forked from derekhoward/nwb_conversion
-
Notifications
You must be signed in to change notification settings - Fork 0
/
utils.py
62 lines (46 loc) · 1.84 KB
/
utils.py
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
from pathlib import Path
import pandas as pd
from ipfx.dataset.create import create_ephys_data_set
import matplotlib.pyplot as plt
import pyabf
def summary_df(path, suffix='.abf'):
# The following provides a dataframe for all abf files found recursively within a directory
# it outputs the filename, path to file and date created
all_files = []
for i in path.rglob(f'*[!.DS_Store]{suffix}'): # searches for all files recursively excluding those named .DS_Store
all_files.append((i.name, i))
columns = ["file_name", "path"]
df = pd.DataFrame.from_records(all_files, columns=columns)
df.path = df.path.astype('str')
return df
def generate_subject_meta(row):
meta = {
'Subject': {
'age': None,
'description': f'{row.abf_comments}',
'species': 'Homo sapiens',
'subject_id': f'Donor_{row.file_id}'}
}
return meta
def load_nwb_ipfx(file_name, ontology):
print('loading dataset into data structure...')
print(file_name)
data_set = create_ephys_data_set(nwb_file=file_name, ontology=ontology) # loads nwb file into ipfx data structure
return(data_set)
def plot_nwb_sweep(file_name, ontology, sweep_plot_index=None, sweep_num=0):
data_set = load_nwb_ipfx(file_name, ontology)
if sweep_plot_index is None:
sweep_plot_index = (len(data_set.sweep_table) // 3)*2
curr_sweep = data_set.sweep_set(sweep_plot_index).sweeps[sweep_num]
t = curr_sweep.t
v = curr_sweep.v
i = curr_sweep.i
fig, axes = plt.subplots(2, 1, sharex=True)
fig.suptitle(f'{file_name}', fontsize=12)
axes[0].plot(t, v)
axes[0].set_xlim(0, 2)
axes[0].set_ylabel("Membrane voltage (mV)")
axes[0].set_title(f'sweep: {sweep_plot_index}')
axes[1].plot(t, i, c="orange")
axes[1].set_ylabel("Injected current (pA)")
return(fig)