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

code/base_chirps.py

@@ -8,45 +8,50 @@ from IPython import embed
 
 
 data_dir = "../data"
-data = ("2018-11-09-ad-invivo-1", "2018-11-09-ae-invivo-1", "2018-11-09-ag-invivo-1", "2018-11-13-aa-invivo-1", "2018-11-13-ac-invivo-1", "2018-11-13-ad-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", "2018-11-13-aj-invivo-1", "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1", "2018-11-14-aa-invivo-1", "2018-11-14-ac-invivo-1", "2018-11-14-ad-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1", "2018-11-14-ah-invivo-1", "2018-11-14-ai-invivo-1", "2018-11-14-ak-invivo-1", "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1", "2018-11-20-aa-invivo-1", "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1", "2018-11-20-ad-invivo-1", "2018-11-20-ae-invivo-1", "2018-11-20-af-invivo-1", "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1") 
+dataset = "2018-11-13-ad-invivo-1"
+data = ["2018-11-09-ad-invivo-1", "2018-11-09-ae-invivo-1", "2018-11-09-ag-invivo-1", "2018-11-13-aa-invivo-1", "2018-11-13-ac-invivo-1", "2018-11-13-ad-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", "2018-11-13-aj-invivo-1", "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1", "2018-11-14-aa-invivo-1", "2018-11-14-ac-invivo-1", "2018-11-14-ad-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1", "2018-11-14-ah-invivo-1", "2018-11-14-ai-invivo-1", "2018-11-14-ak-invivo-1", "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1", "2018-11-20-aa-invivo-1", "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1", "2018-11-20-ad-invivo-1", "2018-11-20-ae-invivo-1", "2018-11-20-af-invivo-1", "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1"]
+
+
+#for dataset in data:
+
+eod = read_chirp_eod(os.path.join(data_dir, dataset))
+times = read_chirp_times(os.path.join(data_dir, dataset))
+df_map = map_keys(eod)
+sort_df = sorted(df_map.keys())
+
+
+eods = chirp_eod_plot(df_map, eod, times)
+plt.show()
+plt.close('all')
 
 
 
-for dataset in data:
+chirp_mods =  {}
-	print(dataset)
+beat_mods = []
-	eod = read_chirp_eod(os.path.join(data_dir, dataset))
+for i in sort_df:
-	times = read_chirp_times(os.path.join(data_dir, dataset))
+	chirp_mods[i] = []
-	df_map = map_keys(eod)
+	freq = list(df_map[i])
-	sort_df = sorted(df_map.keys())
+	ls_mod, beat_mod = cut_chirps(freq, eod, times)
-
+	chirp_mods[i].append(ls_mod)
-
+	beat_mods.append(beat_mod)
-	chirp_eod_plot(df_map, eod, times)
-
-
-	chirp_mods =  []
-	beat_mods = []
-	for i in sort_df:
-		freq = list(df_map[i])
-		ls_mod, beat_mod = cut_chirps(freq, eod, times)
-		chirp_mods.append(ls_mod)
-		beat_mods.append(beat_mod)
-
-
 
 
 	#Chirps einer Phase zuordnen - zusammen plotten
 
-	chirp_spikes = read_chirp_spikes(os.path.join(data_dir, dataset))
+chirp_spikes = read_chirp_spikes(os.path.join(data_dir, dataset))
-	df_map = map_keys(chirp_spikes)
+df_map = map_keys(chirp_spikes)
-	sort_df = sorted(df_map.keys())
+sort_df = sorted(df_map.keys())
-
+example = [-50, 200, 400]
-	#plot_std_chirp(sort_df, df_map, chirp_spikes, chirp_mods)
-
 
+dct_phase = plot_std_chirp(example, df_map, chirp_spikes, chirp_mods)
+plt.show()
+plt.close('all')
 
