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R4670/PySONIC/plt/spikemetrics.py
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spikemetrics.py
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# -*- coding: utf-8 -*-
# @Author: Theo Lemaire
# @Date: 2018-10-01 20:40:28
# @Last Modified by: Theo Lemaire
# @Last Modified time: 2018-10-01 20:42:19
import numpy as np
import matplotlib.pyplot as plt
from ..utils import cm2inch
def plotSpikingMetrics(xvar, xlabel, metrics_dict, logscale=False, spikeamp=True, colors=None,
fs=8, lw=2, ps=4, figsize=cm2inch(7.25, 5.8)):
''' Plot the evolution of key spiking metrics as function of a specific stimulation parameter. '''
ls = {'full': 'o-', 'sonic': 'o--'}
cdefault = {'full': 'silver', 'sonic': 'k'}
# Create figure
naxes = 3 if spikeamp else 2
fig, axes = plt.subplots(naxes, 1, figsize=figsize)
axes[0].set_ylabel('Latency\n (ms)', fontsize=fs, rotation=0, ha='right', va='center')
axes[1].set_ylabel('Firing\n rate (Hz)', fontsize=fs, rotation=0, ha='right', va='center')
if naxes == 3:
axes[2].set_ylabel('Spike amp.\n ($\\rm nC/cm^2$)', fontsize=fs, rotation=0, ha='right',
va='center')
for ax in axes:
ax.spines['top'].set_visible(False)
ax.spines['right'].set_visible(False)
if logscale:
ax.set_xscale('log')
for item in ax.get_yticklabels():
item.set_fontsize(fs)
for ax in axes[:-1]:
ax.spines['bottom'].set_visible(False)
ax.set_xticks([])
ax.get_xaxis().set_tick_params(which='minor', size=0)
ax.get_xaxis().set_tick_params(which='minor', width=0)
axes[-1].set_xlabel(xlabel, fontsize=fs)
if not logscale:
axes[-1].set_xticks([min(xvar), max(xvar)])
for item in axes[-1].get_xticklabels():
item.set_fontsize(fs)
# Plot metrics for each neuron
for i, neuron in enumerate(metrics_dict.keys()):
full_metrics = metrics_dict[neuron]['full']
sonic_metrics = metrics_dict[neuron]['sonic']
c = colors[neuron] if colors is not None else cdefault
# Latency
rf = 10
ax = axes[0]
ax.plot(xvar, full_metrics['latencies (ms)'].values, ls['full'], color=c['full'],
linewidth=lw, markersize=ps)
ax.plot(xvar, sonic_metrics['latencies (ms)'].values, ls['sonic'], color=c['sonic'],
linewidth=lw, markersize=ps, label=neuron)
# Firing rate
rf = 10
ax = axes[1]
ax.errorbar(xvar, full_metrics['mean firing rates (Hz)'].values,
yerr=full_metrics['std firing rates (Hz)'].values,
fmt=ls['full'], color=c['full'], linewidth=lw, markersize=ps)
ax.errorbar(xvar, sonic_metrics['mean firing rates (Hz)'].values,
yerr=sonic_metrics['std firing rates (Hz)'].values,
fmt=ls['sonic'], color=c['sonic'], linewidth=lw, markersize=ps)
# Spike amplitudes
if spikeamp:
ax = axes[2]
rf = 10
ax.errorbar(xvar, full_metrics['mean spike amplitudes (nC/cm2)'].values,
yerr=full_metrics['std spike amplitudes (nC/cm2)'].values,
fmt=ls['full'], color=c['full'], linewidth=lw, markersize=ps)
ax.errorbar(xvar, sonic_metrics['mean spike amplitudes (nC/cm2)'].values,
yerr=sonic_metrics['std spike amplitudes (nC/cm2)'].values,
fmt=ls['sonic'], color=c['sonic'], linewidth=lw, markersize=ps)
# Adapt axes y-limits
rf = 10
for ax in axes:
ax.set_ylim([np.floor(ax.get_ylim()[0] / rf) * rf, np.ceil(ax.get_ylim()[1] / rf) * rf])
ax.set_yticks([max(ax.get_ylim()[0], 0), ax.get_ylim()[1]])
# Legend
if len(metrics_dict.keys()) > 1:
leg = axes[0].legend(fontsize=fs, frameon=False, bbox_to_anchor=(0., 0.9, 1., .102),
loc=8, ncol=2, borderaxespad=0.)
for l in leg.get_lines():
l.set_linestyle('-')
fig.subplots_adjust(hspace=.3, bottom=0.2, left=0.35, right=0.95, top=0.95)
return fig
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