From fffd7226e2545b70a56e7e0e7c9a794f5232a2d8 Mon Sep 17 00:00:00 2001
From: Jan Grewe <jan.grewe@g-node.org>
Date: Mon, 2 Nov 2015 22:54:07 +0100
Subject: [PATCH] improved plotting, xkcd style methods describing the psth
estimation
---
spike_trains/code/firing_rates.py | 29 ++++++++++++----
spike_trains/code/isi_method.py | 56 ++++++++++++++++++-------------
spike_trains/code/sta.py | 17 +++++++---
3 files changed, 67 insertions(+), 35 deletions(-)
diff --git a/spike_trains/code/firing_rates.py b/spike_trains/code/firing_rates.py
index 097250e..faaeb29 100644
--- a/spike_trains/code/firing_rates.py
+++ b/spike_trains/code/firing_rates.py
@@ -1,10 +1,9 @@
import numpy as np
import matplotlib.pyplot as plt
import scipy.io as spio
+import scipy.stats as spst
import scipy as sp
-import seaborn as sb
from IPython import embed
-sb.set_context("paper")
def set_axis_fontsize(axis, label_size, tick_label_size=None, legend_size=None):
@@ -140,7 +139,7 @@ def plot_bin_rate(spike_times, bin_width, max_t=30, dt=1e-4):
def get_convolved_rate(times, sigma, max_t=30., dt=1.e-4):
time = np.arange(0., max_t, dt)
- kernel = sp.stats.norm.pdf(np.arange(-8*sigma, 8*sigma, dt),loc=0,scale=sigma)
+ kernel = spst.norm.pdf(np.arange(-8*sigma, 8*sigma, dt),loc=0,scale=sigma)
indices = np.asarray(times/dt, dtype=int)
rate = np.zeros(time.shape)
rate[indices] = 1.;
@@ -202,6 +201,24 @@ def plot_comparison(spike_times, bin_width, sigma, max_t=30., dt=1e-4):
ax2 = fig.add_subplot(412)
ax3 = fig.add_subplot(413)
ax4 = fig.add_subplot(414)
+ ax1.spines["right"].set_visible(False)
+ ax1.spines["top"].set_visible(False)
+ ax1.yaxis.set_ticks_position('left')
+ ax1.xaxis.set_ticks_position('bottom')
+ ax2.spines["right"].set_visible(False)
+ ax2.spines["top"].set_visible(False)
+ ax2.yaxis.set_ticks_position('left')
+ ax2.xaxis.set_ticks_position('bottom')
+ ax3.spines["right"].set_visible(False)
+ ax3.spines["top"].set_visible(False)
+ ax3.yaxis.set_ticks_position('left')
+ ax3.xaxis.set_ticks_position('bottom')
+ ax4.spines["right"].set_visible(False)
+ ax4.spines["top"].set_visible(False)
+ ax4.yaxis.set_ticks_position('left')
+ ax4.xaxis.set_ticks_position('bottom')
+
+
ax1.vlines(times[times < (100000*dt)], ymin=0, ymax=1, color="dodgerblue", lw=1.5)
ax1.set_ylabel("spikes", fontsize=10)
@@ -211,7 +228,7 @@ def plot_comparison(spike_times, bin_width, sigma, max_t=30., dt=1e-4):
set_axis_fontsize(ax1, 10)
ax1.set_xticklabels([])
- ax2.plot(time, inst_rate, label="instantaneous rate")
+ ax2.plot(time, inst_rate, lw=1.5, label="instantaneous rate")
ax2.set_ylabel("firing rate [Hz]", fontsize=10)
ax2.legend(fontsize=10)
ax2.set_xlim([1.5, 3.5])
@@ -219,7 +236,7 @@ def plot_comparison(spike_times, bin_width, sigma, max_t=30., dt=1e-4):
set_axis_fontsize(ax2, 10)
ax2.set_xticklabels([])
- ax3.plot(time, binn_rate, label="binned rate")
+ ax3.plot(time, binn_rate, lw=1.5, label="binned rate")
ax3.set_ylabel("firing rate [Hz]", fontsize=10)
ax3.legend(fontsize=10)
ax3.set_xlim([1.5, 3.5])
@@ -227,7 +244,7 @@ def plot_comparison(spike_times, bin_width, sigma, max_t=30., dt=1e-4):