 
+'''
 	#Vatriablen speichern, die man für die Übersicht aller Zellen braucht
-	name = str(dataset.strip('invivo-1'))
+	name = str(dataset.replace('-invivo-1', ''))
+	print('saving ../results/Chirpcut/Cc_' + name + '.dat')
 	f = open('../results/Chirpcut/Cc_' + name + '.dat' , 'w') 
 	f.write(str(sort_df)) 
 	f.write(str(df_map)) 
@@ -56,3 +61,4 @@ for dataset in data:
 	#f.write(str(chirp_mods))
 	#f.write(str(beat_mods)) 
 	f.close() 
+'''

code/base_eod.py

@@ -8,14 +8,22 @@ from IPython import embed #Funktionen importieren
 data_dir = "../data"
 dataset = "2018-11-09-aa-invivo-1"
 #data = ("2018-11-09-aa-invivo-1", "2018-11-09-ab-invivo-1", "2018-11-09-ac-invivo-1", "2018-11-09-ad-invivo-1", "2018-11-13-aa-invivo-1", "2018-11-13-ab-invivo-1", "2018-11-13-ad-invivo-1", "2018-11-09-af-invivo-1", "2018-11-09-ag-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", "2018-11-13-aj-invivo-1", "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1", "2018-11-14-aa-invivo-1", "2018-11-14-ab-invivo-1", "2018-11-14-ac-invivo-1", "2018-11-14-ad-invivo-1", "2018-11-14-ae-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1", "2018-11-14-aa-invivo-1", "2018-11-14-aj-invivo-1", "2018-11-14-ak-invivo-1", "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1", "2018-11-20-aa-invivo-1", "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1", "2018-11-20-ad-invivo-1"," 2018-11-20-ae-invivo-1", "2018-11-20-af-invivo-1", "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1")
+
+
 time,eod = read_baseline_eod(os.path.join(data_dir, dataset))
 zeit = np.asarray(time)
 
 
-plt.plot(zeit[0:1000], eod[0:1000])
+
-plt.title('A.lepto EOD')#Plottitelk
+inch_factor = 2.54
-plt.xlabel('time [ms]', fontsize = 12)#Achsentitel
+fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
-plt.ylabel('amplitude[mv]', fontsize = 12)#Achsentitel
+
-plt.xticks(fontsize = 12)
+plt.plot(zeit[0:1000], eod[0:1000], color = 'darkblue')
-plt.yticks(fontsize = 12)
+plt.title('A.lepto EOD', fontsize = 24)#Plottitel
+plt.xlabel('time [ms]', fontsize = 22)#Achsentitel
+plt.ylabel('amplitude[mv]', fontsize = 22)#Achsentitel
+plt.tick_params(axis='both', which='major', labelsize = 22)
+ax.spines['right'].set_visible(False)
+ax.spines['top'].set_visible(False)
+fig.tight_layout()
 plt.show()

code/base_spikes.py

@@ -3,7 +3,7 @@ from read_chirp_data import *
 from func_spike import *
 import matplotlib.pyplot as plt
 import numpy as np
-from IPython import embed #Funktionen imposrtieren
+from IPython import embed #Funktionen importieren
 
 
 
@@ -11,77 +11,89 @@ data_dir = "../data"
 data_base = ("2018-11-09-ab-invivo-1", "2018-11-09-ad-invivo-1", "2018-11-13-aa-invivo-1", "2018-11-13-ab-invivo-1", "2018-11-13-ad-invivo-1", "2018-11-13-af-invivo-1", "2018-11-13-ag-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", "2018-11-13-aj-invivo-1", "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1", "2018-11-14-ab-invivo-1", "2018-11-14-ac-invivo-1", "2018-11-14-ad-invivo-1", "2018-11-14-ae-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1",  "2018-11-14-aj-invivo-1", "2018-11-14-ak-invivo-1", "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1", "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1", "2018-11-20-ad-invivo-1", "2018-11-20-ae-invivo-1", "2018-11-20-af-invivo-1", "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1")
 data_chirps = ("2018-11-09-ad-invivo-1", "2018-11-09-ae-invivo-1", "2018-11-09-ag-invivo-1", "2018-11-13-aa-invivo-1", "2018-11-13-ac-invivo-1", "2018-11-13-ad-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", "2018-11-13-aj-invivo-1", "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1", "2018-11-14-aa-invivo-1", "2018-11-14-ac-invivo-1", "2018-11-14-ad-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1", "2018-11-14-ah-invivo-1", "2018-11-14-ai-invivo-1", "2018-11-14-ak-invivo-1", "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1", "2018-11-20-aa-invivo-1", "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1", "2018-11-20-ad-invivo-1", "2018-11-20-ae-invivo-1", "2018-11-20-af-invivo-1", "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1") 
 
+dataset = "2018-11-13-ad-invivo-1"
+inch_factor = 2.54
 
+#for dataset in data_base:
 
-'''
+spike_times = read_baseline_spikes(os.path.join(data_dir, dataset))	
-for dataset in data_base:
+spike_iv = np.diff(spike_times)
+x = np.arange(0.001, 0.01, 0.0001)
 
