Update values to int64 by teonbrooks · Pull Request #13548 · mne-tools/mne-python

teonbrooks · 2025-12-16T18:56:29Z

Fix attempt as fixing the overflow issue in the read_raw_cnt reader. This error has manifested with numpy upgrade.

Reference issue

Fixes #13547.

What does this implement/fix?

This follows a pattern suggested in #12907 to cast the integer to int64.

larsoner · 2025-12-16T19:05:27Z

To read your file it needs a few more fixes actually... I'll push

larsoner · 2025-12-16T19:16:47Z

Definitely still something wrong here...

$ python -uic "import mne; raw = mne.io.read_raw_cnt('~/Desktop/945flankers_ready.cnt', data_format='int16').load_data(); raw.plot(annotation_regex='aaa')"
Traceback (most recent call last):
  File "<string>", line 1, in <module>
    import mne; raw = mne.io.read_raw_cnt('~/Desktop/945flankers_ready.cnt', data_format='int16').load_data(); raw.plot(annotation_regex='aaa')
                      ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^
  File "<decorator-gen-190>", line 12, in load_data
  File "/home/larsoner/python/mne-python/mne/io/base.py", line 589, in load_data
    self._preload_data(True)
    ~~~~~~~~~~~~~~~~~~^^^^^^
  File "/home/larsoner/python/mne-python/mne/io/base.py", line 601, in _preload_data
    self._data = self._read_segment(data_buffer=data_buffer)
                 ~~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^
  File "<decorator-gen-189>", line 12, in _read_segment
  File "/home/larsoner/python/mne-python/mne/io/base.py", line 420, in _read_segment
    data = _allocate_data(data_buffer, data_shape, dtype)
  File "/home/larsoner/python/mne-python/mne/io/base.py", line 2577, in _allocate_data
    data = np.zeros(shape, dtype)
numpy._core._exceptions._ArrayMemoryError: Unable to allocate 2.06 TiB for an array with shape (66, 4294966564) and data type float64

Same error if I use data_format='int32'. If I remove the .load_data and use data_format='int32' the plot at least looks okay

So need to figure out the n_samples issue, 4294966564 samples for 66 channels is totally unreasonable for a 150MB file...

larsoner · 2025-12-16T19:31:31Z

@teonbrooks I'm done pushing/looking for now, I hope the changes I made help debugging a bit more. Something is wrong with n_samples here, it gets read as 4294966564 ...

teonbrooks · 2025-12-17T14:39:37Z

thanks @larsoner!

came across this post and adding it here for reference in the future
https://paulbourke.net/dataformats/eeg/

teonbrooks · 2025-12-17T14:45:20Z

@teonbrooks I'm done pushing/looking for now, I hope the changes I made help debugging a bit more. Something is wrong with n_samples here, it gets read as 4294966564 ...

according to the link above, it looks like this is not an uncommon occurrence:

Experience has shown that many (most) of the fields are not filled out correctly by the software. In particular, the best way to work out the number of samples is

it looks like n_samples should be calculated as:

nsamples = SETUP.EventTablePos - (900 + 75 * nchannels) / (2 * nchannels)

larsoner · 2025-12-17T15:15:59Z

Great, can you add some comments / links in the code for the next time we dig into this, and try the suggested fix?

teonbrooks · 2025-12-20T00:36:23Z

added a note. after trying it out and I look more closely at the code, it looks as though the n_samples logic is already there starting at https://github.com/mne-tools/mne-python/blob/main/mne/io/cnt/cnt.py#L339.

teonbrooks · 2025-12-20T00:37:41Z

I actually don't know what to do about the n_samples. it looks like the code already is trying to best handle the data without knowing the data_format and with the header not having a reliable header entry for it.

larsoner · 2025-12-29T17:35:54Z

@teonbrooks do you want me to take a look?

it looks like the code already is trying to best handle the data without knowing the data_format and with the header not having a reliable header entry for it.

So we have two potential sources of truth:

n_samples, which is 4294966564 for this dataset
SETUP.EventTablePos - (900 + 75 * nchannels) / (2 * nchannels), which is presumably correct for this dataset (right?)

In main we assume (1) is going to be more correct so we use it incorrectly for this file. Does that sound right?

If so, maybe we should prefer to use (2) if it's available, since it's more likely to be correct.

