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[MRG] Fix copyfile_eeglab type conflicts #1126

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merged 3 commits into from
Mar 8, 2023
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[MRG] Fix copyfile_eeglab type conflicts #1126

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75b6e7e
Fix copyfile_eeglab type conflicts
laemtl Mar 8, 2023
ce70f52
Alternative solution using loadmat option mat_dtype
laemtl Mar 8, 2023
074ea18
Authors/citation updates
laemtl Mar 8, 2023
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3 changes: 3 additions & 0 deletions CITATION.cff
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Original file line number Diff line number Diff line change
Expand Up @@ -155,6 +155,9 @@ authors:
family-names: Gerster
affiliation: 'Max Planck Institute for Human Cognitive and Brain Sciences, Leipzig, Germany'
orcid: 'https://orcid.org/0000-0001-9343-6986'
- given-names: Fesselier
family-names: Laetitia
affiliation: 'McGill Centre for Integrative Neuroscience, McGill University, Montreal, Canada'
- given-names: Alexandre
family-names: Gramfort
affiliation: 'Université Paris-Saclay, Inria, CEA, Palaiseau, France'
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1 change: 1 addition & 0 deletions doc/authors.rst
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Expand Up @@ -40,3 +40,4 @@
.. _Bruno Hebling Vieira: https://bhvieira.github.io/
.. _Daniel McCloy: http://dan.mccloy.info
.. _Moritz Gerster: http://moritz-gerster.com
.. _Laetitia Fesselier: https://github.com/laemtl
1 change: 1 addition & 0 deletions doc/whats_new.rst
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Expand Up @@ -52,6 +52,7 @@ Detailed list of changes
^^^^^^^^^^^^

- Amending a dataset now works in cases where the newly-written data contains additional participant properties (new columns in ``participants.tsv``) not found in the existing dataset, by `Richard Höchenberger`_ (:gh:`1113`)
- Fixes :func:`~mne_bids.copyfiles.copyfile_eeglab` to prevent data type conversion leading to an ``eeg_checkset`` failure when trying to load the file in EEGLAB, by `Laetitia Fesselier`_ (:gh:`1122`)

:doc:`Find out what was new in previous releases <whats_new_previous_releases>`

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5 changes: 3 additions & 2 deletions mne_bids/copyfiles.py
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Expand Up @@ -533,18 +533,19 @@ def copyfile_eeglab(src, dest):
# structure and potentially breaks re-reading of the file
uint16_codec = None
eeg = loadmat(file_name=src, simplify_cells=False,
appendmat=False, uint16_codec=uint16_codec)
appendmat=False, uint16_codec=uint16_codec, mat_dtype=True)
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oldstyle = False
if 'EEG' in eeg:
eeg = eeg['EEG']
oldstyle = True

has_fdt_link = False
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@hoechenberger hoechenberger Mar 8, 2023 •
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I would suggest to revert this change, as it makes the program flow less obvious

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@laemtl laemtl Mar 8, 2023 •
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In the current implementation, there is some potential cases where has_fdt_link will not be set and an error thrown. It happened to me during testing so that's how I tried to fix that. Would you prefer an else case instead?

    try:
        # If the data field is a string, it points to a .fdt file in src dir
        if isinstance(eeg['data'][0, 0][0], str):
            has_fdt_link = True
        else:
            has_fdt_link = False
    except IndexError:
        has_fdt_link = False

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For me both ways are fine. Thanks for figuring out that there is one potential flow that previously lead to an error!

try:
# If the data field is a string, it points to a .fdt file in src dir
if isinstance(eeg['data'][0, 0][0], str):
has_fdt_link = True
except IndexError:
has_fdt_link = False
pass

if has_fdt_link:
fdt_fname = eeg['data'][0, 0][0]
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