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ephys_analysis.py

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+import os
+import numpy as np
+import matplotlib.pyplot as plt
+import nixio as nix
+from IPython import embed
+
+def analyze_sams(filename):
+    print(filename)
+    f = nix.File.open(filename, nix.FileMode.ReadOnly)
+    b = f.blocks[0]
+    b.metadata.pprint(max_depth=-1) # max_depth=-1: alles rausschreiben
+    print(b.groups)
+    for g in b.groups:
+        if 'sam' in g.name.lower():
+            break
+    rtag_data = g.tags[0]
+    rtag_data.metadata.pprint(max_depth=-1)
+    print(40*'*')
+    stim_tag = g.multi_tags[0]
+    stim_pos = stim_tag.positions[:]
+    stim_extent = stim_tag.extents[:]
+
+    for r in rtag_data.references:
+        print(r.name, r.type)
+
+    voltage_trace = rtag_data.references['V-1']
+
+    spike_data = []
+
+    for i in range(len(stim_pos)):
+        spike_data.append(stim_tag.retrieve_data(i, 'Spikes-1')[:])
+
+
+    dims = [[]] * len(voltage_trace)
+    for j in range(len(spike_data)):
+        dims[j] = voltage_trace.dimensions[j]
+    print(spike_data, len(spike_data))
+    f.close()
+    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'
+    stim_pos, stim_extent, spike_data, voltage_trace, dims = analyze_sams(os.path.join(data_dir, data_set, data_set + '.nix'))
+    for i in range(len(stim_pos)):
+        plt.eventplot(dims[i], spike_data[i])
+        plt.show()
+        # spikes = stim_tag.retrieve_data(i, 'Spikes-1')[:]
+        # print(spikes)
+        # embed()
+        # exit()