main.py

# this app allows filtering raw data.
# it loads the raw data, applies a bandpass filter to it using the parameters specified in the config.json file
# it then saves the filtered data and plots the filter response
# it also saves a report of the filtered data

import os
import mne
import json
import helper
import matplotlib.pyplot as plt
from mne.viz import plot_filter, plot_ideal_filter
import re

import matplotlib
matplotlib.use('Agg')
import matplotlib.pyplot as plt

# Load brainlife config.json
with open('config.json','r') as config_f:
    config = helper.convert_parameters_to_None(json.load(config_f))

# == CONFIG PARAMETERS ==
fname = config['mne']
l_freq = config['l_freq']
h_freq = config['h_freq']

picks = config['picks']
filter_length = config['filter_length']
l_trans_bandwidth = config['l_trans_bandwidth']
h_trans_bandwidth = config['h_trans_bandwidth']
method = config['method']
iir_params = config['iir_params']
phase = config['phase']
fir_window = config['fir_window']
fir_design = config['fir_design']
skip_by_annotation = config['skip_by_annotation']
pad = config['pad']


# == LOAD DATA ==
raw = mne.io.read_raw_fif(fname, preload=True)
raw_orig = raw.copy()
sfreq = raw.info['sfreq']

# Create filter
f = mne.filter.create_filter(raw_orig.get_data(),
                             sfreq,
                             l_freq = l_freq,
                             h_freq = h_freq )
'''
                             filter_length = filter_length, 
                             l_trans_bandwidth = l_trans_bandwidth,
                             h_trans_bandwidth = h_trans_bandwidth,
                             method = method,
                             iir_params = iir_params, 
                             phase = phase,
                             fir_window = fir_window,
                             fir_design = fir_design)
'''
plt.figure()
fig = plot_filter(f,sfreq)
plt.savefig(os.path.join('out_figs','filter_response.png'))


if config['notch']:
    config['notch'] = [int(x) for x in re.split("\\W+",config['notch'])]
    raw.notch_filter(freqs=config['notch'], picks=config['picks'])

raw.filter( l_freq = l_freq,
            h_freq = h_freq )

'''
raw.filter(
            l_freq = l_freq,
            h_freq = h_freq,
            picks = picks, 
            filter_length = filter_length, 
            l_trans_bandwidth = l_trans_bandwidth,
            h_trans_bandwidth = h_trans_bandwidth,
            method = method,
            iir_params = iir_params, 
            phase = phase,
            fir_window = fir_window,
            fir_design = fir_design
            skip_by_annotation=config['skip_by_annotation'],
            pad = pad)

raw.filter(picks=config['picks'], 
           l_freq=config['l_freq'],
           h_freq=config['h_freq'],
           filter_length=config['filter_length'],
           l_trans_bandwidth=config['l_trans_bandwidth'],
           h_trans_bandwidth=config['h_trans_bandwidth'],
           method=config['method'],
           iir_params=config['iir_params'],
           phase=config['phase'],
           fir_window=config['fir_window'],
           fir_design=config['fir_design'],
           skip_by_annotation = skip_by_annotation,
           pad = config['pad'])
'''        
raw.save('out_dir/meg.fif',overwrite=True)


# == REPORT ==
report = mne.Report(title='Filtering report')
report.add_figure(fig, title='Filter')
report.add_raw(raw_orig, 'Original unfiltered data', psd=True)
report.add_raw(raw, 'Filtered data', psd=True)
report.save('out_report/report_filter.html', overwrite=True)