Merge branch 'master' of https://whale.am28.uni-tuebingen.de/git/jgrewe/gp_neurobio

code/base_chirps.py

@@ -58,7 +58,7 @@ axs[1,1].set_xlabel('Time [ms]')
 
 freq = list(df_map['-50Hz'])
 ls_mod = []
-beat_mods = []
+ls_beat = []
 for k in freq: 
 	e1 = eod[k]
 	zeit = np.asarray(e1[0])
@@ -69,14 +69,19 @@ for k in freq:
 		time_cut = zeit[(zeit > chirp-10) & (zeit < chirp+10)]
 		eods_cut = ampl[(zeit > chirp-10) & (zeit < chirp+10)]
 		beat_cut = ampl[(zeit > chirp-55) & (zeit < chirp-10)]
-
+		
 		chirp_mod = np.std(eods_cut) #Std vom Bereich um den Chirp
-		beat_mod = np.std(beat_cut) #Std vom Bereich vor dem Chirp
+		ls_mod.append(chirp_mod) #in die richtige Reihenfolge bringen?
-		ls_mod.append(chirp_mod)
+		#momentan nicht nach Chirp-Platz sortiert, sondern nacheinander
-		beat_mods.append(beat_mod)
+
+		#erst beat_cuts auf die gleiche Länge bringen!
+		ls_beat.append(beat_cut)
 
-#Länge des Mods ist 160, 16 Wiederholungen mal 10 Chirps pro Trial
+#beat_mod = np.std(ls_beat) #Std vom Bereich vor dem Chirp
-#Verwendung der Std für die Amplitudenmodulation?
+plt.figure()
+plt.scatter(np.arange(0,len(ls_mod),1), ls_mod)
+plt.scatter(np.arange(0,len(ls_mod),1), np.ones(len(ls_mod))/2, color = 'violet')
+plt.show()
 
 
 

code/base_spikes.py

@@ -4,7 +4,7 @@ from utility import *
 #import nix_helpers as nh 
 import matplotlib.pyplot as plt
 import numpy as np
-from IPython import embed #Funktionen importieren
+from IPython import embed #Funktionen imposrtieren
 
 
 data_dir = "../data"
@@ -40,18 +40,44 @@ plt.show()
 
 chirp_spikes = read_chirp_spikes(os.path.join(data_dir, dataset))
 df_map = map_keys(chirp_spikes)
-
+ls_rate = {}
-
 for i in df_map.keys():
 	freq = list(df_map[i])
+	ls_rate[i] = []
 	for k in freq:
-		spikes = chirp_spikes[k]
+		for phase in chirp_spikes[k]:
-		phase_map = map_keys(spikes)
+			spikes = chirp_spikes[k][phase]
-		for p in phase_map: 
+			rate = len(spikes)/ 1.2
-			spike_rate = 1./ np.diff(p)
+			ls_rate[i].append(rate)
+
+
+plt.figure()
+sort_df =  sorted(df_map.keys(),reverse = False)
+print(sort_df)
+
+for i in sort_df:
+	plt.plot(np.arange(0,len(ls_rate[i]),1),ls_rate[i], label = i)
+
+plt.vlines(10, ymin = 200, ymax = 300)
+plt.vlines(30, ymin = 200, ymax = 300)
+plt.vlines(50, ymin = 200, ymax = 300)
+plt.vlines(70, ymin = 200, ymax = 300)
+plt.vlines(90, ymin = 200, ymax = 300)
+plt.vlines(110, ymin = 200, ymax = 300)
+plt.vlines(130, ymin = 200, ymax = 300)
+plt.vlines(150, ymin = 200, ymax = 300)
+plt.legend()
+plt.show()
+
 
-print(spike_rate)
-#
-#	plt.plot(spikes, rate)
-#	plt.show()
 
+#mittlere Feuerrate einer Frequenz auf Frequenz
+
+plt.figure()
+ls_mean = []
+for i in sort_df:
+	mean = np.mean(ls_rate[i])
+	ls_mean.append(mean)
+
+plt.plot(np.arange(0,len(ls_mean),1),ls_mean)
+plt.show()

code/spikes_analysis.py

@@ -10,8 +10,10 @@ data_dir = "../data"
 dataset = "2018-11-09-ad-invivo-1"
 # parameters for binning, smoothing and plotting
 num_bin = 12
-window = sampling_rate
+window = 1
 time_axis = np.arange(-50, 50, 1/sampling_rate)
+bin_size = 1
+spike_bins = np.arange(-50, 50+bin_size, bin_size)
 
 # read data from files
 spikes = read_chirp_spikes(os.path.join(data_dir, dataset))
@@ -60,22 +62,43 @@ for deltaf in df_map.keys():
                         df_phase_time[deltaf][idx] = [spikes_cut]
                         df_phase_binary[deltaf][idx] = binary_spikes
 
-# for plotting iterate over delta f and phases
+# for plotting and calculating iterate over delta f and phases
 for df in df_phase_time.keys():
     for phase in df_phase_time[df].keys():
+
+        # plot
         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)
+        # calculation
+        overall_spikerate = (np.sum(plot_trials_binary)/len(plot_trials_binary))*sampling_rate*1000
+
+        '''
+        spike_rate = np.zeros(len(spike_bins)-1)
+        for idx in range(len(spike_bins)-1):
+            bin_start = spike_bins[idx]*sampling_rate
+            bin_end = spike_bins[idx+1]*sampling_rate
+            spike_rate[idx] = np.sum(plot_trials_binary[bin_start:bin_end])/bin_size*sampling_rate
+
+        print(np.std(spike_rate))
+        plt.plot(spike_rate)
+        plt.show()
+
+        embed()
+        exit()
+        '''
+
+        smoothed_spikes = smooth(plot_trials_binary, window, 1./sampling_rate)
 
-        fig, ax = plt.subplots(2, 1)
+        fig, ax = plt.subplots(2, 1, sharex=True)
         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[1].plot(time_axis, smoothed_spikes*1000)
 
         ax[0].set_title(df)
         ax[0].set_ylabel('repetition', fontsize=12)
 
         ax[1].set_xlabel('time [ms]', fontsize=12)
-        ax[1].set_ylabel('firing rate [?]', fontsize=12)
+        ax[1].set_ylabel('firing rate [Hz]', fontsize=12)
+        print(overall_spikerate)
         plt.show()

code/utility.py

@@ -20,18 +20,16 @@ def vector_strength(spike_times, eod_durations):
 	return vs
 
 
-def gaussian(x, mu, sig):
+def gaussian(x, sig):
-	y = np.exp(-np.power(x - mu, 2.) / (2 * np.power(sig, 2.)))
+	y = np.exp(-0.5 * (x/sig)**2) / np.sqrt(2*np.pi)/sig
 	return y
 
 
-def smooth(data, window):
+def smooth(data, window, dt):
-	mu = 1
 	sigma = window
-	time_gauss = np.arange(-4 * sigma, 4 * sigma, 1)
+	time_gauss = np.arange(-4 * sigma, 4 * sigma, dt)
-	gauss = gaussian(time_gauss, mu, sigma)
+	gauss = gaussian(time_gauss, sigma)
-	gauss_norm = gauss/(np.sum(gauss)/len(gauss))
+	smoothed_data = np.convolve(data, gauss, 'same')
-	smoothed_data = np.convolve(data, gauss_norm, 'same')
 	return smoothed_data