-	print(dataset)
+fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
-	spike_times = read_baseline_spikes(os.path.join(data_dir, dataset))	
+plt.hist(spike_iv,x, color = 'darkblue')
-	spike_iv = np.diff(spike_times)
-	x = np.arange(0.001, 0.01, 0.0001)
-	plt.hist(spike_iv,x)
 
-	mu = np.mean(spike_iv)
+mu = np.mean(spike_iv)
-	sigma = np.std(spike_iv)
+sigma = np.std(spike_iv)
-	cv = sigma/mu
+cv = sigma/mu
 
-	plt.title('A.lepto ISI Histogramm', fontsize = 14)
+plt.title('A.lepto ISI Histogramm', fontsize = 24)
-	plt.xlabel('duration ISI[ms]', fontsize = 12)
+plt.xlabel('duration ISI[ms]', fontsize = 22)
-	plt.ylabel('number of ISI', fontsize = 12)
+plt.ylabel('number of ISI', fontsize = 22)
-
+plt.tick_params(axis='both', which='major', labelsize = 22)
-	plt.xticks(fontsize = 12)
+ax.spines['right'].set_visible(False)
-	plt.yticks(fontsize = 12)
+ax.spines['top'].set_visible(False)
-'''
+plt.tight_layout()
+plt.show()
 
 
 
-for dataset in data_chirps:
+#for dataset in data_chirps:
 
 	#Nyquist-Theorem Plot:
-	print(dataset)
+chirp_spikes = read_chirp_spikes(os.path.join(data_dir, dataset))
-	chirp_spikes = read_chirp_spikes(os.path.join(data_dir, dataset))
+times = read_chirp_times(os.path.join(data_dir, dataset))
-	times = read_chirp_times(os.path.join(data_dir, dataset))
+eod = read_chirp_eod(os.path.join(data_dir, dataset))
-	eod = read_chirp_eod(os.path.join(data_dir, dataset))
+df_map = map_keys(chirp_spikes)
-	df_map = map_keys(chirp_spikes)
+sort_df = sorted(df_map.keys())
-	sort_df = sorted(df_map.keys())
 
-	dct_rate, over_r = spike_rates(sort_df, df_map, chirp_spikes)
+dct_rate, over_r = spike_rates(sort_df, df_map, chirp_spikes)
-
-	plt.figure()
-	ls_mean = plot_df_spikes(sort_df, dct_rate)
 
+plt.figure()
+fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
+ls_mean = plot_df_spikes(sort_df, dct_rate)
+plt.show()
 
 
 
 	#mittlere Feuerrate einer Frequenz auf Frequenz:
 
-	plt.figure()
+fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
-	plt.plot(np.arange(0,len(ls_mean),1),ls_mean)
+plt.plot(np.arange(0,len(ls_mean),1),ls_mean, color = 'darkblue')
-	plt.scatter(np.arange(0,len(ls_mean),1), np.ones(len(ls_mean))*over_r)
+plt.scatter(np.arange(0,len(ls_mean),1), np.ones(len(ls_mean))*over_r, color = 'green')
-	plt.title('Mean firing rate of a cell for a range of frequency differences')
+plt.title('Mean firing rate of a cell for a range of frequency differences', fontsize = 24)
-	plt.xticks(np.arange(1,len(sort_df),1), (sort_df))
+plt.xticks(np.arange(1,len(sort_df),1), (sort_df))
-	plt.xlabel('Range of frequency differences [Hz]')
+plt.xlabel('Range of frequency differences [Hz]', fontsize = 22)
-	plt.ylabel('Mean firing rate of the cell')
+plt.ylabel('Mean firing rate of the cell', fontsize = 22)
-
+plt.tick_params(axis='both', which='major', labelsize = 18)
+ax.spines['right'].set_visible(False)
+ax.spines['top'].set_visible(False)
+plt.tight_layout()
+plt.show()
 
 
 
 	#Adaption der Zellen:
 	#wie viel Prozent der Anfangsrate macht die Adaption von Zellen aus?
 
