ENH: read EGI MFF channelStatus into raw.info["bads"] - #14156
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PragnyaKhandelwal wants to merge 8 commits into
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ENH: read EGI MFF channelStatus into raw.info["bads"]#14156PragnyaKhandelwal wants to merge 8 commits into
channelStatus into raw.info["bads"]#14156PragnyaKhandelwal wants to merge 8 commits into
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When categories.xml is present in an MFF directory, collect the union of all channels marked exclusion="badChannels" across every category segment and populate raw.info["bads"] with their MNE channel names.
PragnyaKhandelwal
marked this pull request as ready for review
August 13, 2026 20:16
PragnyaKhandelwal
requested review from
agramfort,
drammock and
larsoner
as code owners
August 13, 2026 20:16
19 tasks
…, goodChannels, unknown signalBin, PNS, and corrupted XML cases
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| cats_path = op.join(filepath, "categories.xml") | ||
| if not op.isfile(cats_path): |
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@PragnyaKhandelwal can you please remove the str call on _check_fname on Line 498, and then swap out op for Path methods? in modern MNE we try to use pathlib for file handling. If there are other uses of op on file strings in this module, you can swap those out too.
Suggested change
| cats_path = op.join(filepath, "categories.xml") | |
| if not op.isfile(cats_path): | |
| cats_path = filepath / "categories.xml" | |
| if not cats_path.isfile(): |
…move str() from _check_fname
…rop os.path import
| info_filepath = op.join(filepath, "info.xml") | ||
| info_obj = XML.from_file(info_filepath) | ||
| info_filepath = Path(filepath) / "info.xml" | ||
| info_obj = XML.from_file(str(info_filepath)) |
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Suggested change
| info_obj = XML.from_file(str(info_filepath)) | |
| info_obj = XML.from_file(info_filepath) # ty: ignore[invalid-argument-type] |
@larsoner is this the way you like to silence ty errors in MNE? In this case we'd have to use this comment 3 times in this module, but seems safer than suppressing this error at the module level.
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mffpy's type annotation says from_file takes a string as input, but looks like it handles Path objects just fine.
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Reference issue (if any)
Part of #13926 (GSoC 2026 meta-issue, Phase 1).
What does this implement/fix?
EGI NetStation marks bad channels per recording epoch inside
categories.xmlusing<channelStatus>elements withexclusion="badChannels". Previously,read_raw_egiignored this file entirely and always returnedraw.info["bads"] == [].This PR adds a helper
_read_channel_status_badsthat:categories.xmlexists in the MFF directory (gracefully skips if absent or unparseable)CategoriesXML class to iterate over every category and segmentexclusion="badChannels"across all segments (both EEGsignalBin=1and PNSsignalBin=2)raw.info["bads"]A test is added that copies an existing test MFF file to a temp directory, injects a minimal
categories.xmlwith two EEG channels marked bad, reads the file, and asserts the bads list is set correctly.Additional information
categories.xmlis absent in most of the existing test MFF files (it is only present intest_egi_evoked.mff, which is an averaged file handled byread_evokeds_mff). The new test therefore constructs a minimalcategories.xmlin a temp copy of the paused multi-epoch test file to exercise the raw reader path.All 26 EGI tests pass.