We could add some parameter to control which of these to prefer, too, if needed. We can even make it like n_samples="computed" (new default, option 2 above) | "read" (default on main, option 1 above) and change the default without a deprecation cycle since I think we can consider this a bugfix given the unreliability of "read"

teonbrooks · 2026-01-02T19:00:52Z

@larsoner, yes, that would be a great help if you could take a look at it. and yep, I agree with your assessment on the number of samples

* upstream/main: BUG: Fix bug with error message check (mne-tools#13579) Add QC + Full MNE Report tutorial (mne-tools#13532) FIX: adding kit_system_id info to forward solution (mne-tools#13520) MAINT: Update code credit (mne-tools#13572) MAINT: Fix Circle (mne-tools#13574) DOC: Clarify read_raw_nirx expects directory path, not file path (mne-tools#13541)

larsoner · 2026-01-09T16:42:54Z

Yikes this is a bit of a nightmare. Looks like in the header for event_table_offset and n_samples:

Sometimes they are both correct, and consistent
Sometimes event_table_offset is correct and n_samples is incorrect (like in the linked docs)
Sometimes event_table_offset is incorrect and n_samples is correct (like in some of our test datasets)
event_table_offset will always be wrong for file sizes > 2 GB

So when I said before:

If so, maybe we should prefer to use (2) [event_table_offset-computed value] if it's available, since it's more likely to be correct.

I'm no longer convinced this is a good idea, given it's not even the case for our test datasets! To make things worse, all of this stuff interacts with data_format, which we allow to be "auto". So thinking about it more, how about we:

Add n_samples="header" (default) | "computed" where "computed" means "compute it using event_table_offset and data_format"
Only allow data_format="auto" when n_samples="header" or data_format != "auto" and file size < 2GB, because you can't figure out both data_format and n_samples given just an event_table_pos (and event_table_pos is only even potentially usable for file sizes < 2 GB) -- you can just as easily say there are 2 bytes per sample and X samples or 4 bytes per sample and X//2 samples.

Also, looking at the docs from https://paulbourke.net/dataformats/eeg/, their example file has the data offset (SETUP+ELECTLOC) at 5550, which runs to EventTablePos=8511950 for 62 channels. They say this span is n_samples * n_channels * 2 (so data_format="int16"). But if you take their math at the top nsamples = SETUP.EventTablePos - (900 + 75 * nchannels) / (2 * nchannels) you get a very wrong value 8511950-(900+75*62)/(2*62) = 8511905.241935484. Correcting their algebra to be what I think should be correct (EventTablePos-(900+75*n_channels))/(n_channels*n_bytes) we get a more reasonable 68675.0 (note the whole value on this float div, which is good / suggests possible correctness once we convert to integer arithmetic!)... but according to the doc itself the number of samples is 68600! So somehow there are 75 extra values here. I wondered if this could be the source of #11802, but I also see this is the data @teonbrooks shared -- computing the number of samples from the event_table_offset I see ~1865 samples toward the end of the data that are almost all (but not all!) zeros. Wouldn't be surprised if this is the result of something writing un-zeroed malloc'ed rather than calloc'ed data or something... in any case, we should revisit #11802 once we work out the solutions above since maybe we'll magically fix that issue, too.

@withmywoessner you've worked on this stuff a bit recently... WDYT?

xref previous nightmares #6535 #6537 #11802 #12393

larsoner · 2026-04-07T14:08:02Z

I think this should be an early 1.13 PR, not a last-minute 1.12 one. I am going to look now and hopefully push a commit to have this where I think it can be merged, but given it changes some behavior it seems better to have it in dev for a few months in case we can spot new bugs earlier.

larsoner · 2026-04-07T15:10:27Z

Okay actually I think this could possibly go in for 1.12. Here's what's changed:

Added a recompute_n_samples=None which means "recompute if n_samples from header is negative", and allows a user to set to True if their n_samples is wrong (but positive) and it should be recomputed from the event table offset. This makes the file from Overflow Error with read_raw_cnt reader #13547 be read correctly.
Makes data_format handling more strict. data_format="auto" tries to use the header values to figure out the number of bits per sample. In main, if it couldn't do it correctly, it just chose data_format="int16". This was incorrect for some files. In this PR, we are now more strict -- if it can't be safely computed, we raise an error. The workaround for users is easy enough -- try both options and see which one looks like actual EEG data (it's usually easy to tell by eye). This seems safer than us guessing one or the other.