-	adapt = adaptation_df(sort_df, dct_rate)
+adapt = adaptation_df(sort_df, dct_rate)
-	plt.figure()
+fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
-	plt.boxplot(adapt)
+plt.boxplot(adapt)
-	plt.title('Adaptation of cell firing rate during a trial')
+plt.title('Adaptation of cell firing rate during a trial', fontsize = 24)
-	plt.xlabel('Cell')
+plt.xlabel('Cell', fontsize = 22)
-	plt.ylabel('Adaptation size [Hz]')
+plt.ylabel('Adaptation size [Hz]', fontsize = 22)
+plt.tick_params(axis='both', which='major', labelsize = 18)
+ax.spines['right'].set_visible(False)
+ax.spines['top'].set_visible(False)
+plt.tight_layout()
+plt.show()	
 
 
 
+'''
 
 	#Vatriablen speichern, die man für die Übersicht aller Zellen braucht
-	name = str(dataset.strip('invivo-1'))
+	name = str(dataset.replace('-invivo-1', ''))
 	f = open('../results/Nyquist/Ny_' + name + '.txt' , 'w') 
 	f.write(str(sort_df)) 
 	f.write(str(df_map)) 
@@ -91,3 +103,4 @@ for dataset in data_chirps:
 	f.write(str(over_r)) 
 	f.write(str(adapt))
 	f.close() 
+'''

code/eod_chirp_beat.py

@@ -0,0 +1,96 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import thunderfish.peakdetection as pd
+
+
+def create_chirp(eodf):
+    stimulusrate = eodf  # the eod frequency of the fake fish
+    currentchirptimes = [0.0]
+    chirpwidth = 0.014  # ms
+    chirpsize = 100.
+    chirpampl = 0.02
+    chirpkurtosis = 1.
+    p = 0.
+    stepsize = 0.00001
+
+
+    time = np.arange(-0.05, 0.05, stepsize)
+    signal = np.zeros(time.shape)
+    ampl = np.ones(time.shape)
+    freq = np.ones(time.shape)
+
+    ck = 0
+    csig = 0.5 * chirpwidth / np.power(2.0*np.log(10.0), 0.5/chirpkurtosis)
+
+    for k, t in enumerate(time):
+        a = 1.
+        f = stimulusrate
+        if ck < len(currentchirptimes):
+            if np.abs(t - currentchirptimes[ck]) < 2.0 * chirpwidth:
+                x = t - currentchirptimes[ck]
+                g = np.exp(-0.5 * (x/csig)**2)
+                f = chirpsize * g + stimulusrate
+                a *= 1.0 - chirpampl * g
+            elif t > currentchirptimes[ck] + 2.0 * chirpwidth:
+                ck += 1
+        freq[k] = f
+        ampl[k] = a
+        p += f * stepsize
+        signal[k] = a * np.sin(6.28318530717959 * p)
+
+    return time, signal
+
+
+def plot_chirp(eodf, eodf1, phase, axis):
+    time, chirp_eod = create_chirp(eodf)
+    eod = np.sin(time * 2 * np.pi * eodf1 + phase)
+
+    y = chirp_eod * 0.4 + eod
+    p, t = pd.detect_peaks(y, 0.1)
+    axis.plot(time*1000, y, color = 'royalblue')
+    axis.plot(time[p]*1000, (y)[p], lw=2, color='k')
+    axis.plot(time[t]*1000, (y)[t], lw=2, color='k')
+    axis.spines["top"].set_visible(False)
+    axis.spines["right"].set_visible(False)
+
+
+
+inch_factor = 2.54
+
+fig = plt.figure(figsize=(20 / inch_factor, 10 / inch_factor))
+ax1 = fig.add_subplot(221)
+ax2 = fig.add_subplot(222)
+ax3 = fig.add_subplot(223)
+ax4 = fig.add_subplot(224)
+
+plot_chirp(600, 650, 0, ax2)
+plot_chirp(600, 650, np.pi, ax4)
+
+plot_chirp(600, 620, 0, ax1)
+plot_chirp(600, 620, np.pi, ax3)
+
+ax1.set_ylabel('EOD [mV]', fontsize=22)
+ax1.set_title('$\Delta$f = 20 Hz', fontsize = 18)
+ax1.yaxis.set_tick_params(labelsize=18)
+ax1.set_xticklabels([])
+
+ax2.set_title('$\Delta$f = 50 Hz', fontsize = 18)
+ax2.set_xticklabels([])
+ax2.set_yticklabels([])
+ax3.set_ylabel('EOD [mV]', fontsize=22)
+ax3.xaxis.set_tick_params(labelsize=18)
+ax3.yaxis.set_tick_params(labelsize=18)
+
+ax3.set_xlabel('time [ms]', fontsize=22)
+ax4.set_xlabel('time [ms]', fontsize=22)
+ax4.xaxis.set_tick_params(labelsize=18)
+ax4.set_yticklabels([])
+
+
+
+
+
+
+fig.tight_layout()
+#plt.show()
+plt.savefig('chirps_while_beat.png')

code/eod_freq_beat.py

@@ -2,38 +2,43 @@ from read_baseline_data import *
 from IPython import embed
 import matplotlib.pyplot as plt
 import numpy as np
+import thunderfish.peakdetection as pd
+from IPython import embed
 
