ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair by bruAristimunha · Pull Request #13884 · mne-tools/mne-python

bruAristimunha · 2026-05-03T18:48:44Z

Adds opt-in overrides=dict | None to read_raw_brainvision for non-spec .vhdr files. Closes mne-tools/mne-bids#1598. Mirrors read_raw_edf(units=...) (#11099).

Nine keys cover failure modes with no escape hatch on main:

`main` error	Override
`FileNotFoundError` (renamed `.eeg`)	`data_fname`
`NoOptionError` / `FileNotFoundError` (missing `MarkerFile=` or `.vmrk`)	`marker_fname` (path or `False`)
`NoOptionError` on `NumberOfChannels=` / `SamplingInterval=` / `DataOrientation=` / `DataFormat=` / `BinaryFormat=`	`n_channels`, `sfreq`, `data_orientation`, `data_format`, `binary_format`
`RuntimeError("Missing channel units")` (truncated `[Channel Infos]`)	`units_fallback`
Wrong channel labels	`ch_names`

Each applied override is logged at INFO; None / {} preserves current behavior.

Spec note

The nine keys cover every spec-required header field per the BrainVision Core Data Format 1.0 spec (Brain Products GmbH, Document Version 2.5, 2019-12-12).

One default-behavior change is intentional and brings the reader closer to the spec it claims to read: a header without MarkerFile= (or with an empty value) now reads with no annotations instead of raising NoOptionError. From §1 General Statements:

An EEG recording consists of three files: the header file, the marker file and the EEG data file.
a. Header file and EEG data file are mandatory.
b. Marker file is optional.

i.e., on main the reader rejects spec-compliant headers. The override-supplied path is unaffected; marker_fname=False still works.

Tests

53 brainvision tests pass: pre-existing coverage + table-driven override validation, a 7-case parametrized missing-header-key recovery (one per spec-required key), default-unchanged guard, file-path / units-fallback / empty-MarkerFile= cases.

Affected dataset list in mne-tools/mne-bids#1519; open design questions in mne-tools/mne-bids#1598.

cc @cbrnr @sappelhoff @hoechenberger @drammock @larsoner

… repair Adds an opt-in dict parameter for reading non-spec-compliant .vhdr files where the header contradicts the actual layout (e.g. renamed BIDS siblings, missing MarkerFile=, truncated [Channel Infos]). Six keys: data_fname, marker_fname, n_channels, sfreq, ch_names, units_fallback. Each applied override emits a RuntimeWarning; unknown keys raise ValueError. None / {} keep stock behavior. Mirrors the read_raw_edf(units=...) precedent. Closes mne-tools/mne-bids#1598.

Reduce 7 test functions / 18 scenarios down to 5 functions / 10 scenarios by collapsing the marker_fname split, dropping the absolute-path parametrize on data_fname, dropping the truncation-warn edge case, and trimming the validation parametrize. Add an explicit test_overrides_default_unchanged that asserts overrides=None and overrides={} produce identical (nchan, sfreq, ch_names, meas_date, annotation count) to the no-overrides call. Verified manually with warnings.simplefilter('error') that the default read path emits zero warnings.

…logger.info Fixes test_docdict_order CI failure (key was alphabetically misplaced between brain_kwargs and brain_update). Also addresses review feedback: override warnings become logger.info messages that show original vs. override values, and the docstring uses a definition list.

…lure)

bruAristimunha · 2026-05-05T09:12:18Z

@scott-huberty, @larsoner, @drammock, if we merge this, this will unlock many fixes on the mne-bids, and will not even need a PR in mne-bids :)

btw, @larsoner, thank you for point me extra_parameter of the read at mne :)

…all spec-required keys The override branches called cfg.get(..., key) purely to log the original header value before announcing the override; that lookup raised NoOptionError exactly in the case the override was meant to recover from. Wrap the log-only lookups (DataFile, MarkerFile, NumberOfChannels) and the required SamplingInterval lookup in _aux_hdr_info so the override actually takes effect when the header lacks the key. Extend overrides to every spec-required header key with three new options: data_orientation ([Common Infos] DataOrientation), data_format ([Common Infos] DataFormat), and binary_format ([Binary Infos] BinaryFormat). Treat a missing or empty MarkerFile= entry as "no markers" (per the BV Core Data Format spec, MarkerFile= is optional). Collapse the six per-key override+log+fallback blocks behind one _hdr_get helper, and refactor _validate_overrides into three dispatch tables (type / range / enum) plus the two genuinely irregular cases (marker_fname=False sentinel, ch_names per-element + uniqueness). Tests: parametrize test_overrides_recover_missing_header_keys across all seven file-/header-key keys; add validation cases for the three new enum keys; add test_empty_marker_file_means_no_markers for the spec-compliant empty-MarkerFile= path.

