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I have EEG data with 5 columns (1 per each electrode) and I need to denoise it and extract features from it using Python. I tried to find relevant packages but my search kept leading me to MNE which takes as input data in a format that I don't have. My data is in a pandas dataframe.

my questions are:

  1. How do you denoise such dataset?
  2. How do you do feature extraction for it?

Thanks :)

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    $\begingroup$ Are you asking for a different python package, or a reference for how to do these, or a general explanation? If it's the last two, then you don't need the word "Python" in the title. $\endgroup$
    – uhoh
    Commented Feb 24, 2019 at 4:24
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    $\begingroup$ If you are looking for a python-based EEG analyzing toolbox, have you tried PyEEG (pyeeg.sourceforge.net)? $\endgroup$
    – Cloudy
    Commented Feb 25, 2019 at 12:49
  • $\begingroup$ I recommend updating the Q based on the comments, as the Q is vague; do you need Python script or general help? If the latter, the question is too broad to begin with. $\endgroup$
    – AliceD ♦
    Commented Feb 26, 2019 at 19:45
  • $\begingroup$ Wow this is so exciting topic $\endgroup$
    – user13859
    Commented Sep 10, 2019 at 13:50

1 Answer 1

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you can convert your data frame to numpy array using 

data=df.to_numpy()

If your data is single trial meanining two dimensional dataset, you can use

channel_names=df.columns.tolist()
channel_types=len(channel_names)*['eeg']
sfreq = 1000  # in Hertz
montage = 'standard_1005'
info = mne.create_info(channel_names, sfreq, channel_types, montage)
raw = mne.io.RawArray(data, info)

If you have multitrials dataset

channel_names=df.columns.tolist()
channel_types=len(channel_names)*['eeg']
sfreq = 1000  # in Hertz
montage = 'standard_1005'
info = mne.create_info(channel_names, sfreq, channel_types, montage)
data=data.reshape(len(channel_names),-1,sfreq*time)
data=np.swapaxes(data,0,1)
epochs = mne.EpochsArray(sub, info)

Once you convert your dataset to mne structure, you can use mne filters and mne features

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