = {
|
||||||
|
'neuron_idx': IntSlider(min=0, max=binned_spike_matrix.shape[2] - 1, description='neuron #', layout=Layout(width='800px'), continuous_update=continuous_update)
|
||||||
|
}
|
||||||
|
|
||||||
|
interact(update_plot, **sliders)
|
||||||
|
|
||||||
|
|
||||||
|
def plot_neuron_by_coherence(mat_data):
|
||||||
|
setup_matplotlib_magic()
|
||||||
|
|
||||||
|
time, binned_spike_matrix = get_binned_spike_matrix(mat_data)
|
||||||
|
|
||||||
|
correct_trials_mask = (mat_data['targ_cho'].flatten() == mat_data['targ_cor'].flatten())
|
||||||
|
coherences = np.sort(
|
||||||
|
np.unique(mat_data['dot_coh'])
|
||||||
|
)
|
||||||
|
coherences = coherences[[0, 3, 5]]
|
||||||
|
|
||||||
|
def setup():
|
||||||
|
fig, axes = plt.subplots(1, 2, figsize=(8, 4), sharex=True)
|
||||||
|
|
||||||
|
choices = ['right choice', 'left choice']
|
||||||
|
correct_lines = []
|
||||||
|
for coherence in coherences:
|
||||||
|
correct_line = axes[0].plot([], [], label=f'{coherence = :.1%}')[0]
|
||||||
|
correct_lines += [correct_line]
|
||||||
|
|
||||||
|
incorrect_lines = []
|
||||||
|
for coherence in coherences:
|
||||||
|
incorrect_line = axes[1].plot([], [], label=f'{coherence = :.1%}')[0]
|
||||||
|
incorrect_lines += [incorrect_line]
|
||||||
|
|
||||||
|
axes[0].set(
|
||||||
|
title='correct trials',
|
||||||
|
ylabel=r'$\sqrt{N_\mathrm{spikes}}$',
|
||||||
|
xlabel='time [ms]',
|
||||||
|
xlim=(0, 800)
|
||||||
|
)
|
||||||
|
axes[1].set(
|
||||||
|
title='incorrect trials',
|
||||||
|
xlabel='time [ms]'
|
||||||
|
)
|
||||||
|
axes[0].legend(loc='upper right')
|
||||||
|
axes[1].legend(loc='upper right')
|
||||||
|
|
||||||
|
return {'fig': fig, 'axes': axes, 'correct_lines': correct_lines, 'incorrect_lines': incorrect_lines}
|
||||||
|
|
||||||
|
state = setup()
|
||||||
|
|
||||||
|
|
||||||
|
def update_plot(neuron_idx):
|
||||||
|
maybe_setup(setup, state)
|
||||||
|
|
||||||
|
for i, coherence in enumerate(coherences):
|
||||||
|
coherence_mask = (mat_data['dot_coh'].flatten() == coherence)
|
||||||
|
state['correct_lines'][i].set_data(time, binned_spike_matrix[correct_trials_mask & coherence_mask].mean(axis=0)[:, neuron_idx])
|
||||||
|
state['incorrect_lines'][i].set_data(time, binned_spike_matrix[~correct_trials_mask & coherence_mask].mean(axis=0)[:, neuron_idx])
|
||||||
|
|
||||||
|
state['axes'][0].relim()
|
||||||
|
state['axes'][1].relim()
|
||||||
|
state['axes'][0].autoscale(axis='y')
|
||||||
|
state['axes'][1].autoscale(axis='y')
|
||||||
|
state['fig'].suptitle(f'Neuron #{neuron_idx}', fontsize='small')
|
||||||
|
state['fig'].tight_layout()
|
||||||
|
draw_figure(state['fig'])
|
||||||
|
|
||||||
|
sliders = {
|
||||||
|
'neuron_idx': IntSlider(min=0, max=binned_spike_matrix.shape[2] - 1, description='neuron #', layout=Layout(width='800px'), continuous_update=continuous_update)
|
||||||
|
}
|
||||||
|
|
||||||
|
interact(update_plot, **sliders)
|
||||||
|
|
||||||
|
|
||||||
|
def calculate_deltas(mat_data):
|
||||||
|
time, binned_spike_matrix = get_binned_spike_matrix(mat_data)
|
||||||
|
right_choice = (mat_data['targ_cho'].flatten() == 1)
|
||||||
|
|
||||||
|
mean_spikes_right = binned_spike_matrix[right_choice].mean(axis=0)
|
||||||
|
mean_spikes_left = binned_spike_matrix[~right_choice].mean(axis=0)
|
||||||
|
|
||||||
|
deltas = (
|
||||||
|
trapezoid(mean_spikes_right, axis=0) -
|
||||||
|
trapezoid(mean_spikes_left, axis=0)
|
||||||
|
)
|
||||||
|
|
||||||
|
return deltas
|
||||||
|
|
||||||
|
|
||||||
|
def plot_deltas(deltas):
|
||||||
|
setup_matplotlib_magic()
|
||||||
|
|
||||||
|
fig, axes = plt.subplots(1, 2, figsize=(8, 4), sharey=True)
|
||||||
|
|
||||||
|
axes[0].hist(deltas, bins=16, range=(-4, 4))
|
||||||
|
axes[1].hist(np.abs(deltas), bins=15, range=(0, 4.2))
|
||||||
|
|
||||||
|
axes[0].set(
|
||||||
|
ylabel='counts',
|
||||||
|
xlabel=r'$\Delta$'
|
||||||
|
)
|
||||||
|
axes[1].set(
|
||||||
|
xlabel=r'|$\Delta$|'
|
||||||
|
)
|
||||||
|
plt.tight_layout()
|
||||||
|
|
||||||
|
|
||||||
|
def plot_aggregated_neurons(mat_data):
|
||||||
|
setup_matplotlib_magic()
|
||||||
|
|
||||||
|
time, binned_spike_matrix = get_binned_spike_matrix(mat_data)
|
||||||
|
right_choice = (mat_data['targ_cho'].flatten() == 1)
|
||||||
|
mean_spikes_right = binned_spike_matrix[right_choice].mean(axis=0)
|
||||||
|
mean_spikes_left = binned_spike_matrix[~right_choice].mean(axis=0)
|
||||||
|
|
||||||
|
deltas = calculate_deltas(mat_data)
|
||||||
|
|
||||||
|
def setup():
|
||||||
|
fig, axes = plt.subplots()
|
||||||
|
|
||||||
|
lines = [
|
||||||
|
axes.plot([], [], label='right choice')[0],
|
||||||
|
axes.plot([], [], label='left choice')[0]
|
||||||
|
]
|
||||||
|
|
||||||
|
axes.set(
|
||||||
|
ylabel=r'$\sqrt{N_\mathrm{spikes}}$',
|
||||||
|
xlabel='time [ms]',
|
||||||
|
xlim=(0, 800)
|
||||||
|
)
|
||||||
|
axes.legend(loc='upper right')
|
||||||
|
|
||||||
|
return {'fig': fig, 'axes': axes, 'lines': lines}
|
||||||
|
|
||||||
|
state = setup()
|
||||||
|
|
||||||
|
def update_plot(delta_threshold):
|
||||||
|
maybe_setup(setup, state)
|
||||||
|
|
||||||
|
state['lines'][0].set_data(time, (mean_spikes_right * np.sign(deltas))[:, np.abs(deltas) > delta_threshold].mean(axis=1))
|
||||||
|
state['lines'][1].set_data(time, (mean_spikes_left * np.sign(deltas))[:, np.abs(deltas) > delta_threshold].mean(axis=1))
|
||||||
|
|
||||||
|
state['axes'].relim()
|
||||||
|
state['axes'].autoscale(axis='y')
|
||||||
|
state['axes'].set(
|
||||||
|
title=f'|Δ| > {delta_threshold:.2f}'
|
||||||
|
)
|
||||||
|
state['fig'].tight_layout()
|
||||||
|
draw_figure(state['fig'])
|
||||||
|
|
||||||
|
sliders = {
|
||||||
|
'delta_threshold': FloatSlider(min=0, max=np.abs(deltas).max() - 1e-3, description='threshold |Δ|', layout=Layout(width='800px'), continuous_update=continuous_update)
|
||||||
|
}
|
||||||
|
|
||||||
|
interact(update_plot, **sliders)
|
||||||
|
|
||||||
|
|
||||||
|
def simulate_conditions(mat_data, alpha, sigma_a, sigma_s, lambda_):
|
||||||
|
dot_coh = mat_data['dot_coh'].flatten()
|
||||||
|
dot_dir = mat_data['dot_dir'].flatten()
|
||||||
|
targ_cor = mat_data['targ_cor'].flatten()
|
||||||
|
|
||||||
|
C = np.array([0] + [1]*16)
|
||||||
|
|
||||||
|
dot_coh[dot_coh == 0] = 1e-12
|
||||||
|
k = np.unique(dot_coh)
|
||||||
|
|
||||||
|
# map directions: 0 -> 1 (right), 180 -> -1 (left)
|
||||||
|
d = np.copy(dot_dir)
|
||||||
|
d[dot_dir == 0] = 1
|
||||||
|
d[dot_dir == 180] = -1
|
||||||
|
|
||||||
|
a, _, tau, dt = generate_sims(np.outer(d, C), dot_coh, alpha, sigma_a, sigma_s, lambda_)
|
||||||
|
a = a[:, tau-1::tau]
|
||||||
|
|
||||||
|
# determine choices and correctness
|
||||||
|
cho = (a[:, -1] > 0).astype(int)
|
||||||
|
cho[cho == 0] = 2 # 2 is left, 1 is right
|
||||||
|
isCorr = cho == targ_cor
|
||||||
|
|
||||||
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# separate correct and incorrect trials
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a_Cor = a[isCorr, :]
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d_Cor = d[isCorr]
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|