The previous fix tolerated a missing SamplingInterval= header by parsing NaN inside _aux_hdr_info and re-raising NoOptionError from _get_hdr_info when no sfreq override was supplied. Replace that sentinel dance with an explicit sfreq_override parameter on _aux_hdr_info: when set, skip the cfg lookup entirely; when not set, the natural NoOptionError surfaces. The second _aux_hdr_info call (impedance parsing in __init__) reuses the resolved info['sfreq'] so it never re-parses the missing key.

larsoner

Okay for me and failures are unrelated. @scott-huberty do you want to look?

scott-huberty

Kind of a big diff so I did not review everything. and I am not very familiar with this module, but I have left a few comments!

- Defensive sfreq extraction: catch NoSectionError/NoOptionError in _aux_hdr_info; raise an informative RuntimeError when neither cfg nor overrides['sfreq'] supply a value. - Richer override log: report original cfg sfreq alongside override value (or note that the header was unparseable). - Flatten _OVERRIDES_VALID_KEYS into a single set. - Replace overrides=None round-trip test with an inspect.signature default check; keep the empty-dict equivalence test as its own case.

drammock · 2026-05-05T21:33:10Z

+    """``overrides={}`` matches the no-overrides read exactly."""
+    baseline = read_raw_brainvision(vhdr_path)
+    raw = read_raw_brainvision(vhdr_path, overrides={})


this is fine as-is, but just want to call attention to mne.utils.object_diff which should be able to diff Raw files. Might be overkill here (vs. 5 assert statements) but can be nice if you want to compare more attrs

When the MarkerFile= path declared in a .vhdr does not exist, fall back to the co-located <stem>.vmrk and warn; if no sibling exists, warn and read without annotations instead of raising FileNotFoundError.

bruAristimunha · 2026-05-05T21:50:07Z

hey @drammock, @scott-huberty and @larsoner!

I am so sorry for my last commit. I was just planning to do another PR, but then by accident here, but as was just 5 line, if you can forgive, and review this very small detail, i think i am done with PR at mne-python about the brainvsion.

* upstream/main: ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair (mne-tools#13884)

