From 9150263bdd512feadbc14a4219c8537487928ac5 Mon Sep 17 00:00:00 2001
From: Lisa <lisa-ruth.vial@student.uni-tuebingen.de>
Date: Wed, 7 Aug 2019 15:49:57 +0200
Subject: [PATCH] still struggling

---
 ephys_analysis.py | 38 ++++++++++++++++++++------------------
 1 file changed, 20 insertions(+), 18 deletions(-)

diff --git a/ephys_analysis.py b/ephys_analysis.py
index a579d30..468ce20 100644
--- a/ephys_analysis.py
+++ b/ephys_analysis.py
@@ -5,24 +5,25 @@ import nixio as nix
 from IPython import embed
 
 def analyze_sams(filename):
-    print(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)
+    # print(b.groups)
     for g in b.groups:
-        if 'sam' in g.name.lower():
+        if 'sam' in g.name.lower(): # go through loop, until 'sam' is found
             break
     rtag_data = g.tags[0]
     rtag_data.metadata.pprint(max_depth=-1)
-    print(40*'*')
+    # print(40*'*')
     stim_tag = g.multi_tags[0]
     stim_pos = stim_tag.positions[:] # beginnings of stimulations
     stim_extent = stim_tag.extents[:] # duration of stimulations
 
     for r in rtag_data.references:
         print(r.name, r.type)
-
+    # embed()
+    # exit()
     voltage_trace = rtag_data.references['V-1']
 
     spike_data = []
@@ -30,25 +31,26 @@ def analyze_sams(filename):
     for idx in range(len(stim_pos)):
         spike_data.append(stim_tag.retrieve_data(idx, 'Spikes-1')[:])
 
+    # embed()
+    # exit()
+    dims = voltage_trace.dimensions[0].axis(len(voltage_trace))
 
-    # dims = [[]] * len(spike_data)
-    # for j in range(len(spike_data)):
-    #     dims[j] = spike_data.dimensions[j]
-    # print(spike_data, len(spike_data))
+    # # f.close()
     # embed()
     # exit()
-    f.close()
-    return stim_pos, stim_extent, spike_data, voltage_trace
+    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 = analyze_sams(os.path.join(data_dir, data_set, data_set + '.nix'))
-    for i in range(len(stim_pos)):
-        plt.scatter(voltage_trace.dimensions[i].axis(1000), spike_data[i][:1000])
-        plt.show()
-        # spikes = stim_tag.retrieve_data(i, 'Spikes-1')[:]
-        # print(spikes)
+    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))
+    stims = []
+    # for i in range(len(stim_pos)):
         # embed()
-        # exit()
\ No newline at end of file
+        # plt.plot(stim_pos)
+    plt.plot(dims[:-1], voltage_trace[:-1])
+    plt.scatter(spike_data[:-1], np.ones(len(spike_data)-1)*np.max(voltage_trace))
+    plt.show()
\ No newline at end of file