cho_Cor = cho[isCorr]
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coh_Cor = dot_coh[isCorr]
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|
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|
a_Inc = a[~isCorr, :]
|
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|
d_Inc = d[~isCorr]
|
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|
cho_Inc = cho[~isCorr]
|
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coh_Inc = dot_coh[~isCorr]
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|
|
||||||
|
# plot average accumulation for correct trials by direction
|
||||||
|
unq_dir = np.unique(d)
|
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|
|
||||||
|
means_a = []
|
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|
for dir_ in unq_dir:
|
||||||
|
mean_a = np.mean(a_Cor[d_Cor == dir_, :], axis=0)
|
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|
means_a += [mean_a]
|
||||||
|
|
||||||
|
return means_a
|
||||||
|
|
||||||
|
|
||||||
|
def plot_sims_conditions(mat_data):
|
||||||
|
setup_matplotlib_magic()
|
||||||
|
|
||||||
|
def setup():
|
||||||
|
fig, axes = plt.subplots(figsize=(6.5, 5))
|
||||||
|
|
||||||
|
evidence_line = axes.plot([], [], color='C2', alpha=1)[0]
|
||||||
|
sim_lines = []
|
||||||
|
for choice in ['right choice', 'left choice']:
|
||||||
|
sim_line = axes.plot([], [], label=choice)[0]
|
||||||
|
sim_lines += [sim_line]
|
||||||
|
|
||||||
|
axes.set(
|
||||||
|
ylabel="mean $a$",
|
||||||
|
xlabel="time $t$",
|
||||||
|
xlim=(0, 800),
|
||||||
|
ylim=(-0.5, .5)
|
||||||
|
)
|
||||||
|
|
||||||
|
axes.legend(loc='upper right')
|
||||||
|
plt.tight_layout()
|
||||||
|
|
||||||
|
return {'fig': fig, 'axes': axes, 'sim_lines': sim_lines}
|
||||||
|
|
||||||
|
state = setup()
|
||||||
|
state['random_seed'] = 42
|
||||||
|
|
||||||
|
def update_plot(alpha, sigma_a, sigma_s, lambda_, fixed_noise):
|
||||||
|
maybe_setup(setup, state)
|
||||||
|
|
||||||
|
if fixed_noise == 'redraw noise':
|
||||||
|
state['random_seed'] = np.random.randint(0, 2**32)
|
||||||
|
np.random.seed(state['random_seed'])
|
||||||
|
|
||||||
|
means_a = simulate_conditions(mat_data, alpha, sigma_a, sigma_s, lambda_)
|
||||||
|
|
||||||
|
for mean_a, line in zip(means_a[::-1], state['sim_lines'], strict=True):
|
||||||
|
line.set_data(np.arange(len(mean_a)) * 50, mean_a)
|
||||||
|
|
||||||
|
state['axes'].relim()
|
||||||
|
state['axes'].autoscale(axis='y')
|
||||||
|
state['fig'].tight_layout()
|
||||||
|
draw_figure(state['fig'])
|
||||||
|
|
||||||
|
style = {'description_width': '150px'}
|
||||||
|
layout = Layout(width='600px')
|
||||||
|
sliders = {
|
||||||
|
'sigma_s': FloatSlider(min=0, max=3, step=0.01, value=0., description='fast noise (input)', style=style, layout=layout, continuous_update=continuous_update),
|
||||||
|
'alpha': FloatSlider(min=0, max=1, step=0.01, value=0., description='slow noise (brain)', style=style, layout=layout, continuous_update=continuous_update),
|
||||||
|
'sigma_a': FloatSlider(min=0, max=1, step=0.01, value=0., description='fast inner noise (brain)', style=style, layout=layout, continuous_update=continuous_update),
|
||||||
|
'lambda_': FloatSlider(min=-5, max=5, step=0.01, value=0., description='leakiness', style=style, layout=layout, continuous_update=continuous_update),
|
||||||
|
'fixed_noise': ToggleButtons(options=['fix noise', 'redraw noise'], value='fix noise', description=' '),
|
||||||
|
}
|
||||||
|
|
||||||
|
interact(update_plot, **sliders)
|
||||||
Loading…
Reference in New Issue