* [pre-commit.ci] pre-commit autoupdate (mne-tools#13646) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Fix and extend anonymize_info (mne-tools#13647) * Fix epochs.plot() scrollbar issue (mne-tools#13654) * ENH: Add optional channel name overlay to plot_alignment (mne-tools#13570) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * Fix docstrings for get_data() (mne-tools#13652) * DOC: Add detail to make_watershed_bem volume parameter (mne-tools#13658) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13663) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * update maintainers lists (mne-tools#13631) * Fixes make_scalp_surfaces (mne-tools#13024) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Marijn van Vliet <[email protected]> Co-authored-by: Eric Larson <[email protected]> * DOC: Add pybvrf [skip azp] [skip actions] (mne-tools#13665) * Expose bem submodule (mne-tools#13669) * Rename `Epochs.reset_drop_log_selection()` to `Epochs.reset_index()` (mne-tools#13675) * MAINT: Work around NumPy deprecation (mne-tools#13677) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13678) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Allow reading alternative nasion label (Nz) from snirf file (mne-tools#13672) Co-authored-by: Daniel McCloy <[email protected]> * use a lockfile for "old" CI job (mne-tools#13490) Co-authored-by: Carina Forster <[email protected]> Co-authored-by: Thomas S. 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Binns <[email protected]> * Change syncing of dependencies with `README` (mne-tools#13832) * DOC: Fix changelog [circle deploy] (mne-tools#13833) Co-authored-by: Thomas S. Binns <[email protected]> * Exclude private submodules (e.g., _edf) from Credits page (mne-tools#13673) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * BUG: Fix bug with backward compat [circle deploy] (mne-tools#13835) * Fix bug with credit [circle deploy] (mne-tools#13841) * ENH: broaden OPM coil handling for colocated topomaps (mne-tools#13825) * DOC: Add artifact-cleaning note to epoch quality example. (mne-tools#13827) * [pre-commit.ci] pre-commit autoupdate (mne-tools#13839) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * FIX: Ref [skip azp] [skip actions] * BUG: Fix bug with logging level (mne-tools#13843) * fix env var in actions (mne-tools#13844) Co-authored-by: Scott Huberty <[email protected]> * TST: Add regression coverage for OPM topomap grouping via `plot_joint()` and `ICA` (mne-tools#13842) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * Customize annotation colors (mne-tools#13838) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * DOC: Remove invalid ndarray option from colormap docstrings (mne-tools#13797) * Fix versionadded for annotation_colors (mne-tools#13853) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13852) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13854) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Links [circle deploy] [skip azp] [skip actions] * MAINT: add OPM overlap grouping helper (mne-tools#13847) * FIX: Correct fNIRS interpolation with reordered picks (mne-tools#13856) * MAINT: Modernize numpydoc checks (mne-tools#13865) * Allow concatenating `BaseRaw` objects (mne-tools#13263) Co-authored-by: Copilot <[email protected]> Co-authored-by: Eric Larson <[email protected]> * Add dark theme to Matplotlib-based raw.plot (mne-tools#13861) Co-authored-by: Copilot <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * FIX: Check [ci skip] * FIX: Sets [ci skip] * Update towncrier change type descriptions (mne-tools#13829) * fix numpydoc (missed YD01 ignore) (mne-tools#13868) * FIX: correct label orientation for 0-90 deg nodes in plot_connectivity_circle (mne-tools#13855) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Daniel McCloy <[email protected]> * [dependabot]: Bump the actions group with 3 updates (mne-tools#13871) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13873) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * Add preload keyward argument to Inst.load_data() method call (mne-tools#13858) * MAINT: Make test dir read-only (mne-tools#13872) * BUG: improve FreeSurfer error message when executable not found (mne-tools#13874) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * add CI description to contributing guide (mne-tools#13837) Co-authored-by: Daniel McCloy <[email protected]> * Fix grammar [ci skip] (mne-tools#13881) * FIX: handle missing __version__ in check_version (mne-tools#13870) Co-authored-by: Claude Sonnet 4.6 <[email protected]> * apply diataxis to tutorials/inverse/80_brainstorm_phantom_elekta.py (mne-tools#13584) Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> * add AI policy (mne-tools#13883) * MAINT: Switch to pip for macOS and minimal jobs (mne-tools#13882) * MAINT: Update code credit (mne-tools#13878) * ENH: Allow passing source detector distances to beer lambert law (mne-tools#13875) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> * MAINT: Update for vtk deprecation (mne-tools#13886) * ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair (mne-tools#13884) * Fix bug with ica.plot_properties (mne-tools#13885) * Fix `picks` being ignored in `Epochs.apply_function()` (mne-tools#13894) * Update describing changes in contributing guide (mne-tools#13895) * Add Zuna to related software list (mne-tools#13849) Co-authored-by: Daniel McCloy <[email protected]> * [dependabot]: Bump github/codeql-action from 4.35.2 to 4.35.3 in the actions group (mne-tools#13897) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Eric Larson <[email protected]> * DOC: Fix apply_function shape description for Epochs (mne-tools#13891) Co-authored-by: Eric Larson <[email protected]> * Raise warning and errors when np.nan provided to mne.stats.permutation_t_test(). (mne-tools#13813) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Erica R Peterson <[email protected]> * MAINT: Update dependency specifiers (mne-tools#13899) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * [dependabot]: Bump github/codeql-action from 4.35.3 to 4.35.4 in the actions group (mne-tools#13901) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13902) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Remove workaround for old PySide6 (mne-tools#13900) * Add spherical montages (mne-tools#13903) * [dependabot]: Bump the actions group with 2 updates (mne-tools#13918) Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * [pre-commit.ci] pre-commit autoupdate (mne-tools#13919) Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> * MAINT: Update dependency specifiers (mne-tools#13916) Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Eric Larson <[email protected]> * BUG: set_eeg_reference list ch_type now applies per-type CAR by default (mne-tools#13920) * FIX: Avoid iteration errors caused by None when reading Nihon Kohden .LOG files (mne-tools#13915) * Fix drop_log dtype (mne-tools#13923) * Doc: add guidance on taking over a stale pull request (mne-tools#13877) Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> * FIX: Make set_eeg_reference working with a string for a channel name (mne-tools#13917) --------- Signed-off-by: dependabot[bot] <[email protected]> Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: mne[bot] <[email protected]> Co-authored-by: Clemens Brunner <[email protected]> Co-authored-by: Aman Srivastava <[email protected]> Co-authored-by: Daniel McCloy <[email protected]> Co-authored-by: Himanshu Mahor <[email protected]> Co-authored-by: Scott Huberty <[email protected]> Co-authored-by: Victor Férat <[email protected]> Co-authored-by: Marijn van Vliet <[email protected]> Co-authored-by: Eric Larson <[email protected]> Co-authored-by: Aniket <[email protected]> Co-authored-by: Carina Forster <[email protected]> Co-authored-by: Thomas S. Binns <[email protected]> Co-authored-by: Erica Peterson <[email protected]> Co-authored-by: Horizon_Architect_07 <[email protected]> Co-authored-by: Pragnya <[email protected]> Co-authored-by: Benedikt Ehinger <[email protected]> Co-authored-by: Kay Robbins <[email protected]> Co-authored-by: Bru <[email protected]> Co-authored-by: Stefan Appelhoff <[email protected]> Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com> Co-authored-by: Johannes Herforth <[email protected]> Co-authored-by: Hansuja <[email protected]> Co-authored-by: Simon Kern <[email protected]> Co-authored-by: autofix-ci[bot] <114827586+autofix-ci[bot]@users.noreply.github.com> Co-authored-by: Akhilesh <[email protected]> Co-authored-by: CHH <[email protected]> Co-authored-by: Teon L Brooks <[email protected]> Co-authored-by: Lifeng <[email protected]> Co-authored-by: Kalle Mäkelä <[email protected]> Co-authored-by: Copilot <[email protected]> Co-authored-by: Pavel Popov <[email protected]> Co-authored-by: Ayushi Satodiya <[email protected]> Co-authored-by: Seth Bashford <[email protected]> Co-authored-by: Baris <[email protected]> Co-authored-by: Claude Sonnet 4.6 <[email protected]> Co-authored-by: Jonas Mago <[email protected]> Co-authored-by: Bhargav Kowshik <[email protected]> Co-authored-by: Erica R Peterson <[email protected]> Co-authored-by: Ben Tang <[email protected]> Co-authored-by: myd7349 <[email protected]> Co-authored-by: Michael Straube <[email protected]>

