moving and some work

programming/lectures/Makefile

@@ -1,5 +1,5 @@
 TEXFILES=$(wildcard *.tex)
-TEXFILES=boolean_logical_indexing.tex control_structures.tex data_structures.tex plotting_spike_trains.tex programming_basics.tex scripts_functions.tex sta_stc.tex variables_datatypes.tex vectors_matrices.tex
+TEXFILES=boolean_logical_indexing.tex control_structures.tex data_structures.tex plotting.tex programming_basics.tex scripts_functions.tex sta_stc.tex variables_datatypes.tex vectors_matrices.tex
 
 PDFFILES=$(TEXFILES:.tex=.pdf)
 

spike_trains/code/firing_rates.py

@@ -62,7 +62,7 @@ def plot_isi_rate(spike_times, max_t=30, dt=1e-4):
     ax1.vlines(times[times < (50000*dt)], ymin=0, ymax=1, color="dodgerblue", lw=1.5)
     ax1.set_ylabel("skpikes", fontsize=12)
     set_axis_fontsize(ax1, 12)
-
+    ax1.set_xlim([0, 5])
     ax2.plot(time, rate, label="instantaneous rate, trial 1")
     ax2.set_ylabel("firing rate [Hz]", fontsize=12)
     ax2.legend(fontsize=12)
@@ -191,8 +191,61 @@ def plot_conv_rate(spike_times, sigma=0.05, max_t=30, dt=1e-4):
     plt.close()
 
 
+def plot_comparison(spike_times, bin_width, sigma, max_t=30., dt=1e-4):
+    times = np.squeeze(spike_times[0][0])
+    time, conv_rate = get_convolved_rate(times, sigma)
+    time, inst_rate = get_instantaneous_rate(times)
+    time, binn_rate = get_binned_rate(times, bin_width)
+   
+    fig = plt.figure()
+    ax1 = fig.add_subplot(411)
+    ax2 = fig.add_subplot(412)
+    ax3 = fig.add_subplot(413)
+    ax4 = fig.add_subplot(414)
+
+    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_ylim([0, 1])
+    ax1.set_yticks([0, 1])
+    set_axis_fontsize(ax1, 10)
+    ax1.set_xticklabels([])
+
+    ax2.plot(time, inst_rate, label="instantaneous rate")
+    ax2.set_ylabel("firing rate [Hz]", fontsize=10)
+    ax2.legend(fontsize=10)
+    ax2.set_xlim([1.5, 3.5])
+    ax2.set_ylim([0, 300])
+    set_axis_fontsize(ax2, 10)
+    ax2.set_xticklabels([])
+
+    ax3.plot(time, binn_rate, label="binned rate")
+    ax3.set_ylabel("firing rate [Hz]", fontsize=10)
+    ax3.legend(fontsize=10)
+    ax3.set_xlim([1.5, 3.5])
+    ax3.set_ylim([0, 300])
+    set_axis_fontsize(ax3, 10)
+    ax3.set_xticklabels([])
+
+    ax4.plot(time, conv_rate, label="convolved rate")
+    ax4.set_xlabel("times [s]", fontsize=10)
+    ax4.set_ylabel("firing rate [Hz]", fontsize=10)
+    ax4.legend(fontsize=10)
+    ax4.set_xlim([1.5, 3.5])
+    ax4.set_ylim([0, 300])
+    set_axis_fontsize(ax4, 10)
+
+    fig.set_size_inches(7.5, 5)
+    fig.subplots_adjust(left=0.1, bottom=0.125, top=0.95, right=0.95, )
+    fig.set_facecolor("white")
+    fig.savefig("../lecture/images/psth_comparison.pdf")
+    plt.close()
+
+
 if __name__ == "__main__":
     spike_times =  spio.loadmat('lifoustim.mat')["spikes"]
-    plot_isi_rate(spike_times)
-    plot_bin_rate(spike_times, 0.05)
-    plot_conv_rate(spike_times, 0.025)
+    # plot_isi_rate(spike_times)
+    # plot_bin_rate(spike_times, 0.05)
+    # plot_conv_rate(spike_times, 0.025)
+    plot_comparison(spike_times, 0.05, 0.025)
+

spike_trains/lecture/psth_sta-slides.tex

@@ -383,7 +383,7 @@
   \item Tuningkurven.
   \item Stimulusrekonstruktion mittels STA.
   \item Kreuzkorrelation.
-  \item Fourier Analyse, Transferfunktion, Kohärenz.
+  \item Fourier Analyse, Transferfunktion, Kohärenz.
   \item Reverse Rekonstruktion. 
   \end{enumerate}
 \end{frame}