 ## beat
 
 data_dir = '../data'
 dataset = '2018-11-09-ad-invivo-1'
+inch_factor = 2.54
 
 time, eod = read_baseline_eod(os.path.join(data_dir, dataset))
 eod_norm = eod - np.mean(eod)
+eod_norm = eod_norm[10000:20000]
 
-# calculate eod times and indices by zero crossings
+x = np.arange(0., len(eod_norm))
-threshold = 0
-shift_eod = np.roll(eod_norm, 1)
-eod_times = time[(eod_norm >= threshold) & (shift_eod < threshold)]
 
-#x = eod_times*40000
+y = np.sin(time[10000:20000]*2*np.pi*600)*0.5
-x = np.arange(0., len(eod_times)-1)
+ampl = eod_norm + y
-y = np.sin(x*2*np.pi*600)
+p, t = pd.detect_peaks(ampl, 0.1)
-eod_freq_beat = 1/(np.diff(eod_times) + y)
 
-# glätten
+time_axis = np.arange(len(ampl))
-kernel = np.ones(7)/7
+
-smooth_eod_freq_beat = np.convolve(eod_freq_beat, kernel, mode = 'valid')
+
-time_axis = np.arange(len(smooth_eod_freq_beat))
+fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
+plt.plot(time[10000:20000], ampl)
+plt.plot(time[10000:20000][p], ampl[p], lw=2, color='k')
+plt.plot(time[10000:20000][t], ampl[t], lw=2, color='k')
+ax.set_xlabel("time [ms]", fontsize = 22)
+plt.xticks(fontsize = 18)
+ax.set_ylabel("eod amplitude [mV]", fontsize = 22)
+plt.yticks(fontsize = 18)
+ax.spines["top"].set_visible(False)
+ax.spines["right"].set_visible(False)
+fig.tight_layout()
 
-plt.plot(time_axis, smooth_eod_freq_beat)
 plt.show()
+#plt.savefig('beat.png')
+
 
 
-#eod_freq_beat = eod_freq_normal + y
-#smooth_eod_freq_beat = np.convolve(eod_freq_beat, kernel, mode = 'valid')
-#fig = plt.plot(time_axis,smooth_eod_freq_beat)
-#plt.xlabel("time [ms]")
-#plt.ylabel("eod frequency [mV]")
-#plt.show()
 

code/func_chirp.py

@@ -2,8 +2,10 @@ from read_baseline_data import *
 from read_chirp_data import *
 from utility import *
 import matplotlib.pyplot as plt
+import math
 import numpy as np
 
+inch_factor = 2.54
 
 def chirp_eod_plot(df_map, eod, times):
 	#die äußere Schleife geht für alle Keys durch und somit durch alle dfs
@@ -11,7 +13,7 @@ def chirp_eod_plot(df_map, eod, times):
 
 	for i in df_map.keys():
 		freq = list(df_map[i]) 
-		fig,axs = plt.subplots(2, 2, sharex = True, sharey = True)
+		fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
 
 		for idx, k in enumerate(freq):
 			ct = times[k]
@@ -19,25 +21,29 @@ def chirp_eod_plot(df_map, eod, times):
 			zeit = e1[0]
 			eods = e1[1]
 	
