LisaVial/torus_ephys
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity

still struggling

Browse Source
This commit is contained in:
Lisa 2019-08-07 15:49:57 +02:00
parent 646eaccb9b
commit 9150263bdd
1 changed files with 20 additions and 18 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

38
ephys_analysis.py
View File

@ -5,24 +5,25 @@ import nixio as nix
from IPython import embed from IPython import embed
def analyze_sams(filename): def analyze_sams(filename):
print(filename) # print(filename)
f = nix.File.open(filename, nix.FileMode.ReadOnly) f = nix.File.open(filename, nix.FileMode.ReadOnly)
b = f.blocks[0] b = f.blocks[0]
b.metadata.pprint(max_depth=-1) # max_depth=-1: alles rausschreiben b.metadata.pprint(max_depth=-1) # max_depth=-1: alles rausschreiben
print(b.groups) # print(b.groups)
for g in 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 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
for r in rtag_data.references: for r in rtag_data.references:
print(r.name, r.type) print(r.name, r.type)
# embed()
# exit()
voltage_trace = rtag_data.references['V-1'] voltage_trace = rtag_data.references['V-1']
spike_data = [] spike_data = []
@ -30,25 +31,26 @@ def analyze_sams(filename):
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()
# exit()
dims = voltage_trace.dimensions[0].axis(len(voltage_trace))
# dims = [[]] * len(spike_data) # # f.close()
# for j in range(len(spike_data)):
# dims[j] = spike_data.dimensions[j]
# print(spike_data, len(spike_data))
# embed() # embed()
# exit() # exit()
f.close() return stim_pos, stim_extent, spike_data, voltage_trace, dims
return stim_pos, stim_extent, spike_data, voltage_trace
if __name__ == '__main__': if __name__ == '__main__':
data_dir = '/home/lisa/data' data_dir = '/home/lisa/data'
data_set = '2019-06-24-aa-invivo-1' 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')) stim_pos, stim_extent, spike_data, voltage_trace, dims = analyze_sams(os.path.join(data_dir, data_set,
for i in range(len(stim_pos)): data_set + '.nix'))
plt.scatter(voltage_trace.dimensions[i].axis(1000), spike_data[i][:1000]) print(len(spike_data))
plt.show() stims = []
# spikes = stim_tag.retrieve_data(i, 'Spikes-1')[:] # for i in range(len(stim_pos)):
# print(spikes)
# embed() # embed()
# exit() # 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()