app-eventslog/main.py at master · dnacombo/app-eventslog · GitHub

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import os
import numpy as np
import mne
import json
import helper
from mne_bids.write import _events_tsv
import shutil
import matplotlib.pyplot as plt

#workaround for -- _tkinter.TclError: invalid command name ".!canvas"
import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

with open('config.json') as config_json:
    config = helper.convert_parameters_to_None(json.load(config_json))

data_file = config['mne']
raw = mne.io.read_raw_fif(data_file,verbose=False)

events = mne.find_events(raw,stim_channel=config['stim_channel'],
                            output=config['output'],
                            consecutive=config['consecutive'],
                            min_duration=config['min_duration'],
                            shortest_event=config['shortest_event'],
                            mask=config['mask'],
                            uint_cast=config['uint_cast'],
                            mask_type=config['mask_type'],
                            initial_event=config['initial_event'])

events = mne.pick_events(events,include=config['include'],exclude=config['exclude'])

report = mne.Report(title='Events')

report.add_events(events=events, title='Events',sfreq=raw.info['sfreq'])

fig = mne.viz.plot_events(events, sfreq=raw.info['sfreq'],
                          first_samp=raw.first_samp)

_events_tsv(events, np.repeat(0.,events.shape[0]), raw, 'out_dir/events.tsv', trial_type=None, overwrite=True)

# == SAVE REPORT ==
report.save('out_dir_report/report.html', overwrite=True)