figure updates: interspike intervals in isimethod, more detailed view in firingrates

pointprocesses/lecture/firingrates.py

@@ -218,38 +218,43 @@ def plot_comparison(spike_times, bin_width, sigma, max_t=30., dt=1e-4):
     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)
-    ax1.set_xlim([1.5, 3.5])
+    ax1.set_xlim([2.5, 3.5])
     ax1.set_ylim([0, 1])
     ax1.set_yticks([0, 1])
     set_axis_fontsize(ax1, 10)
+    ax1.set_xticks([2.5, 2.75, 3.0, 3.25, 3.5])
     ax1.set_xticklabels([])
 
     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])
+    ax2.set_xlim([2.5, 3.5])
     ax2.set_ylim([0, 300])
+    ax2.set_yticks(np.arange(0, 400, 100))
     set_axis_fontsize(ax2, 10)
+    ax2.set_xticks([2.5, 2.75, 3.0, 3.25, 3.5])
     ax2.set_xticklabels([])
 
     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])
+    ax3.set_xlim([2.5, 3.5])
     ax3.set_ylim([0, 300])
+    ax3.set_yticks(np.arange(0, 400, 100))
     set_axis_fontsize(ax3, 10)
+    ax3.set_xticks([2.5, 2.75, 3.0, 3.25, 3.5])
     ax3.set_xticklabels([])
 
     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)
-    ax4.set_xlim([1.5, 3.5])
+    ax4.set_xlim([2.5, 3.5])
+    ax4.set_xticks([2.5, 2.75, 3.0, 3.25, 3.5])
     ax4.set_ylim([0, 300])
+    ax4.set_yticks(np.arange(0, 400, 100))
     set_axis_fontsize(ax4, 10)
 
     fig.set_size_inches(7.5, 5)

pointprocesses/lecture/isimethod.py

@@ -17,9 +17,9 @@ def set_rc():
     plt.rcParams['ytick.direction'] = "out"
 
 
-def create_spikes(isi=0.08, duration=0.5):
+def create_spikes(isi=0.08, duration=0.5, seed=57111):
     times = np.arange(0., duration, isi)
-    rng = np.random.RandomState(57281)
+    rng = np.random.RandomState(seed)
     times += rng.randn(len(times)) * (isi / 2.5)
     times = np.delete(times, np.nonzero(times < 0))
     times = np.delete(times, np.nonzero(times > duration))
@@ -42,14 +42,18 @@ def setup_axis(spikes_ax, rate_ax):
     spikes_ax.set_ylim([0, 1.05])
     spikes_ax.set_ylabel("spikes", fontsize=9)
     spikes_ax.text(-0.125, 1.2, "A", transform=spikes_ax.transAxes, size=10)
+    spikes_ax.set_xlim([0, 0.5])
+    spikes_ax.set_xticklabels(np.arange(0., 600, 100))
 
     rate_ax.spines["right"].set_visible(False)
     rate_ax.spines["top"].set_visible(False)
     rate_ax.yaxis.set_ticks_position('left')
     rate_ax.xaxis.set_ticks_position('bottom')
-    rate_ax.set_xlabel('time[s]', fontsize=9)
+    rate_ax.set_xlabel('time[ms]', fontsize=9)
     rate_ax.set_ylabel('firing rate [Hz]', fontsize=9)
     rate_ax.text(-0.125, 1.15, "B", transform=rate_ax.transAxes, size=10)   
+    rate_ax.set_xlim([0, 0.5])
+    rate_ax.set_xticklabels(np.arange(0., 600, 100))
 
 
 def plot_bin_method():
@@ -75,7 +79,7 @@ def plot_bin_method():
     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.text(bins[i] + bins[1]/2, 1.05, str(c), fontdict={'color':'red', 'size':9})
     spikes.set_xlim([0, duration])
 
     rate = count / 0.05
@@ -124,7 +128,7 @@ def plot_conv_method():
 
 
 def plot_isi_method():
-    spike_times = create_spikes(0.09, 0.5)
+    spike_times = create_spikes(0.055, 0.5, 1000)
     
     plt.xkcd()
     set_rc()
@@ -142,12 +146,15 @@ def plot_isi_method():
         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='<->'), color='red')
+        spikes.text(t_start+0.01, 0.75, 
+                    "{0:.1f}".format((t - t_start)*1000),
+                    fontdict={'color':'red', 'size':7})
 
     i_rate = 1./np.diff(spike_times)
 
     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_ylim([0, 50])
-    rate.set_yticks(np.arange(0,100,25))
+    rate.set_yticks(np.arange(0,75,25))
     
     fig.tight_layout()
     fig.savefig("isimethod.pdf")

pointprocesses/lecture/pointprocesses.tex

@@ -257,12 +257,12 @@ Abbildung \ref{psthfig} n\"aher erl\"autert.
 \begin{figure}[tp]
   \includegraphics[width=\columnwidth]{isimethod}
   \titlecaption{Bestimmung des zeitabh\"angigen Feuerrate aus dem
-      Interspike Intervall.}{\textbf{A)} Skizze eines Rasterplots einer
+    Interspike Intervall.}{\textbf{A)} Skizze eines Rasterplots einer
     einzelnen neuronalen Antwort. Jeder vertikale Strich notiert den
     Zeitpunkt eines Aktionspotentials. Die Pfeile zwischen
-    aufeinanderfolgenden Aktionspotentialen illustrieren das
+    aufeinanderfolgenden Aktionspotentialen und die Zahlen
-    Interspike Interval. \textbf{B)} Der Kehrwert des Interspike
+    illustrieren das Interspike Interval.  \textbf{B)} Der Kehrwert
-    Intervalls ist die Feuerrate.}\label{instrate}
+    des Interspike Intervalls ist die Feuerrate.}\label{instrate}
 \end{figure}
 
 Ein sehr einfacher Weg, die zeitabh\"angige Feuerrate zu bestimmen ist