bruAristimunha requested review from agramfort, drammock, larsoner and sappelhoff as code owners May 3, 2026 18:48

bruAristimunha added 2 commits May 3, 2026 20:55

Merge branch 'main' into feat/brainvision-units-fallback

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bruAristimunha added 3 commits May 4, 2026 17:52

ci: retrigger CircleCI build_docs (transient mne-qt-browser clone fai…

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Merge branch 'main' into feat/brainvision-units-fallback

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drammock enabled auto-merge (squash) May 5, 2026 21:35

ENH: Recover from stale MarkerFile= references after BIDS renames

aa899c8

When the MarkerFile= path declared in a .vhdr does not exist, fall back to the co-located <stem>.vmrk and warn; if no sibling exists, warn and read without annotations instead of raising FileNotFoundError.

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drammock merged commit b5cfff0 into mne-tools:main May 5, 2026
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larsoner added a commit to larsoner/mne-python that referenced this pull request May 6, 2026

Merge remote-tracking branch 'upstream/main' into ica

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* upstream/main: ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair (mne-tools#13884)

bruAristimunha mentioned this pull request Sep 1, 2026

fix(nemar): pair each resolved dependency URI with its own destination eegdash/EEGDash#409

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ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair - #13884

ENH: Add overrides= parameter to read_raw_brainvision for BIDS header repair#13884
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