WDYT @drammock , safe enough for 1.12 or you want to wait? I'm okay either way\

drammock

in the end it was just adding code comments and changing one var name, then it all made sense

Co-authored-by: Daniel McCloy <[email protected]>

* upstream/main: MAINT: Update code credit [ci skip] (mne-tools#13823)

teonbrooks · 2026-04-07T20:02:18Z

thanks @larsoner for bringing this home!

mne-tools/mne-python#13548 removed auto-detection of data_format in read_raw_cnt, causing the mne-main CI tests on scan41_short.cnt to fail with "Could not automatically compute number of bytes per sample". Pass data_format="int16" explicitly when the test wrapper sees a .cnt file.

…te if you can (#1556) * FIX: resolve the timezone from the historical date if you can * TST: set data_format="int16" for CNT reader in test_write mne-tools/mne-python#13548 removed auto-detection of data_format in read_raw_cnt, causing the mne-main CI tests on scan41_short.cnt to fail with "Could not automatically compute number of bytes per sample". Pass data_format="int16" explicitly when the test wrapper sees a .cnt file. --------- Co-authored-by: Bru <[email protected]>

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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(). (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]>

larsoner requested review from agramfort, dengemann, drammock and larsoner as code owners December 16, 2025 19:17

larsoner reviewed Dec 16, 2025

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Comment thread mne/io/cnt/_utils.py Outdated

teonbrooks force-pushed the cnt-overflow-fix branch from a5c1f92 to 603dd01 Compare December 20, 2025 00:36

teonbrooks force-pushed the cnt-overflow-fix branch from 603dd01 to 66c24ca Compare December 20, 2025 00:44

teonbrooks and others added 8 commits January 2, 2026 14:01

Update values to int64

dbf6fd2

FIX: Numbers

4169a00

[autofix.ci] apply automated fixes

61c4a8d

FIX: Unify

272ba47

Remove code used for debugging

f7d648e

added note

a71392a

revert back to "<i4" for n_samples

a762526

formatting

74d66ba

teonbrooks force-pushed the cnt-overflow-fix branch from 66c24ca to 74d66ba Compare January 2, 2026 19:01

larsoner added 3 commits January 8, 2026 09:50

TST: Skip

246da2f

TST: Skip [ci skip]

5191067

DOC: Update docs

9934507

larsoner added 5 commits April 7, 2026 10:52

FIX: Better

d2038e6

FIX: Desc

d86f94e

FIX: Exp

ceb9dca

FIX: Test

dc984c7

FIX: Doc

8c7a5cc

larsoner changed the title ~~Update values to int64~~ Update values to int32 Apr 7, 2026

larsoner changed the title ~~Update values to int32~~ Update values to int64 Apr 7, 2026

FIX: Order

ebc8611

larsoner modified the milestones: 1.12, 1.13 Apr 7, 2026

drammock approved these changes Apr 7, 2026

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Comment thread mne/io/cnt/_utils.py Outdated

Comment thread mne/io/cnt/_utils.py

Comment thread mne/io/cnt/_utils.py Outdated

Comment thread mne/io/cnt/_utils.py Outdated

Comment thread mne/io/cnt/_utils.py Outdated

Apply suggestions from code review

007b91b

Co-authored-by: Daniel McCloy <[email protected]>

larsoner enabled auto-merge (squash) April 7, 2026 17:01

larsoner added 2 commits April 7, 2026 13:12

Merge remote-tracking branch 'upstream/main' into cnt-overflow-fix

7325dd1

* upstream/main: MAINT: Update code credit [ci skip] (mne-tools#13823)

FIX: Change

300a8c6

larsoner modified the milestones: 1.13, 1.12 Apr 7, 2026

larsoner added the skip-changelog-checks label Apr 7, 2026

FIX: Match formatting

a8d76a8

larsoner merged commit 77d0960 into mne-tools:main Apr 7, 2026
32 checks passed

teonbrooks deleted the cnt-overflow-fix branch April 7, 2026 20:03

larsoner mentioned this pull request Apr 12, 2026

FIX: scans.tsv: resolve the timestamp timezone from the historical date if you can mne-tools/mne-bids#1556

Merged

bruAristimunha mentioned this pull request Apr 13, 2026

TST: pass data_format="int16" for CNT reader in test_write scott-huberty/mne-bids#1

Merged

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teonbrooks commented Dec 16, 2025

Reference issue

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larsoner commented Apr 7, 2026 •

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