-			if idx <= 3:
+			if idx <= 1:
-				axs[0, 0].plot(zeit, eods, color= 'blue', linewidth = 0.25)
+				ax.plot(zeit, eods, color= 'darkblue')
-				axs[0, 0].scatter(np.asarray(ct), np.ones(len(ct))*3, color = 'green', s= 22)
+				ax.scatter(np.asarray(ct), np.ones(len(ct))*np.mean(eods), color = 'green', s= 22)
-			elif 4<= idx <= 7:
+			#elif 4<= idx <= 7:
-				axs[0, 1].plot(zeit, eods, color= 'blue', linewidth = 0.25)
+			#	axs[0, 1].plot(zeit, eods, color= 'blue', linewidth = 0.25)
-				axs[0, 1].scatter(np.asarray(ct), np.ones(len(ct))*3, color = 'green', s= 22)
+			#	axs[0, 1].scatter(np.asarray(ct), np.ones(len(ct))*np.mean(eods), color = 'green', s= 22)
-			elif 8<= idx <= 11:
+			#elif 8<= idx <= 11:
-				axs[1, 0].plot(zeit, eods, color= 'blue', linewidth = 0.25)
+			#	axs[1, 0].plot(zeit, eods, color= 'blue', linewidth = 0.25)
-				axs[1, 0].scatter(np.asarray(ct), np.ones(len(ct))*3, color = 'green', s= 22)
+			#	axs[1, 0].scatter(np.asarray(ct), np.ones(len(ct))*np.mean(eods), color = 'green', s= 22)
-			else: 
+			else: 	
-				axs[1, 1].plot(zeit, eods, color= 'blue', linewidth = 0.25)
+				continue
-				axs[1, 1].scatter(np.asarray(ct), np.ones(len(ct))*3, color = 'green', s= 22)
+				#axs[1, 1].plot(zeit, eods, color= 'blue', linewidth = 0.25)
+				#axs[1, 1].scatter(np.asarray(ct), np.ones(len(ct))*np.mean(eods), color = 'green', s= 22)
+
+		ax.set_ylabel('Amplitude [mV]', fontsize = 22)
+		ax.set_xlabel('Time [ms]', fontsize = 22)		
+		ax.tick_params(axis='both', which='major', labelsize = 18)
+		ax.spines['right'].set_visible(False)
+		ax.spines['top'].set_visible(False)
+		fig.suptitle('EOD for chirps', fontsize = 24)
+		fig.tight_layout()
+
 
-	fig.suptitle('EOD for chirps', fontsize = 16)
-	axs[0,0].set_ylabel('Amplitude [mV]') 
-	axs[0,1].set_xlabel('Amplitude [mV]')
-	axs[1,0].set_xlabel('Time [ms]')
-	axs[1,1].set_xlabel('Time [ms]')
-	plt.close()
 
 
 
@@ -60,16 +66,18 @@ def cut_chirps(freq, eod, times):
 			ls_beat.extend(beat_cut)
 
 	beat_mod = np.std(ls_beat) #Std vom Bereich vor dem Chirp
-	plt.figure()
+	#plt.figure()
-	plt.scatter(np.arange(0,len(ls_mod),1), ls_mod)
+	#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))*beat_mod, color = 'violet')
+	#plt.scatter(np.arange(0,len(ls_mod),1), np.ones(len(ls_mod))*beat_mod, color = 'violet')
-	plt.close()
 	return(ls_mod, beat_mod)
 
 
 
-def plot_std_chirp(sort_df, df_map, chirp_spikes, ls_mod):
+
-	plt.figure()	
+
+def plot_std_chirp(sort_df, df_map, chirp_spikes, chirp_mods):
+		
+	fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
 	dct_phase = {}
 	num_bin = 12
 	phase_vec = np.arange(0, 1+1/num_bin, 1/num_bin)
@@ -80,8 +88,15 @@ def plot_std_chirp(sort_df, df_map, chirp_spikes, ls_mod):
 		for k in freq:
 			for phase in chirp_spikes[k]:
 				dct_phase[i].append(phase[1])
-
+	
-		plt.scatter(dct_phase[i], ls_mod[i])
+	for i in sort_df:
-	plt.title('Change of std depending on the phase where the chirp occured')
+		norm = np.asarray(dct_phase[i]) *2*math.pi
-	plt.close()
+		plt.scatter(norm, chirp_mods[i], label = i, s = 22)
+	plt.title('Change of std depending on the phase where the chirp occured', fontsize = 24)	
+	plt.xlabel('Phase', fontsize = 22)
+	plt.ylabel('Standard deviation of the amplitude modulation', fontsize = 22)
+	plt.xticks([0, math.pi/2, math.pi, math.pi*1.5, math.pi*2], ('0', '$\pi$ /2', '$\pi$', '1.5 $\pi$', '2$\pi$'))
+	plt.tick_params(axis='both', which='major', labelsize = 18)
+	plt.legend()
+	return(dct_phase)
 

code/func_spike.py

@@ -43,6 +43,8 @@ def spike_rates(sort_df, df_map, chirp_spikes):
 
