still mistakes when normalizing

code/spikes_analysis.py

@@ -4,14 +4,21 @@ from read_chirp_data import *
 from utility import *
 from IPython import embed
 
+# define sampling rate and data path
 sampling_rate = 40 #kHz
 data_dir = "../data"
 dataset = "2018-11-09-ad-invivo-1"
+# parameters for binning, smoothing and plotting
+num_bin = 12
+window = sampling_rate
+time_axis = np.arange(-50, 50, 1/sampling_rate)
 
+# read data from files
 spikes = read_chirp_spikes(os.path.join(data_dir, dataset))
 eod = read_chirp_eod(os.path.join(data_dir, dataset))
 chirp_times = read_chirp_times(os.path.join(data_dir, dataset))
 
+# make a delta f map for the quite more complicated keys
 df_map = {}
 for k in spikes.keys():
     df = k[1]
@@ -20,56 +27,55 @@ for k in spikes.keys():
     else:
         df_map[df] = [k]
 
-# make phases together, 12 phases
-phase_vec = np.arange(0, 1+1/12, 1/12)
+# differentiate between phases
+phase_vec = np.arange(0, 1+1/num_bin, 1/num_bin)
 cut_range = np.arange(-50*sampling_rate, 50*sampling_rate, 1)
 
+# make dictionaries for spiketimes
 df_phase_time = {}
 df_phase_binary = {}
 
+# iterate over delta f, repetition, phases and a single chirp
 for deltaf in df_map.keys():
     df_phase_time[deltaf] = {}
     df_phase_binary[deltaf] = {}
     for rep in df_map[deltaf]:
         for phase in spikes[rep]:
-            #print(phase)
-            for idx in range(len(phase_vec)-1):
+            for idx in np.arange(num_bin):
+                # check the phase
                 if phase[1] > phase_vec[idx] and phase[1] < phase_vec[idx+1]:
 
+                    # get spikes between 50 ms befor and after the chirp
                     spikes_to_cut = np.asarray(spikes[rep][phase])
                     spikes_cut = spikes_to_cut[(spikes_to_cut > -50) & (spikes_to_cut < 50)]
                     spikes_idx = np.round(spikes_cut*sampling_rate)
+                    # also save as binary, 0 no spike, 1 spike
                     binary_spikes = np.isin(cut_range, spikes_idx)*1
 
-                    if phase_vec[idx] in df_phase_time[deltaf].keys():
-                        df_phase_time[deltaf][phase_vec[idx]].append(spikes_cut)
-                        df_phase_binary[deltaf][phase_vec[idx]] = np.vstack((df_phase_binary[deltaf][phase_vec[idx]], binary_spikes))
+                    # add the spikes to the dictionaries with the correct df and phase
+                    if idx in df_phase_time[deltaf].keys():
+                        df_phase_time[deltaf][idx].append(spikes_cut)
+                        df_phase_binary[deltaf][idx] = np.vstack((df_phase_binary[deltaf][idx], binary_spikes))
                     else:
-                        df_phase_time[deltaf][phase_vec[idx]] = [spikes_cut]
-                        df_phase_binary[deltaf][phase_vec[idx]] = binary_spikes
-
-
-
-plot_trials = df_phase_time['-50Hz'][0.0]
-plot_trials_binary = np.mean(df_phase_binary['-50Hz'][0.0], axis=0)
-
-window = 100
-smoothed_spikes = smooth(plot_trials_binary, window)
-time_axis = np.arange(-50, 50, 1/sampling_rate)
+                        df_phase_time[deltaf][idx] = [spikes_cut]
+                        df_phase_binary[deltaf][idx] = binary_spikes
 
-fig, ax = plt.subplots()
-for i, trial in enumerate(plot_trials):
-    ax.scatter(trial, np.ones(len(trial))+i, marker='|', color='k')
-ax.plot(time_axis, smoothed_spikes)
-plt.show()
+# for plotting iterate over delta f and phases
+for df in df_phase_time.keys():
+    for phase in df_phase_time[df].keys():
+        plot_trials = df_phase_time[df][phase]
+        plot_trials_binary = np.mean(df_phase_binary[df][phase], axis=0)
 
+        smoothed_spikes = smooth(plot_trials_binary, window)
 
-#window = np.mean(np.diff(plot_spikes))
-#time_vec = np.arange(plot_spikes[0], plot_spikes[-1]+window, window)
+        fig, ax = plt.subplots(2, 1)
+        for i, trial in enumerate(plot_trials):
+            ax[0].scatter(trial, np.ones(len(trial))+i, marker='|', color='k')
+        ax[1].plot(time_axis, smoothed_spikes)
 
-#ax.plot(time_vec, smoothed_spikes)
+        ax[0].set_title(df)
+        ax[0].set_ylabel('repetition', fontsize=12)
 
-#embed()
-#exit()
-#hist_data = plt.hist(plot_spikes, bins=np.arange(-200, 400, 20))
-#ax.plot(hist_data[1][:-1], hist_data[0])
+        ax[1].set_xlabel('time [ms]', fontsize=12)
+        ax[1].set_ylabel('firing rate [?]', fontsize=12)
+        plt.show()

code/utility.py

@@ -1,4 +1,5 @@
 import numpy as np
+from IPython import embed
 
 
 def zero_crossing(eod, time):
@@ -29,7 +30,8 @@ def smooth(data, window):
 	sigma = window
 	time_gauss = np.arange(-4 * sigma, 4 * sigma, 1)
 	gauss = gaussian(time_gauss, mu, sigma)
-	smoothed_data = np.convolve(data, gauss, 'same')
+	gauss_norm = gauss/(np.sum(gauss)/len(gauss))
+	smoothed_data = np.convolve(data, gauss_norm, 'same')
 	return smoothed_data