set_axis_fontsize(ax3, 10)
ax3.set_xticklabels([])
- ax4.plot(time, conv_rate, label="convolved rate")
+ ax4.plot(time, conv_rate, lw=1.5, label="convolved rate")
ax4.set_xlabel("time [s]", fontsize=10)
ax4.set_ylabel("firing rate [Hz]", fontsize=10)
ax4.legend(fontsize=10)
diff --git a/spike_trains/code/isi_method.py b/spike_trains/code/isi_method.py
index 776c68e..e4b95e3 100644
--- a/spike_trains/code/isi_method.py
+++ b/spike_trains/code/isi_method.py
@@ -55,31 +55,36 @@ def plot_bin_method():
dt = 1e-5
duration = 0.5
- spike_times = create_spikes(0.025, duration)
+ spike_times = create_spikes(0.018, duration)
t = np.arange(0., duration, dt)
- bins = np.arange(0, 0.5, 0.05)
+ bins = np.arange(0, 0.55, 0.05)
count, _ = np.histogram(spike_times, bins)
plt.xkcd()
+ set_rc()
fig = plt.figure()
fig.set_size_inches(5., 2.5)
fig.set_facecolor('white')
- spikes = plt.subplot2grid((3,1), (0,0), rowspan=1, colspan=1)
- rate_ax = plt.subplot2grid((3,1), (1,0), rowspan=2, colspan=1)
+ spikes = plt.subplot2grid((7,1), (0,0), rowspan=3, colspan=1)
+ rate_ax = plt.subplot2grid((7,1), (3,0), rowspan=4, colspan=1)
setup_axis(spikes, rate_ax)
+ spikes.set_ylim([0., 1.25])
- spikes.vlines(spike_times, 0., 1., color="darkblue", lw=1)
- spikes.vlines(bins, 0., 1.05, color="red", lw = 2)
- for c in count:
- spikes.text(bins-(bins[1]-bins[0])/2, 0.75, str(c), fontdict={"color":"red"})
+ spikes.vlines(spike_times, 0., 1., color="darkblue", lw=1.25)
+ spikes.vlines(np.hstack((0,bins)), 0., 1.25, color="red", lw=1.5, linestyles='--')
+ for i,c in enumerate(count):
+ spikes.text(bins[i] + bins[1]/2, 1.05, str(c), fontdict={'color':'red'})
spikes.set_xlim([0, duration])
-
- #rate_ax.step(bins[1:], count/0.05)
-
+
+ rate = count / 0.05
+ rate_ax.step(bins, np.hstack((rate, rate[-1])), where='post')
+ rate_ax.set_xlim([0., duration])
+ rate_ax.set_ylim([0., 100.])
+ rate_ax.set_yticks(np.arange(0,105,25))
fig.tight_layout()
- plt.show()
- #fig.savefig("bin_method.pdf")
+ fig.savefig("../lecture/images/bin_method.pdf")
+ plt.close()
def plot_conv_method():
@@ -94,11 +99,13 @@ def plot_conv_method():
rate = np.convolve(rate, kernel, mode='same')
rate = np.roll(rate, -1)
+ plt.xkcd()
+ set_rc()
fig = plt.figure()
fig.set_size_inches(5., 2.5)
fig.set_facecolor('white')
- spikes = plt.subplot2grid((3,1), (0,0), rowspan=1, colspan=1)
- rate_ax = plt.subplot2grid((3,1), (1,0), rowspan=2, colspan=1)
+ spikes = plt.subplot2grid((7,1), (0,0), rowspan=3, colspan=1)
+ rate_ax = plt.subplot2grid((7,1), (3,0), rowspan=4, colspan=1)
setup_axis(spikes, rate_ax)
spikes.vlines(spike_times, 0., 1., color="darkblue", lw=1.5, zorder=2)
@@ -112,11 +119,11 @@ def plot_conv_method():
rate_ax.set_ylim([0, 50])
rate_ax.set_yticks(np.arange(0,75,25))
fig.tight_layout()
- fig.savefig("conv_method.pdf")
+ fig.savefig("../lecture/images/conv_method.pdf")
def plot_isi_method():
- spike_times = create_spikes(0.08, 0.5)
+ spike_times = create_spikes(0.09, 0.5)
plt.xkcd()
set_rc()
@@ -124,8 +131,8 @@ def plot_isi_method():
