stimuli figures

ephys_analysis.py

@@ -2,6 +2,8 @@ import os
 import numpy as np
 import matplotlib.pyplot as plt
 import nixio as nix
+import glob
+import os
 from IPython import embed
 
 def analyze_sams(filename):
@@ -13,37 +15,39 @@ def analyze_sams(filename):
     for g in b.groups:
         if 'sam' in g.name.lower(): # go through loop, until 'sam' is found
             break
-    rtag_data = g.tags[0]
+        rtag_data = g.tags[0]
-    rtag_data.metadata.pprint(max_depth=-1)
+        rtag_data.metadata.pprint(max_depth=-1)
-    # print(40*'*')
+        # print(40*'*')
-    stim_tag = g.multi_tags[0]
+        stim_tag = g.multi_tags[0]
-    stim_pos = stim_tag.positions[:] # beginnings of stimulations
+        stim_pos = stim_tag.positions[:] # beginnings of stimulations
-    stim_extent = stim_tag.extents[:] # duration of stimulations
+        stim_extent = stim_tag.extents[:] # duration of stimulations
-
+        # embed()
-    for r in rtag_data.references:
+        # exit()
-        print(r.name, r.type)
+        for r in rtag_data.references:
-    # embed()
+            print(r.name, r.type)
-    # exit()
+        # embed()
-    voltage_trace = rtag_data.references['V-1']
+        # exit()
+        voltage_trace = rtag_data.references['V-1']
 
-    spike_data = []
+        spike_data = []
 
-    for idx in range(len(stim_pos)):
+        for idx in range(len(stim_pos)):
-        spike_data.append(stim_tag.retrieve_data(idx, 'Spikes-1')[:])
+            spike_data.append(stim_tag.retrieve_data(idx, 'Spikes-1')[:])
 
-    # embed()
+        # embed()
-    # exit()
+        # exit()
-    dims = voltage_trace.dimensions[0].axis(len(voltage_trace))
+        dims = voltage_trace.dimensions[0].axis(len(voltage_trace))
 
-    # # f.close()
+        # # f.close()
-    # embed()
+        # embed()
     # exit()
     return stim_pos, stim_extent, spike_data, voltage_trace, dims
 
 
 if __name__ == '__main__':
     data_dir = '/home/lisa/data'
-    data_set = '2019-06-24-aa-invivo-1'
+    os.chdir(data_dir)
+    data_set = glob.glob('2019-*')
     stim_pos, stim_extent, spike_data, voltage_trace, dims = analyze_sams(os.path.join(data_dir, data_set,
                                                                                        data_set + '.nix'))
     print(len(spike_data))
@@ -59,5 +63,5 @@ if __name__ == '__main__':
         for k in range(len(spike_data[j])):
             print('current spike time is: ', spike_data[j][k])
             plt.plot(spike_data[j][k], -40, 'o', color='k')
-    plt.ylim([-100, -30])
+    # plt.ylim([-45, 0])
     plt.show()

stimuli_figures.py

@@ -0,0 +1,33 @@
+import glob
+import matplotlib.pyplot as plt
+
+filenames = glob.glob('*.dat')
+
+for i in range(len(filenames)):
+    with open(filenames[i], 'r') as f:
+        lines = f.readlines()
+        time = []
+        amplitude = []
+        for l in lines:
+            if len(l.strip()) > 0 and '#' not in l:
+                l = l.strip().split()
+                time.append(float(l[0]))
+                amplitude.append(float(l[1]))
+        plt.figure(figsize=(20/2.54, 12/2.54), facecolor='white', edgecolor='white')
+        ax = plt.subplot(111)
+        ax.spines["top"].set_visible(False)
+        # ax.spines["bottom"].set_visible(False)
+        ax.spines["right"].set_visible(False)
+        # ax.spines["left"].set_visible(False)
+        ax.get_xaxis().tick_bottom()
+        ax.get_yaxis().tick_left()
+        if filenames[i] == 'zap.dat':
+            ax.set_xlim([0, 1])
+        else:
+            ax.set_xlim([0, .2])
+        ax.set_title(filenames[i])
+        ax.set_xlabel('time')
+        ax.set_ylabel('amplitude')
+        ax.plot(time, amplitude)
+        plt.savefig(filenames[i]+'.pdf')
+        plt.show()