Hilbert Detector

[1]:
# first let's load in all our packages
import matplotlib
import matplotlib.pyplot as plt
import numpy as np
import sys
import os
import re
import pandas as pd


from mne_bids import (read_raw_bids, BIDSPath,
                      get_entity_vals, get_datatypes,
                      make_report)
from mne_bids.stats import count_events

import mne
from mne import make_ad_hoc_cov

basepath = os.path.join(os.getcwd(), "../..")
sys.path.append(basepath)
from mne_hfo import HilbertDetector
[2]:
%%capture
# this may change depending on where you store the data
root = "C:/Users/patri/Dropbox/fedele_hfo_data"
subjects = get_entity_vals(root, 'subject')
sessions = get_entity_vals(root, 'session')
subjectID = subjects[0]
sessionID = sessions[0]
bids_path = BIDSPath(subject=subjectID, session=sessionID,
                     datatype='ieeg',
                     suffix='ieeg',
                     extension='.vhdr', root=root)

# get first matching dataset
fpath = bids_path.match()[0]
# load dataset into mne Raw object
extra_params = dict(preload=True)
raw = read_raw_bids(fpath, extra_params)
[3]:
def convert_to_bipolar(raw, drop_originals=True):
    original_ch_names = raw.ch_names
    ch_names_sorted = sorted(original_ch_names)
    ch_pairs = []
    for first, second in zip(ch_names_sorted, ch_names_sorted[1:]):
        firstName = re.sub(r'[0-9]+', '', first)
        secondName = re.sub(r'[0-9]+', '', second)
        if firstName == secondName:
            ch_pairs.append((first,second))
    for ch_pair in ch_pairs:
        raw = mne.set_bipolar_reference(raw, ch_pair[0], ch_pair[1], drop_refs=False)
    if drop_originals:
        raw = raw.drop_channels(original_ch_names)
    return raw
[4]:
%%capture
raw = convert_to_bipolar(raw)

---------------------------------------------------------------------------
TypeError                                 Traceback (most recent call last)
<ipython-input-4-f6e3da9a949b> in <module>
      2 info = raw.info
      3 sfreq = info['sfreq']
----> 4 data = raw.get_data(start=0, stop=30*sfreq)
      5 raw = mne.io.RawArray(data, info=info)

<decorator-gen-170> in get_data(self, picks, start, stop, reject_by_annotation, return_times, verbose)

~\.virtualenvs\mne-hfo-tjBZjdVA\lib\site-packages\mne\io\base.py in get_data(self, picks, start, stop, reject_by_annotation, return_times, verbose)
    823         stop = min(self.n_times if stop is None else stop, self.n_times)
    824         if len(self.annotations) == 0 or reject_by_annotation is None:
--> 825             data, times = self[picks, start:stop]
    826             return (data, times) if return_times else data
    827         _check_option('reject_by_annotation', reject_by_annotation.lower(),

~\.virtualenvs\mne-hfo-tjBZjdVA\lib\site-packages\mne\io\base.py in __getitem__(self, item)
    770         sel, start, stop = self._parse_get_set_params(item)
    771         if self.preload:
--> 772             data = self._data[sel, start:stop]
    773         else:
    774             data = self._read_segment(start=start, stop=stop, sel=sel,

TypeError: slice indices must be integers or None or have an __index__ method
[7]:
info = raw.info
sfreq = info['sfreq']
data = raw.get_data(start=0, stop=int(30*sfreq))
raw = mne.io.RawArray(data, info=info)
Creating RawArray with float64 data, n_channels=43, n_times=60000
    Range : 0 ... 59999 =      0.000 ...    30.000 secs
Ready.
[8]:
kwargs = {
    'band_method': 'log',
    'filter_band': (80, 250), # (l_freq, h_freq)
    'threshold': 3, # Number of st. deviations
    'hfo_name': "ripple",
    'n_jobs': 1,
}
hil_detector = HilbertDetector(**kwargs)
[9]:
raw.n_times
[9]:
60000
[10]:
# perform the fits
hil_detector = hil_detector.fit(raw)
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[12]:
hil_detector.df_
[12]:
onset duration label channels sample
0 10.4095 0.6320 ripple AHR1-AHR2 20819.0
1 14.2345 0.2995 ripple AHR1-AHR2 28469.0
2 16.0610 0.3110 ripple AHR1-AHR2 32122.0
3 23.8995 0.4905 ripple AHR1-AHR2 47799.0
4 10.4225 0.5130 ripple AHR2-AHR3 20845.0
... ... ... ... ... ...
69 16.0450 0.5025 ripple PHR4-PHR5 32090.0
70 23.9560 0.5325 ripple PHR4-PHR5 47912.0
71 6.4010 0.1840 ripple PHR5-PHR6 12802.0
72 1.4250 0.1630 ripple PHR7-PHR8 2850.0
73 28.2535 0.3480 ripple PHR7-PHR8 56507.0

74 rows × 5 columns

[ ]: