Improve handling of dropped epochs in ica.plot_properties by cbrnr · Pull Request #13746 · mne-tools/mne-python

cbrnr · 2026-03-13T12:34:11Z

I frequently run into the issue that calling ica.plot_properties(raw) fails because raw contains many "bad" annotations such that the fake 2 second epochs (that are part of the properties plot) cannot be contructed.

Here's a minimal reproducible example:

from pathlib import Path

import mne
from mne import Annotations
from mne.io import read_raw_fif
from mne.preprocessing import ICA

raw_fname = Path(mne.__file__).parent / "io" / "tests" / "data" / "test_raw.fif"

raw = read_raw_fif(raw_fname, preload=True, verbose=False)
raw.crop(0, 8).pick("eeg")
raw.del_proj()

annot = Annotations(
    onset=[0.5, 2.5, 4.5, 6.5],
    duration=[1.0, 1.0, 1.0, 1.0],
    description=["BAD"] * 4,
)
raw.set_annotations(annot)

ica = ICA(n_components=2, max_iter=1, random_state=0)
ica.fit(raw)

ica.plot_properties(raw, picks=[0])

Here, I am fitting ICA on the good segments only (because the default is reject_by_annotation=True), which works fine. However, when trying to visualize the ICA properties with the same data that I fit the model with, I get the following error:

<stdin-15>:1: RuntimeWarning: All epochs were dropped!
You might need to alter reject/flat-criteria or drop bad channels to avoid this. You can use Epochs.plot_drop_log() to see which channels are responsible for the dropping of epochs.
<stdin-15>:1: RuntimeWarning: epochs._get_data() can't run because this Epochs-object is empty. You might want to check Epochs.drop_log or Epochs.plot_drop_log() to see why epochs were dropped.
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
    ica.plot_properties(raw, picks=[0])
    ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
  File "/Users/clemens/Projects/mne-python/mne/preprocessing/ica.py", line 2558, in plot_properties
    return plot_ica_properties(
        self,
    ...<14 lines>...
        verbose=verbose,
    )
  File "<decorator-gen-297>", line 12, in plot_ica_properties
  File "/Users/clemens/Projects/mne-python/mne/viz/ica.py", line 516, in plot_ica_properties
    return _fast_plot_ica_properties(
        ica,
    ...<15 lines>...
        precomputed_data=None,
    )
  File "/Users/clemens/Projects/mne-python/mne/viz/ica.py", line 621, in _fast_plot_ica_properties
    spectrum = epochs_src.compute_psd(picks=picks, **psd_args)
  File "<decorator-gen-249>", line 12, in compute_psd
  File "/Users/clemens/Projects/mne-python/mne/epochs.py", line 2588, in compute_psd
    return EpochsSpectrum(
        self,
    ...<11 lines>...
        **method_kw,
    )
  File "/Users/clemens/Projects/mne-python/mne/time_frequency/spectrum.py", line 1448, in __init__
    data = self.inst._get_data(picks=self._picks, on_empty="raise")[
           ~~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<decorator-gen-243>", line 12, in _get_data
  File "/Users/clemens/Projects/mne-python/mne/epochs.py", line 1662, in _get_data
    self._handle_empty(on_empty, "_get_data")
    ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/clemens/Projects/mne-python/mne/epochs.py", line 1623, in _handle_empty
    _on_missing(on_empty, msg, error_klass=RuntimeError)
    ~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/Users/clemens/Projects/mne-python/mne/utils/check.py", line 1221, in _on_missing
    raise error_klass(msg)
RuntimeError: epochs._get_data() can't run because this Epochs-object is empty. You might want to check Epochs.drop_log or Epochs.plot_drop_log() to see why epochs were dropped.

I fixed this issue by constructing the fake 2s epochs a bit more cleverly. If the normal approach yields empty epochs, I first stitch together the good segments and only then create the fake epochs.

hoechenberger · 2026-03-17T15:41:57Z

LGTM!

hoechenberger · 2026-03-17T15:42:29Z

I think you need a changelog entry still

larsoner

This can lead to some interesting mechanics where you might end up with more epochs shown if there is an additional bad annot added (e.g., if there are many good 1s-length segments separated by bad ones plus one good 2.1s segment, then you add a bad annot in the middle of that one and it kicks into the new logic) but we can always improve the logic here later to accomodate that sort of thing. In the meantime this seems like a clear improvement since ICA doesn't care about temporal structure anyway

…a.plot_properties

…epochs in ica.plot_properties) (#13768) Co-authored-by: Clemens Brunner <[email protected]>

* [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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(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(). 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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]>

Improve handling of dropped epochs in ica.plot_properties

ee59d9a

cbrnr requested a review from drammock as a code owner March 13, 2026 12:34

cbrnr added the backport-candidate on-merge: backport to maint/1.13 label Mar 13, 2026

Rewrap comment

4324ed8

cbrnr mentioned this pull request Mar 13, 2026

Workaround ica.plot_properties() issue cbrnr/mnelab#596

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hoechenberger approved these changes Mar 17, 2026

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cbrnr added 2 commits March 17, 2026 17:47

Merge branch 'main' into ica-properties

d5e729b

Add changelog entry

6222bca

cbrnr requested review from agramfort and larsoner as code owners March 17, 2026 16:52

cbrnr added 2 commits March 18, 2026 07:09

Fix RST

1e10d06

Merge branch 'main' into ica-properties

890161e

larsoner approved these changes Mar 18, 2026

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larsoner merged commit 2c008ad into mne-tools:main Mar 18, 2026
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meeseeksmachine pushed a commit to meeseeksmachine/mne-python that referenced this pull request Mar 18, 2026

Backport PR mne-tools#13746: Improve handling of dropped epochs in ic…

318b0ba

…a.plot_properties

meeseeksmachine mentioned this pull request Mar 18, 2026

Backport PR #13746 on branch maint/1.11 (Improve handling of dropped epochs in ica.plot_properties) #13768

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larsoner pushed a commit that referenced this pull request Mar 18, 2026

Backport PR #13746 on branch maint/1.11 (Improve handling of dropped …

ccbe909

…epochs in ica.plot_properties) (#13768) Co-authored-by: Clemens Brunner <[email protected]>

pjdurka mentioned this pull request May 1, 2026

ica.plot_properties(reject='auto') raises IndexError when fit-time reject dropped any segments #13879

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cbrnr deleted the ica-properties branch June 18, 2026 05:55

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Improve handling of dropped epochs in ica.plot_properties - #13746

Improve handling of dropped epochs in ica.plot_properties#13746
larsoner merged 6 commits into
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cbrnr commented Mar 13, 2026 •

edited

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cbrnr commented Mar 13, 2026 •

edited

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