fix ignoring sessions that have no data #1035
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| @@ -159,9 +172,9 @@ def get_subjects_sessions(config: SimpleNamespace) -> dict[str, list[str] | list | |||
| f"{tuple(sorted(missing_sessions))}, and " | |||
| "`config.allow_missing_sessions` is False" | |||
| ) | |||
| subj_sessions[subject] = sorted(set(cfg_sessions) & set(valid_sessions_subj)) | |||
| if subj_sessions[subject] == []: | |||
| subj_sessions[subject] = [None] | |||
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this wasn't doing what was intended. We want [None] (or (None,)) for datasets where sessions aren't tracked (ie there's just one session). But for datasets where sessions are tracked, we should omit an entry from this subj_sessions dict if there aren't any sessions found for that subj.
| ignore_acquisitions=("calibration", "crosstalk"), | ||
| ignore_suffixes=("scans", "coordsystem"), |
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These two lines are the important bit, for getting MNE-BIDS to only tell us if data files are present.
This ignore_suffixes line requires upstream mne-tools/mne-bids@41ce36a to work, so we'll need to pin MNE-BIDS to that commit, or wait for the next MNE-BIDS release before merging here.
I'm also not really sure if coordsystems.json and scans.tsv are the only possible sidecars that could have the undesirous effect (of having get_entity_vals return a false positive when no data files are actually present for the requested session --- cf. discussion at mne-tools/mne-bids#1351). If you can think of other sidecar suffixes to exclude, speak now.
The addition of
allow_missing_sessionsin #1000 had some problems:[None]in thesubjs_sessionsdict in cases where a subject had no valid sessions; this was not behaving as expectedmne_bids.get_entity_valswas not working as expected, because even if a subject had no data for a session for a given task, the presence ofcoordsystem.jsonorscans.tsvsidecars was causing it to report that the subject had some files for that session.Item (2) was fixed in mne-tools/mne-bids#1362; item (1) is fixed here. Works on my data, but will self-review to add some questions about implementation/testing.
Before merging …
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