Raising meaningful warnings/errors for interpolate_bads, when supplie… by 1himan · Pull Request #13518 · mne-tools/mne-python

1himan · 2025-12-01T14:10:25Z

Raising meaningful warnings/errors for interpolate_bads, when supplied loc field with missing or invalid data.

What does this implement/fix?

Fixes #13363

Additional information

…d loc field with missing or invalid data

for more information, see https://pre-commit.ci

1himan · 2025-12-02T07:24:07Z

Should we update the user about what's going on, on a deeper level or is it going to be too verbose.

Because if we look, that why the bug exists, its primarily because of how create_info creates the info dict structure - its all NaN for the loc field. Of course we're not expecting the user to provide the exact positions of the sensor but we should also give the user a heads up about this.

Also in the add_channels, something like:
Warning: Channel 'MEG2112' was added without valid sensor position (loc) information. Interpolation or spatial filtering will fail silently or raise an error unless position data is manually supplied.

And something similar for the interpolate_bads.

If that's the case then we should create a separate utility method for this, something like:

def _is_invalid_loc(loc):
    return np.allclose(loc, 0.0, atol=1e-16) or np.isnan(loc).any()

And use that, wherever its required to warn the user about this.

scott-huberty · 2025-12-02T22:47:20Z

@1himan I haven't followed this ticket super closely but if I understand correctly it seems like you are talking about 2 or 3 different ideas here:

1: "Should we update the user about what's going on on a deeper level [during the `interpolate_bads_function`]"

Generally We want to:

Let the user know what is wrong, e.g. "We don't have the spatial coordinates for bad sensor(s) ['X1', 'X2'] so we can't interpolate them using the signal of neighboring channels".
Let the user know how to fix or work around it.. something like "Please use the set_montage method to set the sensor locations, or pass on_no_position='warn', which will set bad channel(s) ['X1', 'X2'] to np.nan" .

We don't want to bog the user down with details about the loc array because I don't think that we expect the typical user to even know about it, let alone manually change it. If you want to communicate details that can help with debugging to super-users or other devs, you can use logger.debug

2: Should we add a similar warning to add_channels (if the user adds a channel without providing spatial sensor coordinates)

I'm -1 on this. Not all MNE functionality requires sensor locations, so I don' think we need to eagerly warn about missing sensor info during add_channels. I think it's okay to stay focused on the interpolation use-case, and if down the road we decide that we want raise/warn in other places, then we can put this warning message in a re-usable helper function!

3: the bug exists primarily because of how create_info creates the info dict structure

I'm not sure I agree, but anyways I don't think you need to worry about the internals of create_info!

Once you address/integrate the open maintainer feedback, or once you have other questions for, feel free to ping us!

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…, Parameters {on_no_position} not found - fix

…ne-python into interpolate_bads_bugfix

1himan · 2026-01-06T09:41:26Z

Ready to run rest of the tests?

drammock

Thanks for the contribution!

there should be a test (or modification of an existing test) to ensure that this works as intended. For example, a pytest.raises() context around a call when the value is "raise", a pytest.warns() context around a call when the value is "warn", and no context (or a null context) when called with the value "ignore". Should also assert that the invalid chs end up as all NaN (though since that's current behavior I'm guessing that's already tested, but please confirm)

1himan · 2026-01-07T11:55:25Z

I've made the suggested changes @drammock. and yes, the assertion for bad channel interpolated to all nan values is already implemented.

tsbinns · 2026-02-20T09:22:07Z

@1himan Do you think this is ready to be reviewed again?

1himan · 2026-02-20T09:59:28Z

@1himan Do you think this is ready to be reviewed again?

Hey @tsbinns, could you read unresolved conversation above and tell what is your opinion about the warning message? Wether it is clear or not.

Otherwise its ready to review again.

drammock

approving to clear my "changes requested" status, but see below, there are still 2 minor things to fix.

Thanks @1himan

1himan · 2026-02-25T10:24:01Z

Hey @drammock, I've added the final suggested changes. thanks for your guidance.

tsbinns · 2026-03-12T12:19:09Z

@1himan Those final comments from @drammock were addressed, but I think there should also be a .. versionadded: 1.12 tag for the new on_bad_position param.

1himan · 2026-03-12T12:44:58Z

here it is, @tsbinns. And now its hopefully ready 🤔

tsbinns · 2026-03-12T14:04:39Z

@1himan 9512936 added a number of changes to report.py that seem unrelated to this PR. Please revert these.

1himan · 2026-03-12T15:01:06Z

Thanks for correcting 😅, I actually pushed the changes from a different branch I was working on. Now I checked this one out in a completely separate working tree, so... this won't happen again :).

scott-huberty · 2026-03-12T15:45:44Z

    assert raw.info["bads"] == ch_to_interp

+    store = raw.info["chs"][1]["loc"]
+    # for on_bad_position="raise"
+    raw.info["bads"] = ch_to_interp


isn't this assignment to raw.info["bads"] unnecessary since we just verified that raw.info["bads"] already equals ch_to_interp above?

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(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]>

Raising meaningful warnings/errors for interpolate_bads, when supplie…

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…d loc field with missing or invalid data

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Improved logic and error message

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Merge branch 'main' into interpolate_bads_bugfix

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Merge branch 'main' into interpolate_bads_bugfix

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Validation warning while processing docstring for .interpolate_bads()…

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Change on_bad_position behavior from 'raise' to 'warn'

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fixed ruff error

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Raising meaningful warnings/errors for interpolate_bads, when supplie… (

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1himan commented Dec 1, 2025 • edited Loading Uh oh! There was an error while loading. Please reload this page.

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1himan commented Dec 2, 2025

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scott-huberty commented Dec 2, 2025

1: "Should we update the user about what's going on on a deeper level [during the interpolate_bads_function]"

2: Should we add a similar warning to add_channels (if the user adds a channel without providing spatial sensor coordinates)

3: the bug exists primarily because of how create_info creates the info dict structure

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1himan commented Feb 25, 2026

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1himan commented Dec 1, 2025 •

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1: "Should we update the user about what's going on on a deeper level [during the `interpolate_bads_function`]"

1himan commented Jan 7, 2026 •

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1himan commented Mar 12, 2026 •

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