mne-tools / mne-tools/mne-python

can't pickle Epochs with preload=False

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BUG
Dominant language
Python
Stars
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Forks
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Avg merge
1d 6h
Merged PRs (30d)
100

Description

To replicate:

from pathlib import Path
import mne
import pickle

sample_dir = Path(mne.datasets.sample.data_path())
sample_fname = sample_dir / 'MEG' / 'sample' / 'sample_audvis_raw.fif'

raw = mne.io.read_raw_fif(sample_fname)
raw.crop(tmax=60)

events = mne.find_events(raw, stim_channel='STI 014')
event_id = {'auditory/left': 1}
epochs = mne.Epochs(raw, events=events, event_id=event_id,
                    tmin=-0.2, tmax=0.5, baseline=(None, 0),
                    preload=True)

epochs.save('toto-epo.fif', overwrite=True)
epochs = mne.read_epochs('toto-epo.fif', preload=False)

# del epochs._raw[0].fid  # uncomment this line to fix it

fname = "toto.pkl"
with open(fname, 'wb') as fid:
    pickle.dump(epochs, fid)

it's due to the fid in epochs._raw[0].fid

@larsoner thoughts?

reported by @gemeinl in braindecode

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Research direction

Start by running the provided Python reproduction with MNE's sample dataset and inspect the loaded Epochs object's epochs._raw[0].fid after read_epochs(..., preload=False). Done means an Epochs object loaded with preload=False can be serialized with pickle without requiring the manual fid deletion shown in the report.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
data
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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