 def plot_df_spikes(sort_df, dct_rate):
 #gibt die Feuerrate gegen die Frequenz aufgetragen
+	inch_factor = 2.54
+	fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
 	ls_mean = []
 	for h in sort_df:	
 		mean = np.mean(dct_rate[h])
@@ -50,9 +52,13 @@ def plot_df_spikes(sort_df, dct_rate):
 		plt.plot(np.arange(0,len(dct_rate[h]),1),dct_rate[h], label = h)
 
 	plt.legend()
-	plt.title('Firing rate of the cell for all trials, sorted by df')
+	plt.title('Firing rate of the cell for all trials, sorted by df', fontsize = 24)
-	plt.xlabel('# of trials')
+	plt.xlabel('# of trials', fontsize = 22)
-	plt.ylabel('Instant firing rate of the cell')
+	plt.ylabel('Instant firing rate of the cell', fontsize = 22)
+	plt.tick_params(axis='both', which='major', labelsize = 18)
+	ax.spines['right'].set_visible(False)
+	ax.spines['top'].set_visible(False)
+	plt.tight_layout()
 	return(ls_mean)
 
 

code/order_eff.py

@@ -0,0 +1,48 @@
+from read_chirp_data import *
+from func_spike import *
+import matplotlib.pyplot as plt
+import numpy as np
+from IPython import embed #Funktionen importieren
+
+
+
+
+data_dir = "../data"
+data_chirps = ("2018-11-09-ad-invivo-1", "2018-11-09-ae-invivo-1", "2018-11-09-ag-invivo-1", "2018-11-13-aa-invivo-1", "2018-11-13-ac-invivo-1", "2018-11-13-ad-invivo-1", "2018-11-13-ah-invivo-1", "2018-11-13-ai-invivo-1", "2018-11-13-aj-invivo-1", "2018-11-13-ak-invivo-1", "2018-11-13-al-invivo-1", "2018-11-14-aa-invivo-1", "2018-11-14-ac-invivo-1", "2018-11-14-ad-invivo-1", "2018-11-14-af-invivo-1", "2018-11-14-ag-invivo-1", "2018-11-14-ah-invivo-1", "2018-11-14-ai-invivo-1", "2018-11-14-ak-invivo-1", "2018-11-14-al-invivo-1", "2018-11-14-am-invivo-1", "2018-11-14-an-invivo-1", "2018-11-20-aa-invivo-1", "2018-11-20-ab-invivo-1", "2018-11-20-ac-invivo-1", "2018-11-20-ad-invivo-1", "2018-11-20-ae-invivo-1", "2018-11-20-af-invivo-1", "2018-11-20-ag-invivo-1", "2018-11-20-ah-invivo-1", "2018-11-20-ai-invivo-1") 
+
+
+
+inch_factor = 2.54
+data_rate_dict = {}
+for dataset in data_chirps:
+	
+	data_rate_dict[dataset] = []
+	chirp_spikes = read_chirp_spikes(os.path.join(data_dir, dataset))
+	times = read_chirp_times(os.path.join(data_dir, dataset))
+	eod = read_chirp_eod(os.path.join(data_dir, dataset))
+	df_map = map_keys(chirp_spikes)
+
+
+	for i in df_map.keys():
+		freq = list(df_map[i])
+		k = freq[0]
+		phase = list(chirp_spikes[k].keys())[0]
+
+		spikes = chirp_spikes[k][phase]
+		rate = len(spikes)/ 1.2
+		data_rate_dict[dataset].append(rate)		
+
+fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
+for dataset in data_rate_dict:
+	plt.plot(data_rate_dict[dataset])
+
+plt.title('Test for sequence effects', fontsize = 24)
+plt.xlabel('Number of stimulus presentations', fontsize = 22)
+plt.ylabel('Firing rates of cells', fontsize = 22)
+plt.tick_params(axis='both', which='major', labelsize = 22)
+ax.spines['right'].set_visible(False)
+ax.spines['top'].set_visible(False)
+fig.tight_layout()
+plt.show()
+
+

code/plot_eodform_spikehist.py

@@ -14,6 +14,9 @@ dataset = '2018-11-14-ad-invivo-1'
 
 # read eod and time of baseline
 time, eod = read_baseline_eod(os.path.join(data_dir, dataset))
+
+
+
 eod_norm = eod - np.mean(eod)
 