fig.set_size_inches(5., 2.5)
fig.set_facecolor('white')
- spikes = plt.subplot2grid((3,1), (0,0), rowspan=1, colspan=1)
- rate = plt.subplot2grid((3,1), (1,0), rowspan=2, colspan=1)
+ spikes = plt.subplot2grid((7,1), (0,0), rowspan=3, colspan=1)
+ rate = plt.subplot2grid((7,1), (3,0), rowspan=4, colspan=1)
setup_axis(spikes, rate)
spikes.vlines(spike_times, 0., 1., color="darkblue", lw=1.25)
@@ -133,18 +140,19 @@ def plot_isi_method():
for i in range(1, len(spike_times)):
t_start = spike_times[i-1]
t = spike_times[i]
- spikes.annotate(s='', xy=(t_start, 0.5), xytext=(t,0.5), arrowprops=dict(arrowstyle='<->'))
+ spikes.annotate(s='', xy=(t_start, 0.5), xytext=(t,0.5), arrowprops=dict(arrowstyle='<->'), color='red')
+
i_rate = 1./np.diff(spike_times)
- rate.step(spike_times[1:], i_rate,color="darkblue", lw=1.25, where="pre")
+ rate.step(spike_times, np.hstack((i_rate, i_rate[-1])),color="darkblue", lw=1.25, where="post")
rate.set_ylim([0, 75])
rate.set_yticks(np.arange(0,100,25))
fig.tight_layout()
- fig.savefig("isi_method.pdf")
+ fig.savefig("../lecture/images/isi_method.pdf")
if __name__ == '__main__':
- #plot_isi_method()
- #plot_conv_method()
+ plot_isi_method()
+ plot_conv_method()
plot_bin_method()
diff --git a/spike_trains/code/sta.py b/spike_trains/code/sta.py
index 5b14083..d373820 100644
--- a/spike_trains/code/sta.py
+++ b/spike_trains/code/sta.py
@@ -1,9 +1,7 @@
import numpy as np
import matplotlib.pyplot as plt
import scipy.io as scio
-import seaborn as sb
from IPython import embed
-sb.set_context("paper")
def plot_sta(times, stim, dt, t_min=-0.1, t_max=.1):
@@ -31,10 +29,15 @@ def plot_sta(times, stim, dt, t_min=-0.1, t_max=.1):
fig.set_facecolor("white")
ax = fig.add_subplot(111)
- ax.plot(time, sta, color="darkblue")
+ ax.plot(time, sta, color="darkblue", lw=1)
ax.set_xlabel("time [s]")
ax.set_ylabel("stimulus")
ax.xaxis.grid('off')
+ ax.spines["right"].set_visible(False)
+ ax.spines["top"].set_visible(False)
+ ax.yaxis.set_ticks_position('left')
+ ax.xaxis.set_ticks_position('bottom')
+
ylim = ax.get_ylim()
xlim = ax.get_xlim()
ax.plot(list(xlim), [0., 0.], zorder=1, color='darkgray', ls='--')
@@ -56,13 +59,17 @@ def reconstruct_stimulus(spike_times, sta, stimulus, t_max=30., dt=1e-4):
s_est[i, :] = np.convolve(y, sta, mode='same')
plt.plot(np.arange(0, t_max, dt), stimulus[:,1], label='stimulus', color='darkblue', lw=2.)
- plt.plot(np.arange(0, t_max, dt), np.mean(s_est, axis=0), label='reconstruction', color='silver', lw=1.5)
+ plt.plot(np.arange(0, t_max, dt), np.mean(s_est, axis=0), label='reconstruction', color='gray', lw=1.5)
plt.xlabel('time[s]')
plt.ylabel('stimulus')
plt.xlim([0.0, 0.25])
plt.ylim([-1., 1.])
plt.legend()
- plt.plot([0.0, 0.25], [0., 0.], color="darkgray", lw=1, ls='--', zorder=1)
+ plt.plot([0.0, 0.25], [0., 0.], color="darkgray", lw=1.5, ls='--', zorder=1)
+ plt.gca().spines["right"].set_visible(False)
+ plt.gca().spines["top"].set_visible(False)
+ plt.gca().yaxis.set_ticks_position('left')
+ plt.gca().xaxis.set_ticks_position('bottom')
fig = plt.gcf()
fig.set_size_inches(7.5, 5)