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Exporting epochs is not working if epochs have been concatenated #11434

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Description

@Gabrock94

Description of the problem

Hi all,
I ma facing this error for which exporting epochs using mne.export_epochs() will fail if epochs were concatenated using mne.concatenate_epochs.

I understand from previous issues (e.g. #11131) that this is because mne.concatenate_epochs has no support for annotations, however either the concatenate function should generate empty annotations, or the export function should handle missing annotations.

I tried to solve it myself using the second approach as I needed it rapidly, by editing the file mne-python/mne/export/_eeglab.py. See https://github.com/Gabrock94/mne-python

The workaround I used is to edit Line 45 from:
if len(epochs.annotations) > 0:

to:

if (type(epochs.annotations)!=None.__class__):
        if (len(epochs.annotations) > 0):

however probably fixing the concatenation function would be a better approach.

Steps to reproduce

import mne
mne.datasets.sample.data_path(verbose=True)

raw = mne.io.read_raw_fif('~/mne_data/MNE-sample-data/MEG/sample/sample_audvis_raw.fif', verbose=False).load_data()
events = mne.find_events(raw, shortest_event=1)

epochs = mne.Epochs(raw, events, tmin=-1, tmax = 1, detrend = 0, event_id={'LA':1, 'RA':2})
epochsCombined =  mne.concatenate_epochs([epochs['LA'], epochs['RA']])
mne.export.export_epochs('~/mne_data/MNE-sample-data/MEG/sample/test.set', epochsCombined, fmt='auto')

Link to data

No response

Expected results

Epochs should be exported with no annotations.

Actual results

Traceback (most recent call last):

File "/usr/local/lib/python3.8/dist-packages/spyder_kernels/py3compat.py", line 356, in compat_exec
exec(code, globals, locals)

File "/home/giulio/Repositories/spinrec_giulio/Scripts/untitled4.py", line 16, in
mne.export.export_epochs('~/mne_data/MNE-sample-data/MEG/sample/test.set', epochsCombined, fmt='auto')

File "", line 12, in export_epochs

File "/usr/local/lib/python3.8/dist-packages/mne/export/_export.py", line 105, in export_epochs
_export_epochs(fname, epochs)

File "/usr/local/lib/python3.8/dist-packages/mne/export/_eeglab.py", line 45, in _export_epochs
if len(epochs.annotations) > 0:

TypeError: object of type 'NoneType' has no len()

Additional information

mne.sys_info()
Platform: Linux-5.15.0-58-generic-x86_64-with-glibc2.29
Python: 3.8.10 (default, Nov 14 2022, 12:59:47) [GCC 9.4.0]
Executable: /usr/bin/python3
CPU: x86_64: 20 cores
Memory: 31.1 GB

mne: 1.3.0
numpy: 1.22.3 {OpenBLAS 0.3.18 with 20 threads}
scipy: 1.8.0
matplotlib: 3.5.1 {backend=Qt5Agg}

sklearn: 1.0.2
numba: Not found
nibabel: Not found
nilearn: Not found
dipy: Not found
openmeeg: Not found
cupy: 10.3.0
pandas: 1.4.2
pyvista: Not found
pyvistaqt: Not found
ipyvtklink: Not found
vtk: Not found
qtpy: 2.0.1 {PyQt5=5.15.2}
ipympl: Not found
pyqtgraph: Not found
pooch: v1.6.0

mne_bids: Not found
mne_nirs: Not found
mne_features: Not found
mne_qt_browser: Not found
mne_connectivity: Not found
mne_icalabel: Not found

Activity

  1. welcome commented on Jan 30, 2023

    @welcome

    Hello! 👋 Thanks for opening your first issue here! ❤️ We will try to get back to you soon. 🚴🏽‍♂️

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