 # calculate eod times and indices by zero crossings
@@ -23,6 +26,10 @@ eod_times = time[(eod_norm >= threshold) & (shift_eod < threshold)]
 
 eod_duration = eod_times[2]- eod_times[1] #time in s
 
+eod_duration = eod_times[2]- eod_times[1]
+
+
+
 # read spikes during baseline activity
 spikes = read_baseline_spikes(os.path.join(data_dir, dataset)) #spikes in s
 # calculate interpike intervals and plot them
@@ -37,9 +44,8 @@ plt.yticks(fontsize = 18)
 ax.spines["top"].set_visible(False)
 ax.spines["right"].set_visible(False)
 fig.tight_layout()
-plt.show()
+#plt.show()
 #plt.savefig('isis.pdf')
-exit()
 plt.savefig('isis.png')
 
 
@@ -93,10 +99,10 @@ plt.yticks(fontsize=18)
 ax1.spines['top'].set_visible(False)
 
 ax2 = ax1.twinx()
-ax2.fill_between(time_axis, mu_eod+std_eod, mu_eod-std_eod, color='navy', alpha=0.5)
+ax2.fill_between(time_axis, mu_eod+std_eod, mu_eod-std_eod, color='royalblue', alpha=0.5)
 ax2.plot(time_axis, mu_eod, color='black', lw=2)
 ax2.set_ylabel('voltage [mV]', fontsize=22)
-ax2.tick_params(axis='y', labelcolor='navy')
+ax2.tick_params(axis='y', labelcolor='royalblue')
 ax2.spines['top'].set_visible(False)
 
 plt.yticks(fontsize=18)

code/plot_spikesduringbaselineactivity.py

@@ -17,6 +17,7 @@ interspikeintervals = np.diff(spikes)*1000
 
 fig, ax = plt.subplots(figsize=(20/inch_factor, 10/inch_factor))
 plt.hist(interspikeintervals, bins=np.arange(0, np.max(interspikeintervals), 0.0001), color='darkblue')
+#Titel fehlt!!
 plt.xlabel("time [ms]", fontsize = 22)
 plt.xticks(fontsize = 18)
 plt.ylabel("Number of \n Interspikeinterval", fontsize = 22)

code/stimulus_chirp.py

@@ -35,13 +35,13 @@ for k, t in enumerate(time):
     p += f * stepsize
     signal[k] = a * np.sin(6.28318530717959 * p)
 
-fig = plt.figure(figsize = (20/inch_factor, 15/inch_factor))
+fig = plt.figure(figsize = (20/inch_factor, 12/inch_factor))
 ax1 = fig.add_subplot(211)
 plt.yticks(fontsize=18)
 ax2 = fig.add_subplot(212, sharex=ax1)
 plt.setp(ax1.get_xticklabels(), visible=False)
-ax1.plot(time*1000, signal, color = 'midnightblue', lw = 1)
+ax1.plot(time*1000, signal, color = 'royalblue', lw = 1)
-ax2.plot(time*1000, freq, color = 'midnightblue', lw = 3)
+ax2.plot(time*1000, freq, color = 'royalblue', lw = 3)
 
 ax1.set_ylabel("field [mV]", fontsize = 22)
 
@@ -53,5 +53,5 @@ ax2.yaxis.set_label_coords(-0.1, 0.5)
 plt.xticks(fontsize=18)
 plt.yticks(fontsize=18)
 fig.tight_layout()
-#plt.show()
+plt.show()
-plt.savefig('stimulus_chirp.png')
+#plt.savefig('stimulus_chirp.png')

code/vector_phase.py

@@ -1,25 +0,0 @@
-from read_baseline_data import *
-from utility import *
-#import nix_helpers as nh 
-import matplotlib.pyplot as plt
-import numpy as np
-from IPython import embed #Funktionen importieren
-
-
-#Zeitpunkte einer EOD über Zero-crossings finden, die in einer Steigung liegen
-data_dir = "../data"
-dataset = "2018-11-09-ad-invivo-1"
-time,eod = read_baseline_eod(os.path.join(data_dir, dataset))
-spike_times = read_baseline_spikes(os.path.join(data_dir, dataset))
-print(len(spike_times))
-
-eod_times = zero_crossing(eod,time)
-eod_durations = np.diff(eod_times)
-print(len(spike_times))
-print(len(eod_durations))
-
-#for st in spike_times:
-	#et = eod_times[eod_times < st]
-	#dt = st - et
-	
-#vs = vector_strength(spike_times, eod_durations)